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For: Durham TJ, Libbrecht MW, Howbert JJ, Bilmes J, Noble WS. PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition. Nat Commun 2018;9:1402. [PMID: 29643364 DOI: 10.1038/s41467-018-03635-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 03/02/2018] [Indexed: 11/24/2022]  Open
Number Cited by Other Article(s)
1
Maciejewski E, Horvath S, Ernst J. CMImpute: cross-species and tissue imputation of species-level DNA methylation samples across mammalian species. Genome Biol 2025;26:133. [PMID: 40394556 PMCID: PMC12090574 DOI: 10.1186/s13059-025-03561-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/26/2025] [Indexed: 05/22/2025]  Open
2
López-Hernández L, Toolan-Kerr P, Bannister AJ, Millán-Zambrano G. Dynamic histone modification patterns coordinating DNA processes. Mol Cell 2025;85:225-237. [PMID: 39824165 DOI: 10.1016/j.molcel.2024.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 10/02/2024] [Accepted: 10/25/2024] [Indexed: 01/20/2025]
3
Murphy AE, Beardall W, Rei M, Phuycharoen M, Skene NG. Predicting cell type-specific epigenomic profiles accounting for distal genetic effects. Nat Commun 2024;15:9951. [PMID: 39550354 PMCID: PMC11569248 DOI: 10.1038/s41467-024-54441-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 11/06/2024] [Indexed: 11/18/2024]  Open
4
Wen W, Zhong J, Zhang Z, Jia L, Chu T, Wang N, Danko CG, Wang Z. dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility. Brief Bioinform 2024;25:bbae459. [PMID: 39316943 PMCID: PMC11421843 DOI: 10.1093/bib/bbae459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/13/2024] [Accepted: 09/04/2024] [Indexed: 09/26/2024]  Open
5
Tan ZC, Meyer AS. The structure is the message: Preserving experimental context through tensor decomposition. Cell Syst 2024;15:679-693. [PMID: 39173584 PMCID: PMC11366223 DOI: 10.1016/j.cels.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 06/25/2024] [Accepted: 07/22/2024] [Indexed: 08/24/2024]
6
Min A, Schreiber J, Kundaje A, Noble WS. Predicting chromatin conformation contact maps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589240. [PMID: 38645064 PMCID: PMC11030330 DOI: 10.1101/2024.04.12.589240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
7
Xiang G, Guo Y, Bumcrot D, Sigova A. JMnorm: a novel joint multi-feature normalization method for integrative and comparative epigenomics. Nucleic Acids Res 2024;52:e11. [PMID: 38055833 PMCID: PMC10810286 DOI: 10.1093/nar/gkad1146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023]  Open
8
Yu X, Zhao H, Wang R, Chen Y, Ouyang X, Li W, Sun Y, Peng A. Cancer epigenetics: from laboratory studies and clinical trials to precision medicine. Cell Death Discov 2024;10:28. [PMID: 38225241 PMCID: PMC10789753 DOI: 10.1038/s41420-024-01803-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/23/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024]  Open
9
Fadri MTM, Lee JB, Keung AJ. Summary of ChIP-Seq Methods and Description of an Optimized ChIP-Seq Protocol. Methods Mol Biol 2024;2842:419-447. [PMID: 39012609 DOI: 10.1007/978-1-0716-4051-7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
10
Hawkins-Hooker A, Visonà G, Narendra T, Rojas-Carulla M, Schölkopf B, Schweikert G. Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning. Nat Commun 2023;14:4750. [PMID: 37550323 PMCID: PMC10406842 DOI: 10.1038/s41467-023-40211-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/18/2023] [Indexed: 08/09/2023]  Open
11
Schreiber JM, Boix CA, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom RS, Farrell NP, Halow JM, Lee K, Jiang L, Yang X, Epstein CB, Strattan JS, Bernstein BE, Snyder MP, Kellis M, Noble WS, Kundaje AB. The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biol 2023;24:79. [PMID: 37072822 PMCID: PMC10111747 DOI: 10.1186/s13059-023-02915-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/24/2023] [Indexed: 04/20/2023]  Open
12
Llera A, Brammer M, Oakley B, Tillmann J, Zabihi M, Amelink JS, Mei T, Charman T, Ecker C, Dell'Acqua F, Banaschewski T, Moessnang C, Baron-Cohen S, Holt R, Durston S, Murphy D, Loth E, Buitelaar JK, Floris DL, Beckmann CF. Evaluation of data imputation strategies in complex, deeply-phenotyped data sets: the case of the EU-AIMS Longitudinal European Autism Project. BMC Med Res Methodol 2022;22:229. [PMID: 35971088 PMCID: PMC9380301 DOI: 10.1186/s12874-022-01656-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/02/2022] [Indexed: 12/19/2022]  Open
13
Dsouza KB, Li AY, Bhargava VK, Libbrecht MW. Latent Representation of the Human Pan-Celltype Epigenome Through a Deep Recurrent Neural Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2313-2323. [PMID: 34043510 DOI: 10.1109/tcbb.2021.3084147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
14
Albrecht S, Andreani T, Andrade-Navarro MA, Fontaine JF. Single-cell specific and interpretable machine learning models for sparse scChIP-seq data imputation. PLoS One 2022;17:e0270043. [PMID: 35776722 PMCID: PMC9249201 DOI: 10.1371/journal.pone.0270043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/02/2022] [Indexed: 11/19/2022]  Open
15
Luo K, Zhong J, Safi A, Hong LK, Tewari AK, Song L, Reddy TE, Ma L, Crawford GE, Hartemink AJ. Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data. Genome Res 2022;32:1183-1198. [PMID: 35609992 PMCID: PMC9248881 DOI: 10.1101/gr.272203.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/06/2022] [Indexed: 11/24/2022]
16
Hesami M, Alizadeh M, Jones AMP, Torkamaneh D. Machine learning: its challenges and opportunities in plant system biology. Appl Microbiol Biotechnol 2022;106:3507-3530. [PMID: 35575915 DOI: 10.1007/s00253-022-11963-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/14/2022] [Accepted: 05/07/2022] [Indexed: 12/25/2022]
17
Daneshpajouh H, Chen B, Shokraneh N, Masoumi S, Wiese KC, Libbrecht MW. Continuous chromatin state feature annotation of the human epigenome. Bioinformatics 2022;38:3029-3036. [PMID: 35451453 PMCID: PMC9154241 DOI: 10.1093/bioinformatics/btac283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 12/02/2022]  Open
18
Li H, Guan Y. Asymmetric predictive relationships across histone modifications. NAT MACH INTELL 2022;4:288-299. [DOI: 10.1038/s42256-022-00455-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
19
Wang Z, Chivu AG, Choate LA, Rice EJ, Miller DC, Chu T, Chou SP, Kingsley NB, Petersen JL, Finno CJ, Bellone RR, Antczak DF, Lis JT, Danko CG. Prediction of histone post-translational modification patterns based on nascent transcription data. Nat Genet 2022;54:295-305. [PMID: 35273399 PMCID: PMC9444190 DOI: 10.1038/s41588-022-01026-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 01/24/2022] [Indexed: 01/01/2023]
20
Ni Z, Zheng X, Zheng X, Zou X. scLRTD : A Novel Low Rank Tensor Decomposition Method for Imputing Missing Values in Single-Cell Multi-Omics Sequencing Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1144-1153. [PMID: 32960767 DOI: 10.1109/tcbb.2020.3025804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
21
Arslan E, Schulz J, Rai K. Machine Learning in Epigenomics: Insights into Cancer Biology and Medicine. Biochim Biophys Acta Rev Cancer 2021;1876:188588. [PMID: 34245839 PMCID: PMC8595561 DOI: 10.1016/j.bbcan.2021.188588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 02/01/2023]
22
Morrow A, Hughes J, Singh J, Joseph A, Yosef N. Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning. Nucleic Acids Res 2021;49:e110. [PMID: 34379786 PMCID: PMC8565335 DOI: 10.1093/nar/gkab676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/19/2021] [Accepted: 07/25/2021] [Indexed: 01/04/2023]  Open
23
Libbrecht MW, Chan RCW, Hoffman MM. Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns. PLoS Comput Biol 2021;17:e1009423. [PMID: 34648491 PMCID: PMC8516206 DOI: 10.1371/journal.pcbi.1009423] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
24
Zhou W, Hongkai J. Genome-wide Prediction of Chromatin Accessibility Based on Gene Expression. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL STATISTICS 2021;13:e1544. [PMID: 39391743 PMCID: PMC11466374 DOI: 10.1002/wics.1544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 11/28/2020] [Indexed: 10/12/2024]
25
Nieboer MM, Nguyen L, de Ridder J. Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning. Sci Rep 2021;11:14411. [PMID: 34257393 PMCID: PMC8277903 DOI: 10.1038/s41598-021-93917-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022]  Open
26
Bayat F, Libbrecht M. VSS: Variance-stabilized signals for sequencing-based genomic signals. Bioinformatics 2021;37:4383-4391. [PMID: 34165492 PMCID: PMC8652025 DOI: 10.1093/bioinformatics/btab457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 04/28/2021] [Accepted: 06/17/2021] [Indexed: 11/12/2022]  Open
27
Schreiber J, Singh R. Machine learning for profile prediction in genomics. Curr Opin Chem Biol 2021;65:35-41. [PMID: 34107341 DOI: 10.1016/j.cbpa.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 02/08/2023]
28
Schreiber J, Bilmes J, Noble WS. Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data. Bioinformatics 2021;37:439-447. [PMID: 32966546 PMCID: PMC8088321 DOI: 10.1093/bioinformatics/btaa830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 07/28/2020] [Accepted: 09/09/2020] [Indexed: 12/03/2022]  Open
29
Nakato R, Sakata T. Methods for ChIP-seq analysis: A practical workflow and advanced applications. Methods 2021;187:44-53. [PMID: 32240773 DOI: 10.1016/j.ymeth.2020.03.005] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/13/2022]  Open
30
Pei G, Hu R, Dai Y, Manuel AM, Zhao Z, Jia P. Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations. Nucleic Acids Res 2021;49:53-66. [PMID: 33300042 PMCID: PMC7797043 DOI: 10.1093/nar/gkaa1137] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/22/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023]  Open
31
Pei G, Wang YY, Simon LM, Dai Y, Zhao Z, Jia P. Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders. Genome Res 2020;31:146-158. [PMID: 33272935 PMCID: PMC7849392 DOI: 10.1101/gr.265769.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022]
32
Schreiber J, Singh R, Bilmes J, Noble WS. A pitfall for machine learning methods aiming to predict across cell types. Genome Biol 2020;21:282. [PMID: 33213499 PMCID: PMC7678316 DOI: 10.1186/s13059-020-02177-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/07/2020] [Indexed: 01/19/2023]  Open
33
Song M, Greenbaum J, Luttrell J, Zhou W, Wu C, Shen H, Gong P, Zhang C, Deng HW. A Review of Integrative Imputation for Multi-Omics Datasets. Front Genet 2020;11:570255. [PMID: 33193667 PMCID: PMC7594632 DOI: 10.3389/fgene.2020.570255] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 09/16/2020] [Indexed: 01/05/2023]  Open
34
Sahu A, Li N, Dunkel I, Chung HR. EPIGENE: genome-wide transcription unit annotation using a multivariate probabilistic model of histone modifications. Epigenetics Chromatin 2020;13:20. [PMID: 32264931 PMCID: PMC7137282 DOI: 10.1186/s13072-020-00341-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/28/2020] [Indexed: 11/10/2022]  Open
35
Schreiber J, Bilmes J, Noble WS. Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples. Genome Biol 2020;21:82. [PMID: 32228713 PMCID: PMC7104481 DOI: 10.1186/s13059-020-01978-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 02/26/2020] [Indexed: 12/16/2022]  Open
36
Schreiber J, Durham T, Bilmes J, Noble WS. Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome. Genome Biol 2020;21:81. [PMID: 32228704 PMCID: PMC7104480 DOI: 10.1186/s13059-020-01977-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 02/26/2020] [Indexed: 02/08/2023]  Open
37
Zhang S, Chasman D, Knaack S, Roy S. In silico prediction of high-resolution Hi-C interaction matrices. Nat Commun 2019;10:5449. [PMID: 31811132 PMCID: PMC6898380 DOI: 10.1038/s41467-019-13423-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/07/2019] [Indexed: 11/28/2022]  Open
38
Zhang Y, Mahony S. Direct prediction of regulatory elements from partial data without imputation. PLoS Comput Biol 2019;15:e1007399. [PMID: 31682602 PMCID: PMC6855516 DOI: 10.1371/journal.pcbi.1007399] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/14/2019] [Accepted: 09/12/2019] [Indexed: 01/07/2023]  Open
39
Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. AN INTERNATIONAL JOURNAL ON INFORMATION FUSION 2019;50:71-91. [PMID: 30467459 PMCID: PMC6242341 DOI: 10.1016/j.inffus.2018.09.012] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
40
Nair S, Kim DS, Perricone J, Kundaje A. Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts. Bioinformatics 2019;35:i108-i116. [PMID: 31510655 PMCID: PMC6612838 DOI: 10.1093/bioinformatics/btz352] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
41
Keilwagen J, Posch S, Grau J. Accurate prediction of cell type-specific transcription factor binding. Genome Biol 2019;20:9. [PMID: 30630522 PMCID: PMC6327544 DOI: 10.1186/s13059-018-1614-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/18/2018] [Indexed: 01/11/2023]  Open
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Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends Genet 2018;34:790-805. [PMID: 30143323 PMCID: PMC6309559 DOI: 10.1016/j.tig.2018.07.003] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/01/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022]
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