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Rossini R, Oshaghi M, Nekrasov M, Bellanger A, Domaschenz R, Dijkwel Y, Abdelhalim M, Collas P, Tremethick D, Paulsen J. Multi-level 3D genome organization deteriorates during breast cancer progression. bioRxiv 2023:2023.11.26.568711. [PMID: 38076897 PMCID: PMC10705249 DOI: 10.1101/2023.11.26.568711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Breast cancer entails intricate alterations in genome organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from a normal to a breast cancer malignant state remains unknown. To address this, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identify a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene is inserted into a highly active subcompartment on chromosome 10. This insertion leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing novel relationships between genome 3D structure and oncogenic processes.
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Affiliation(s)
- Roberto Rossini
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Mohammadsaleh Oshaghi
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Maxim Nekrasov
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Aurélie Bellanger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Renae Domaschenz
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Yasmin Dijkwel
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424 Oslo, Norway
| | - David Tremethick
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jonas Paulsen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
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2
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Raffo A, Paulsen J. The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data. Brief Bioinform 2023; 24:bbad302. [PMID: 37646128 PMCID: PMC10516369 DOI: 10.1093/bib/bbad302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/05/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023] Open
Abstract
The three-dimensional organization of chromatin plays a crucial role in gene regulation and cellular processes like deoxyribonucleic acid (DNA) transcription, replication and repair. Hi-C and related techniques provide detailed views of spatial proximities within the nucleus. However, data analysis is challenging partially due to a lack of well-defined, underpinning mathematical frameworks. Recently, recognizing and analyzing geometric patterns in Hi-C data has emerged as a powerful approach. This review provides a summary of algorithms for automatic recognition and analysis of geometric patterns in Hi-C data and their correspondence with chromatin structure. We classify existing algorithms on the basis of the data representation and pattern recognition paradigm they make use of. Finally, we outline some of the challenges ahead and promising future directions.
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Affiliation(s)
- Andrea Raffo
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Jonas Paulsen
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
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3
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Rossini R, Kumar V, Mathelier A, Rognes T, Paulsen J. MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biol 2022; 23:247. [PMID: 36451166 PMCID: PMC9710047 DOI: 10.1186/s13059-022-02815-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.
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Affiliation(s)
- Roberto Rossini
- grid.5510.10000 0004 1936 8921Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Vipin Kumar
- grid.5510.10000 0004 1936 8921Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Anthony Mathelier
- grid.5510.10000 0004 1936 8921Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Torbjørn Rognes
- grid.5510.10000 0004 1936 8921Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0424 Oslo, Norway
| | - Jonas Paulsen
- grid.5510.10000 0004 1936 8921Department of Biosciences, University of Oslo, 0316 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
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Abstract
The three-dimensional (3D) organization of the genome is shaped by interactions with multiple structures within the nucleus, affecting gene expression outcomes. Technological breakthroughs in recent years have generated vast data reflecting various aspects of nuclear genome architecture in space and time. Integrating these datasets into comprehensive 3D genome models can reveal new insights into genome structure and regulation in normal and disease states. In this chapter, we provide a step-by-step guide on how to generate publication-ready integrated 3D genome models from (raw) Hi-C data and from lamin-genome (LAD) contacts.
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Affiliation(s)
- Jonas Paulsen
- EVOGENE, Department of Biosciences, Faculty of Natural Sciences, University of Oslo, Oslo, Norway.
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
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5
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Abstract
BACKGROUND Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and interactions with the nuclear lamina dynamically act on chromatin at multiple levels. Here, we explore long-range interaction patterns between topologically associated domains (TADs) in several cell types. RESULTS We find that TAD long-range interactions are connected to many key features of chromatin organization, including open and closed compartments, compaction and loop extrusion processes. Domains that form large TAD cliques tend to be repressive across cell types, when comparing gene expression, LINE/SINE repeat content and chromatin subcompartments. Further, TADs in large cliques are larger in genomic size, less dense and depleted of convergent CTCF motifs, in contrast to smaller and denser TADs formed by a loop extrusion process. CONCLUSIONS Our results shed light on the organizational principles that govern repressive and active domains in the human genome.
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Affiliation(s)
- Tharvesh M Liyakat Ali
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Annaël Brunet
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
| | - Jonas Paulsen
- Institute of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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6
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Abstract
The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in regulating DNA transcription, replication, and damage-repair among other nuclear functions. With this increased awareness, reinforced over the last ten years, many new experimental techniques, mainly based on microscopy and chromosome conformation capture, have been introduced to study the genome in space and time. Owing to the increasing complexity of these cutting-edge techniques, computational approaches have become of paramount importance to interpret, contextualize, and complement such experiments with new insights. Hence, it is becoming crucial for experimental biologists to have a clear understanding of the diverse theoretical modeling approaches available and the biological information each of them can provide.
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Affiliation(s)
- Marco Di Stefano
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
| | - Jonas Paulsen
- EVOGENE, Department of Biosciences, Faculty of Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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7
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Paulsen J, Liyakat Ali TM, Nekrasov M, Delbarre E, Baudement MO, Kurscheid S, Tremethick D, Collas P. Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation. Nat Genet 2019; 51:835-843. [PMID: 31011212 DOI: 10.1038/s41588-019-0392-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/12/2019] [Indexed: 01/01/2023]
Abstract
Genomic information is selectively used to direct spatial and temporal gene expression during differentiation. Interactions between topologically associating domains (TADs) and between chromatin and the nuclear lamina organize and position chromosomes in the nucleus. However, how these genomic organizers together shape genome architecture is unclear. Here, using a dual-lineage differentiation system, we report long-range TAD-TAD interactions that form constitutive and variable TAD cliques. A differentiation-coupled relationship between TAD cliques and lamina-associated domains suggests that TAD cliques stabilize heterochromatin at the nuclear periphery. We also provide evidence of dynamic TAD cliques during mouse embryonic stem-cell differentiation and somatic cell reprogramming and of inter-TAD associations in single-cell high-resolution chromosome conformation capture (Hi-C) data. TAD cliques represent a level of four-dimensional genome conformation that reinforces the silencing of repressed developmental genes.
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Affiliation(s)
- Jonas Paulsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tharvesh M Liyakat Ali
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maxim Nekrasov
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.,Biomolecular Research Facility, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Erwan Delbarre
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marie-Odile Baudement
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sebastian Kurscheid
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - David Tremethick
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
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8
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Briand N, Guénantin AC, Jeziorowska D, Shah A, Mantecon M, Capel E, Garcia M, Oldenburg A, Paulsen J, Hulot JS, Vigouroux C, Collas P. The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks. Hum Mol Genet 2019; 27:1447-1459. [PMID: 29438482 DOI: 10.1093/hmg/ddy055] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 02/08/2018] [Indexed: 12/21/2022] Open
Abstract
The p.R482W hotspot mutation in A-type nuclear lamins causes familial partial lipodystrophy of Dunnigan-type (FPLD2), a lipodystrophic syndrome complicated by early onset atherosclerosis. Molecular mechanisms underlying endothelial cell dysfunction conferred by the lamin A mutation remain elusive. However, lamin A regulates epigenetic developmental pathways and mutations could perturb these functions. Here, we demonstrate that lamin A R482W elicits endothelial differentiation defects in a developmental model of FPLD2. Genome modeling in fibroblasts from patients with FPLD2 caused by the lamin A R482W mutation reveals repositioning of the mesodermal regulator T/Brachyury locus towards the nuclear center relative to normal fibroblasts, suggesting enhanced activation propensity of the locus in a developmental model of FPLD2. Addressing this issue, we report phenotypic and transcriptional alterations in mesodermal and endothelial differentiation of induced pluripotent stem cells we generated from a patient with R482W-associated FPLD2. Correction of the LMNA mutation ameliorates R482W-associated phenotypes and gene expression. Transcriptomics links endothelial differentiation defects to decreased Polycomb-mediated repression of the T/Brachyury locus and over-activation of T target genes. Binding of the Polycomb repressor complex 2 to T/Brachyury is impaired by the mutated lamin A network, which is unable to properly associate with the locus. This leads to a deregulation of vascular gene expression over time. By connecting a lipodystrophic hotspot lamin A mutation to a disruption of early mesodermal gene expression and defective endothelial differentiation, we propose that the mutation rewires the fate of several lineages, resulting in multi-tissue pathogenic phenotypes.
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Affiliation(s)
- Nolwenn Briand
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway.,Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France
| | - Anne-Claire Guénantin
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Dorota Jeziorowska
- Sorbonne Université, UPMC Université Paris 6, UMR-S1166 ICAN, 75013 Paris, France
| | - Akshay Shah
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Matthieu Mantecon
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France
| | - Emilie Capel
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France
| | - Marie Garcia
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France
| | - Anja Oldenburg
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Jonas Paulsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Jean-Sebastien Hulot
- Sorbonne Université, UPMC Université Paris 6, UMR-S1166 ICAN, 75013 Paris, France
| | - Corinne Vigouroux
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France.,AP-HP Saint-Antoine Hospital, Molecular Biology and Genetics Laboratory, Endocrinology Department, National Reference Center for Insulin Secretion and Insulin Sensitivity Rare Diseases, 75012 Paris, France
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway.,Department of Immunology and Transfusion Medicine, Norwegian Center for Stem Cell Research, Oslo University Hospital, 0424 Oslo, Norway
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9
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Briand N, Cahyani I, Madsen-Østerbye J, Paulsen J, Rønningen T, Sørensen AL, Collas P. Lamin A, Chromatin and FPLD2: Not Just a Peripheral Ménage-à-Trois. Front Cell Dev Biol 2018; 6:73. [PMID: 30057899 PMCID: PMC6053905 DOI: 10.3389/fcell.2018.00073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/21/2018] [Indexed: 11/13/2022] Open
Abstract
At the nuclear periphery, the genome is anchored to A- and B-type nuclear lamins in the form of heterochromatic lamina-associated domains. A-type lamins also associate with chromatin in the nuclear interior, away from the peripheral nuclear lamina. This nucleoplasmic lamin A environment tends to be euchromatic, suggesting distinct roles of lamin A in the regulation of gene expression in peripheral and more central regions of the nucleus. The hot-spot lamin A R482W mutation causing familial partial lipodystrophy of Dunnigan-type (FPLD2), affects lamin A association with chromatin at the nuclear periphery and in the nuclear interior, and is associated with 3-dimensional (3D) rearrangements of chromatin. Here, we highlight features of nuclear lamin association with the genome at the nuclear periphery and in the nuclear interior. We address recent data showing a rewiring of such interactions in cells from FPLD2 patients, and in adipose progenitor and induced pluripotent stem cell models of FPLD2. We discuss associated epigenetic and genome conformation changes elicited by the lamin A R482W mutation at the gene level. The findings argue that the mutation adversely impacts both global and local genome architecture throughout the nucleus space. The results, together with emerging new computational modeling tools, mark the start of a new era in our understanding of the 3D genomics of laminopathies.
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Affiliation(s)
- Nolwenn Briand
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Norwegian Center for Stem Cell Research, Oslo University Hospital, Oslo, Norway
| | - Inswasti Cahyani
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Julia Madsen-Østerbye
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jonas Paulsen
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Torunn Rønningen
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anita L Sørensen
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Norwegian Center for Stem Cell Research, Oslo University Hospital, Oslo, Norway
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10
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García-Nieto PE, Schwartz EK, King DA, Paulsen J, Collas P, Herrera RE, Morrison AJ. Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis. EMBO J 2017; 36:2829-2843. [PMID: 28814448 PMCID: PMC5623849 DOI: 10.15252/embj.201796717] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 07/05/2017] [Accepted: 07/14/2017] [Indexed: 12/12/2022] Open
Abstract
The development of many sporadic cancers is directly initiated by carcinogen exposure. Carcinogens induce malignancies by creating DNA lesions (i.e., adducts) that can result in mutations if left unrepaired. Despite this knowledge, there has been remarkably little investigation into the regulation of susceptibility to acquire DNA lesions. In this study, we present the first quantitative human genome-wide map of DNA lesions induced by ultraviolet (UV) radiation, the ubiquitous carcinogen in sunlight that causes skin cancer. Remarkably, the pattern of carcinogen susceptibility across the genome of primary cells significantly reflects mutation frequency in malignant melanoma. Surprisingly, DNase-accessible euchromatin is protected from UV, while lamina-associated heterochromatin at the nuclear periphery is vulnerable. Many cancer driver genes have an intrinsic increase in carcinogen susceptibility, including the BRAF oncogene that has the highest mutation frequency in melanoma. These findings provide a genome-wide snapshot of DNA injuries at the earliest stage of carcinogenesis. Furthermore, they identify carcinogen susceptibility as an origin of genome instability that is regulated by nuclear architecture and mirrors mutagenesis in cancer.
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Affiliation(s)
| | - Erin K Schwartz
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Devin A King
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jonas Paulsen
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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11
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Paulsen J, Sekelja M, Oldenburg AR, Barateau A, Briand N, Delbarre E, Shah A, Sørensen AL, Vigouroux C, Buendia B, Collas P. Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts. Genome Biol 2017; 18:21. [PMID: 28137286 PMCID: PMC5278575 DOI: 10.1186/s13059-016-1146-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/23/2016] [Indexed: 01/09/2023] Open
Abstract
Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells. Chrom3D reveals unexpected spatial features of LAD regulation in cells from patients with a laminopathy-causing lamin mutation. Chrom3D is freely available on github.
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Affiliation(s)
- Jonas Paulsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Monika Sekelja
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anja R Oldenburg
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Nolwenn Briand
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Erwan Delbarre
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Akshay Shah
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita L Sørensen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Corinne Vigouroux
- INSERM, UMR S938, Centre de Recherches Saint-Antoine, Paris, France.,UPMC Université Paris 6 UMR S938, Paris, France.,ICAN, Paris, France.,AP-HP Hôpital Tenon, Paris, France
| | | | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Oslo University Hospital, Oslo, Norway.
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12
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Di Stefano M, Paulsen J, Lien TG, Hovig E, Micheletti C. Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization. Sci Rep 2016; 6:35985. [PMID: 27786255 PMCID: PMC5081523 DOI: 10.1038/srep35985] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/30/2016] [Indexed: 11/10/2022] Open
Abstract
Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based constraints for large-scale three-dimensional models of the human diploid genome. The resulting models remain minimally entangled and acquire several functional features that are observed in vivo and that were never used as input for the model. We find, for instance, that gene-rich, active regions are drawn towards the nuclear center, while gene poor and lamina associated domains are pushed to the periphery. These and other properties persist upon adding local contact constraints, suggesting their compatibility with non-local constraints for the genome organization. The results show that suitable combinations of data analysis and physical modelling can expose the unexpectedly rich functionally-related properties implicit in chromosome-chromosome contact data. Specific directions are suggested for further developments based on combining experimental data analysis and genomic structural modelling.
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Affiliation(s)
- Marco Di Stefano
- SISSA, International School for Advanced Studies, Trieste, I-34136, Italy
| | - Jonas Paulsen
- Institute of Basic Medical Sciences, University of Oslo, Oslo, 0317, Norway
| | - Tonje G. Lien
- University of Oslo, Department of Mathematics, Oslo, 0316, Norway
| | - Eivind Hovig
- Institute for Cancer Research, Oslo University Hospital, Department of Tumor Biology, Oslo, 0310, Norway
- University of Oslo, Department of Informatics, Oslo, 0316, Norway
- Institute of Cancer Genetics and Informatics, Oslo, 0310, Norway
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Bos L, Schouten L, van Vught L, Wiewel M, Ong D, Cremer O, Artigas A, Martin-Loeches I, Hoogendijk A, van der Poll T, Horn J, Juffermans N, Schultz M, de Prost N, Pham T, Carteaux G, Dessap AM, Brun-Buisson C, Fan E, Bellani G, Laffey J, Mercat A, Brochard L, Maitre B, Howells PA, Thickett DR, Knox C, Park DP, Gao F, Tucker O, Whitehouse T, McAuley DF, Perkins GD, Pham T, Laffey J, Bellani G, Fan E, Pisani L, Roozeman JP, Simonis FD, Giangregorio A, Schouten LR, Van der Hoeven SM, Horn J, Neto AS, Festic E, Dondorp AM, Grasso S, Bos LD, Schultz MJ, Koster-Brouwer M, Verboom D, Scicluna B, van de Groep K, Frencken J, Schultz M, van der Poll T, Bonten M, Cremer O, Ko JI, Kim KS, Suh GJ, Kwon WY, Kim K, Shin JH, Ranzani OT, Prina E, Menendez R, Ceccato A, Mendez R, Cilloniz C, Gabarrus A, Ferrer M, Torres A, Urbano A, Zhang LA, Swigon D, Pike F, Parker RS, Clermont G, Scheer C, Kuhn SO, Modler A, Vollmer M, Fuchs C, Hahnenkamp K, Rehberg S, Gründling M, Taggu A, Darang N, Öveges N, László I, Tánczos K, Németh M, Lebák G, Tudor B, Érces D, Kaszaki J, Huber W, Oerding H, Holst R, Toft P, Nedergaard HK, Haberlandt T, Jensen HI, Toft P, Park S, Kim S, Cho YJ, Trásy D, Lim YJ, Chan A, Tang S, Nunes SL, Forsberg S, Blomqvist H, Berggren L, Sörberg M, Sarapohja T, Wickerts CJ, Molnár Z, Hofhuis JGM, Rose L, Blackwood B, Akerman E, Mcgaughey J, Egerod I, Fossum M, Foss H, Georgiou E, Graff HJ, Ferrara G, Kalafati M, Sperlinga R, Schafer A, Wojnicka AG, Spronk PE, Zand F, Khalili F, Afshari R, Sabetian G, Masjedi M, Edul VSK, Maghsudi B, Khodaei HH, Javadpour S, Petramfar P, Nasimi S, Vazin A, Ziaian B, Tabei H, Gunther A, Hansen JO, Canales HS, Sackey P, Storm H, Bernhardsson J, Sundin Ø, Bjärtå A, Bienert A, Smuszkiewicz P, Wiczling P, Przybylowski K, Borsuk A, Martins E, Trojanowska I, Matysiak J, Kokot Z, Paterska M, Grzeskowiak E, Messina A, Bonicolini E, Colombo D, Moro G, Romagnoli S, Canullán C, De Gaudio AR, Corte FD, Romano SM, Silversides JA, Major E, Mann EE, Ferguson AJ, Mcauley DF, Marshall JC, Blackwood B, Murias G, Fan E, Diaz-Rodriguez JA, Silva-Medina R, Gomez-Sandoval E, Gomez-Gonzalez N, Soriano-Orozco R, Gonzalez-Carrillo PL, Hernández-Flores M, Pilarczyk K, Lubarksi J, Pozo MO, Wendt D, Dusse F, Günter J, Huschens B, Demircioglu E, Jakob H, Palmaccio A, Dell’Anna AM, Grieco DL, Torrini F, Eguillor JFC, Iaquaniello C, Bongiovanni F, Antonelli M, Toscani L, Antonakaki D, Bastoni D, Aya HD, Rhodes A, Cecconi M, Jozwiak M, Buscetti MG, Depret F, Teboul JL, Alphonsine J, Lai C, Richard C, Monnet X, László I, Demeter G, Öveges N, Tánczos K, Ince C, Németh M, Trásy D, Kertmegi I, Érces D, Tudor B, Kaszaki J, Molnár Z, Hasanin A, Lotfy A, El-adawy A, Dubin A, Nassar H, Mahmoud S, Abougabal A, Mukhtar A, Quinty F, Habchi S, Luzi A, Antok E, Hernandez G, Lara B, Aya HD, Enberg L, Ortega M, Leon P, Kripper C, Aguilera P, Kattan E, Bakker J, Huber W, Lehmann M, Sakka S, Rhodes A, Bein B, Schmid RM, Preti J, Creteur J, Herpain A, Marc J, 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Chiang CC, Huang WC, Lilot M, Lin KC, Lin SC, Cheng CC, Kang PL, Wann SR, Mar GY, Liu CP, Carranza ML, Fernandez HS, Roman JAS, Neidecker J, Lucena F, Garcia AC, Vazquez AL, Serrano AL, Moreira LS, Vidal-Perez R, Herranz UA, Acuna JMG, Gil CP, Allut JLG, Fellahi JL, Sedes PR, Lopez CM, Paz ES, Rodriguez CG, Gonzalez-Juanatey JR, Vallejo-Baez A, de la Torre-Prados MV, Nuevo-Ortega P, Fernández-Porcel A, Cámara-Sola E, Escoresca-Ortega A, Tsvetanova-Spasova T, Rueda-Molina C, Salido-Díaz L, García-Alcántara A, Aron J, Marharaj R, Gervasio K, Bottiroli M, Mondino M, De Caria D, Gutiérrez-Pizarraya A, Calini A, Montrasio E, Milazzo F, Gagliardone MP, Vallejo-Báez A, de la Torre-Prados MV, Nuevo-Ortega P, Fernández-Porcel A, Cámara-Sola E, Tsvetanova-Spasova T, Charris-Castro L, Rueda-Molina C, Salido-Díaz L, García-Alcántara A, Moreira LS, Vidal-Perez R, Anido U, Gil CP, Acuna JMG, Sedes PR, Lopez CM, Corcia-Palomo Y, Paz ES, Allut JLG, Rodriguez CG, Gonzalez-Juanatey JR, Hamdaoui Y, Khedher A, Cheikh-Bouhlel M, Ayachi J, Meddeb K, Sma N, Fernandez-Delgado E, Fraj N, Aicha NB, Romdhani S, Bouneb R, Chouchene I, Boussarsar M, Dela Cruz MPRDL, Bernardo JM, Galfo F, Dyson A, Garnacho-Montero J, Singer M, Marino A, Dyson A, Singer M, Chao CC, Hou P, Huang WC, Hung CC, Chiang CH, Hung WT, Roger C, Lin KC, Lin SC, Liou YJ, Hung SM, Lin YS, Cheng CC, Kuo FY, Chiou KR, Chen CJ, Yan LS, Muller L, Liu CY, Wang HH, Kang PL, Chen HL, Ho CK, Mar GY, Liu CP, Grewal S, Gopal S, Corbett C, Elotmani L, Wilson A, Capps J, Ayoub W, Lomas A, Ghani S, Moore J, Atkinson D, Sharman M, Swinnen W, Pauwels J, Lipman J, Mignolet K, Pannier E, Koch A, Sarens T, Temmerman W, Elmenshawy AM, Fayed AM, Elboriuny M, Hamdy E, Zakaria E, Lefrant JY, Falk AC, Petosic A, Olafsen K, Wøien H, Flaatten H, Sunde K, Agra JJC, Cabrera JLS, Santana JDM, Alzola LM, Roberts JA, Pérez HR, Pires TC, Calderón H, Pereira A, Castro S, Granja C, Norkiene I, Urbanaviciute I, Kezyte G, Ringaitiene D, Muñoz-Bermúdez R, 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P, Socolovsky CS, Cauley RP, Frankel JE, Beam AL, Olaniran KO, Gibbons FK, Christopher KB, Tuinman PR, Pennington J, Zolfaghari P, King HS, Kong HHY, Shum HP, Yan WW, Kaymak C, Okumus N, Sari A, Erdogdu B, de Waard MC, Aksun S, Basar H, Ozcan A, Ozcan N, Oztuna D, Malmgren JA, Lundin S, Torén K, Eckerström M, Wallin A, Oudemans-van Straaten HM, Waldenström AC, Riccio FC, Pogson D, Antonio ACP, Leivas AF, Kenji F, James E, Morgan P, Carroll G, Gemmell L, Liberatore AMA, MacKay A, Wright C, Ballantyne J, Jonnada S, Gerrard CS, Jones N, Salciccioli JD, Marshall DC, Komorowski M, Hartley A, Souza RB, Sykes MC, Goodson R, Shalhoub J, Villanueva JRF, Garda RF, Lago AML, Ruiz ER, Vaquero RH, Rodríguez CG, Pérez EV, Martins AMCRPF, Hilasque C, Oliva I, Sirgo G, Martin MC, Olona M, Gilavert MC, Bodí M, Ebm C, Aggarwal G, Huddart S, Vieira JCF, Quiney N, Cecconi M, Fernandes SM, Silva JS, Gouveia J, Silva D, Marques R, Bento H, Alvarez A, Silva ZC, Koh IHJ, Diaz DD, Martínez MV, Herrejon EP, de la Gandara AM, Gonzalo G, Lopez MA, de Gopegui Miguelena PR, Matilla CIB, Chueca PS, Longares MDCR, Martínez MG, Abril RR, Aguilar ALR, de Murillas RGL, Fernández RF, Laborías PM, Castellanos MAD, Laborías MEM, Cho J, Kim J, Park J, Sánchez RJ, Woo S, West T, Powell E, Rimmer A, Orford C, Jones N, Williams J, Matilla CIB, de Gopegui Miguelena PR, Chueca PS, Gascón LM, Abril RR, Longares MDCR, Aguilar ALR, de Murillas RGL, Bourne RS, Shulman R, Tomlin M, Mills GH, Borthwick M, Berry W, Mulero MDR, Huertas DG, Manzano F, Villagrán-Ramírez F, Ruiz-Perea A, Rodríguez-Mejías C, Santiago-Ruiz F, Colmenero-Ruiz M, König C, Matt B, Kortgen A, Freire AO, Hartog CS, Wong A, Balan C, Barker G, Srisawat N, Peerapornratana S, Laoveeravat P, Tachaboon S, Eiam-ong S, Paratz J, Muñoz AO, Kayambu G, Boots R, Arzapalo MFA, Vlasenko R, Gromova E, Loginov S, Kiselevskiy M, Dolgikova Y, Tang KB, Chau CM, Acebes SR, Lam KN, Gil E, Suh GY, Park CM, Park J, Chung CR, Lee CT, Chao A, Shih PY, Chang YF, Martínez ÁF, Lai CH, Hsu YC, Yeh YC, Cheng YJ, Colella V, Zarrillo N, D’Amico M, Forfori F, Pezza B, Laddomada T, Aliaga SM, Beltramelli V, Pizzaballa ML, Doronzio A, Balicco B, Kiers D, van der Heijden W, Gerretsen J, de Mast Q, el Messaoudi S, Rongen G, Para LH, Gomes M, Kox M, Pickkers P, Riksen NP, Kashiwagi Y, Okada M, Hayashi K, Inagaki Y, Fujita S, Nakamae MN, Payá JM, Kang YR, Souza RB, Liberatore AMA, Koh IHJ, Blet A, Sadoune M, Lemarié J, Bihry N, Bern R, Polidano E, Mulero FR, Merval R, Launay JM, Lévy B, Samuel JL, Mebazaa A, Hartmann J, Harm S, Weber V, Guerci P, Ince Y, Heeman P, Ergin B, Ince C, Uz Z, Massey M, Ince Y, Papatella R, Bulent E, Guerci P, Toraman F, Ince C, Longbottom ER, Torrance HD, Owen HC, Hinds CJ, Pearse RM, O’Dywer MJ, Trogrlic Z, van der Jagt M, Lingsma H, Ponssen HH, Schoonderbeek JF, Schreiner F, Verbrugge SJ, Duran S, van Achterberg T, Bakker J, Gommers DAMPJ, Ista E, Krajčová A, Waldauf P, Duška F, Shah A, Roy N, McKechnie S, Doree C, Fisher S, Stanworth SJ, Jensen JF, Overgaard D, Bestle MH, Christensen DF, Egerod I, Pivkina A, Gusarov V, Zhivotneva I, Pasko N, Zamyatin M, Jensen JF, Egerod I, Bestle MH, Christensen DF, Alklit A, Hansen RL, Knudsen H, Grode LB, Overgaard D, Hravnak M, Chen L, Dubrawski A, Clermont G, Pinsky MR, Parry SM, Knight LD, Connolly BC, Baldwin CE, Puthucheary ZA, Denehy L, Hart N, Morris PE, Mortimore J, Granger CL, Jensen HI, Piers R, Van den Bulcke B, Malmgren J, Metaxa V, Reyners AK, Darmon M, Rusinova K, Talmor D, Meert AP, Cancelliere L, Zubek L, Maia P, Michalsen A, Decruyenaere J, Kompanje E, Vanheule S, Azoulay E, Vansteelandt S, Benoit D, Van den Bulcke B, Piers R, Jensen HI, Malmgren J, Metaxa V, Reyners AK, Darmon M, Rusinova K, Talmor D, Meert AP, Cancelliere L, Zubek L, Maia P, Michalsen A, Decruyenaere J, Kompanje E, Vanheule S, Azoulay E, Vansteelandt S, Benoit D, Ryan C, Dawson D, Ball J, Noone K, Aisling B, Prudden S, Ntantana A, Matamis D, Savvidou S, Giannakou M, Gouva M, Nakos G, Koulouras V, Aron J, Lumley G, Milliken D, Dhadwal K, McGrath BA, Lynch SJ, Bovento B, Sharpe G, Grainger E, Pieri-Davies S, Wallace S, McGrath B, Lynch SJ, Bovento B, Grainger E, Pieri-Davies S, Sharpe G, Wallace S, Jung M, Cho J, Park H, Suh G, Kousha O, Paddle J, Gripenberg LG, Rehal MS, Wernerman J, Rooyackers O, de Grooth HJ, Choo WP, Spoelstra-de Man AM, Swart EL, Oudemans-van Straaten HM, Talan L, Güven G, Altıntas ND, Padar M, Uusvel G, Starkopf L, Starkopf J, Blaser AR, Kalaiselvan MS, Arunkumar AS, Renuka MK, Shivkumar RL, Volbeda M, ten Kate D, Hoekstra M, van der Maaten JM, Nijsten MW, Komaromi A, Rooyackers O, Wernerman J, Norberg Å, Smedberg M, Mori M, Pettersson L, Norberg Å, Rooyackers O, Wernerman J, Theodorakopoulou M, Christodoulopoulou T, Diamantakis A, Frantzeskaki F, Kontogiorgi M, Chrysanthopoulou E, Lygnos M, Diakaki C, Armaganidis A, Gundogan K, Dogan E, Coskun R, Muhtaroglu S, Sungur M, Ziegler T, Guven M, Kleyman A, Khaliq W, Andreas D, Singer M, Meierhans R, Schuepbach R, De Brito-Ashurst I, Zand F, Sabetian G, Nikandish R, Hagar F, Masjedi M, Maghsudi B, Vazin A, Ghorbani M, Asadpour E, Kao KC, Chiu LC, Hung CY, Chang CH, Li SH, Hu HC, El Maraghi S, Ali M, Rageb D, Helmy M, Marin-Corral J, Vilà C, Masclans JR, Vàzquez A, Martín-Loeches I, Díaz E, Yébenes JC, Rodriguez A, Álvarez-Lerma F, Varga N, Cortina-Gutiérrez A, Dono L, Martínez-Martínez M, Maldonado C, Papiol E, Pérez-Carrasco M, Ferrer R, Nweze K, Morton B, Welters I, Houard M, Voisin B, Ledoux G, Six S, Jaillette E, Nseir S, Romdhani S, Bouneb R, Loghmari D, Aicha NB, Ayachi J, Meddeb K, Chouchène I, Khedher A, Boussarsar M, Chan KS, Yu WL, Marin-Corral J, Vilà C, Masclans JR, Nolla J, Vidaur L, Bonastre J, Suberbiola B, Guerrero JE, Rodriguez A, Coll NR, Jiménez GJ, Brugger SC, Calero JC, Garrido BB, García M, Martínez MP, Vidal MV, de la Torre MC, Vendrell E, Palomera E, Güell E, Yébenes JC, Serra-Prat M, Bermejo-Martín JF, Almirall J, Tomas E, Escoval A, Froe F, Pereira MHV, Velez N, Viegas E, Filipe E, Groves C, Reay M, Chiu LC, Hu HC, Hung CY, Chang CH, Li SH, Kao KC, Ballin A, Facchin F, Sartori G, Zarantonello F, Campello E, Radu CM, Rossi S, Ori C, Simioni P, Umei N, Shingo I, Santos AC, Candeias C, Moniz I, Marçal R, e Silva ZC, Ribeiro JM, Georger JF, Ponthus JP, Tchir M, Amilien V, Ayoub M, Barsam E, Martucci G, Panarello G, Tuzzolino F, Capitanio G, Ferrazza V, Carollo T, Giovanni L, Arcadipane A, Sánchez ML, González-Gay MA, Díaz FJL, López MIR, Zogheib E, Villeret L, Nader J, Bernasinski M, Besserve P, Caus T, Dupont H, Morimont P, Habran S, Hubert R, Desaive T, Blaffart F, Janssen N, Guiot J, Pironet A, Dauby P, Lambermont B, Zarantonello F, Ballin A, Facchin F, Sartori G, Campello E, Pettenuzzo T, Citton G, Rossi S, Simioni P, Ori C, Kirakli C, Ediboglu O, Ataman S, Yarici M, Tuksavul F, Keating S, Gibson A, Gilles M, Dunn M, Price G, Young N, Remeta P, Bishop P, Zamora MDF, Muñoz-Bono J, Curiel-Balsera E, Aguilar-Alonso E, Hinojosa R, Gordillo-Brenes A, Arboleda-Sánchez JA, Skorniakov I, Vikulova D, Whiteley C, Shaikh O, Jones A, Ostermann M, Forni L, Scott M, Sahatjian J, Linde-Zwirble W, Hansell D, Laoveeravat P, Srisawat N, Kongwibulwut M, Peerapornrattana S, Suwachittanont N, Wirotwan TO, Chatkaew P, Saeyub P, Latthaprecha K, Tiranathanagul K, Eiam-ong S, Kellum JA, Berthelsen RE, Perner A, Jensen AEK, Jensen JU, Bestle MH, Gebhard DJ, Price J, Kennedy CE, Akcan-Arikan A, Liberatore AMA, Souza RB, Martins AMCRPF, Vieira JCF, Kang YR, Nakamae MN, Koh IHJ, Hamed K, Khaled MM, Soliman RA, Mokhtar MS, Seller-Pérez G, Arias-Verdú D, Llopar-Valdor E, De-Diós-Chacón I, Quesada-García G, Herrera-Gutierrez ME, Hafes R, Carroll G, Doherty P, Wright C, Vera IGG, Ralston M, Gemmell ML, MacKay A, Black E, Wright C, Docking RI, Appleton R, Ralston MR, Gemmell L, Appleton R, Wright C, Docking RI, Black E, Mackay A, Rozemeijer S, Mulier JLGH, Röttgering JG, Elbers PWG, Spoelstra-de Man AME, Tuinman PR, de Waard MC, Oudemans-van Straaten HM, Mejeni N, Nsiala J, Kilembe A, Akilimali P, Thomas G, Egerod I, Andersson AE, Fagerdahl AM, Knudsen V, Meddeb K, Cheikh AB, Hamdaoui Y, Ayachi J, Guiga A, Fraj N, Romdhani S, Sma N, Bouneb R, Chouchene I, Khedher A, Bouafia N, Boussarsar M, Amirian A, Ziaian B, Masjedi M, Fleischmann C, Thomas-Rueddel DO, Schettler A, Schwarzkopf D, Stacke A, Reinhart K, Filipe E, Escoval A, Martins A, Sousa P, Velez N, Viegas E, Tomas E, Snell G, Matsa R, Paary TTS, Kalaiselvan MS, Cavalheiro AM, Rocha LL, Vallone CS, Tonilo A, Lobato MDS, Malheiro DT, Sussumo G, Lucino NM, Zand F, Rosenthal VD, Masjedi M, Sabetian G, Maghsudi B, Ghorbani M, Dashti AS, Yousefipour A, Goodall JR, Williamson M, Tant E, Thomas N, Balci C, Gonen C, Haftacı E, Gurarda H, Karaca E, Paldusová B, Zýková I, Šímová D, Houston S, D’Antona L, Lloyd J, Garnelo-Rey V, Sosic M, Sotosek-Tokmazic V, Kuharic J, Antoncic I, Dunatov S, Sustic A, Chong CT, Sim M, Lyovarin T, Díaz FMA, Galdó SN, Garach MM, Romero OM, Bailón AMP, Pinel AC, Colmenero M, Gritsan A, Gazenkampf A, Korchagin E, Dovbish N, Lee RM, Lim MPP, Chong CT, Lim BCL, See JJ, Assis R, Filipe F, Lopes N, Pessoa L, Pereira T, Catorze N, Aydogan MS, Aldasoro C, Marchio P, Jorda A, Mauricio MD, Guerra-Ojeda S, Gimeno-Raga M, Colque-Cano M, Bertomeu-Artecero A, Aldasoro M, Valles SL, Tonon D, Triglia T, Martin JC, Alessi MC, Bruder N, Garrigue P, Velly L, Spina S, Scaravilli V, Marzorati C, Colombo E, Savo D, Vargiolu A, Cavenaghi G, Citerio G, Andrade AHV, Bulgarelli P, Araujo JAP, Gonzalez V, Souza VA, Costa A, Massant C, Filho CACA, Morbeck RA, Burgo LE, van Groenendael R, van Eijk LT, Leijte GP, Koeneman B, Kox M, Pickkers P, García-de la Torre A, de la Torre-Prados M, Fernández-Porcel A, Rueda-Molina C, Nuevo-Ortega P, Tsvetanova-Spasova T, Cámara-Sola E, García-Alcántara A, Salido-Díaz L, Liao X, Feng T, Zhang J, Cao X, Wu Q, Xie Z, Li H, Kang Y, Winkler MS, Nierhaus A, Mudersbach E, Bauer A, Robbe L, Zahrte C, Schwedhelm E, Kluge S, Zöllner C, Morton B, Mitsi E, Pennington SH, Reine J, Wright AD, Parker R, Welters ID, Blakey JD, Rajam G, Ades EW, Ferreira DM, Wang D, Kadioglu A, Gordon SB, Koch R, Kox M, Rahamat-Langedoen J, Schloesser J, de Jonge M, Pickkers P, Bringue J, Guillamat-Prats R, Torrents E, Martinez ML, Camprubí-Rimblas M, Artigas A, Blanch L, Park SY, Park YB, Song DK, Shrestha S, Park SH, Koh Y, Park MJ, Hong CW, Lesur O, Coquerel D, Sainsily X, Cote J, Söllradl T, Murza A, Dumont L, Dumaine R, Grandbois M, Sarret P, Marsault E, Salvail D, Auger-Messier M, Chagnon F, Lauretta MP, Greco E, Dyson A, Singer M, Preau S, Ambler M, Sigurta A, Saeed S, Singer M, Sarıca LT, Zibandeh N, Genc D, Gul F, Akkoc T, Kombak E, Cinel L, Akkoc T, Cinel I, Pollen SJ, Arulkumaran N, Singer M, Torrance HD, Longbottom ER, Warnes G, Hinds CJ, Pennington DJ, Brohi K, O’Dwyer MJ, Kim HY, Na S, Kim J, Chang YF, Chao A, Shih PY, Lee CT, Yeh YC, Chen LW, Adriaanse M, Trogrlic Z, Ista E, Lingsma H, Rietdijk W, Ponssen HH, Schoonderbeek JF, Schreiner F, Verbrugge SJ, Duran S, Gommers DAMPJ, van der Jagt M, Funcke S, Sauerlaender S, Saugel B, Pinnschmidt H, Reuter DA, Nitzschke R, Perbet S, Biboulet C, Lenoire A, Bourdeaux D, Pereira B, Plaud B, Bazin JE, Sautou V, Mebazaa A, Constantin JM, Legrand M, Boyko Y, Jennum P, Nikolic M. ESICM LIVES 2016: part one. Intensive Care Med Exp 2016. [PMCID: PMC5042924 DOI: 10.1186/s40635-016-0098-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
Genome-wide sequencing technologies enable investigations of the structural properties of the genome in various spatial dimensions. Here, we review computational techniques developed to model the three-dimensional genome in single cells versus ensembles of cells and assess their underlying assumptions. We further address approaches to study the spatio-temporal aspects of genome organization from single-cell data.
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Affiliation(s)
- Monika Sekelja
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112, Blindern, 0317, Oslo, Norway
| | - Jonas Paulsen
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112, Blindern, 0317, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112, Blindern, 0317, Oslo, Norway.
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Børnich C, Grytten I, Hovig E, Paulsen J, Čech M, Sandve GK. Galaxy Portal: interacting with the galaxy platform through mobile devices. Bioinformatics 2016; 32:1743-5. [PMID: 26819474 PMCID: PMC4892412 DOI: 10.1093/bioinformatics/btw042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 01/20/2016] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED : We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general. AVAILABILITY AND IMPLEMENTATION The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer. CONTACT geirksa@ifi.uio.no.
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Affiliation(s)
- Claus Børnich
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ivar Grytten
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway, Department of Tumor Biology, Institute of Cancer Research, Oslo, Norway, Department of Cancer Genetics and Informatics, Radium Hospital, Part of Oslo University Hospital, Oslo, Norway and
| | - Jonas Paulsen
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Martin Čech
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802, USA
| | - Geir Kjetil Sandve
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway
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Paulsen J, Gramstad O, Collas P. Manifold Based Optimization for Single-Cell 3D Genome Reconstruction. PLoS Comput Biol 2015; 11:e1004396. [PMID: 26262780 PMCID: PMC4532452 DOI: 10.1371/journal.pcbi.1004396] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/08/2015] [Indexed: 11/18/2022] Open
Abstract
The three-dimensional (3D) structure of the genome is important for orchestration of gene expression and cell differentiation. While mapping genomes in 3D has for a long time been elusive, recent adaptations of high-throughput sequencing to chromosome conformation capture (3C) techniques, allows for genome-wide structural characterization for the first time. However, reconstruction of "consensus" 3D genomes from 3C-based data is a challenging problem, since the data are aggregated over millions of cells. Recent single-cell adaptations to the 3C-technique, however, allow for non-aggregated structural assessment of genome structure, but data suffer from sparse and noisy interaction sampling. We present a manifold based optimization (MBO) approach for the reconstruction of 3D genome structure from chromosomal contact data. We show that MBO is able to reconstruct 3D structures based on the chromosomal contacts, imposing fewer structural violations than comparable methods. Additionally, MBO is suitable for efficient high-throughput reconstruction of large systems, such as entire genomes, allowing for comparative studies of genomic structure across cell-lines and different species. Understanding how the genome is folded in three-dimensional (3D) space is crucial for unravelling the complex regulatory mechanisms underlying the differentiation and proliferation of cells. With recent high-throughput adaptations of chromosome conformation capture in techniques such as single-cell Hi-C, it is now possible to probe 3D information of chromosomes genome-wide. Such experiments, however, only provide sparse information about contacts between regions in the genome. We have developed a tool, based on manifold based optimization (MBO), that reconstructs 3D structures from such contact information. We show that MBO allows for reconstruction of 3D genomes more consistent with the original contact map, and with fewer structural violations compared to other, related methods. Since MBO is also computationally fast, it can be used for high-throughput and large-scale 3D reconstruction of entire genomes.
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Affiliation(s)
- Jonas Paulsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway
| | - Odin Gramstad
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway
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17
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Smekens J, Paulsen J, Yang W, Omar N, Deconinck J, Hubin A, Van Mierlo J. A Modified Multiphysics model for Lithium-Ion batteries with a LixNi1/3Mn1/3Co1/3O2 electrode. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Thiel M, Paulsen J, Mayer S, Rasch C. Unterdrucklungenödem. Monatsschr Kinderheilkd 2015. [DOI: 10.1007/s00112-015-3360-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Håkelien AM, Bryne JC, Harstad KG, Lorenz S, Paulsen J, Sun J, Mikkelsen TS, Myklebost O, Meza-Zepeda LA. The regulatory landscape of osteogenic differentiation. Stem Cells 2015; 32:2780-93. [PMID: 24898411 DOI: 10.1002/stem.1759] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 04/20/2014] [Indexed: 01/08/2023]
Abstract
Differentiation of osteoblasts from mesenchymal stem cells (MSCs) is an integral part of bone development and homeostasis, and may when improperly regulated cause disease such as bone cancer or osteoporosis. Using unbiased high-throughput methods we here characterize the landscape of global changes in gene expression, histone modifications, and DNA methylation upon differentiation of human MSCs to the osteogenic lineage. Furthermore, we provide a first genome-wide characterization of DNA binding sites of the bone master regulatory transcription factor Runt-related transcription factor 2 (RUNX2) in human osteoblasts, revealing target genes associated with regulation of proliferation, migration, apoptosis, and with a significant overlap with p53 regulated genes. These findings expand on emerging evidence of a role for RUNX2 in cancer, including bone metastases, and the p53 regulatory network. We further demonstrate that RUNX2 binds to distant regulatory elements, promoters, and with high frequency to gene 3' ends. Finally, we identify TEAD2 and GTF2I as novel regulators of osteogenesis.
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Affiliation(s)
- Anne-Mari Håkelien
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital
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Mehl A, Harthug S, Lydersen S, Paulsen J, Åsvold BO, Solligård E, Damås JK, Edna TH. Prior statin use and 90-day mortality in Gram-negative and Gram-positive bloodstream infection: a prospective observational study. Eur J Clin Microbiol Infect Dis 2014; 34:609-17. [PMID: 25373530 PMCID: PMC4356896 DOI: 10.1007/s10096-014-2269-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/20/2014] [Indexed: 01/31/2023]
Abstract
In several studies on patients with bloodstream infection (BSI), prior use of statins has been associated with improved survival. Gram-positive and Gram-negative bacteria alert the innate immune system in different ways. We, therefore, studied whether the relation between prior statin use and 90-day total mortality differed between Gram-positive and Gram-negative BSI. We conducted a prospective observational cohort study of 1,408 adults with BSI admitted to Levanger Hospital between January 1, 2002, and December 31, 2011. Data on the use of statins and other medications at admission, comorbidities, functional status, treatment, and outcome were obtained from the patients’ hospital records. The relation of statin use with 90-day mortality differed between Gram-negative and Gram-positive BSI (p-value for interaction 0.01). Among patients with Gram-negative BSI, statin users had significantly lower 90-day total mortality [odds ratio (OR) 0.42, 95 % confidence interval (CI) 0.23–0.75, p = 0.003]. The association remained essentially unchanged after adjusting for the effect of sex, age, functional status before the infection, and underlying diseases that were considered confounders (adjusted OR 0.38, 95 % CI 0.20–0.72, p = 0.003). A similar analysis of patients with Gram-positive BSI showed no association of statin use with mortality (adjusted OR 1.22, 95 % CI 0.69–2.17, p = 0.49). The present study suggests that prior statin use is associated with a lower 90-day total mortality in Gram-negative BSI, but not in Gram-positive BSI.
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Affiliation(s)
- A Mehl
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Post Box 333, 7601, Levanger, Norway,
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Paulsen J, Rødland EA, Holden L, Holden M, Hovig E. A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. Nucleic Acids Res 2014; 42:e143. [PMID: 25114054 PMCID: PMC4191384 DOI: 10.1093/nar/gku738] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/10/2014] [Accepted: 08/01/2014] [Indexed: 12/23/2022] Open
Abstract
Identification of three-dimensional (3D) interactions between regulatory elements across the genome is crucial to unravel the complex regulatory machinery that orchestrates proliferation and differentiation of cells. ChIA-PET is a novel method to identify such interactions, where physical contacts between regions bound by a specific protein are quantified using next-generation sequencing. However, determining the significance of the observed interaction frequencies in such datasets is challenging, and few methods have been proposed. Despite the fact that regions that are close in linear genomic distance have a much higher tendency to interact by chance, no methods to date are capable of taking such dependency into account. Here, we propose a statistical model taking into account the genomic distance relationship, as well as the general propensity of anchors to be involved in contacts overall. Using both real and simulated data, we show that the previously proposed statistical test, based on Fisher's exact test, leads to invalid results when data are dependent on genomic distance. We also evaluate our method on previously validated cell-line specific and constitutive 3D interactions, and show that relevant interactions are significant, while avoiding over-estimating the significance of short nearby interactions.
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Affiliation(s)
- Jonas Paulsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway
| | - Einar A Rødland
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway
| | - Lars Holden
- Statistics for Innovation, Norwegian Computing Center, N-0314 Oslo, Norway
| | - Marit Holden
- Statistics for Innovation, Norwegian Computing Center, N-0314 Oslo, Norway
| | - Eivind Hovig
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway
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Kim J, Long J, Mills J, Downing N, Williams J, Paulsen J. J25 Performance Of The 36-item And 12-item Whodas 2.0 In Prodromal Huntington Disease. Journal of Neurology, Neurosurgery & Psychiatry 2014. [DOI: 10.1136/jnnp-2014-309032.208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kim R, Matsui J, Wassermann D, Vaidya J, Johnson H, Magnotta V, Long J, Mills J, Lowe M, Sakaie K, Rao S, Smith M, Paulsen J. E17 Diffusion Weighted Imaging Study Of Prefrontal Cortex White Matter In Prodromal Huntington Disease. Journal of Neurology, Neurosurgery & Psychiatry 2014. [DOI: 10.1136/jnnp-2014-309032.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Paulsen J, Long J, Ross C, Harrington D, Erwin C, Williams J, Westervelt H, Johnson H, Aylward E, Zhang Y, Bockholt J, Barker R. J01 Improving Prediction Of Huntington Disease Onset With Clinical And Imaging Measures: A 10-year Preopective Study Of Converters. Journal of Neurology, Neurosurgery & Psychiatry 2014. [DOI: 10.1136/jnnp-2014-309032.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Miller A, Epping E, Kim J, Long J, Brashers-Krug T, Craufurd D, Paulsen J. H06 Longitudinal Psychiatric Symptoms in Premanifest HD: Psychiatric Progression and Unawareness in a Decade of Data. Journal of Neurology, Neurosurgery & Psychiatry 2014. [DOI: 10.1136/jnnp-2014-309032.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Aylward E, Long J, MacDonald M, Lee JM, Paulsen J, Gusella J. E01 CAG Repeat Length Predicts Rate of Striatal Atrophy, but Relationship is Nonlinear. Journal of Neurology, Neurosurgery & Psychiatry 2014. [DOI: 10.1136/jnnp-2014-309032.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Han SH, Cho FH, Song YK, Paulsen J, Song YQ, Kim YR, Kim JK, Cho G, Cho H. Ultrafast 3D spin-echo acquisition improves Gadolinium-enhanced MRI signal contrast enhancement. Sci Rep 2014; 4:5061. [PMID: 24863102 PMCID: PMC4034007 DOI: 10.1038/srep05061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/07/2014] [Indexed: 11/27/2022] Open
Abstract
Long scan times of 3D volumetric MR acquisitions usually necessitate ultrafast in vivo gradient-echo acquisitions, which are intrinsically susceptible to magnetic field inhomogeneities. This is especially problematic for contrast-enhanced (CE)-MRI applications, where non-negligible T2* effect of contrast agent deteriorates the positive signal contrast and limits the available range of MR acquisition parameters and injection doses. To overcome these shortcomings without degrading temporal resolution, ultrafast spin-echo acquisitions were implemented. Specifically, a multiplicative acceleration factor from multiple spin echoes (×32) and compressed sensing (CS) sampling (×8) allowed highly-accelerated 3D Multiple-Modulation-Multiple-Echo (MMME) acquisition. At the same time, the CE-MRI of kidney with Gd-DOTA showed significantly improved signal enhancement for CS-MMME acquisitions (×7) over that of corresponding FLASH acquisitions (×2). Increased positive contrast enhancement and highly accelerated acquisition of extended volume with reduced RF irradiations will be beneficial for oncological and nephrological applications, in which the accurate in vivo 3D quantification of contrast agent concentration is necessary with high temporal resolution.
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Affiliation(s)
- S H Han
- Department of Biomedical Engineering, UNIST, Ulsan, South Korea
| | - F H Cho
- Department of Biomedical Engineering, UNIST, Ulsan, South Korea
| | - Y K Song
- Department of Biomedical Engineering, UNIST, Ulsan, South Korea
| | - J Paulsen
- Schlumberger Doll Research Center, Cambridge, MA, USA
| | - Y Q Song
- Schlumberger Doll Research Center, Cambridge, MA, USA
| | - Y R Kim
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - J K Kim
- Department of Radiology, Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - G Cho
- Korea Basic Science Institute, Ochang, South Korea
| | - H Cho
- Department of Biomedical Engineering, UNIST, Ulsan, South Korea
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Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E. HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. ACTA ACUST UNITED AC 2014; 30:1620-2. [PMID: 24511080 PMCID: PMC4029040 DOI: 10.1093/bioinformatics/btu082] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Summary: Recently developed methods that couple next-generation sequencing with chromosome conformation capture-based techniques, such as Hi-C and ChIA-PET, allow for characterization of genome-wide chromatin 3D structure. Understanding the organization of chromatin in three dimensions is a crucial next step in the unraveling of global gene regulation, and methods for analyzing such data are needed. We have developed HiBrowse, a user-friendly web-tool consisting of a range of hypothesis-based and descriptive statistics, using realistic assumptions in null-models. Availability and implementation: HiBrowse is supported by all major browsers, and is freely available at http://hyperbrowser.uio.no/3d. Software is implemented in Python, and source code is available for download by following instructions on the main site. Contact:jonaspau@ifi.uio.no Supplementary Information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jonas Paulsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway
| | - Geir Kjetil Sandve
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway
| | - Sveinung Gundersen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway
| | - Tonje G Lien
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway
| | - Kai Trengereid
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway
| | - Eivind Hovig
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, NorwayInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, NorwayInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway
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Parke E, Hart J, Baldock D, Barchard K, Etcoff L, Allen D, Stolberg P, Nardi N, Cohen J, Jones W, Loe S, Etcoff L, Delgaty L, Tan A, Bunner M, Delgaty L, Tan A, Bunner M, Tan A, Delgaty L, Bunner M, Tan A, Delgaty L, Bunner M, Goodman G, Kim W, Nolty A, Marion S, Davis A, Finch W, Piehl J, Moss L, Nogin R, Dean R, Davis J, Lindstrom W, Poon M, Fonseca F, Bure-Reyes A, Stewart J, Golden C, Fonseca F, Bure-Reyes A, Stewart J, Golden C, Fields K, Hill B, Corley E, Russ K, Boettcher A, Musso M, Rohling M, Rowden A, Downing K, Benners M, Miller D, Maricle D, Dugbartey T, Anum A, Anderson J, Daniel M, Hoskins L, Gillis K, Khen S, Carter K, Ayers C, Neeland I, Cullum M, Weiner M, Rossetti H, Buddin W, Mahal S, Schroeder R, Baade L, Macaluso M, Phelps K, Evans C, Clark J, Vickery C, Chow J, Stokic D, Phelps K, Evans C, Watson S, Odom R, Clark J, Clark J, Odom R, Evans C, Vickery C, Thompson J, Noggle C, Kane C, Kecala N, Lane E, Raymond M, Woods S, Iudicello J, Dawson M, Ghias A, Choe M, Yudovin S, McArthur D, Asarnow R, Giza C, Babikian T, Tun S, O'Neil M, Ensley M, Storzbach D, Ellis R, O'Neil M, Carlson K, Storzbach D, Brenner L, Freeman M, Quinones A, Motu'apuaka M, Ensley M, Kansagara D, Brickell T, Grant I, Lange R, Kennedy J, Ivins B, Marshall K, Prokhorenko O, French L, Brickell T, Lange R, Bhagwat A, French L, Weber E, Nemeth D, Songy C, Gremillion A, Lange R, Brubacher J, Shewchuk J, Heran M, Jarrett M, Rauscher A, Iverson G, Woods S, Ukueberuwa D, Medaglia J, Hillary F, Meyer J, Vargas G, Rabinowitz A, Barwick F, Arnett P, Levan A, Gale S, Atkinson J, Boettcher A, Hill B, Rohling M, Stolberg P, Hart J, Allen D, Mayfield J, Ellis M, Marion SD, Houshyarnejad A, Grant I, Akarakian R, Kernan C, Babikian T, Asarnow R, Bens M, Fisher M, Garrett C, Vinogradov S, Walker K, Torstrick A, Uderman J, Wellington R, Zhao L, Fromm N, Dahdah M, Salisbury D, Monden K, Lande E, Wanlass R, Fong G, Smith K, Miele A, Novakovic-Agopian T, Chen A, Rome S, Rossi A, Abrams G, Murphy M, Binder D, Muir J, Carlin G, Loya F, Rabinovitz B, Bruhns M, Adler M, Schleicher-Dilks S, Messerly J, Babika C, Ukpabi C, Golden C, Schleicher-Dilks S, Coad S, Messerly J, Schaffer S, Babika C, Golden C, Cowad S, Paisley S, Fontanetta R, Messerly J, Golden C, Holder C, Kloezeman K, Henry B, Burns W, Patt V, Minassian A, Perry W, Cooper L, Allen D, Vogel S, Woolery H, Ciobanu C, Simone A, Bedard A, Olivier T, O'Neill S, Rajendran K, Halperin J, Rudd-Barnard A, Steenari M, Murry J, Le M, Becker T, Mucci G, Zupanc M, Shapiro E, Santos O, Cadavid N, Giese E, Londono N, Osmon D, Zamzow J, Culnan E, D'Argenio D, Mosti C, Spiers M, Schleicher-Dilks S, Kloss J, Curiel A, Miller K, Olmstead R, Gottuso A, Saucier C, Miller J, Dye R, Small G, Kent A, Andrews P, Puente N, Terry D, Faraco C, Brown C, Patel A, Siegel J, Miller L, Lee B, Joan M, Thaler N, Fontanetta R, Carla F, Allen D, Nguyen T, Glass L, Coles C, Julie K, May P, Sowell E, Jones K, Riley E, Demsky Y, Mattson S, Allart A, Freer B, Tiersky L, Sunderaraman P, Sylvester P, Ang J, Schultheis M, Newton S, Holland A, Burns K, Bunting J, Taylor J, Muetze H, Coe M, Harrison D, Putnam M, Tiersky L, Freer B, Holland A, Newton S, Sakamoto M, Bunting J, Taylor J, Coe M, Harrison D, Musso M, Hill B, Barker A, Pella R, Gouvier W, Davis J, Woods S, Wall J, Etherton J, Brand T, Hummer B, O'Shea C, Segovia J, Thomlinson S, Schulze E, Roskos P, Gfeller J, Loftis J, Fogel T, Barrera K, Sherzai A, Chappell A, Harrison A, Armstrong I, Flaro L, Pedersen H, Shultz LS, Roper B, Huckans M, Basso M, Silk-Eglit G, Stenclik J, Miele A, Lynch J, McCaffrey R, Silk-Eglit G, Stenclik J, Miele A, Lynch J, Musso M, McCaffrey R, Martin P, VonDran E, Baade L, Heinrichs R, Schroeder R, Hunter B, Calloway J, Rolin S, Akeson S, Westervelt H, Mohammed S, An K, Jeffay E, Zakzanis K, Lynch A, Drasnin D, Ikanga J, Graham O, Reid M, Cooper D, Long J, Lange R, Kennedy J, Hopewell C, Lukaszewska B, Pachalska M, Bidzan M, Lipowska M, McCutcheon L, Kaup A, Park J, Morgan E, Kenton J, Norman M, Martin P, Netson K, Woods S, Smith M, Paulsen J, Hahn-Ketter A, Paxton J, Fink J, Kelley K, Lee R, Pliskin N, Segala L, Vasilev G, Bozgunov K, Naslednikova R, Raynov I, Gonzalez R, Vassileva J, Bonilla X, Fedio A, Johnson K, Sexton J, Blackstone K, Weber E, Moore D, Grant I, Woods S, Pimental P, Welch M, Ring M, Stranks E, Crowe S, Jaehnert S, Ellis C, Prince C, Wheaton V, Schwartz D, Loftis J, Fuller B, Hoffman W, Huckans M, Turecka S, McKeever J, Morse C, Schultheis M, Dinishak D, Dasher N, Vik P, Hachey D, Bowman B, Van Ness E, Williams C, Zamzow J, Sunderaraman P, Kloss J, Spiers M, Swirsky-Sacchetti T, Alhassoon O, Taylor M, Sorg S, Schweinsburg B, Stricker N, Kimmel C, Grant I, Alhassoon O, Taylor M, Sorg S, Schweinsburg B, Stephan R, Stricker N, Grant I, Hertza J, Tyson K, Northington S, Loughan A, Perna R, Davis A, Collier M, Schroeder R, Buddin W, Schroeder R, Moore C, Andrew W, Ghelani A, Kim J, Curri M, Patel S, Denney D, Taylor S, Huberman S, Greenberg B, Lacritz L, Brown D, Hughes S, Greenberg B, Lacritz L, Vargas V, Upshaw N, Whigham K, Peery S, Casto B, Barker L, Otero T, La D, Nunan-Saah J, Phoong M, Gill S, Melville T, Harley A, Gomez R, Adler M, Tsou J, Schleicher-Dilks S, Golden C, Tsou J, Schleicher-Dilks S, Adler M, Golden C, Cowad S, Link J, Barker T, Gulliver K, Golden C, Young K, Moses J, Lum J, Vik P, Legarreta M, Van Ness E, Williams C, Dasher N, Williams C, Vik P, Dasher N, Van Ness E, Bowman B, Nakhutina L, Margolis S, Baek R, Gonzalez J, Hill F, England H, Horne-Moyer L, Stringer A, DeFilippis N, Lyon A, Giovannetti T, Fanning M, Heverly-Fitt S, Stambrook E, Price C, Selnes O, Floyd T, Vogt E, Thiruselvam I, Quasney E, Hoelzle J, Grant N, Moses J, Matevosyan A, Delano-Wood L, Alhassoon O, Hanson K, Lanni E, Luc N, Kim R, Schiehser D, Benners M, Downing K, Rowden A, Miller D, Maricle D, Kaminetskaya M, Moses J, Tai C, Kaminetskaya M, Melville T, Poole J, Scott R, Hays F, Walsh B, Mihailescu C, Douangratdy M, Scott B, Draffkorn C, Andrews P, Schmitt A, Waksmunski C, Brady K, Andrews A, Golden C, Olivier T, Espinoza K, Sterk V, Spengler K, Golden C, Olivier T, Spengler K, Sterk V, Espinoza K, Golden C, Gross J, DeFilippis N, Neiman-Kimel J, Romers C, Isaacs C, Soper H, Sordahl J, Tai C, Moses J, D'Orio V, Glukhovsky L, Beier M, Shuman M, Spat J, Foley F, Guatney L, Bott N, Moses J, Miranda C, Renteria MA, Rosario A, Sheynin J, Fuentes A, Byrd D, Mindt MR, Batchelor E, Meyers J, Patt V, Thomas M, Minassian A, Geyer M, Brown G, Perry W, Smith C, Kiefel J, Rooney A, Gouaux B, Ellis R, Grant I, Moore D, Graefe A, Wyman-Chick K, Daniel M, Beene K, Jaehnert S, Choi A, Moses J, Iudicello J, Henry B, Minassian A, Perry W, Marquine M, Morgan E, Letendre S, Ellis R, Woods S, Grant I, Heaton R, Constantine K, Fine J, Palewjala M, Macher R, Guatney L, Earleywine M, Draffkorn C, Scott B, Andrews P, Schmitt A, Dudley M, Silk-Eglit G, Stenclik J, Miele A, Lynch J, McCaffrey R, Scharaga E, Gomes W, McGinley J, Miles-Mason E, Colvin M, Carrion L, Romers C, Soper H, Zec R, Kohlrus S, Fritz S, Robbs R, Ala T, Zec R, Fritz S, Kohlrus S, Robbs R, Ala T, Edwards M, Hall J, O'Bryant S, Miller J, Dye R, Miller K, Baerresen K, Small G, Moskowitz J, Puente A, Ahmed F, Faraco C, Brown C, Evans S, Chu K, Miller L, Young-Bernier M, Tanguay A, Tremblay F, Davidson P, Duda B, Puente A, Terry D, Kent A, Patel A, Miller L, Junod A, Marion SD, Harrington M, Fonteh A, Gurnani A, John S, Gavett B, Diaz-Santos M, Mauro S, Beaute J, Cronin-Golomb A, Fazeli P, Gouaux B, Rosario D, Heaton R, Moore D, Puente A, Lindbergh C, Chu K, Evans S, Terry D, Duda B, Mackillop J, Miller S, Greco S, Klimik L, Cohen J, Robbins J, Lashley L, Schleicher-Dilks S, Golden C, Kunkes I, Culotta V, Kunkes I, Griffits K, Loughan A, Perna R, Hertza J, Cohen M, Northington S, Tyson K, Musielak K, Fine J, Kaczorowski J, Doty N, Braaten E, Shah S, Nemanim N, Singer E, Hinkin C, Levine A, Gold A, Evankovich K, Lotze T, Yoshida H, O'Bryan S, Roberg B, Glusman M, Ness A, Thelen J, Wilson L, Feaster T, Bruce J, Lobue C, Brown D, Hughes S, Greenberg B, Lacritz L, Bristow-Murray B, Andrews A, Bermudez C, Golden C, Moore R, Pulver A, Patterson T, Bowie C, Harvey P, Jeste D, Mausbach B, Wingo J, Fink J, Lee R, Pliskin N, Legenkaya A, Henry B, Minassian A, Perry W, McKeever J, Morse C, Thomas F, Schultheis M, Ruocco A, Daros A, Gill S, Grimm D, Saini G, Relova R, Hoblyn J, Lee T, Stasio C, Mahncke H, Drag L, Grimm D, Gill S, Saini G, Relova R, Hoblyn J, Lee T, Stasio C, Mahncke H, Drag L, Verbiest R, Ringdahl E, Thaler N, Sutton G, Vogel S, Reyes A, Ringdahl E, Vogel S, Freeman A, Call E, Allen D, March E, Salzberg M, Vogel S, Ringdahl E, Freeman A, Dadis F, Allen D, Sisk S, Ringdahl E, Vogel S, Freeman A, Allen D, DiGangi J, Silva L, Pliskin N, Thieme B, Daniel M, Jaehnert S, Noggle C, Thompson J, Kecala N, Lane E, Kane C, Noggle C, Thompson J, Lane E, Kecala N, Kane C, Palmer G, Happe M, Paxson J, Jurek B, Graca J, Olson S, Melville T, Harley A, La D, Phoong M, Gill S, Jocson VA, Nunan-Saah J, Keller J, Gomez R, Melville T, Kaminetskaya M, Poole J, Vernon A, Van Vleet T, DeGutis J, Chen A, Marini C, Dabit S, Gallegos J, Zomet A, Merzenich M, Thaler N, Linck J, Heyanka D, Pastorek N, Miller B, Romesser J, Sim A, Allen D, Zimmer A, Marcinak J, Hibyan S, Webbe F, Rainwater B, Francis J, Baum L, Sautter S, Donders J, Hui E, Barnes K, Walls G, Erikson S, Bailie J, Schwab K, Ivins B, Boyd C, Neff J, Cole W, Lewis S, Bailie J, Schwab K, Ivins B, Boyd C, Neff J, Cole W, Lewis S, Ramirez C, Oganes M, Gold S, Tanner S, Pina D, Merritt V, Arnett P, Heyanka D, Linck J, Thaler N, Pastorek N, Miller B, Romesser J, Sim A, Parks A, Roskos P, Gfeller J, Clark A, Isham K, Carter J, McLeod J, Romero R, Dahdah M, Barisa M, Schmidt K, Barnes S, Dubiel R, Dunklin C, Harper C, Callender L, Wilson A, Diaz-Arrastia R, Shafi S, Jacquin K, Bolshin L, Jacquin K, Romers C, Gutierrez E, Messerly J, Tsou J, Adler M, Golden C, Harmell A, Mausbach B, Moore R, Depp C, Jeste D, Palmer B, Hoadley R, Hill B, Rohling M, Mahdavi S, Fine J, daCruz K, Dinishak D, Richardson G, Vertinski M, Allen D, Mayfield J, Margolis S, Miele A, Rabinovitz B, Schaffer S, Kline J, Boettcher A, Hill B, Hoadley R, Rohling M, Eichstaedt K, Vale F, Benbadis S, Bozorg A, Rodgers-Neame N, Rinehardt E, Mattingly M, Schoenberg M, Fares R, Fares R, Carrasco R, Grups J, Evans B, Simco E, Mittenberg W, Carrasco R, Grups J, Evans B, Simco E, Mittenberg W, Rach A, Baughman B, Young C, Bene E, Irwin C, Li Y, Poulin R, Jerram M, Susmaras T, Gansler D, Ashendorf L, Miarmi L, Fazio R, Cantor J, Fernandez A, Godoy-Garcete G, Marchetti P, Harrison A, Armstrong I, Harrison L, Iverson G, Brinckman D, Ayaz H, Schultheis M, Heinly M, Vitelli K, Russler K, Sanchez I, Jones W, Loe S, Raines T, Hart J, Bene E, Li Y, Irwin C, Baughman B, Rach A, Bravo J, Schilling B, Weiss L, Lange R, Shewchuk J, Heran M, Rauscher A, Jarrett M, Brubacher J, Iverson 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Steed A, Kark S, Lafleche G, Brown T, Bogdanova Y, Strongin E, Spickler C, Drasnin D, Strongin C, Poreh A, Houshyarnejad A, Ellis M, Babikian T, Kernan C, Asarnow R, Didehbani N, Cullum M, Loneman L, Mansinghani S, Hart J, Fischer J. POSTER SESSIONS SCHEDULE. Arch Clin Neuropsychol 2013. [DOI: 10.1093/arclin/act054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalaš M, Lien T, Rye MB, Frigessi A, Hovig E. The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Res 2013; 41:W133-41. [PMID: 23632163 PMCID: PMC3692097 DOI: 10.1093/nar/gkt342] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/27/2013] [Accepted: 04/10/2013] [Indexed: 11/14/2022] Open
Abstract
The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome.
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Affiliation(s)
- Geir K. Sandve
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Sveinung Gundersen
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Morten Johansen
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Ingrid K. Glad
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Krishanthi Gunathasan
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Lars Holden
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Marit Holden
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Knut Liestøl
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Ståle Nygård
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Vegard Nygaard
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Jonas Paulsen
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Halfdan Rydbeck
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Kai Trengereid
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Trevor Clancy
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Finn Drabløs
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Egil Ferkingstad
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Matúš Kalaš
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Tonje Lien
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Morten B. Rye
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Arnoldo Frigessi
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Eivind Hovig
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, PO Box 4950, Nydalen, 0424 Oslo, Norway, Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway, Department of Mathematics, University of Oslo, PO Box 1053, Blindern, 0316 Oslo, Norway, Department of Medical Biology, Faculty of Health Science, University of Tromsø, 9037 Tromsø, Norway, Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway, Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, PO Box 4950 Nydalen, N-0424 Oslo, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, 5020 Bergen, Norway and Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
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Paulsen J, Lien TG, Sandve GK, Holden L, Borgan O, Glad IK, Hovig E. Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Res 2013; 41:5164-74. [PMID: 23571755 PMCID: PMC3664813 DOI: 10.1093/nar/gkt227] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The study of chromatin 3D structure has recently gained much focus owing to novel techniques for detecting genome-wide chromatin contacts using next-generation sequencing. A deeper understanding of the architecture of the DNA inside the nucleus is crucial for gaining insight into fundamental processes such as transcriptional regulation, genome dynamics and genome stability. Chromatin conformation capture-based methods, such as Hi-C and ChIA-PET, are now paving the way for routine genome-wide studies of chromatin 3D structure in a range of organisms and tissues. However, appropriate methods for analyzing such data are lacking. Here, we propose a hypothesis test and an enrichment score of 3D co-localization of genomic elements that handles intra- or interchromosomal interactions, both separately and jointly, and that adjusts for biases caused by structural dependencies in the 3D data. We show that maintaining structural properties during resampling is essential to obtain valid estimation of P-values. We apply the method on chromatin states and a set of mutated regions in leukemia cells, and find significant co-localization of these elements, with varying enrichment scores, supporting the role of chromatin 3D structure in shaping the landscape of somatic mutations in cancer.
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Affiliation(s)
- Jonas Paulsen
- Section for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, PO Box 4950, Nydalen, N-0424 Oslo, Norway
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Nordstrand LM, Furu K, Paulsen J, Rognes T, Klungland A. Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes. Nucleic Acids Res 2012; 40:10950-63. [PMID: 22965116 PMCID: PMC3505970 DOI: 10.1093/nar/gks839] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Piwi proteins and Piwi-interacting small RNAs (piRNAs) have known functions in transposon silencing in the male germline of fetal and newborn mice. Both are also present in adult testes; however, their function here remains a mystery. Here, we confirm that most piRNAs in meiotic spermatocytes originate from clusters in non-repeat intergenic regions of DNA. The regulation of these piRNA clusters, including the processing of the precursor transcripts into individual piRNAs, is accomplished through mostly unknown processes. We present a possible regulatory mechanism for one such cluster, named cluster 1082B, located on chromosome 7 in the mouse genome. The 1082B precursor transcript and its 788 unique piRNAs are repressed by the Alkbh1 dioxygenase and the testis-specific transcription repressor Tzfp. We observe a remarkable >1000-fold upregulation of individual piRNAs in pachytene spermatocytes isolated from Alkbh1- and Tzfp-deficient murine testes. Repression of cluster 1082B is further supported by the identification of a 10-bp Tzfp recognition sequence contained within the precursor transcript. Downregulation of LINE1 and IAP transcripts in the Alkbh1- and Tzfp-deficient mice leads us to propose a potential role for the 1082B-encoded piRNAs in transposon control.
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Affiliation(s)
- Line M Nordstrand
- Department of Microbiology, Centre for Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, NO-0424 Oslo, Norway
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Nopoulos P, Mathews K, Paulsen J, Epping E, Conrad A, Perlmutter J, Schlaggar B. I02 Effect of CAG length on motor scores of children at risk for huntington's disease. J Neurol Neurosurg Psychiatry 2012. [DOI: 10.1136/jnnp-2012-303524.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Nopoulos P, Lee J, Mathews K, Epping E, Paulsen J, Conrad A. K01 Behaviour assessments in children at risk for huntington's disease. J Neurol Psychiatry 2012. [DOI: 10.1136/jnnp-2012-303524.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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McCusker E, Gunn D, Epping E, Loy C, Long J, Radford K, Griffith J, Mills J, Paulsen J. I01 Unawareness of motor phenoconversion in huntington disease. J Neurol Psychiatry 2012. [DOI: 10.1136/jnnp-2012-303524.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Valerio L, Di Donato S, Long J, Juhl A, Paulsen J. F13 Progressive reduction of plasma 24S-hydroxycholestrol in prodromal HD subjects according with clinical and MRI features in the PREDICT-HD study. J Neurol Psychiatry 2012. [DOI: 10.1136/jnnp-2012-303524.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Nopoulos P, Epping E, Conrad A, Mathews K, Perlmutter J, Schlaggar B, Paulsen J, Byars J, Magnotta V. G04 Brain structure in children at risk for Huntington's disease. J Neurol Psychiatry 2012. [DOI: 10.1136/jnnp-2012-303524.84] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Fallows R, McCoy K, Hertza J, Klosson E, Estes B, Stroescu I, Salinas C, Stringer A, Aronson S, MacAllister W, Spurgin A, Morriss M, Glasier P, Stavinoha P, Houshyarnejad A, Jacobus J, Norman M, Peery S, Mattingly M, Pennuto T, Anderson-Hanley C, Miele A, Dunnam M, Edwards M, O'Bryant S, Johnson L, Barber R, Inscore A, Kegel J, Kozlovsky A, Tarantino B, Goldberg A, Herrera-Pino J, Jubiz-Bassi N, Rashid K, Noniyeva Y, Vo K, Stephens V, Gomez R, Sanders C, Kovacs M, Walton B, Schmitter-Edgecombe M, Schmitter-Edgecombe M, Parsey C, Cook D, Woods S, Weinborn M, Velnoweth A, Rooney A, Bucks R, Adalio C, White S, Blair J, Barber B, Marcy S, Barber B, Marcy S, Boseck J, McCormick C, Davis A, Berry K, Koehn E, Tiberi N, Gelder B, Brooks B, Sherman E, Garcia M, Robillard R, Gunner J, Miele A, Lynch J, McCaffrey R, Hamilton J, Froming K, Nemeth D, Steger A, Lebby P, Harrison J, Mounoutoua A, Preiss J, Brimager A, Gates E, Chang J, Cisneros H, Long J, Petrauskas V, Casey J, Picard E, Long J, Petrauskas V, Casey J, Picard E, Miele A, Gunner J, Lynch J, McCaffrey R, Rodriguez M, Fonseca F, Golden C, Davis J, Wall J, DeRight J, Jorgensen R, Lewandowski L, Ortigue S, Etherton J, Axelrod B, Green C, Snead H, Semrud-Clikeman M, Kirk J, Connery A, Kirkwood M, Hanson ML, Fazio R, Denney R, Myers W, McGuire A, Tree H, Waldron-Perrine B, Goldenring Fine J, Spencer R, Pangilinan P, Bieliauskas L, Na S, Waldron-Perrine B, Tree H, Spencer R, Pangilinan P, Bieliauskas L, Peck C, Bledsoe J, Schroeder R, Boatwright B, Heinrichs R, Baade L, Rohling M, Hill B, Ploetz D, Womble M, Shenesey J, Schroeder R, Semrud-Clikeman M, Baade L, VonDran E, Webster B, Brockman C, Burgess A, Heinrichs R, Schroeder R, Baade L, VonDran E, Webster B, Goldenring Fine J, Brockman C, Heinrichs R, Schroeder R, Baade L, VonDran E, Webster B, Brockman C, Heinrichs R, Schroeder R, Baade L, Bledsoe J, VonDran E, Webster B, Brockman C, Heinrichs R, Schroeder R, Baade L, VonDran E, Webster B, Brockman C, Heinrichs R, Thaler N, Strauss G, White T, Gold J, Tree H, Waldron-Perrine B, Spencer R, McGuire A, Na S, Pangilinan P, Bieliauskas L, Allen D, Vincent A, Roebuck-Spencer T, Cooper D, Bowles A, Gilliland K, Watts A, Ahmed F, Miller L, Yon A, Gordon B, Bello D, Bennett T, Yon A, Gordon B, Bennett T, Wood N, Etcoff L, Thede L, Oraker J, Gibson F, Stanford L, Gray S, Vroman L, Semrud-Clikeman M, Taylor T, Seydel K, Bure-Reyes A, Stewart J, Tourgeman I, Demsky Y, Golden C, Burns W, Gray S, Burns K, Calderon C, Tourgeman I, Golden C, Neblina C, San Miguel Montes L, Allen D, Strutt A, Scott B, Strutt A, Scott B, Armstrong P, Booth C, Blackstone K, Moore D, Gouaux B, Ellis R, Atkinson J, Grant I, Brennan L, Schultheis M, Hurtig H, Weintraub D, Duda J, Moberg P, Chute D, Siderowf A, Brescian N, Gass C, Brewster R, King T, Morris R, Krawiecki N, Dinishak D, Richardson G, Estes B, Knight M, Hertza J, Fallows R, McCoy K, Garcia S, Strain G, Devlin M, Cohen R, Paul R, Crosby R, Mitchell J, Gunstad J, Hancock L, Bruce J, Roberg B, Lynch S, Hertza J, Klosson E, Varnadore E, Schiff W, Estes B, Hertza J, Varnadore E, Estes B, Kaufman R, Rinehardt E, Schoenberg M, Mattingly M, Rosado Y, Velamuri S, LeBlanc M, Pimental P, Lynch-Chee S, Broshek D, Lyons P, McKeever J, Morse C, Ang J, Leist T, Tracy J, Schultheis M, Morgan E, Woods S, Rooney A, Perry W, Grant I, Letendre S, Morse C, McKeever J, Schultheis M, Musso M, Jones G, Hill B, Proto D, Barker A, Gouvier W, Nersesova K, Drexler M, Cherkasova E, Sakamoto M, Marcotte T, Hilsabeck R, Perry W, Carlson M, Barakat F, Hassanein T, Shevchik K, McCaw W, Schrock B, Smith M, Moser D, Mills J, Epping E, Paulsen J, Somogie M, Bruce J, Bryan F, Buscher L, Tyrer J, Stabler A, Thelen J, Lovelace C, Spurgin A, Graves D, Greenberg B, Harder L, Szczebak M, Glisky M, Thelen J, Lynch S, Hancock L, Bruce J, Ukueberuwa D, Arnett P, Vahter L, Ennok M, Pall K, Gross-Paju K, Vargas G, Medaglia J, Chiaravalloti N, Zakrzewski C, Hillary F, Andrews A, Golden C, Belloni K, Nicewander J, Miller D, Johnson S, David Z, Weideman E, Lawson D, Currier E, Morton J, Robinson J, Musso M, Hill B, Barker A, Pella R, Jones G, Proto D, Gouvier W, Vertinski M, Allen D, Thaler N, Heisler D, Park B, Barney S, Kucukboyaci N, Girard H, Kemmotsu N, Cheng C, Kuperman J, McDonald C, Carroll C, Odland A, Miller L, Mittenberg W, Coalson D, Wahlstrom D, Raiford S, Holdnack J, Ennok M, Vahter L, Gardner E, Dasher N, Fowler B, Vik P, Grajewski M, Lamar M, Penney D, Davis R, Korthauer L, Libon D, Kumar A, Holdnack J, Iverson G, Chelune G, Hunter C, Zimmerman E, Klein R, Prathiba N, Hopewell A, Cooper D, Kennedy J, Long M, Moses J, Lutz J, Tiberi N, Dean R, Miller J, Axelrod B, Van Dyke S, Rapport L, Schutte C, Hanks R, Pella R, Fallows R, McCoy K, O'Rourke J, Hilsabeck R, Petrauskas V, Bowden S, Romero R, Hulkonen R, Boivin M, Bangirana P, John C, Shapiro E, Slonaker A, Pass L, Smigielski J, Biernacka J, Geske J, Hall-Flavin D, Loukianova L, Schneekloth T, Abulseoud O, Mrazek D, Karpyak V, Terranova J, Safko E, Heisler D, Thaler N, Allen D, Van Dyke S, Axelrod B, Zink D, Puente A, Ames H, LePage J, Carroll C, Knee K, Mittenberg W, Cummings T, Webbe F, Shepherd E, Marcinak J, Diaz-Santos M, Seichepine D, Sullivan K, Neargarder S, Cronin-Golomb A, Franchow E, Suchy Y, Kraybill M, Holland A, Newton S, Hinson D, Smith A, Coe M, Carmona J, Harrison D, Hyer L, Atkinson M, Dalibwala J, Yeager C, Hyer L, Scott C, Atkinson M, Yeager C, Jacobson K, Olson K, Pella R, Fallows R, McCoy K, O'Rourke J, Hilsabeck R, Rosado Y, Kaufman R, Velamuri S, Rinehardt E, Mattingly M, Sartori A, Clay O, Ovalle F, Rothman R, Crowe M, Schmid A, Horne L, Horn G, Johnson-Markve B, Gorman P, Stewart J, Bure-Reyes A, Golden C, Tam J, McAlister C, Schmitter-Edgecombe M, Wagner M, Brenner L, Walker A, Armstrong L, Inman E, Grimmett J, Gray S, Cornelius A, Hertza J, Klosson E, Varnadore E, Schiff W, Estes B, Johnson L, Willingham M, Restrepo L, Bolanos J, Patel F, Golden C, Rice J, Dougherty M, Golden C, Sharma V, Martin P, Golden C, Bradley E, Dinishak D, Lockwood C, Poole J, Brickell T, Lange R, French L, Chao L, Klein S, Dunnam M, Miele A, Warner G, Donnelly K, Donnelly J, Kittleson J, Bradshaw C, Alt M, England D, Denney R, Meyers J, Evans J, Lynch-Chee S, Kennedy C, Moore J, Fedor A, Spitznagel M, Gunstad J, Ferland M, Guerrero NK, Davidson P, Collins B, Marshall S, Herrera-Pino J, Samper G, Ibarra S, Parrott D, Steffen F, Backhaus S, Karver C, Wade S, Taylor H, Brown T, Kirkwood M, Stancin T, Krishnan K, Culver C, Arenivas A, Bosworth C, Shokri-Kojori E, Diaz-Arrastia R, Marquez de la PC, Lange R, Ivins B, Marshall K, Schwab K, Parkinson G, Iverson G, Bhagwat A, French L, Lichtenstein J, Adams-Deutsch Z, Fleischer J, Goldberg K, Lichtenstein J, Adams-Deutsch Z, Fleischer J, Goldberg K, Lichtenstein J, Fleischer J, Goldberg K, Lockwood C, Ehrler M, Hull A, Bradley E, Sullivan C, Poole J, Lockwood C, Sullivan C, Hull A, Bradley E, Ehrler M, Poole J, Marcinak J, Schuster D, Al-Khalil K, Webbe F, Myers A, Ireland S, Simco E, Carroll C, Mittenberg W, Palmer E, Poole J, Bradley E, Dinishak D, Piecora K, Marcinak J, Al-Khalil K, Mroczek N, Schuster D, Snyder A, Rabinowitz A, Arnett P, Schatz P, Cameron N, Stolberg P, Hart J, Jones W, Mayfield J, Allen D, Sullivan K, Edmed S, Vanderploeg R, Silva M, Vaughan C, McGuire E, Gerst E, Fricke S, VanMeter J, Newman J, Gioia G, Vaughan C, VanMeter J, McGuire E, Gioia G, Newman J, Gerst E, Fricke S, Wahlberg A, Zelonis S, Chatterjee A, Smith S, Whipple E, Mace L, Manning K, Ang J, Schultheis M, Wilk J, Herrell R, Hoge C, Zakzanis K, Yu S, Jeffay E, Zimmer A, Webbe F, Piecora K, Schuster D, Zimmer A, Piecora K, Schuster D, Webbe F, Adler M, Holster J, Golden C, Andrews A, Schleicher-Dilks S, Golden C, Arffa S, Thornton J, Arffa S, Thornton J, Arffa S, Thornton J, Arffa S, Thornton J, Canas A, Sevadjian C, Fournier A, Miller D, Maricle D, Donders J, Larsen T, Gidley Larson J, Sheehan J, Suchy Y, Higgins K, Rolin S, Dunham K, Akeson S, Horton A, Reynolds C, Horton A, Reynolds C, Jordan L, Gonzalez S, Heaton S, McAlister C, Tam J, Schmitter-Edgecombe M, Olivier T, West S, Golden C, Prinzi L, Martin P, Robbins J, Bruzinski B, Golden C, Riccio C, Blakely A, Yoon M, Reynolds C, Robbins J, Prinzi L, Martin P, Golden C, Schleicher-Dilks S, Andrews A, Adler M, Pearlson J, Golden C, Sevadjian C, Canas A, Fournier A, Miller D, Maricle D, Sheehan J, Gidley LJ, Suchy Y, Sherman E, Carlson H, Gaxiola-Valdez I, Wei X, Beaulieu C, Hader W, Brooks B, Kirton A, Barlow K, Hrabok M, Mohamed I, Wiebe S, Smith K, Ailion A, Ivanisevic M, King T, Smith K, King T, Thorgusen S, Bowman D, Suchy Y, Walsh K, Mitchell F, Jill G, Iris P, Ross K, Madan-Swain A, Gioia G, Isquith P, Webber D, DeFilippis N, Collins M, Hill F, Weber R, Johnson A, Wiley C, Zimmerman E, Burns T, DeFilippis N, Ritchie D, Odland A, Stevens A, Mittenberg W, Hartlage L, Williams B, Weidemann E, Demakis G, Avila J, Razani J, Burkhart S, Adams W, Edwards M, O'Bryant S, Hall J, Johnson L, Grammas P, Gong G, Hargrave K, Mattevada S, Barber R, Hall J, Vo H, Johnson L, Barber R, O'Bryant S, Hill B, Davis J, O'Connor K, Musso M, Rehm-Hamilton T, Ploetz D, Rohling M, Rodriguez M, Potter E, Loewenstein D, Duara R, Golden C, Velamuri S, Rinehardt E, Schoenberg M, Mattingly M, Kaufman R, Rosado Y, Boseck J, Tiberi N, McCormick C, Davis A, Hernandez Finch M, Gelder B, Cannon M, McGregor S, Reitman D, Rey J, Scarisbrick D, Holdnack J, Iverson G, Thaler N, Bello D, Whoolery H, Etcoff L, Vekaria P, Whittington L, Nemeth D, Gremillion A, Olivier T, Amirthavasagam S, Jeffay E, Zakzanis K, Barney S, Umuhoza D, Strauss G, Knatz-Bello D, Allen D, Bolanos J, Bell J, Restrepo L, Frisch D, Golden C, Hartlage L, Williams B, Iverson G, McIntosh D, Kjernisted K, Young A, Kiely T, Tai C, Gomez R, Schatzberg A, Keller J, Rhodes E, Ajilore O, Zhang A, Kumar A, Lamar M, Ringdahl E, Sutton G, Turner A, Snyder J, Allen D, Verbiest R, Thaler N, Strauss G, Allen D, Walkenhorst E, Crowe S, August-Fedio A, Sexton J, Cummings S, Brown K, Fedio P, Grigorovich A, Fish J, Gomez M, Leach L, Lloyd H, Nichols M, Goldberg M, Novakovic-Agopian T, Chen A, Abrams G, Rossi A, Binder D, Muir J, Carlin G, Murphy M, McKim R, Fitsimmons R, D'Esposito M, Shevchik K, McCaw W, Schrock B, Vernon A, Frank R, Ona PZ, Freitag E, Weber E, Woods S, Kellogg E, Grant I, Basso M, Dyer B, Daniel M, Michael P, Fontanetta R, Martin P, Golden C, Gass C, Stripling A, Odland A, Holster J, Corsun-Ascher C, Olivier T, Golden C, Legaretta M, Vik P, Van Ness E, Fowler B, Noll K, Denney D, Wiechman A, Stephanie T, Greenberg B, Lacritz L, Padua M, Sandhu K, Moses J, Sordahl J, Anderson J, Wheaton V, Anderson J, Berggren K, Cheung D, Luber H, Loftis J, Huckans M, Bennett T, Dawson C, Soper H, Bennett T, Soper H, Carter K, Hester A, Ringe W, Spence J, Posamentier M, Hart J, Haley R, Fallows R, Pella R, McCoy K, O'Rourke J, Hilsabeck R, Fallows R, Pella R, McCoy K, O'Rourke J, Hilsabeck R, Gass C, Curiel R, Gass C, Stripling A, Odland A, Goldberg M, Lloyd H, Gremillion A, Nemeth D, Whittington L, Hu E, Vik P, Dasher N, Fowler B, Jeffay E, Zakzanis K, Jordan S, DeFilippis N, Collins M, Goetsch V, Small S, Mansoor Y, Homer-Smith E, Lockwood C, Moses J, Martin P, Odland A, Fontanetta R, Sharma V, Golden C, Odland A, Martin P, Perle J, Gass C, Simco E, Mittenberg W, Patt V, Minassian A, Perry W, Polott S, Webbe F, Mulligan K, Shaneyfelt K, Wall J, Thompson J, Tai C, Kiely T, Compono V, Trettin L, Gomez R, Schatzberg A, Keller J, Tsou J, Pearlson J, Sharma V, Tourgeman I, Golden C, Waldron-Perrine B, Tree H, Spencer R, McGuire A, Na S, Pangilinan P, Bieliauskas L, You S, Moses J, An K, Jeffay E, Zakzanis K, Biddle C, Fazio R, Willett K, Rolin S, O'Grady M, Denney R, Bresnan K, Erlanger D, Seegmiller R, Kaushik T, Brooks B, Krol A, Carlson H, Sherman E, Davis J, McHugh T, Axelrod B, Hanks R. Grand Rounds. Arch Clin Neuropsychol 2011. [DOI: 10.1093/arclin/acr056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel JH, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, Nepal C, Previti C, Karlsen BO, Moum T, Skage M, Berg PR, Gjøen T, Kuhl H, Thorsen J, Malde K, Reinhardt R, Du L, Johansen SD, Searle S, Lien S, Nilsen F, Jonassen I, Omholt SW, Stenseth NC, Jakobsen KS. The genome sequence of Atlantic cod reveals a unique immune system. Nature 2011; 477:207-10. [PMID: 21832995 DOI: 10.1038/nature10342] [Citation(s) in RCA: 527] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 06/28/2011] [Indexed: 01/24/2023]
Abstract
Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.
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Affiliation(s)
- Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
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Hamelryck T, Borg M, Paluszewski M, Paulsen J, Frellsen J, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J. Potentials of mean force for protein structure prediction vindicated, formalized and generalized. PLoS One 2010; 5:e13714. [PMID: 21103041 PMCID: PMC2978081 DOI: 10.1371/journal.pone.0013714] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 10/04/2010] [Indexed: 11/26/2022] Open
Abstract
Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge-based potentials based on pairwise distances – so-called “potentials of mean force” (PMFs) – have been center stage in the prediction and design of protein structure and the simulation of protein folding. However, the validity, scope and limitations of these potentials are still vigorously debated and disputed, and the optimal choice of the reference state – a necessary component of these potentials – is an unsolved problem. PMFs are loosely justified by analogy to the reversible work theorem in statistical physics, or by a statistical argument based on a likelihood function. Both justifications are insightful but leave many questions unanswered. Here, we show for the first time that PMFs can be seen as approximations to quantities that do have a rigorous probabilistic justification: they naturally arise when probability distributions over different features of proteins need to be combined. We call these quantities “reference ratio distributions” deriving from the application of the “reference ratio method.” This new view is not only of theoretical relevance but leads to many insights that are of direct practical use: the reference state is uniquely defined and does not require external physical insights; the approach can be generalized beyond pairwise distances to arbitrary features of protein structure; and it becomes clear for which purposes the use of these quantities is justified. We illustrate these insights with two applications, involving the radius of gyration and hydrogen bonding. In the latter case, we also show how the reference ratio method can be iteratively applied to sculpt an energy funnel. Our results considerably increase the understanding and scope of energy functions derived from known biomolecular structures.
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Affiliation(s)
- Thomas Hamelryck
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (TH); (JFB)
| | - Mikael Borg
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Paluszewski
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Paulsen
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jes Frellsen
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christian Andreetta
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Wouter Boomsma
- Biomedical Engineering, Technical University of Denmark (DTU) Elektro, Technical University of Denmark, Lyngby, Denmark
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sandro Bottaro
- Biomedical Engineering, Technical University of Denmark (DTU) Elektro, Technical University of Denmark, Lyngby, Denmark
| | - Jesper Ferkinghoff-Borg
- Biomedical Engineering, Technical University of Denmark (DTU) Elektro, Technical University of Denmark, Lyngby, Denmark
- * E-mail: (TH); (JFB)
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Sills T, Geraci J, Vaccarino A, Anderson K, Borowsky B, Giuliano J, Guttman M, Ho AK, Paulsen J, van Kammen DP, Evans K. F09 Progression of motor symptoms prior to diagnosis in HD-gene carriers. J Neurol Neurosurg Psychiatry 2010. [DOI: 10.1136/jnnp.2010.222620.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Evans K, Anderson K, Borowsky B, Giuliano J, Guttman M, Ho A, Paulsen J, Sills T, Vaccarino A, van Kammen D. F08 The functional rating taskforce for pre-huntington's disease: results so far. J Neurol Psychiatry 2010. [DOI: 10.1136/jnnp.2010.222620.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Duff K, Paulsen J, Mills J, Beglinger LJ, Moser DJ, Smith MM, Langbehn D, Stout J, Queller S, Harrington DL. Mild cognitive impairment in prediagnosed Huntington disease. Neurology 2010; 75:500-7. [PMID: 20610833 DOI: 10.1212/wnl.0b013e3181eccfa2] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Cognitive decline has been reported in Huntington disease (HD), as well as in the period before diagnosis of motor symptoms (i.e., pre-HD). However, the severity, frequency, and characterization of cognitive difficulties have not been well-described. Applying similar cutoffs to those used in mild cognitive impairment (MCI) research, the current study examined the rates of subtle cognitive dysfunction (e.g., dysfunction that does not meet criteria for dementia) in pre-HD. METHODS Using baseline data from 160 non-gene-expanded comparison participants, normative data were established for cognitive tests of episodic memory, processing speed, executive functioning, and visuospatial perception. Cutoff scores at 1.5 standard deviations below the mean of the comparison group were then applied to 575 gene-expanded pre-HD participants from the observational study, PREDICT-HD, who were stratified by motor signs and genetic risk for HD. RESULTS Nearly 40% of pre-HD individuals met criteria for MCI, and individuals closer to HD diagnosis had higher rates of MCI. Nonamnestic MCI was more common than amnestic MCI. Single-domain MCI was more common than multiple-domain MCI. Within the nonamnestic single-domain subtype, impairments in processing speed were most frequent. CONCLUSIONS Consistent with the Alzheimer disease literature, MCI as a prodromal period is a valid concept in pre-HD, with nearly 40% of individuals showing this level of impairment before diagnosis. Future studies should examine the utility of MCI as a marker of cognitive decline in pre-HD.
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Affiliation(s)
- K Duff
- University of Utah, Salt Lake City, USA
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Weiss E, Paulsen J, Rudolph R, Hoffmann R. C-Typ Viruspartikel in Blutlymphozytenkulturen von zwei Schafen mit persistierender Lymphozytose. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1439-0450.1971.tb00353.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Paulsen J, Bertelsmann KF, Schliesser T. Weitere Untersuchungen zum Vorkommen von Antikörpern gegen C-Typ-Virus spezifisches Antigen in Seren von Rindern aus leukoseverseuchten, -verdächtigen und -unverdächtigen Beständen. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1439-0450.1975.tb00624.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Langbehn D, Paulsen J. Platform presentation—Late-breaking research—Multivariate Clinical Predictors of Huntington Disease (HD): Prospective Results from the PREDICT-HD Study. Neurotherapeutics 2010. [DOI: 10.1016/j.nurt.2009.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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