Sushmita Roy, Ph.D. - Publications

Affiliations: 
2009 Computer Science University of New Mexico, Albuquerque, NM, United States 
Area:
Computer Science, Bioinformatics Biology

41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
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 Khatri R, Krishnan S, Roy S, Chattopadhyay S, Kumar V, Mukhopadhyay A. Reactive oxygen species limit the ability of bone marrow stromal cells to support hematopoietic reconstitution in aging mice. Stem Cells and Development. PMID 27140293 DOI: 10.1089/scd.2015.0391  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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
2015 Dittenhafer-Reed KE, Richards AL, Fan J, Smallegan MJ, Fotuhi Siahpirani A, Kemmerer ZA, Prolla TA, Roy S, Coon JJ, Denu JM. SIRT3 mediates multi-tissue coupling for metabolic fuel switching. Cell Metabolism. 21: 637-46. PMID 25863253 DOI: 10.1016/j.cmet.2015.03.007  0.64
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  0.64
2014 Plis SM, Sui J, Lane T, Roy S, Clark VP, Potluru VK, Huster RJ, Michael A, Sponheim SR, Weisend MP, Calhoun VD. High-order interactions observed in multi-task intrinsic networks are dominant indicators of aberrant brain function in schizophrenia. Neuroimage. 102: 35-48. PMID 23876245 DOI: 10.1016/j.neuroimage.2013.07.041  0.64
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  0.64
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  0.64
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  0.64
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  0.64
2013 Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon AJ, Higbee AJ, Westphall MS, Pagliarini DJ, Prolla TA, Assadi-Porter F, Roy S, et al. Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Molecular Cell. 49: 186-99. PMID 23201123 DOI: 10.1016/j.molcel.2012.10.024  0.64
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  0.64
2012 Roy S, Tripathy M, Mathur N, Jain A, Mukhopadhyay A. Hypoxia improves expansion potential of human cord blood-derived hematopoietic stem cells and marrow repopulation efficiency. European Journal of Haematology. 88: 396-405. PMID 22268587 DOI: 10.1111/j.1600-0609.2012.01759.x  0.64
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  0.64
2011 Roy S, Bingle L, Marshall JF, Bass R, Ellis V, Speight PM, Whawell SA. The role of α9β1 integrin in modulating epithelial cell behaviour. Journal of Oral Pathology & Medicine : Official Publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology. 40: 755-61. PMID 21615501 DOI: 10.1111/j.1600-0714.2011.01050.x  0.64
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  0.64
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  0.64
2011 Zawada JF, Yin G, Steiner AR, Yang J, Naresh A, Roy SM, Gold DS, Heinsohn HG, Murray CJ. Microscale to manufacturing scale-up of cell-free cytokine production--a new approach for shortening protein production development timelines. Biotechnology and Bioengineering. 108: 1570-8. PMID 21337337 DOI: 10.1002/bit.23103  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
2008 Roy S, Josephson SA, Fridlyand J, Karch J, Kadoch C, Karrim J, Damon L, Treseler P, Kunwar S, Shuman MA, Jones T, Becker CH, Schulman H, Rubenstein JL. Protein biomarker identification in the CSF of patients with CNS lymphoma. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 26: 96-105. PMID 18056677 DOI: 10.1200/JCO.2007.12.1053  0.64
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  0.64
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  0.4
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  0.64
2006 O'Connor KC, Roy SM, Becker CH, Hafler DA, Kantor AB. Comprehensive phenotyping in multiple sclerosis: discovery based proteomics and the current understanding of putative biomarkers. Disease Markers. 22: 213-25. PMID 17124343  0.64
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  0.64
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  0.64
2006 Tierney RJ, Edwards RH, Sitki-Green D, Croom-Carter D, Roy S, Yao QY, Raab-Traub N, Rickinson AB. Multiple Epstein-Barr virus strains in patients with infectious mononucleosis: comparison of ex vivo samples with in vitro isolates by use of heteroduplex tracking assays. The Journal of Infectious Diseases. 193: 287-97. PMID 16362894 DOI: 10.1086/498913  0.64
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  0.64
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  0.64
2002 Hastings CA, Norton SM, Roy S. New algorithms for processing and peak detection in liquid chromatography/mass spectrometry data. Rapid Communications in Mass Spectrometry : Rcm. 16: 462-7. PMID 11857732 DOI: 10.1002/rcm.600  0.64
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