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Kwon D, Park N, Wy S, Lee D, Park W, Chai HH, Cho IC, Lee J, Kwon K, Kim H, Moon Y, Kim J, Kim J. Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies. BMC Genomics 2024; 25:299. [PMID: 38515031 PMCID: PMC10956321 DOI: 10.1186/s12864-024-10225-1] [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: 01/19/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities. RESULTS By applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues. CONCLUSIONS Whole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngbeen Moon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Juyeon Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Kwon D, Park N, Wy S, Lee D, Chai HH, Cho IC, Lee J, Kwon K, Kim H, Moon Y, Kim J, Park W, Kim J. A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa). Sci Data 2023; 10:761. [PMID: 37923776 PMCID: PMC10624824 DOI: 10.1038/s41597-023-02661-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
As plentiful high-quality genome assemblies have been accumulated, reference-guided genome assembly can be a good approach to reconstruct a high-quality assembly. Here, we present a chromosome-level genome assembly of the Korean crossbred pig called Nanchukmacdon (the NCMD assembly) using the reference-guided assembly approach with short and long reads. The NCMD assembly contains 20 chromosome-level scaffolds with a total size of 2.38 Gbp (N50: 138.77 Mbp). Its BUSCO score is 93.1%, which is comparable to the pig reference assembly, and a total of 20,588 protein-coding genes, 8,651 non-coding genes, and 996.14 Mbp of repetitive elements are annotated. The NCMD assembly was also used to close many gaps in the pig reference assembly. This NCMD assembly and annotation provide foundational resources for the genomic analyses of pig and related species.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngbeen Moon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Juyeon Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Moon SW, Zhao L, Matloff W, Hobel S, Berger R, Kwon D, Kim J, Toga AW, Dinov ID. Brain structure and allelic associations in Alzheimer's disease. CNS Neurosci Ther 2023; 29:1034-1048. [PMID: 36575854 PMCID: PMC10018103 DOI: 10.1111/cns.14073] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD), the most prevalent form of dementia, affects 6.5 million Americans and over 50 million people globally. Clinical, genetic, and phenotypic studies of dementia provide some insights of the observed progressive neurodegenerative processes, however, the mechanisms underlying AD onset remain enigmatic. AIMS This paper examines late-onset dementia-related cognitive impairment utilizing neuroimaging-genetics biomarker associations. MATERIALS AND METHODS The participants, ages 65-85, included 266 healthy controls (HC), 572 volunteers with mild cognitive impairment (MCI), and 188 Alzheimer's disease (AD) patients. Genotype dosage data for AD-associated single nucleotide polymorphisms (SNPs) were extracted from the imputed ADNI genetics archive using sample-major additive coding. Such 29 SNPs were selected, representing a subset of independent SNPs reported to be highly associated with AD in a recent AD meta-GWAS study by Jansen and colleagues. RESULTS We identified the significant correlations between the 29 genomic markers (GMs) and the 200 neuroimaging markers (NIMs). The odds ratios and relative risks for AD and MCI (relative to HC) were predicted using multinomial linear models. DISCUSSION In the HC and MCI cohorts, mainly cortical thickness measures were associated with GMs, whereas the AD cohort exhibited different GM-NIM relations. Network patterns within the HC and AD groups were distinct in cortical thickness, volume, and proportion of White to Gray Matter (pct), but not in the MCI cohort. Multinomial linear models of clinical diagnosis showed precisely the specific NIMs and GMs that were most impactful in discriminating between AD and HC, and between MCI and HC. CONCLUSION This study suggests that advanced analytics provide mechanisms for exploring the interrelations between morphometric indicators and GMs. The findings may facilitate further clinical investigations of phenotypic associations that support deep systematic understanding of AD pathogenesis.
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Affiliation(s)
- Seok Woo Moon
- Department of Neuropsychiatry, Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea.,USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, California, Los Angeles, USA
| | - Lu Zhao
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, California, Los Angeles, USA
| | - William Matloff
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, California, Los Angeles, USA
| | - Sam Hobel
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, California, Los Angeles, USA
| | - Ryan Berger
- Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Korea
| | - Arthur W Toga
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, California, Los Angeles, USA
| | - Ivo D Dinov
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, California, Los Angeles, USA.,Department of Health Behavior and Biological Sciences, Statistics Online Computational Resource (SOCR), Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, Michigan, USA.,Department of Statistics, University of California, Los Angeles, California, USA
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Sim M, Lee J, Kwon D, Lee D, Park N, Wy S, Ko Y, Kim J. Reference-based read clustering improves the de novo genome assembly of microbial strains. Comput Struct Biotechnol J 2022; 21:444-451. [PMID: 36618978 PMCID: PMC9804104 DOI: 10.1016/j.csbj.2022.12.032] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Constructing accurate microbial genome assemblies is necessary to understand genetic diversity in microbial genomes and its functional consequences. However, it still remains as a challenging task especially when only short-read sequencing technologies are used. Here, we present a new read-clustering algorithm, called RBRC, for improving de novo microbial genome assembly, by accurately estimating read proximity using multiple reference genomes. The performance of RBRC was confirmed by simulation-based evaluation in terms of assembly contiguity and the number of misassemblies, and was successfully applied to existing fungal and bacterial genomes by improving the quality of the assemblies without using additional sequencing data. RBRC is a very useful read-clustering algorithm that can be used (i) for generating high-quality genome assemblies of microbial strains when genome assemblies of related strains are available, and (ii) for upgrading existing microbial genome assemblies when the generation of additional sequencing data, such as long reads, is difficult.
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Affiliation(s)
- Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Gyeonggi-do 17035, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea,Corresponding author.
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Graf GH, Li X, Kwon D, Belsky DW, Widom CS. Biological aging in maltreated children followed up into middle adulthood. Psychoneuroendocrinology 2022; 143:105848. [PMID: 35779342 DOI: 10.1016/j.psyneuen.2022.105848] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Childhood adversity has been linked to many indicators of shorter healthy lifespan, including earlier onset of disease and disability as well as early mortality. These observations suggest the hypothesis that childhood maltreatment may accelerate aging. OBJECTIVE To characterize the relationship between childhood maltreatment and accelerated biological aging in a prospective cohort of 357 individuals with documented cases of childhood maltreatment and 250 controls matched on demographic and socioeconomic factors. METHODS Cases were drawn from juvenile and adult court records from the years 1967 through 1971 in a large Midwest metropolitan geographic area. Cases were defined as having court-substantiated cases of childhood physical or sexual abuse, or neglect occurring at age 11 or younger. Controls were selected from the same schools and hospitals of birth and matched on age, sex, race, and approximate socioeconomic status. We compared biological aging in these two groups using two blood-chemistry algorithms, the Klemera-Doubal method Biological Age (KDM BA) and the PhenoAge. Algorithms were developed and validated in data from the National Health and Nutrition Examination Surveys (NHANES) using published methods and publicly available software. RESULTS Participants (55% women, 49% non-White) had mean age of 41 years (SD=4). Those with court substantiated childhood maltreatment history exhibited more advanced biological aging as compared with matched controls, although this difference was statistically different for only the KDM BA measure (KDM BA Cohen's D=0.20, 95% CI=[0.03,0.36], p = 0.02; PhenoAge Cohen's D=0.09 95% CI=[-0.08,0.25], p = 0.296). In subgroup analyses, maltreatment effect sizes were larger for women as compared to men and for White participants as compared to non-White participants, although these differences were not statistically significant at the α= 0.05 level. CONCLUSIONS AND RELEVANCE As of midlife, effects of childhood maltreatment on biological aging are small in magnitude but discernible. Interventions to treat psychological and behavioral sequelae of exposure to childhood maltreatment, including in midlife adults, have potential to protect survivors from excess burden of disease, disability, and mortality in later life.
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Affiliation(s)
- G H Graf
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA; Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY 10032, USA.
| | - X Li
- Psychology Department, John Jay College, City University of New York, New York, USA; Graduate Center, City University of New York, New York, USA
| | - D Kwon
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA; Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - D W Belsky
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA; Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY 10032, USA.
| | - C S Widom
- Psychology Department, John Jay College, City University of New York, New York, USA; Graduate Center, City University of New York, New York, USA.
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Deshmukh P, De Kouchkovsky I, Zhang L, Jindal T, Reyes K, Hernandez Romero E, Chan E, Desai A, Borno H, Kwon D, Wong A, Bose R, Aggarwal R, Porten S, Fong L, Small E, Chou J, Friedlander T, Koshkin V. 1751P Impact of squamous histology on clinical outcomes and molecular profiling in metastatic urothelial carcinoma (mUC) patients (pts) treated with newer therapies. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1829] [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] Open
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Jindal T, Han H, Deshmukh P, De Kouchkovsky I, Kwon D, Borno H, Koshkin V, Desai A, Bose R, Chou J, Friedlander T, Small E, Angelidakis A, Johnson M, Feng S, Patnaik A, Fong L, Alumkal J, Aggarwal R. 1404P A phase II study of ZEN-3694 (ZEN), enzalutamide (ENZ), and pembrolizumab (P) in metastatic castration resistant prostate cancer (mCRPC): Interim safety results. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1890] [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: 11/01/2022] Open
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Aggarwal R, Trihy L, Hernandez Romero E, Luch Sam S, Rastogi M, De Kouchkovsky I, Small E, Feng F, Kwon D, Friedlander T, Borno H, Bose R, Chou J, Koshkin V, Desai A, Feng S, Angelidakis A, Johnson M, Fong L, Hope T. 1379P A phase Ib study of a single priming dose of 177Lu-PSMA-617 coupled with pembrolizumab in metastatic castration resistant prostate cancer (mCRPC). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Sim M, Lee J, Wy S, Park N, Lee D, Kwon D, Kim J. Generation and application of pseudo-long reads for metagenome assembly. Gigascience 2022; 11:giac044. [PMID: 35579554 PMCID: PMC9112764 DOI: 10.1093/gigascience/giac044] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/10/2022] [Accepted: 04/03/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads. RESULTS In this study, we present a new method called PLR-GEN. It creates pseudo-long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo-long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo-long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes. CONCLUSIONS PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.
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Affiliation(s)
- Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
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Wy S, Kwon D, Kwon K, Kim J. DLEB: a web application for building deep learning models in biological research. Nucleic Acids Res 2022; 50:W254-W260. [PMID: 35552439 PMCID: PMC9252827 DOI: 10.1093/nar/gkac369] [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] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/28/2022] [Indexed: 11/15/2022] Open
Abstract
Deep learning has been applied for solving many biological problems, and it has shown outstanding performance. Applying deep learning in research requires knowledge of deep learning theories and programming skills, but researchers have developed diverse deep learning platforms to allow users to build deep learning models without programming. Despite these efforts, it is still difficult for biologists to use deep learning because of limitations of the existing platforms. Therefore, a new platform is necessary that can solve these challenges for biologists. To alleviate this situation, we developed a user-friendly and easy-to-use web application called DLEB (Deep Learning Editor for Biologists) that allows for building deep learning models specialized for biologists. DLEB helps researchers (i) design deep learning models easily and (ii) generate corresponding Python code to run directly in their machines. DLEB provides other useful features for biologists, such as recommending deep learning models for specific learning tasks and data, pre-processing of input biological data, and availability of various template models and example biological datasets for model training. DLEB can serve as a highly valuable platform for easily applying deep learning to solve many important biological problems. DLEB is freely available at http://dleb.konkuk.ac.kr/.
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Affiliation(s)
- Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
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Chuong M, Kirsch C, Herrera R, Rubens M, Gungor G, Schaff E, Dolan J, Kim J, Mittauer K, Kotecha R, Gutierrez A, Doemer A, Ugurluer G, Kwon D, Khan G, Alvarez D, Ucar A, Asbun H, Ozyar E, Parikh P. Long-Term Multi-Institutional Outcomes of 5-Fraction Ablative Stereotactic MR-Guided Adaptive Radiation Therapy (SMART) for Inoperable Pancreas Cancer With Median Prescribed Biologically Effective Dose of 100 Gy10. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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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Khakoo N, Levy M, Uribe LP, Wang J, Kuker R, Kwon D, Dooley S, Portelance L, Azzam G, Isrow D, Wolfson A. The Predictive Value of Post-Treatment PET-CT Imaging for Patients With Curable Anal Canal Cancer. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.384] [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: 11/27/2022]
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Peters V, Gurayah A, Kwon D, Zhao W, Jin W, Patel N, Markoe A, Correa Z, Studenski M, Harbour J, Samuels S. Clinical Characteristics and Post-Operative Complications as Predictors of Radiation Toxicity After Treatment With I125 Eye Plaque Brachytherapy for Uveal Melanomas. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1617] [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: 11/24/2022]
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Soni Y, Rich B, Kwon D, Zhao W, John D, Seldon C, Benjamin C, Benveniste R, Komotar R, Prieto P, Fuente MDL, Azzam G, Mellon E, Diwanji T. Disparities in Use of Salvage Whole Brain Radiation Therapy vs. Salvage Stereotactic Radiosurgery After Initial Stereotactic Radiosurgery for Brain Metastases. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1560] [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]
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Gurayah A, Peters V, Kwon D, Zhao W, Jin W, Patel N, Markoe A, Correa Z, Studenski M, Harbour J, Samuels S. Predictors of Outcomes in Iodine-125 Brachytherapy-Treated Uveal Melanomas: A Modern Institutional Study. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1147] [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]
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Delgadillo R, Spieler B, Deana A, Ford J, Kwon D, Yang F, Studenski M, Padgett K, Abramowitz M, Pra A, Stoyanova R, Dogan N. Cone Beam CT Based Delta-Radiomics of Prostate Cancer Patients and Their Correlation to Quality of Life, Genitourinary and Gastrointestinal Toxicities. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.880] [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: 11/17/2022]
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Jang M, Seong S, Jung J, Kwon D, Lee K, Park J, Suh K. 648 Dermoscopic findings and HPV genotypes of genital keratotic lesions: Bowenoid papulosis, seborrheic keratosis, and condyloma acuminatum. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.02.678] [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: 10/21/2022]
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Dawar R, Gawri K, Rodriguez E, Thammineni V, Saul E, Lima Filho JO, Dempsey N, Khan K, Torres T, Kwon D, Lopes G. P01.09 Improved Outcomes With Ramucirumab & Docetaxel in Metastatic Non-Small Cell Lung Cancer After Failure of Immunotherapy. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.333] [Citation(s) in RCA: 1] [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: 11/16/2022]
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Mihaylov I, Lopes G, Saravia D, Kwon D, Yechieli R, Pra AD, Freedman L, Diwanji T, Spieler B. PO-1006: Immunotherapy related pneumonitis correlates with radiomics in NSCLC patients treated with Nivolumab. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)01023-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Rich B, Schumacher L, Sargi Z, Masforroll M, Kwon D, Zhao W, Rueda-Lara M, Elsayyad N, Freedman L, Samuels S, Abramowitz M, Samuels M. Opioid Use Patterns In Head/Neck Cancer Patients Receiving Radiation Therapy: A Single-Institution Retrospective Analysis Characterizing Patients Who Did Not Require Opioid Therapy. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.373] [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: 10/23/2022]
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21
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Spieler B, Azzam G, Kwon D, Saravia D, Lopes G, Dal Pra A, Diwanji T, Yechieli R, Freedman L, Mihaylov I. Checkpoint Inhibitor Pneumonitis in Patients with Advanced NSCLC on Nivolumab Monotherapy is Underreported and Associated with Prior Radiotherapy History. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Seldon C, Shrivastava G, Jarboe J, Fine J, Conway S, Pretell J, Freedman L, Wolfson A, Zhao W, Kwon D, Rosenberg A, Trent J, Yechieli R. Tumor Necrosis Following Multi-Modality Neoadjuvant Therapy for Sarcoma: A Single Institution Series. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1009] [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: 11/27/2022]
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Meshman J, Farnia B, Stoyanova R, Dal Pra A, Abramowitz M, Reis I, Kwon D, Punnen S, Horwitz E, Pollack A. Post-Treatment Biopsy Positivity In Prostate Cancer Patients Undergoing MpMRI-Targeted Radiation Dose Escalation. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.448] [Citation(s) in RCA: 1] [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: 11/29/2022]
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Barkdull S, Yechieli R, Van Wyhe R, Abad M, Hidalgo M, Kwon D, Samuels S. FRAIL Questionnaire Predicts Treatment Delivery Deviations in Patients Receiving Radiotherapy. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1470] [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: 10/23/2022]
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Schaff E, Gartrelle K, Kirsch C, Siddiqui F, Ajlouni M, Dragovic J, Aref I, Shah M, Kwon D, Dobrosotskaya I, Shah R, Khan G, Parikh P. Magnetic Resonance Guided Stereotactic Ablative Radiation Therapy Versus External Beam RT with Chemotherapy For Pancreatic Cancer: Single Institution Toxicity Analysis Of Patients Treated In An Urban Academic Center. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1789] [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: 11/16/2022]
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Stoyanova R, Lopez C, Breto A, Xu I, Kwon D, Franco G, Pra AD, Abramowitz M, Punnen S, Pollack A. The Effects of Androgen-Deprivation Therapy on MRI Delta Radiomics Features in a Prospective Radiotherapy Treatment Trial for Prostate Cancer. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2341] [Citation(s) in RCA: 1] [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: 11/27/2022]
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Ramchand J, Chahine J, Alnajjar H, Chetrit M, Cremer P, Johnston D, Kwon D, Jellis C, Klein A. Long-term natural history of transient constrictive pericarditis. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.2163] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
In recent years, there has been increasing recognition of a potentially-reversible, transient/ subacute form of constrictive pericarditis (CP). To date, studies have been small with lack of long-term longitudinal follow-up.
Purpose
We aimed to elucidate the causes and natural history of subacute CP.
Methods
Patients were included if (1) they had a diagnosis of CP, (2) had cardiac magnetic resonance (CMR) within 12 months of symptom onset with evidence of pericardial delayed enhancement/ inflammation (Figure) (3) received anti-inflammatory medications.
Results
A total of 78 individuals were included, comprising 61 men (78%) with a mean age of 59±14 years. Causes of subacute CP included idiopathic/ viral pericarditis (58%), post-pericardiotomy (29%), autoimmune (6%), radiation therapy (3%) and others (4%). After median follow-up of 4.4 years, 31 (40%) required pericardiectomy. There were no deaths.
Patients who underwent pericardiectomy had longer duration of symptoms at presentation [6 (4–9) vs. 3 (2–5) months, P<0.01], were more likely to be on diuretic therapy (87 vs. 45%, P<0.001), had lower ultra-sensitive C-reactive protein [4.4 (2.6–13.1) vs. 11.95 (1.8–61.55) mg/dl, P<0.001] and lower erythrocyte sedimentation rate [5 (2–10) vs. 25 (6–43 mm/hr), P=0.031] compared to those who were managed medically. There were no other significant differences in clinical characteristics or baseline anti-inflammatory therapy. The presence of elevated inflammatory markers (HR: 0.18; 95% CI: 0.06–0.58, P<0.01) was an independent predictor of freedom from pericardiectomy after adjustment for relevant clinical and imaging parameters.
Conclusions
We present the original observations of the largest cohort of patients with transient CP to date and demonstrate that increased inflammatory markers were independently associated with long-term freedom from pericardiectomy. Our results suggest that a trial of anti-inflammatory therapy in the setting of elevated inflammatory markers may be appropriate prior to referral for surgery given the possible reversibility.
Pericardial delayed enhancement
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
- J Ramchand
- Cleveland Clinic Foundation, Cleveland, United States of America
| | - J Chahine
- Cleveland Clinic Foundation, Cleveland, United States of America
| | - H Alnajjar
- Cleveland Clinic Foundation, Cleveland, United States of America
| | - M Chetrit
- Cleveland Clinic Foundation, Cleveland, United States of America
| | - P Cremer
- Cleveland Clinic Foundation, Cleveland, United States of America
| | - D Johnston
- Cleveland Clinic Foundation, Cleveland, United States of America
| | - D Kwon
- Cleveland Clinic Foundation, Cleveland, United States of America
| | - C Jellis
- Cleveland Clinic Foundation, Cleveland, United States of America
| | - A Klein
- Cleveland Clinic Foundation, Cleveland, United States of America
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Dooley S, Khakoo N, Perlow H, Kwon D, Nicolli E, Yechieli R, Samuels M, Mora M, Freedman L, Samuels S. Improved Care for Patients Evaluated in a Head and Neck Multidisciplinary Clinic at a Safety Net Hospital. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.326] [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: 10/23/2022]
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Ford J, Simpson G, Spieler B, Portelance L, Mellon E, Kwon D, Yang F, Dogan N. Radiomics of 0.35T Magnetic Resonance Images for Predicting Pancreatic Cancer Response to Radiotherapy. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2132] [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: 11/26/2022]
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Azzam G, Toomeh D, Kwon D, Mihaylov I, Samuels S. CT Dose-weighted Textures Indicate Radiation Induced Fibrosis (RIF) in Patients Treated for Head and Neck Cancers. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2339] [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: 10/23/2022]
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Jang M, Seong S, Kwon D, Jang J, Park J, Suh K. 368 Epidemiology and clinical outcomes of 151 patients with mycosis fungoides at the Kosin University Gospel Hospital: Retrospective 27-year review. J Invest Dermatol 2020. [DOI: 10.1016/j.jid.2020.03.376] [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: 10/24/2022]
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Bhat AS, Wang L, Kaur S, Nawabit R, Highland K, Park M, Jellis C, Kwon D, Hill N, Mehra R, Pvdomics P. 0558 Sleep Disordered Breathing and Right Ventricular Electrocardiographic and Functional Characteristics in Group 1 Pulmonary Arterial Hypertension. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.555] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
Right ventricular (RV) electrophysiologic and functional alterations related to sleep disordered breathing (SDB) in pulmonary arterial hypertension (PAH) are not well understood. We hypothesize an association between SDB and RV electrophysiological/functional measures in World Symposium of Pulmonary Hypertension (WSPH) Group 1 PAH.
Methods
The NHLBI multicenter PVDOMICS study (NCT02980887) enrolls patients with PAH undergoing a battery of assessments including home sleep apnea testing(NOX-T3, Carefusion®) or with historical sleep study data. Logistic(OR,95%CI) and linear(beta coefficients,95%CI) regression models adjusted for age, sex, race, body mass index (BMI, kg/m2), PAH medications, supplemental oxygen(O2), positive airway pressure(PAP) were used to assess associations of SDB(apnea hypopnea index,(AHI), ≥3% desaturations(hypopnea), percentage recording time with SaO2<90% (TRT<90%) with electrocardiographic measures: RV hypertrophy(RVH), right bundle branch block(RBBB), and right axis deviation(RAD), echocardiographically-derived RV systolic pressure(RVSP) and RV ejection fraction(RVEF) from cardiac MRI. Analyses were performed based on an overall significance level of 0.05, using SAS software (version 9.4, Cary, NC).
Results
The analysis consisted of 182 PAH participants with age: 52.5±13.9 years, 71.4% female, 88.9% Caucasian, BMI:30.3±7.8 kg/m2, RVEF: 37.3±11.6, and RVSP: 67.0±23.4. None of the electrocardiographic measures were associated with AHI and only RVH was significantly associated with TRT<90% (1.25:1.09,1.43),p=0.001. Although AHI was not associated with RVSP, a 10% increase in TRT<90% was associated with a 2.60mmHg increase in RVSP (2.60:1.44,3.76),p<0.001. Each 10-unit increase in AHI was associated with a 2.72% reduction of RVEF (-2.72:-4.89,-0.56),p=0.014, and each 10-unit increase in TRT<90% was associated with a 0.72% reduction of RVEF (-0.72:-1.38,-0.06),p=0.033.
Conclusion
We identify nocturnal hypoxia as a predictor of RV electrophysiological and functional alterations even after consideration of confounding factors. SDB as determined by AHI was also more so associated with reduced RVEF than hypoxia. Future mechanistic studies should focus on further elucidation of SDB and nocturnal hypoxia on pathogenesis of RV dysfunction in PAH.
Support
U01HL125218/U01HL125205/U01HL125212/U01HL125208/U01HL125175/U01HL125215, U01HL125177/Pulmonary Hypertension Association
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Affiliation(s)
- A S Bhat
- Cleveland Clinic Neurologic Institute, Cleveland, OH
| | - L Wang
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - S Kaur
- Cleveland Clinic Neurologic Institute, Cleveland, OH
| | - R Nawabit
- Cleveland Clinic Neurologic Institute, Cleveland, OH
| | - K Highland
- Cleveland Clinic Respiratory Institute, Cleveland, OH
| | - M Park
- Cleveland Clinic Heart and Vascular Institute, Cleveland, OH
| | - C Jellis
- Cleveland Clinic Heart and Vascular Institute, Cleveland, OH
| | - D Kwon
- Cleveland Clinic Heart and Vascular Institute, Cleveland, OH
| | - N Hill
- Tufts Medical Center Pulmonary, Critical Care & Sleep Divission, Boston, MA
| | - R Mehra
- Cleveland Clinic Neurologic Institute, Cleveland, OH
| | - P Pvdomics
- National Heart, Lung, Blood Institute (NHLBI), Bethesda, MD
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Sim M, Lee J, Lee D, Kwon D, Kim J. TAMA: improved metagenomic sequence classification through meta-analysis. BMC Bioinformatics 2020; 21:185. [PMID: 32397982 PMCID: PMC7218625 DOI: 10.1186/s12859-020-3533-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/16/2020] [Accepted: 05/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microorganisms are important occupants of many different environments. Identifying the composition of microbes and estimating their abundance promote understanding of interactions of microbes in environmental samples. To understand their environments more deeply, the composition of microorganisms in environmental samples has been studied using metagenomes, which are the collections of genomes of the microorganisms. Although many tools have been developed for taxonomy analysis based on different algorithms, variability of analysis outputs of existing tools from the same input metagenome datasets is the main obstacle for many researchers in this field. RESULTS Here, we present a novel meta-analysis tool for metagenome taxonomy analysis, called TAMA, by intelligently integrating outputs from three different taxonomy analysis tools. Using an integrated reference database, TAMA performs taxonomy assignment for input metagenome reads based on a meta-score by integrating scores of taxonomy assignment from different taxonomy classification tools. TAMA outperformed existing tools when evaluated using various benchmark datasets. It was also successfully applied to obtain relative species abundance profiles and difference in composition of microorganisms in two types of cheese metagenome and human gut metagenome. CONCLUSION TAMA can be easily installed and used for metagenome read classification and the prediction of relative species abundance from multiple numbers and types of metagenome read samples. TAMA can be used to more accurately uncover the composition of microorganisms in metagenome samples collected from various environments, especially when the use of a single taxonomy analysis tool is unreliable. TAMA is an open source tool, and can be downloaded at https://github.com/jkimlab/TAMA.
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Affiliation(s)
- Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Azzam G, Perlow H, Cerbon D, Sargi Z, Abramowitz M, Elsayyad N, Freedman L, Nicolli E, Kwon D, Huang L, Samuels M, Samuels S. Quality of Life Impact and Dosimetric Predictors of Radiation-induced Fibrosis of the Neck in Patients Treated for Head and Neck Cancer. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2019.11.055] [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: 10/24/2022]
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35
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Khakoo N, Dooley S, Perlow H, Nicolli E, Kwon D, Samuels M, Mora M, Freedman L, Samuels S. Improvement in Time-to-Treatment Initiation and Use of Ancillary Services for Patients Seen in a Head and Neck Multidisciplinary Clinic at a Safety Net Hospital. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2019.11.072] [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: 11/27/2022]
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Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J. Using INTERSPIA to Explore the Dynamics of Protein-Protein Interactions Among Multiple Species. ACTA ACUST UNITED AC 2019; 68:e88. [PMID: 31751498 DOI: 10.1002/cpbi.88] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
INTER-Species Protein Interaction Analysis (INTERSPIA) is a web application for identifying diverse patterns of protein-protein interactions (PPIs) in different species. Given a set of proteins of interest to the user, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins as well as different or common patterns of PPIs among the proteins in multiple species through a server-side pipeline. Second, it visualizes the dynamics of PPIs in multiple species via an easy-to-use web interface. This article contains a basic protocol describing how to visualize diverse patterns of PPIs of input proteins in multiple species, and how to use them for functional analysis in the web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/. © 2019 by John Wiley & Sons, Inc. Basic Protocol: Running INTERSPIA using a list of input proteins.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Juyeon Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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Spieler B, Azzam G, Asher D, Lopes G, Saravia D, Kwon D, Yechieli R, Pra AD, Diwanji T, Mihaylov I. Overall Survival of Patients with Advanced NSCLC Treated with Nivolumab Correlates with Texture Features on Pre-Immunotherapy CT Imaging and Radiotherapy History. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2438] [Citation(s) in RCA: 3] [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: 11/24/2022]
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Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang GI, Cherry JM, Kim J. Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies. PLoS One 2019; 14:e0221858. [PMID: 31454399 PMCID: PMC6711525 DOI: 10.1371/journal.pone.0221858] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 08/18/2019] [Indexed: 11/29/2022] Open
Abstract
Background Genomic data have become major resources to understand complex mechanisms at fine-scale temporal and spatial resolution in functional and evolutionary genetic studies, including human diseases, such as cancers. Recently, a large number of whole genomes of evolving populations of yeast (Saccharomyces cerevisiae W303 strain) were sequenced in a time-dependent manner to identify temporal evolutionary patterns. For this type of study, a chromosome-level sequence assembly of the strain or population at time zero is required to compare with the genomes derived later. However, there is no fully automated computational approach in experimental evolution studies to establish the chromosome-level genome assembly using unique features of sequencing data. Methods and results In this study, we developed a new software pipeline, the integrative meta-assembly pipeline (IMAP), to build chromosome-level genome sequence assemblies by generating and combining multiple initial assemblies using three de novo assemblers from short-read sequencing data. We significantly improved the continuity and accuracy of the genome assembly using a large collection of sequencing data and hybrid assembly approaches. We validated our pipeline by generating chromosome-level assemblies of yeast strains W303 and SK1, and compared our results with assemblies built using long-read sequencing and various assembly evaluation metrics. We also constructed chromosome-level sequence assemblies of S. cerevisiae strain Sigma1278b, and three commonly used fungal strains: Aspergillus nidulans A713, Neurospora crassa 73, and Thielavia terrestris CBS 492.74, for which long-read sequencing data are not yet available. Finally, we examined the effect of IMAP parameters, such as reference and resolution, on the quality of the final assembly of the yeast strains W303 and SK1. Conclusions We developed a cost-effective pipeline to generate chromosome-level sequence assemblies using only short-read sequencing data. Our pipeline combines the strengths of reference-guided and meta-assembly approaches. Our pipeline is available online at http://github.com/jkimlab/IMAP including a Docker image, as well as a Perl script, to help users install the IMAP package, including several prerequisite programs. Users can use IMAP to easily build the chromosome-level assembly for the genome of their interest.
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Affiliation(s)
- Giltae Song
- School of Computer Science and Engineering, Pusan National University, Busan, South Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Juyeon Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Seokwoo Kang
- School of Computer Science and Engineering, Pusan National University, Busan, South Korea
| | - Hoyong Lee
- School of Computer Science and Engineering, Pusan National University, Busan, South Korea
| | - Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Gregory I. Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, United States of America
| | - J. Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- * E-mail:
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Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J. INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. Nucleic Acids Res 2019; 46:W89-W94. [PMID: 29746660 PMCID: PMC6031021 DOI: 10.1093/nar/gky378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 01/31/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023] Open
Abstract
Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes during evolution can give us new insight into the evolution of functions. Although many algorithms, databases and websites have been developed to help the study of PPIs, most of them are limited to visualize the structure and features of PPIs in a chosen single species with limited functions in the visualization perspective. This leads to difficulties in the identification of different patterns of PPIs in different species and their functional consequences. To resolve these issues, we developed a web application, called INTER-Species Protein Interaction Analysis (INTERSPIA). Given a set of proteins of user's interest, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Juyeon Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
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Kwon Y, Lee H, Kwon D, Kim D, Koo H, Yoo K, Lee M. Effect of interferon-γ-primed mesenchymal stem cells on the growth of acute lymphoblastic leukemia cells in an in vivo model. Cytotherapy 2019. [DOI: 10.1016/j.jcyt.2019.04.042] [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: 11/28/2022]
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Lin W, Bullen J, Soltesz E, Estep J, Tang W, Sabe M, Joyce E, Kwon D. Predictors of Change in Mitral Regurgitation Severity after Left Ventricular Assist Device Implantation. J Heart Lung Transplant 2019. [DOI: 10.1016/j.healun.2019.01.899] [Citation(s) in RCA: 1] [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: 11/26/2022] Open
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Abstract
BACKGROUND Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have been developed to generate high quality de novo assemblies using the NGS reads, but their output is very different because of algorithmic differences. However, there are not properly structured measures to show the similarity or difference in assemblies. RESULTS We developed a new measure, called the GMASS score, for comparing two genome assemblies in terms of their structure. The GMASS score was developed based on the distribution pattern of the number and coverage of similar regions between a pair of assemblies. The new measure was able to show structural similarity between assemblies when evaluated by simulated assembly datasets. The application of the GMASS score to compare assemblies in recently published benchmark datasets showed the divergent performance of current assemblers as well as its ability to compare assemblies. CONCLUSION The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, South Korea.
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Fox B, Swersky A, Sandhu J, Amin A, Chang D, Kwon D, Mohan P. 03:27 PM Abstract No. 182 Microwave ablation (MWA) in cirrhotic patients: prediction of underablation or overablation based on the energy and volume of ablation. J Vasc Interv Radiol 2019. [DOI: 10.1016/j.jvir.2018.12.236] [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: 11/25/2022] Open
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45
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Park B, Silk M, Kwon D, Nadolski G, Hunt S, Gade T. 03:27 PM Abstract No. 289 Registration of 3D holographic models of patient imaging onto a CT grid: assessment of manual and automatic techniques using HoloLens. J Vasc Interv Radiol 2019. [DOI: 10.1016/j.jvir.2018.12.354] [Citation(s) in RCA: 1] [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: 11/25/2022] Open
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46
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Choksi N, Hayward M, Kwon D, Marrazzo J, Mitchell C. Genetic variation of lactobacilllus crispatus strains isolated from a woman during and after bacterial vaginosis. Am J Obstet Gynecol 2018. [DOI: 10.1016/j.ajog.2018.10.061] [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: 10/27/2022]
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47
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Perlow H, Alford S, Kwon D, Griggs J, Ciraula S, Quintana J, Awerbuch A, Cassidy V, Yechieli R, Samuels S. Consideration of Functional Status as a Tool to Predict Treatment Interruptions for Patients Receiving Palliative Radiation for Bone and Brain Metastases. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1292] [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: 10/28/2022]
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48
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Spieler B, El-Bared N, Padgett K, Brown K, Kwon D, Portelance L. Daily Adaptive Magnetic Resonance Image Guidance Protects the Duodenum from Dose Constraint Violations Associated with Interfraction Stomach Deformation in Stereotactic Body Radiation Therapy for Locally Advanced Pancreatic Cancer. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.441] [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: 11/26/2022]
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49
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Mehta S, Ramey S, Kwon D, Rich B, Wolfson A, Yechieli R, Portelance L, Mellon E. Effect of Radiation Therapy Duration on Overall Survival in Anal Squamous Cell Carcinoma: A National Analysis. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.220] [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: 11/24/2022]
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50
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Pollack A, Giret T, Chinea F, Kwon D, Udayakumar T, Cote R, Stortz J, Lam L, Davicioni E, Buerki C, Abramowitz M, Stoyanova R. Association of Circulating Tumor Cells (CTCs) and Genomic Signatures in Prostate Cancer Patients. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.06.123] [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: 11/17/2022]
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