Year |
Citation |
Score |
2023 |
Baur B, Shin J, Schreiber J, Zhang S, Zhang Y, Manjunath M, Song JS, Stafford Noble W, Roy S. Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation. Plos Computational Biology. 19: e1011286. PMID 37428809 DOI: 10.1371/journal.pcbi.1011286 |
0.344 |
|
2023 |
Zhang S, Pyne S, Pietrzak S, Halberg S, McCalla SG, Siahpirani AF, Sridharan R, Roy S. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nature Communications. 14: 3064. PMID 37244909 DOI: 10.1038/s41467-023-38637-9 |
0.369 |
|
2023 |
Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, et al. Publisher Correction: Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Scientific Reports. 13: 7522. PMID 37160896 DOI: 10.1038/s41598-023-33284-y |
0.553 |
|
2023 |
Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, et al. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Scientific Reports. 13: 5420. PMID 37012431 DOI: 10.1038/s41598-023-32568-7 |
0.602 |
|
2022 |
Knaack SA, Conde D, Chakraborty S, Balmant KM, Irving TB, Maia LGS, Triozzi PM, Dervinis C, Pereira WJ, Maeda J, Schmidt HW, Ané JM, Kirst M, Roy S. Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula. Bmc Biology. 20: 252. PMID 36352404 DOI: 10.1186/s12915-022-01450-9 |
0.304 |
|
2022 |
Fotuhi Siahpirani A, Knaack S, Chasman D, Seirup M, Sridharan R, Stewart R, Thomson J, Roy S. Dynamic regulatory module networks for inference of cell type-specific transcriptional networks. Genome Research. PMID 35705328 DOI: 10.1101/gr.276542.121 |
0.34 |
|
2022 |
Zhang S, Knaack S, Roy S. Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE. Methods in Molecular Biology (Clifton, N.J.). 2477: 439-455. PMID 35524131 DOI: 10.1007/978-1-0716-2257-5_24 |
0.323 |
|
2022 |
Pereira WJ, Knaack S, Chakraborty S, Conde D, Folk RA, Triozzi PM, Balmant KM, Dervinis C, Schmidt HW, Ané JM, Roy S, Kirst M. Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade. The New Phytologist. PMID 35092309 DOI: 10.1111/nph.18006 |
0.339 |
|
2021 |
Mehta TK, Koch C, Nash W, Knaack SA, Sudhakar P, Olbei M, Bastkowski S, Penso-Dolfin L, Korcsmaros T, Haerty W, Roy S, Di-Palma F. Evolution of regulatory networks associated with traits under selection in cichlids. Genome Biology. 22: 25. PMID 33419455 DOI: 10.1186/s13059-020-02208-8 |
0.323 |
|
2020 |
Baur B, Shin J, Zhang S, Roy S. Data integration for inferring context-specific gene regulatory networks. Current Opinion in Systems Biology. 23: 38-46. PMID 33225112 DOI: 10.1016/j.coisb.2020.09.005 |
0.405 |
|
2020 |
Manjunath M, Zhang Y, Zhang S, Roy S, Perez-Pinera P, Song JS. ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants. Frontiers in Genetics. 11: 730. PMID 32765587 DOI: 10.3389/Fgene.2020.00730 |
0.37 |
|
2020 |
Sinha D, Steyer B, Shahi PK, Mueller KP, Valiauga R, Edwards KL, Bacig C, Steltzer SS, Srinivasan S, Abdeen A, Cory E, Periyasamy V, Siahpirani AF, Stone EM, Tucker BA, ... Roy S, et al. Human iPSC Modeling Reveals Mutation-Specific Responses to Gene Therapy in a Genotypically Diverse Dominant Maculopathy. American Journal of Human Genetics. PMID 32707085 DOI: 10.1016/J.Ajhg.2020.06.011 |
0.365 |
|
2020 |
Li M, Shin J, Risgaard RD, Parries MJ, Wang J, Chasman D, Liu S, Roy S, Bhattacharyya A, Zhao X. Identification of FMR1-regulated molecular networks in human neurodevelopment. Genome Research. PMID 32179589 DOI: 10.1101/Gr.251405.119 |
0.435 |
|
2019 |
Zhang S, Chasman D, Knaack S, Roy S. In silico prediction of high-resolution Hi-C interaction matrices. Nature Communications. 10: 5449. PMID 31811132 DOI: 10.1038/S41467-019-13423-8 |
0.423 |
|
2019 |
Zhang Y, Manjunath M, Yan J, Baur BA, Zhang S, Roy S, Song JS. The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment. Frontiers in Genetics. 10: 754. PMID 31507631 DOI: 10.3389/Fgene.2019.00754 |
0.324 |
|
2019 |
Chasman D, Iyer N, Fotuhi Siahpirani A, Estevez Silva M, Lippmann E, McIntosh B, Probasco MD, Jiang P, Stewart R, Thomson JA, Ashton RS, Roy S. Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. Cell Systems. PMID 31302154 DOI: 10.1016/J.Cels.2019.05.012 |
0.427 |
|
2019 |
Tran KA, Pietrzak SJ, Zaidan NZ, Siahpirani AF, McCalla SG, Zhou AS, Iyer G, Roy S, Sridharan R. Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency. Cell Reports. 27: 1726-1741.e5. PMID 31067459 DOI: 10.1016/J.Celrep.2019.04.056 |
0.408 |
|
2019 |
Wheeler HE, Ploch S, Barbeira AN, Bonazzola R, Andaleon A, Fotuhi Sishpirani A, Saha A, Battle A, Roy S, Im HK. Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits. Genetic Epidemiology. PMID 30950127 DOI: 10.1002/Gepi.22205 |
0.411 |
|
2019 |
Siahpirani AF, Chasman D, Roy S. Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks. Methods in Molecular Biology (Clifton, N.J.). 1883: 161-194. PMID 30547400 DOI: 10.1007/978-1-4939-8882-2_7 |
0.5 |
|
2018 |
Zhang Y, Manjunath M, Zhang S, Chasman D, Roy S, Song JS. Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer-associated genetic variant rs4415084. Cancer Research. PMID 29351903 DOI: 10.1158/0008-5472.Can-17-3486 |
0.353 |
|
2018 |
Zhang Y, Manjunath M, Zhang S, Chasman D, Roy S, Song JS. Abstract 1220: Integrative genomic analysis discovers the causative regulatory mechanisms of a breast cancer-associated genetic variant Epidemiology. 78: 1220-1220. DOI: 10.1158/1538-7445.Am2018-1220 |
0.355 |
|
2017 |
Chasman D, Roy S. Inference of cell type specific regulatory networks on mammalian lineages. Current Opinion in Systems Biology. 2: 130-139. PMID 29082337 DOI: 10.1016/J.Coisb.2017.04.001 |
0.513 |
|
2017 |
Koch C, Konieczka J, Delorey T, Lyons A, Socha A, Davis K, Knaack SA, Thompson D, O'Shea EK, Regev A, Roy S. Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies. Cell Systems. 4: 543-558.e8. PMID 28544882 DOI: 10.1016/J.Cels.2017.04.010 |
0.438 |
|
2017 |
Roy S, Sridharan R. Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes. Genome Research. PMID 28424352 DOI: 10.1101/Gr.215004.116 |
0.373 |
|
2017 |
Garcia K, Chasman D, Roy S, Ane JM. Physiological responses and gene co-expression network of mycorrhizal roots under K+ deprivation. Plant Physiology. PMID 28159827 DOI: 10.1104/Pp.16.01959 |
0.327 |
|
2016 |
Siahpirani AF, Roy S. A prior-based integrative framework for functional transcriptional regulatory network inference. Nucleic Acids Research. PMID 27794550 DOI: 10.1093/Nar/Gkw963 |
0.444 |
|
2016 |
Marx H, Minogue CE, Jayaraman D, Richards AL, Kwiecien NW, Sihapirani AF, Rajasekar S, Maeda J, Garcia K, Del Valle-Echevarria AR, Volkening JD, Westphall MS, Roy S, Sussman MR, Ané JM, et al. A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti. Nature Biotechnology. PMID 27748755 DOI: 10.1038/Nbt.3681 |
0.323 |
|
2016 |
Chasman D, Walters KB, Lopes TJ, Eisfeld AJ, Kawaoka Y, Roy S. Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. Plos Computational Biology. 12: e1005013. PMID 27403523 DOI: 10.1371/Journal.Pcbi.1005013 |
0.407 |
|
2016 |
Fotuhi Siahpirani A, Ay F, Roy S. A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions. Genome Biology. 17: 114. PMID 27233632 DOI: 10.1186/S13059-016-0962-8 |
0.64 |
|
2016 |
Chasman D, Fotuhi Siahpirani A, Roy S. Network-based approaches for analysis of complex biological systems. Current Opinion in Biotechnology. 39: 157-166. PMID 27115495 DOI: 10.1016/J.Copbio.2016.04.007 |
0.395 |
|
2016 |
Niu Z, Chasman D, Eisfeld AJ, Kawaoka Y, Roy S. Multi-task Consensus Clustering of Genome-wide Transcriptomes from Related Biological Conditions. Bioinformatics (Oxford, England). PMID 26801959 DOI: 10.1093/Bioinformatics/Btw007 |
0.421 |
|
2016 |
Knaack SA, Thompson DA, Roy S. Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum. Methods in Molecular Biology (Clifton, N.J.). 1361: 375-89. PMID 26483033 DOI: 10.1007/978-1-4939-3079-1_21 |
0.478 |
|
2015 |
Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R. A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Research. PMID 26546512 DOI: 10.1093/nar/gkv1181 |
0.596 |
|
2015 |
Roy S, Thompson D. Evolution of regulatory networks in Candida glabrata: learning to live with the human host. Fems Yeast Research. PMID 26449820 DOI: 10.1093/Femsyr/Fov087 |
0.4 |
|
2015 |
Thompson D, Regev A, Roy S. Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution. Annual Review of Cell and Developmental Biology. PMID 26355593 DOI: 10.1146/Annurev-Cellbio-100913-012908 |
0.49 |
|
2015 |
Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R. A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Research. PMID 26338778 DOI: 10.1093/Nar/Gkv865 |
0.69 |
|
2015 |
Larrainzar E, Riely B, Kim SC, Carrasquilla-Garcia N, Yu HJ, Hwang HJ, Oh M, Kim GB, Surendrarao A, Chasman D, Siahpirani AF, Penmetsa RV, Lee GS, Kim N, Roy S, et al. Deep sequencing of the Medicago truncatula root transcriptome reveals a massive and early interaction between Nod factor and ethylene signals. Plant Physiology. PMID 26175514 DOI: 10.1104/Pp.15.00350 |
0.378 |
|
2015 |
Tran KA, Jackson SA, Olufs ZP, Zaidan NZ, Leng N, Kendziorski C, Roy S, Sridharan R. Collaborative rewiring of the pluripotency network by chromatin and signalling modulating pathways. Nature Communications. 6: 6188. PMID 25650115 DOI: 10.1038/Ncomms7188 |
0.378 |
|
2014 |
Knaack SA, Siahpirani AF, Roy S. A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components. Cancer Informatics. 13: 69-84. PMID 25374456 DOI: 10.4137/Cin.S14058 |
0.425 |
|
2013 |
Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP. Integrated module and gene-specific regulatory inference implicates upstream signaling networks. Plos Computational Biology. 9: e1003252. PMID 24146602 DOI: 10.1371/Journal.Pcbi.1003252 |
0.476 |
|
2013 |
Thompson DA, Roy S, Chan M, Styczynski MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A. Correction: Evolutionary principles of modular gene regulation in yeasts. Elife. 2: e01114. PMID 23840936 DOI: 10.7554/Elife.01114 |
0.554 |
|
2013 |
Thompson DA, Roy S, Chan M, Styczynsky MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A. Evolutionary principles of modular gene regulation in yeasts. Elife. 2: e00603. PMID 23795289 DOI: 10.7554/Elife.00603 |
0.601 |
|
2013 |
Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A. Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules. Genome Research. 23: 1039-50. PMID 23640720 DOI: 10.1101/Gr.146233.112 |
0.592 |
|
2013 |
Thompson DA, Roy S, Chan M, Styczynsky MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A. Author response: Evolutionary principles of modular gene regulation in yeasts Elife. DOI: 10.7554/Elife.00603.031 |
0.579 |
|
2012 |
Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Research. 22: 1334-49. PMID 22456606 DOI: 10.1101/Gr.127191.111 |
0.769 |
|
2012 |
Werner-Washburne M, Roy S, Davidson GS. Aging and the survival of quiescent and non-quiescent cells in yeast stationary-phase cultures. Sub-Cellular Biochemistry. 57: 123-43. PMID 22094420 DOI: 10.1007/978-94-007-2561-4_6 |
0.669 |
|
2011 |
Roy S, Werner-Washburne M, Lane T. A multiple network learning approach to capture system-wide condition-specific responses. Bioinformatics (Oxford, England). 27: 1832-8. PMID 21551143 DOI: 10.1093/bioinformatics/btr270 |
0.632 |
|
2011 |
Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, et al. Comparative functional genomics of the fission yeasts. Science (New York, N.Y.). 332: 930-6. PMID 21511999 DOI: 10.1126/Science.1203357 |
0.639 |
|
2011 |
Davidson GS, Joe RM, Roy S, Meirelles O, Allen CP, Wilson MR, Tapia PH, Manzanilla EE, Dodson AE, Chakraborty S, Carter M, Young S, Edwards B, Sklar L, Werner-Washburne M. The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures. Molecular Biology of the Cell. 22: 988-98. PMID 21289090 DOI: 10.1091/Mbc.E10-06-0499 |
0.759 |
|
2010 |
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374 |
0.678 |
|
2009 |
Roy S, Plis S, Werner-Washburne M, Lane T. Scalable learning of large networks. Iet Systems Biology. 3: 404-13. PMID 21028930 DOI: 10.1049/Iet-Syb.2008.0161 |
0.679 |
|
2009 |
Roy S, Lane T, Werner-Washburne M. Learning structurally consistent undirected probabilistic graphical models. Proceedings of the ... International Conference On Machine Learning. International Conference On Machine Learning. 382: 905-912. PMID 20485538 DOI: 10.1145/1553374.1553490 |
0.594 |
|
2009 |
Roy S, Martinez D, Platero H, Lane T, Werner-Washburne M. Exploiting amino acid composition for predicting protein-protein interactions. Plos One. 4: e7813. PMID 19936254 DOI: 10.1371/Journal.Pone.0007813 |
0.65 |
|
2009 |
Roy S, Lane T, Werner-Washburne M, Martinez D. Inference of functional networks of condition-specific response--a case study of quiescence in yeast. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 51-62. PMID 19209695 |
0.687 |
|
2008 |
Roy S, Werner-Washburne M, Lane T. A system for generating transcription regulatory networks with combinatorial control of transcription. Bioinformatics (Oxford, England). 24: 1318-20. PMID 18400774 DOI: 10.1093/Bioinformatics/Btn126 |
0.71 |
|
2008 |
Aragon AD, Rodriguez AL, Meirelles O, Roy S, Davidson GS, Tapia PH, Allen C, Joe R, Benn D, Werner-Washburne M. Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-phase cultures. Molecular Biology of the Cell. 19: 1271-80. PMID 18199684 DOI: 10.1091/Mbc.E07-07-0666 |
0.763 |
|
2007 |
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340 |
0.788 |
|
2007 |
Kheradpour P, Stark A, Roy S, Kellis M. Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Research. 17: 1919-31. PMID 17989251 DOI: 10.1101/Gr.7090407 |
0.79 |
|
2006 |
Roy S, Lane T, Allen C, Aragon AD, Werner-Washburne M. A hidden-state Markov model for cell population deconvolution. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 1749-74. PMID 17238843 DOI: 10.1089/Cmb.2006.13.1749 |
0.688 |
|
2006 |
Wentzell PD, Karakach TK, Roy S, Martinez MJ, Allen CP, Werner-Washburne M. Multivariate curve resolution of time course microarray data. Bmc Bioinformatics. 7: 343. PMID 16839419 DOI: 10.1186/1471-2105-7-343 |
0.658 |
|
2006 |
Aragon AD, Quiñones GA, Thomas EV, Roy S, Werner-Washburne M. Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress. Genome Biology. 7: R9. PMID 16507144 DOI: 10.1186/Gb-2006-7-2-R9 |
0.658 |
|
2006 |
Aragon AD, Quiñones GA, Allen C, Thomas J, Roy S, Davidson GS, Wentzell PD, Millier B, Jaetao JE, Rodriguez AL, Werner-Washburne M. An automated, pressure-driven sampling device for harvesting from liquid cultures for genomic and biochemical analyses. Journal of Microbiological Methods. 65: 357-60. PMID 16198434 DOI: 10.1016/J.Mimet.2005.08.015 |
0.63 |
|
2004 |
Martinez MJ, Roy S, Archuletta AB, Wentzell PD, Anna-Arriola SS, Rodriguez AL, Aragon AD, Quiñones GA, Allen C, Werner-Washburne M. Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes. Molecular Biology of the Cell. 15: 5295-305. PMID 15456898 DOI: 10.1091/Mbc.E03-11-0856 |
0.705 |
|
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