1
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Schwarzl T, Sahadevan S, Lang B, Miladi M, Backofen R, Huber W, Hentze MW, Tartaglia GG. Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq. Nucleic Acids Res 2024; 52:e1. [PMID: 37962298 PMCID: PMC10783507 DOI: 10.1093/nar/gkad998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/04/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Enhanced crosslinking and immunoprecipitation (eCLIP) sequencing is a method for transcriptome-wide detection of binding sites of RNA-binding proteins (RBPs). However, identified crosslink sites can deviate from experimentally established functional elements of even well-studied RBPs. Current peak-calling strategies result in low replication and high false positive rates. Here, we present the R/Bioconductor package DEWSeq that makes use of replicate information and size-matched input controls. We benchmarked DEWSeq on 107 RBPs for which both eCLIP data and RNA sequence motifs are available and were able to more than double the number of motif-containing binding regions relative to standard eCLIP processing. The improvement not only relates to the number of binding sites (3.1-fold with known motifs for RBFOX2), but also their subcellular localization (1.9-fold of mitochondrial genes for FASTKD2) and structural targets (2.2-fold increase of stem-loop regions for SLBP. On several orthogonal CLIP-seq datasets, DEWSeq recovers a larger number of motif-containing binding sites (3.3-fold). DEWSeq is a well-documented R/Bioconductor package, scalable to adequate numbers of replicates, and tends to substantially increase the proportion and total number of RBP binding sites containing biologically relevant features.
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Affiliation(s)
- Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Sudeep Sahadevan
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Benjamin Lang
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79098 Freiburg im Breisgau, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79098 Freiburg im Breisgau, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Gian Gaetano Tartaglia
- Center for Life Nano & Neuroscience, Italian Institute of Technology, 00161 Rome, Italy and Department of Biology, Sapienza University of Rome, 00185 Rome, Italy
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2
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Dobos G, Miladi M, Michel L, Ram-Wolff C, Battistella M, Bagot M, de Masson A. Recent advances on cutaneous lymphoma epidemiology. Presse Med 2022; 51:104108. [PMID: 35026392 DOI: 10.1016/j.lpm.2022.104108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/26/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Primary cutaneous lymphomas are a group of T- (CTCL) and B-cell (CBCL) malignancies. These diseases have different clinical presentations and prognosis. Our knowledge on their epidemiology is limited. Aim of this review was to summarise recent findings on the incidence of CTCL and CBCL, how they change over time, and to describe possible causes and consequences. We found that although there are important differences in the epidemiology of cutaneous lymphomas in different countries, the relative frequency of certain, especially rare lymphomas remains stable. Several studies described growing incidences of both CTCL and CBCL. The emergence of new diagnostic criteria, a more precise definition of the entities and new biomarkers enable a better classification of cases.
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Affiliation(s)
- G Dobos
- Dermatology Department, Saint-Louis Hospital, AP-HP, Paris, France; INSERM U976 Human Immunology, Pathophysiology and Immune Therapies, Paris, France; Université de Paris, Paris, France; Department of Dermatology, Venerology and Allergology, Charité-Universitätsmedizin Berlin, Germany
| | - M Miladi
- Dermatology Department, Saint-Louis Hospital, AP-HP, Paris, France
| | - L Michel
- INSERM U976 Human Immunology, Pathophysiology and Immune Therapies, Paris, France; Université de Paris, Paris, France
| | - C Ram-Wolff
- Dermatology Department, Saint-Louis Hospital, AP-HP, Paris, France
| | - M Battistella
- INSERM U976 Human Immunology, Pathophysiology and Immune Therapies, Paris, France; Université de Paris, Paris, France; Pathology Department, Saint-Louis Hospital, AP-HP, Paris, France
| | - M Bagot
- Dermatology Department, Saint-Louis Hospital, AP-HP, Paris, France; INSERM U976 Human Immunology, Pathophysiology and Immune Therapies, Paris, France; Université de Paris, Paris, France.
| | - A de Masson
- Dermatology Department, Saint-Louis Hospital, AP-HP, Paris, France; INSERM U976 Human Immunology, Pathophysiology and Immune Therapies, Paris, France; Université de Paris, Paris, France
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3
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Wallach T, Mossmann ZJ, Szczepek M, Wetzel M, Machado R, Raden M, Miladi M, Kleinau G, Krüger C, Dembny P, Adler D, Zhai Y, Kumbol V, Dzaye O, Schüler J, Futschik M, Backofen R, Scheerer P, Lehnardt S. MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration. Mol Neurodegener 2021; 16:80. [PMID: 34838071 PMCID: PMC8626928 DOI: 10.1186/s13024-021-00498-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 06/11/2021] [Accepted: 11/03/2021] [Indexed: 12/30/2022] Open
Abstract
Background MicroRNA (miRNA) expression in the brain is altered in neurodegenerative diseases. Recent studies demonstrated that selected miRNAs conventionally regulating gene expression at the post-transcriptional level can act extracellularly as signaling molecules. The identity of miRNA species serving as membrane receptor ligands involved in neuronal apoptosis in the central nervous system (CNS), as well as the miRNAs’ sequence and structure required for this mode of action remained largely unresolved. Methods Using a microarray-based screening approach we analyzed apoptotic cortical neurons of C56BL/6 mice and their supernatant with respect to alterations in miRNA expression/presence. HEK-Blue Toll-like receptor (TLR) 7/8 reporter cells, primary microglia and macrophages derived from human and mouse were employed to test the potential of the identified miRNAs released from apoptotic neurons to serve as signaling molecules for the RNA-sensing receptors. Biophysical and bioinformatical approaches, as well as immunoassays and sequential microscopy were used to analyze the interaction between candidate miRNA and TLR. Immunocytochemical and -histochemical analyses of murine CNS cultures and adult mice intrathecally injected with miRNAs, respectively, were performed to evaluate the impact of miRNA-induced TLR activation on neuronal survival and microglial activation. Results We identified a specific pattern of miRNAs released from apoptotic cortical neurons that activate TLR7 and/or TLR8, depending on sequence and species. Exposure of microglia and macrophages to certain miRNA classes released from apoptotic neurons resulted in the sequence-specific production of distinct cytokines/chemokines and increased phagocytic activity. Out of those miRNAs miR-100-5p and miR-298-5p, which have consistently been linked to neurodegenerative diseases, entered microglia, located to their endosomes, and directly bound to human TLR8. The miRNA-TLR interaction required novel sequence features, but no specific structure formation of mature miRNA. As a consequence of miR-100-5p- and miR-298-5p-induced TLR activation, cortical neurons underwent cell-autonomous apoptosis. Presence of miR-100-5p and miR-298-5p in cerebrospinal fluid led to neurodegeneration and microglial accumulation in the murine cerebral cortex through TLR7 signaling. Conclusion Our data demonstrate that specific miRNAs are released from apoptotic cortical neurons, serve as endogenous TLR7/8 ligands, and thereby trigger further neuronal apoptosis in the CNS. Our findings underline the recently discovered role of miRNAs as extracellular signaling molecules, particularly in the context of neurodegeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s13024-021-00498-5.
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Affiliation(s)
- Thomas Wallach
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany.
| | - Zoé J Mossmann
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Michal Szczepek
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography & Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Max Wetzel
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Rui Machado
- Department of Biomedical Sciences and Medicine, University of Algarve, 8005-139, Faro, Portugal
| | - Martin Raden
- Bioinformatics, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Milad Miladi
- Bioinformatics, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Gunnar Kleinau
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography & Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Christina Krüger
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Paul Dembny
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Drew Adler
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Yuanyuan Zhai
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Victor Kumbol
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Omar Dzaye
- Department of Radiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Jutta Schüler
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Matthias Futschik
- Department of Biomedical Sciences and Medicine, University of Algarve, 8005-139, Faro, Portugal.,School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, PL6 8BU, UK.,MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Rolf Backofen
- Bioinformatics, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Patrick Scheerer
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography & Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany.,German Centre for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Seija Lehnardt
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany. .,Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany.
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4
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Maier W, Bray S, van den Beek M, Bouvier D, Coraor N, Miladi M, Singh B, De Argila JR, Baker D, Roach N, Gladman S, Coppens F, Martin DP, Lonie A, Grüning B, Kosakovsky Pond SL, Nekrutenko A. Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nat Biotechnol 2021; 39:1178-1179. [PMID: 34588690 PMCID: PMC8845060 DOI: 10.1038/s41587-021-01069-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
| | - Simon Bray
- University of Freiburg, Freiburg, Germany
| | | | - Dave Bouvier
- The Pennsylvania State University, University Park, PA, USA
| | - Nathan Coraor
- The Pennsylvania State University, University Park, PA, USA
| | | | | | | | - Dannon Baker
- Centre for Genomic Regulation, Viral Beacon Project, Barcelona, Spain
| | | | - Simon Gladman
- University of Melbourne, Melbourne, Victoria, Australia
| | - Frederik Coppens
- Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Andrew Lonie
- University of Melbourne, Melbourne, Victoria, Australia
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5
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Raden M, Wallach T, Miladi M, Zhai Y, Krüger C, Mossmann ZJ, Dembny P, Backofen R, Lehnardt S. Structure-aware machine learning identifies microRNAs operating as Toll-like receptor 7/8 ligands. RNA Biol 2021; 18:268-277. [PMID: 34241565 PMCID: PMC8677043 DOI: 10.1080/15476286.2021.1940697] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNAs) can serve as activation signals for membrane receptors, a recently discovered function that is independent of the miRNAs’ conventional role in post-transcriptional gene regulation. Here, we introduce a machine learning approach, BrainDead, to identify oligonucleotides that act as ligands for single-stranded RNA-detecting Toll-like receptors (TLR)7/8, thereby triggering an immune response. BrainDead was trained on activation data obtained from in vitro experiments on murine microglia, incorporating sequence and intra-molecular structure, as well as inter-molecular homo-dimerization potential of candidate RNAs. The method was applied to analyse all known human miRNAs regarding their potential to induce TLR7/8 signalling and microglia activation. We validated the predicted functional activity of subsets of high- and low-scoring miRNAs experimentally, of which a selection has been linked to Alzheimer’s disease. High agreement between predictions and experiments confirms the robustness and power of BrainDead. The results provide new insight into the mechanisms of how miRNAs act as TLR ligands. Eventually, BrainDead implements a generic machine learning methodology for learning and predicting the functions of short RNAs in any context.
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Affiliation(s)
- Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Thomas Wallach
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Yuanyuan Zhai
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christina Krüger
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Zoé J Mossmann
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Paul Dembny
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany.,Signalling Research Centre CIBSS, University of Freiburg, Freiburg, Germany
| | - Seija Lehnardt
- Department of Neurology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
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6
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Maier W, Bray S, van den Beek M, Bouvier D, Coraor N, Miladi M, Singh B, De Argila JR, Baker D, Roach N, Gladman S, Coppens F, Martin DP, Lonie A, Grüning B, Kosakovsky Pond SL, Nekrutenko A. Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring. bioRxiv 2021:2021.03.25.437046. [PMID: 33791701 PMCID: PMC8010728 DOI: 10.1101/2021.03.25.437046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org .
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Affiliation(s)
- Wolfgang Maier
- University of Freiburg / usegalaxy.eu, Freiburg, Germany
| | - Simon Bray
- University of Freiburg / usegalaxy.eu, Freiburg, Germany
| | | | - Dave Bouvier
- The Pennsylvania State University / usegalaxy.org, University Park, PA, USA
| | - Nathaniel Coraor
- The Pennsylvania State University / usegalaxy.org, University Park, PA, USA
| | - Milad Miladi
- University of Freiburg / usegalaxy.eu, Freiburg, Germany
| | | | | | - Dannon Baker
- Centre for Genomic Regulation, Viral Beacon Project, Barcelona, Spain
| | - Nathan Roach
- Johns Hopkins University / usegalaxy.org, Baltimore, MD, USA
| | - Simon Gladman
- University of Melbourne / usegalaxy.org.au, Melbourne, Australia
| | - Frederik Coppens
- Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Andrew Lonie
- University of Melbourne / usegalaxy.org.au, Melbourne, Australia
| | - Björn Grüning
- University of Freiburg / usegalaxy.eu, Freiburg, Germany
| | | | - Anton Nekrutenko
- The Pennsylvania State University / usegalaxy.org, University Park, PA, USA
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7
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Miladi M, Raden M, Will S, Backofen R. Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. Algorithms Mol Biol 2020; 15:19. [PMID: 33292340 PMCID: PMC7666477 DOI: 10.1186/s13015-020-00179-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 10/16/2020] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Simultaneous alignment and folding (SA&F) of RNAs is the indispensable gold standard for inferring the structure of non-coding RNAs and their general analysis. The original algorithm, proposed by Sankoff, solves the theoretical problem exactly with a complexity of [Formula: see text] in the full energy model. Over the last two decades, several variants and improvements of the Sankoff algorithm have been proposed to reduce its extreme complexity by proposing simplified energy models or imposing restrictions on the predicted alignments. RESULTS Here, we introduce a novel variant of Sankoff's algorithm that reconciles the simplifications of PMcomp, namely moving from the full energy model to a simpler base pair-based model, with the accuracy of the loop-based full energy model. Instead of estimating pseudo-energies from unconditional base pair probabilities, our model calculates energies from conditional base pair probabilities that allow to accurately capture structure probabilities, which obey a conditional dependency. This model gives rise to the fast and highly accurate novel algorithm Pankov (Probabilistic Sankoff-like simultaneous alignment and folding of RNAs inspired by Markov chains). CONCLUSIONS Pankov benefits from the speed-up of excluding unreliable base-pairing without compromising the loop-based free energy model of the Sankoff's algorithm. We show that Pankov outperforms its predecessors LocARNA and SPARSE in folding quality and is faster than LocARNA.
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Affiliation(s)
- Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
| | - Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
| | - Sebastian Will
- Theoretical Biochemistry Group (TBI), Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, Vienna, Austria
- Bioinformatics group (AMIBIO), Laboratoire d’Informatique de l’École Polytechnique (LIX), Institut Polytechnique de Paris (IPP), Batiment Turing, 1 rue d’Estienne d’Orve, Palaiseau, France
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, Freiburg, Germany
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8
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de Koning W, Miladi M, Hiltemann S, Heikema A, Hays JP, Flemming S, van den Beek M, Mustafa DA, Backofen R, Grüning B, Stubbs AP. NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy. Gigascience 2020; 9:giaa105. [PMID: 33068114 PMCID: PMC7568507 DOI: 10.1093/gigascience/giaa105] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/10/2020] [Accepted: 09/16/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies-based long-read sequencing "nanopore" platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatics analysis by enabling easy access and ease-of-use solutions for researchers. RESULTS The Galaxy platform provides a user-friendly interface to computational command line-based tools, handles the software dependencies, and provides refined workflows. The users do not have to possess programming experience or extended computer skills. The interface enables researchers to perform powerful bioinformatics analysis, including the assembly and analysis of short- or long-read sequence data. The newly developed "NanoGalaxy" is a Galaxy-based toolkit for analysing long-read sequencing data, which is suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads. CONCLUSIONS A range of best-practice tools and workflows for long-read sequence genome assembly has been integrated into a NanoGalaxy platform to facilitate easy access and use of bioinformatics tools for researchers. NanoGalaxy is freely available at the European Galaxy server https://nanopore.usegalaxy.eu with supporting self-learning training material available at https://training.galaxyproject.org.
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Affiliation(s)
- Willem de Koning
- Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands
- Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus University Medical Centre, 's Gravendijkwal 230, 3015 CE, Rotterdam, the Netherlands
| | - Milad Miladi
- Department of Computer Science, Bioinformatics Group, University of Freiburg, 79110 Freiburg im Breisgau, Germany
| | - Saskia Hiltemann
- Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands
| | - Astrid Heikema
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, 's Gravendijkwal 230, 3015 CE, Rotterdam, the Netherlands
| | - John P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, 's Gravendijkwal 230, 3015 CE, Rotterdam, the Netherlands
| | - Stephan Flemming
- Department of Computer Science, Bioinformatics Group, University of Freiburg, 79110 Freiburg im Breisgau, Germany
| | - Marius van den Beek
- Department of Stem Cells and Tissue Homeostasis, Institut Curie, PSL Research University, 75005 Paris, France
| | - Dana A Mustafa
- Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus University Medical Centre, 's Gravendijkwal 230, 3015 CE, Rotterdam, the Netherlands
| | - Rolf Backofen
- Department of Computer Science, Bioinformatics Group, University of Freiburg, 79110 Freiburg im Breisgau, Germany
| | - Björn Grüning
- Department of Computer Science, Bioinformatics Group, University of Freiburg, 79110 Freiburg im Breisgau, Germany
| | - Andrew P Stubbs
- Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands
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9
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Miladi M, Raden M, Diederichs S, Backofen R. MutaRNA: analysis and visualization of mutation-induced changes in RNA structure. Nucleic Acids Res 2020; 48:W287-W291. [PMID: 32392303 PMCID: PMC7319544 DOI: 10.1093/nar/gkaa331] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 12/25/2022] Open
Abstract
RNA molecules fold into complex structures as a result of intramolecular interactions between their nucleotides. The function of many non-coding RNAs and some cis-regulatory elements of messenger RNAs highly depends on their fold. Single-nucleotide variants (SNVs) and other types of mutations can disrupt the native function of an RNA element by altering its base pairing pattern. Identifying the effect of a mutation on an RNA’s structure is, therefore, a crucial step in evaluating the impact of mutations on the post-transcriptional regulation and function of RNAs within the cell. Even though a single nucleotide variation can have striking impacts on the structure formation, interpreting and comparing the impact usually needs expertise and meticulous efforts. Here, we present MutaRNA, a web server for visualization and interpretation of mutation-induced changes on the RNA structure in an intuitive and integrative fashion. To this end, probabilities of base pairing and position-wise unpaired probabilities of wildtype and mutated RNA sequences are computed and compared. Differential heatmap-like dot plot representations in combination with circular plots and arc diagrams help to identify local structure abberations, which are otherwise hidden in standard outputs. Eventually, MutaRNA provides a comprehensive and comparative overview of the mutation-induced changes in base pairing potentials and accessibility. The MutaRNA web server is freely available at http://rna.informatik.uni-freiburg.de/MutaRNA.
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Affiliation(s)
- Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Faculty of Medicine, German Cancer Consortium (DKTK), University of Freiburg, 79085 Freiburg, Germany.,Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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Müller T, Miladi M, Hutter F, Hofacker I, Will S, Backofen R. The locality dilemma of Sankoff-like RNA alignments. Bioinformatics 2020; 36:i242-i250. [PMID: 32657398 PMCID: PMC7355259 DOI: 10.1093/bioinformatics/btaa431] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/24/2022] Open
Abstract
Motivation Elucidating the functions of non-coding RNAs by homology has been strongly limited due to fundamental computational and modeling issues. While existing simultaneous alignment and folding (SA&F) algorithms successfully align homologous RNAs with precisely known boundaries (global SA&F), the more pressing problem of identifying new classes of homologous RNAs in the genome (local SA&F) is intrinsically more difficult and much less understood. Typically, the length of local alignments is strongly overestimated and alignment boundaries are dramatically mispredicted. We hypothesize that local SA&F approaches are compromised this way due to a score bias, which is caused by the contribution of RNA structure similarity to their overall alignment score. Results In the light of this hypothesis, we study pairwise local SA&F for the first time systematically—based on a novel local RNA alignment benchmark set and quality measure. First, we vary the relative influence of structure similarity compared to sequence similarity. Putting more emphasis on the structure component leads to overestimating the length of local alignments. This clearly shows the bias of current scores and strongly hints at the structure component as its origin. Second, we study the interplay of several important scoring parameters by learning parameters for local and global SA&F. The divergence of these optimized parameter sets underlines the fundamental obstacles for local SA&F. Third, by introducing a position-wise correction term in local SA&F, we constructively solve its principal issues. Availability and implementation The benchmark data, detailed results and scripts are available at https://github.com/BackofenLab/local_alignment. The RNA alignment tool LocARNA, including the modifications proposed in this work, is available at https://github.com/s-will/LocARNA/releases/tag/v2.0.0RC6. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Teresa Müller
- Bioinformatics Group, University of Freiburg, Freiburg 79110, Germany
| | - Milad Miladi
- Bioinformatics Group, University of Freiburg, Freiburg 79110, Germany
| | - Frank Hutter
- Machine Learning Lab, Department of Computer Science, University of Freiburg, Freiburg 79110, Germany
| | - Ivo Hofacker
- Theoretical Biochemistry Group (TBI), Institute for Theoretical Chemistry, University of Vienna, Vienna, Wien 1090, Austria
| | - Sebastian Will
- Theoretical Biochemistry Group (TBI), Institute for Theoretical Chemistry, University of Vienna, Vienna, Wien 1090, Austria.,Bioinformatics Group AMIBio, LIX-Laboratoire d'Informatique d'École Polytechnique, IPP, Palaiseau 91120, France
| | - Rolf Backofen
- Bioinformatics Group, University of Freiburg, Freiburg 79110, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg 79104, Germany
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Miladi M, Montaseri S, Backofen R, Raden M. Integration of accessibility data from structure probing into RNA-RNA interaction prediction. Bioinformatics 2020; 35:2862-2864. [PMID: 30590479 PMCID: PMC6691327 DOI: 10.1093/bioinformatics/bty1029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/20/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
SUMMARY Experimental structure probing data has been shown to improve thermodynamics-based RNA secondary structure prediction. To this end, chemical reactivity information (as provided e.g. by SHAPE) is incorporated, which encodes whether or not individual nucleotides are involved in intra-molecular structure. Since inter-molecular RNA-RNA interactions are often confined to unpaired RNA regions, SHAPE data is even more promising to improve interaction prediction. Here, we show how such experimental data can be incorporated seamlessly into accessibility-based RNA-RNA interaction prediction approaches, as implemented in IntaRNA. This is possible via the computation and use of unpaired probabilities that incorporate the structure probing information. We show that experimental SHAPE data can significantly improve RNA-RNA interaction prediction. We evaluate our approach by investigating interactions of a spliceosomal U1 snRNA transcript with its target splice sites. When SHAPE data is incorporated, known target sites are predicted with increased precision and specificity. AVAILABILITY AND IMPLEMENTATION https://github.com/BackofenLab/IntaRNA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Milad Miladi
- Department of Computer Science, Bioinformatics Group, University of Freiburg, Freiburg D-79110, Germany
| | - Soheila Montaseri
- Department of Computer Science, Bioinformatics Group, University of Freiburg, Freiburg D-79110, Germany
| | - Rolf Backofen
- Department of Computer Science, Bioinformatics Group, University of Freiburg, Freiburg D-79110, Germany.,Center for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg D-79104, Germany
| | - Martin Raden
- Department of Computer Science, Bioinformatics Group, University of Freiburg, Freiburg D-79110, Germany
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12
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Abstract
Summary SHAPE experiments are used to probe the structure of RNA molecules. We present ShaKer to predict SHAPE data for RNA using a graph-kernel-based machine learning approach that is trained on experimental SHAPE information. While other available methods require a manually curated reference structure, ShaKer predicts reactivity data based on sequence input only and by sampling the ensemble of possible structures. Thus, ShaKer is well placed to enable experiment-driven, transcriptome-wide SHAPE data prediction to enable the study of RNA structuredness and to improve RNA structure and RNA–RNA interaction prediction. For performance evaluation, we use accuracy and accessibility comparing to experimental SHAPE data and competing methods. We can show that Shaker outperforms its competitors and is able to predict high quality SHAPE annotations even when no reference structure is provided. Availability and implementation ShaKer is freely available at https://github.com/BackofenLab/ShaKer.
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Affiliation(s)
- Stefan Mautner
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Soheila Montaseri
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Fabrizio Costa
- Department Computer Science, University of Exeter, Exeter, UK
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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13
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Miladi M, Sokhoyan E, Houwaart T, Heyne S, Costa F, Grüning B, Backofen R. GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. Gigascience 2019; 8:giz150. [PMID: 31808801 PMCID: PMC6897289 DOI: 10.1093/gigascience/giz150] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/23/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND RNA plays essential roles in all known forms of life. Clustering RNA sequences with common sequence and structure is an essential step towards studying RNA function. With the advent of high-throughput sequencing techniques, experimental and genomic data are expanding to complement the predictive methods. However, the existing methods do not effectively utilize and cope with the immense amount of data becoming available. RESULTS Hundreds of thousands of non-coding RNAs have been detected; however, their annotation is lagging behind. Here we present GraphClust2, a comprehensive approach for scalable clustering of RNAs based on sequence and structural similarities. GraphClust2 bridges the gap between high-throughput sequencing and structural RNA analysis and provides an integrative solution by incorporating diverse experimental and genomic data in an accessible manner via the Galaxy framework. GraphClust2 can efficiently cluster and annotate large datasets of RNAs and supports structure-probing data. We demonstrate that the annotation performance of clustering functional RNAs can be considerably improved. Furthermore, an off-the-shelf procedure is introduced for identifying locally conserved structure candidates in long RNAs. We suggest the presence and the sparseness of phylogenetically conserved local structures for a collection of long non-coding RNAs. CONCLUSIONS By clustering data from 2 cross-linking immunoprecipitation experiments, we demonstrate the benefits of GraphClust2 for motif discovery under the presence of biological and methodological biases. Finally, we uncover prominent targets of double-stranded RNA binding protein Roquin-1, such as BCOR's 3' untranslated region that contains multiple binding stem-loops that are evolutionary conserved.
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Affiliation(s)
- Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Eteri Sokhoyan
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, University of Dusseldorf, Universitaetsstr. 1, 40225 Dusseldorf, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Stuebeweg 51, 79108 Freiburg, Germany
| | - Fabrizio Costa
- Department of Computer Science, University of Exeter, North Park Road, EX4 4QF Exeter, UK
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- ZBSA Centre for Biological Systems Analysis, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- ZBSA Centre for Biological Systems Analysis, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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14
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Abdellaoui K, Boussadia O, Miladi M, Boughattas I, Omri G, Mhafdhi M, Hazzoug M, Acheuk F, Brahem M. Olive Leaf Extracts Toxicity to the Migratory Locust, Locusta migratoria: Histopathological Effects on the Alimentary Canal and Acetylcholinesterase and Glutathione S-Transferases Activity. Neotrop Entomol 2019; 48:246-259. [PMID: 30151672 DOI: 10.1007/s13744-018-0628-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
The migratory locust, Locusta migratoria (Linnaeus), is the most widespread locust species. Frequent applications of insecticides have inevitably resulted in environmental pollution and development of resistance in some natural populations of the locust. To find a new and safe alternative to conventional insecticides, experiments were conducted to assess the effect of olive leaf extracts on L. migratoria fifth instar larvae. The methanolic extracts were prepared from the leaves sampled during four phenological growth stages of olive tree which are as follows: Cluster formation (Cf), Swelling inflorescence buds (Sib), Full flowering (Ff), and Endocarp hardening (Eh). The most relevant result was noted with the extract prepared from the leaves collected at the Sib-stage. Results showed that treatment of newly emerged larvae resulted in a significant mortality with a dose-response relationship. The olive leaf extracts toxicity was also demonstrated by histopathological changes in the alimentary canal resulting in a considerable disorganization and serious damage of the midgut, ceca, and proventriculus structure. Epithelial cells alterations, less dense and degraded striated border, disintegrated regeneration crypts, vacuolarized cells, extrusion of cytoplasmic contents, and rupture of muscular layer were evident in the midgut and ceca of treated larvae. Data of biochemical analyzes showed that olive leaf extracts induced a significant decrease of the hemolymph metabolites (proteins, carbohydrates, and lipids). In a second series of experiments, we showed that the olive leaf extracts reduced the activity of acetylcholinesterase and induced the glutathione S-transferases with a dose-response relationship.
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Affiliation(s)
- K Abdellaoui
- Dept of Biological Sciences and Plant Protection, Higher Agronomic Institute of Chott Mariem, Sousse Univ, Sousse, Tunisia.
| | - O Boussadia
- Unit of Sousse, Olive Tree Institute, Sousse, Tunisia
| | - M Miladi
- Dept of Biological Sciences and Plant Protection, Higher Agronomic Institute of Chott Mariem, Sousse Univ, Sousse, Tunisia
| | - I Boughattas
- Dept of Biological Sciences and Plant Protection, Higher Agronomic Institute of Chott Mariem, Sousse Univ, Sousse, Tunisia
| | - G Omri
- Dept of Biological Sciences and Plant Protection, Higher Agronomic Institute of Chott Mariem, Sousse Univ, Sousse, Tunisia
| | - M Mhafdhi
- General Directorate of Plant Health and Agricultural Inputs Control, Ministry of Agriculture, Tunis, Tunisia
| | - M Hazzoug
- Dept of Biological Sciences and Plant Protection, Higher Agronomic Institute of Chott Mariem, Sousse Univ, Sousse, Tunisia
| | - F Acheuk
- Lab of Valorization and Conservation of Biological Resources "Valcore," Dept of Biology, Faculty of Sciences, Univ of Boumerdes, Boumerdes, Algeria
| | - M Brahem
- Unit of Sousse, Olive Tree Institute, Sousse, Tunisia
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15
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Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR, Backofen R. Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Res 2018; 46:W25-W29. [PMID: 29788132 PMCID: PMC6030932 DOI: 10.1093/nar/gky329] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/03/2018] [Accepted: 05/18/2018] [Indexed: 12/20/2022] Open
Abstract
The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.
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Affiliation(s)
- Martin Raden
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Syed M Ali
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Omer S Alkhnbashi
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Fabrizio Costa
- Department of Computer Science, University of Exeter, Exeter EX4 4QF, UK
| | - Jason A Davis
- Coreva Scientific, Kaiser-Joseph-Str 198-200, 79098 Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rick Gelhausen
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Jens Georg
- Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1HH, UK
| | - Robert Kleinkauf
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Steffen C Lott
- Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Mostafa M Mohamed
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Alexander Mattheis
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Milad Miladi
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | | | - Sebastian Will
- Theoretical Biochemistry Group, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria
| | - Joachim Wolff
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Patrick R Wright
- Department of Clinical Research, Clinical Trial Unit, University of Basel Hospital, Schanzenstrasse 55, 4031 Basel, Switzerland
| | - Rolf Backofen
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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17
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Miladi M, Junge A, Costa F, Seemann SE, Havgaard JH, Gorodkin J, Backofen R. RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. Bioinformatics 2017; 33:2089-2096. [PMID: 28334186 PMCID: PMC5870858 DOI: 10.1093/bioinformatics/btx114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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] [Revised: 12/22/2016] [Accepted: 02/23/2017] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION Clustering RNA sequences with common secondary structure is an essential step towards studying RNA function. Whereas structural RNA alignment strategies typically identify common structure for orthologous structured RNAs, clustering seeks to group paralogous RNAs based on structural similarities. However, existing approaches for clustering paralogous RNAs, do not take the compensatory base pair changes obtained from structure conservation in orthologous sequences into account. RESULTS Here, we present RNAscClust , the implementation of a new algorithm to cluster a set of structured RNAs taking their respective structural conservation into account. For a set of multiple structural alignments of RNA sequences, each containing a paralog sequence included in a structural alignment of its orthologs, RNAscClust computes minimum free-energy structures for each sequence using conserved base pairs as prior information for the folding. The paralogs are then clustered using a graph kernel-based strategy, which identifies common structural features. We show that the clustering accuracy clearly benefits from an increasing degree of compensatory base pair changes in the alignments. AVAILABILITY AND IMPLEMENTATION RNAscClust is available at http://www.bioinf.uni-freiburg.de/Software/RNAscClust . CONTACT gorodkin@rth.dk or backofen@informatik.uni-freiburg.de. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany
| | - Alexander Junge
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fabrizio Costa
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stefan E Seemann
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jakob Hull Havgaard
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- Center for Biological Signalling Studies (BIOSS), Cluster of Excellence, University of Freiburg, Freiburg im Breisgau, Germany
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Will S, Otto C, Miladi M, Möhl M, Backofen R. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics 2015; 31:2489-96. [PMID: 25838465 PMCID: PMC4514930 DOI: 10.1093/bioinformatics/btv185] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [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: 11/07/2014] [Accepted: 03/25/2015] [Indexed: 01/19/2023] Open
Abstract
Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact:backofen@informatik.uni-freiburg.de Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sebastian Will
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany, Bioinformatics, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Christina Otto
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Milad Miladi
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Mathias Möhl
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany, Centre for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany, Centre for Non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark and Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
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Ghasemi JB, Miladi M. Association Equilibrium of Methylene Blue by Spectral Titration and Chemometrics Analysis: A Thermodynamic Study. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200900069] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Chebil D, Aissa SK, Latiri HS, Rejeb MB, Jaidane N, Miladi M, Dhidah L. P257: Survey of the prevalence of healthcare associated infection at the Sahloul-Sousse teaching hospital-2010. Antimicrob Resist Infect Control 2013. [PMCID: PMC3688196 DOI: 10.1186/2047-2994-2-s1-p257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Chebil D, Rejeb MB, Latiri H, Jaidane N, Khefacha S, Miladi M, Alaya KB, Dhidah L. P258: Incidence and risk factors of bacteremia associated with care intensive care environment: study in Chu Sahloul (Sousse Tunisia). Antimicrob Resist Infect Control 2013. [PMCID: PMC3687738 DOI: 10.1186/2047-2994-2-s1-p258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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Abstract
Extra-adrenal pheochromocytoma is rare. The diagnosis must be evoked in signs of pheochromocytoma with absence of tumor of the adrenal. We report four cases of ectopic pheochromocytoma while specifying their clinical particularities and diagnosis procedure.
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Affiliation(s)
- M Miladi
- Service d'urologie, hôpital Charles Nicolle, boulevard 9 avril, Tunis, Tunisie.
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Bacha K, Miladi M, Ben Hassine L, Hajri M, Tanazaghti F, Ayed M. [Therapeutic aspects of renal abscess. Report of 50 cases]. Prog Urol 2001; 11:444-9. [PMID: 11512456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
INTRODUCTION Renal abscess often raises therapeutic problems. Based on their experience and a review of the literature, the authors propose a treatment plant for renal abscess. MATERIAL AND METHODS The authors report 50 cases of renal abscess treated between January 1988 and September 1999 in the Department of Urology of Charles Nicolle Hospital in Tunis. The diameter of the abscess was less than or equal to 4 cm in 19 cases, between 4 and 10 cm in 29 cases and greater than 10 cm in 2 cases. Renal ultrasound and intravenous urography are an integral part of the initial morphological assessment. All patients were treated by intravenous antibiotics for a mean duration of 28 days. Complementary percutaneous drainage of the abscess was indicated in 25 patients. Surgical treatment was indicated in 13 patients in the presence of a large perirenal collection or severe sepsis, or following failure of percutaneous drainage. RESULTS Antibiotics alone were proposed in only 17 patients with an abscess less than 4 cm in diameter and 90% of these patients were cured. Percutaneous treatment was performed in 25 patients with an 80% success rate; the other patients underwent open surgery. One patient died after surgery in a context of septic shock despite salvage nephrectomy. The other patients has a favourable outcome. CONCLUSION The treatment of renal abscess is based on antibiotics alone or combined with a percutaneous or surgical drainage procedure depending on the size of the abscess and the clinical course. The authors describe their decisional flow-chart.
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Affiliation(s)
- K Bacha
- Service d'Urologie, Hôpital Charles Nicolle, Boulevard du 9 avril, Tunis, Tunisie.
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Dhidah L, Dhidah M, Miladi M, Kacem N, Troudi M. [The role of surgical wounds in nosocomial infections. Prevalence study at Sahloul university hospital]. Tunis Med 1998; 76:401-7. [PMID: 9881050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- L Dhidah
- Service d'hygiène hospitalière, CHU Sahloul, Sousse
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Dhidah L, Dhidah M, Miladi M, Troudi M. [Hospital infections. Study of positive bacterial case prevalence --University Hospital Center of Sahloul (1992-1996), Sousse, Tunisia]. Tunis Med 1998; 76:996-1000. [PMID: 9577205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- L Dhidah
- Service d'Hygiène Hospitalière-CHU Sahloul, Sousse
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Gharbi L, Miladi M, Cherif I, Ferjani E, Fteriche F, Sebai F. [A rare cause of liver abscess]. Tunis Med 1994; 72:577-9. [PMID: 7778233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- L Gharbi
- Service des urgences Hopital La RABTA-Tunis
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Miladi M, Elleuch MH, Sellami S, Douik M. [Spondyloepiphyseal dysplasia tarda with progressive arthropathy. Apropos of 3 cases]. Int Orthop 1987; 11:271-5. [PMID: 3623766 DOI: 10.1007/bf00271460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Two brothers and a sister with spondyloepiphyseal dysplasia tarda who subsequently developed severe generalised peripheral arthropathy are described. The condition appeared to be transmitted as an autosomal recessive trait.
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Chaabouni H, Douiri H, Abdelkefi MM, Miladi M, Slimane N, Ferchiou A. [Genetic study of eight cases of spondylo-epiphyseal dysplasia tarda and its autosomal recessive transmission]. J Genet Hum 1986; 34:275-84. [PMID: 3760831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Spondylo-epiphyseal dysplasia tarda is an hereditary disease of bone first described by Maroteaux in 1957. The disease affects only boys, then is transmitted on X-linked recessive pattern. The authors describe two tunisians families with 8 patients presenting clinical and radiologic symptoms resembling spondylo-epiphyseal dysplasia tarda but affecting both sexes. Autosomal recessive inheritance is probable in these families. Conclusion is that genetic heterogeneity of the disease must be precise.
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Champeau RJ, Miladi M. Déplacement isotopique relatif dans le spectre d'arc du tungstène. structure hyperfine du niveau 5d5 6s 7s3 de WI. ACTA ACUST UNITED AC 1974. [DOI: 10.1051/jphys:01974003502010500] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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