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Sushmita Roy, Ph.D. - Publications

Affiliations: 
2009 Computer Science University of New Mexico, Albuquerque, NM, United States 
Area:
Computer Science, Bioinformatics Biology
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63 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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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