Publications

  • Roy S, Sridharan R, “Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes,” Genome Research, gr. 215004.116 Available
  • Chasman D, Roy S, “Inference of cell type specific regulatory networks on mammalian lineages,” Current Opinion in Systems Biology Available
  • Garcia K, Chasman D, Roy S, Ané J-M. “Physiological responses and gene co-expression network of mycorrhizal roots under K+ deprivation,” Plant Physiol. American Society of Plant Biologists; 2017 Feb 3;:pp.01959.2016. Available
  • Knaack SA, Thompson DA, Roy S. “Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum,” Methods Mol Biol. New York, NY: Springer New York; 2016;1361(Chapter 21):375–89. Available
  • Siahpirani AF, Roy S. “A prior-based integrative framework for functional transcriptional regulatory network inference,” Nucleic Acids Res. Oxford University Press; 2016 Oct 28;:gkw963. Available
  • Niu Z, Chasman D, Eisfeld AJ, Kawaoka Y, Roy S. “Multi-task Consensus Clustering of Genome-wide Transcriptomes from Related Biological Conditions,” Bioinformatics. Oxford Univ Press; 2016;:btw007. Available
  • Chasman D, Walters KB, Lopes TJS, Eisfeld AJ, Kawaoka Y, Roy S. Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. Leslie CS, editor. PLoS Comput Biol. Public Library of Science; 2016 Jul 12;12(7):e1005013. Available
  • Siahpirani AF, Ay F, Roy S.,” A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions,” Genome Biol. BioMed Central; 2016;17(1):1. Available
  • Marx H, Minogue CE, Jayaraman D, Richards AL, Kwiecien NW, Siahpirani AF, et al., “A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti,” Nature biotechnology. Nature Research; 2016 Nov 1;34(11):1198–205. Available
  • D. Chasman, A. Fotuhi Siahpirani, and S. Roy, “Network-based approaches for analysis of complex biological systems,” Current Opinion in Biotechnology, vol. 39, pp. 157-166, Jun. 2016. [Online]. Available
  • Z. Niu, D. Chasman, A. J. Eisfeld, Y. Kawaoka, and S. Roy (2015), “Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions.” Bioinformatics (Oxford, England), Jan. 2016. [Online]. Available
  • S. Roy, A. F. Siahpirani, D. Chasman, S. Knaack, F. Ay, R. Stewart, M. Wilson, and R. Sridharan (2015), “A predictive modeling approach for cell line-specific long-range regulatory interactions,” Nucleic Acids Research, vol. 43, no. 18, pp. 8694-8712, Oct. 2015. [Online].Available
  • D. Thompson, A. Regev, and S. Roy (2015), “Comparative analysis of gene regulatory networks: From network reconstruction to evolution,” Annual Review of Cell and Developmental Biology, vol. 31, no. 1, pp. null+, 2015. [Online]. Available
  • S. Roy and D. Thompson, “Evolution of regulatory networks in candida glabrata: learning to live with the human host,” FEMS Yeast Research, pp. fov087+, Oct. 2015. [Online]. Available
  • E. Larrainzar, B. Riely, S. C. Kim, N. Carrasquilla-Garcia, H.-J. Yu, H.-J. Hwang, M. Oh, G. B. Kim, A. Surendrarao, D. Chasman, A. F. Siahpirani, R. V. Penmetsa, G.-S. Lee, N. Kim, S. Roy, J.-H. Mun, and D. R. Cook (2015), “Deep sequencing of the medicago truncatula root transcriptome reveals a massive and early interaction between nod factor and ethylene signals,” Plant Physiology, pp. pp.00 350.2015+, Jul. 2015. [Online]. Available
  • K. E. Dittenhafer-Reed, A. L. Richards, J. Fan, M. J. Smallegan, A. Fotuhi Siahpirani, Z. A. Kemmerer, T. A. Prolla, S. Roy, J. J. Coon, and J. M. Denu (2015), “SIRT3 mediates Multi-Tissue coupling for metabolic fuel switching.” Cell metabolism, vol. 21, no. 4, pp. 637-646, Apr. 2015. [Online]. Available
  • K. A. Tran, S. A. Jackson, Z. P. Olufs, N. Z. Z. Zaidan, N. Leng, C. Kendziorski, S. Roy, and R. Sridharan. (2015) “Collaborative rewiring of the pluripotency network by chromatin and signalling modulating pathways.” Nature communications, vol. 6, 2015. [Online]. Available
  • Knaack, S., A. F. Siahpirani, S. Roy (2014). A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components. Cancer informatics, vol. 13, no. Suppl 5, pp. 69-84, 2014. [Online]. Available
  • S. Roy, S. Lagree, Z. Hou, J. A. Thomson, R. Stewart, and A. P. Gasch, “Integrated module and Gene-Specific regulatory inference implicates upstream signaling networks,” PLoS Comput Biol, vol. 9, no. 10, pp. e1 003 252+, Oct. 2013. [Online]. Available
  • D. A. Thompson+, S. Roy+, M. Chan, M. P. Styczynsky, J. Pfiffner, C. French, A. Socha, A. Thielke, S. Napolitano, P. Muller, M. Kellis, J. H. Konieczka, I. Wapinski, A. Regev, and D. Tautz, “Evolutionary principles of modular gene regulation in yeasts,” eLife, vol. 2, Jun. 2013. [Online]. Available +Co-first authors.
  • S.Roy, I.Wapinski, J.Pfiffner, C.French, A.Socha, J.Konieczka, N.Habib, M.Kellis, D.Thompson, and A. Regev (2013). Arboretum: reconstruction and analysis of the evolutionary history of condition- specific transcriptional modules. Genome Research.
  • A. S. Hebert, K. E. Dittenhafer-Reed, W. Yu, D. J. Bailey, E. S. Selen, M. D. Boersma, J. J. Carson, M. Tonelli, A. J. Balloon, A. J. Higbee, M. S. Westphall, D. J. Pagliarini, T. A. Prolla, F. Assadi- Porter, S. Roy, J. M. Denu,1, and J. J. Coon. (2012). Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome. Cell
  • R. Atlas, S. Roy. (2012). A graph-based comparative analysis of three-dimensional organization of chromosomes in yeast and mammals. 5th Annual RECOMB Conference on Regulatory and Systems Genomics with DREAM Challenges.
  • D. Marbach+, S. Roy+, F. Ay, P. E. Meyer, R. Candeias, T. Kahveci, C. A. Bristow, M. Kellis (2012). Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Research. +Equal contribution
  • N. Rhind, Z. Chen, M. Yassour+, D. A. Thompson+, B. J. Haas+, N. Habib+, I. Wapinski+, S. Roy+, M. F. Lin, D. I. Heiman, et al. (2011). Comparative Functional Genomics of the Fission Yeasts. Science 332, 930. +Equal contribution
  • G. S. Davidson, R. M. Joe, S. Roy, O. Meirelles, C. P. Allen, M. R. Wilson, P. H. Tapia, E. E. Manzanilla, A. E. Dodson, S. Chakraborty, M. Carter, S. Young, B. Edwards, L. Sklar, and M. Werner-Washburne (2011). The proteomics of quiescent and non-quiescent cell differentiation in yeast stationary-phase cultures. Molecular Biology of the Cell
  • The modENCODE Consortium, S. Roy+, J. Ernst+, P. V. Kharchenko+, P. Kheradpour+, N. Negre+, M. L. Eaton+, J.M. Landolin+, C. A. Bristow+, L. Ma+, M. F. Lin+, S. Washietl+, B. I. Arshinoff+, F. Ay+, P. E. Meyer+, N. Robine+, N. L. Washington+, L. D. Stefano+, E. Berezikov, C. D. Brown, R. Candeias, J. W. Carlson, A. Carr, I. Jungreis, D. Marbach, R. Sealfon, M. Y. Tolstorukov, S.Will, A. Alekseyenko, C. Artieri, B.W. Booth, A. N. Brooks, Qi. Dai, C. A. Davis, M. O. Duff, X. Feng, A. Gorchakov, T. Gu, J. G. Henikoff, P. Kapranov, R. Li, H. MacAlpine, J. Malone, A. Minoda, J. Nordman, K. Okamura, M. Perry, S. Powell, N. C. Riddle, A. Sakai, A. Samsonova, J. E. Sandler, Y. Schwartz, N. Sher, R. Spokony, D. Sturgill, M. van Baren, K. H. Wan, L.Yang, C. Yu, E. Feingold, P. Good, M. Guyer, R. Lowdon, K. Ahmad, J. Andrews, B. Berger, S. E. Brenner, M. R. Brent, L. Cherbas, S. C. R. Elgin, T. R. Gingeras, R. Grossman, R. A. Hoskins, T. C. Kaufman, W. Kent, M. Kuroda, T. Orr-Weaver, N. Perrimon, V. Pirrotta, J. W. Posakony, B. Ren, S. Russell, P. Cherbas, B. R. Graveley, S. Lewis, G. Micklem, B. Oliver, P. J. Park S. E. Celniker, S. Henikoff, G. H. Karpen, E. C. Lai, D. M. MacAlpine, L. D. Stein, K. P. White, and M. Kellis (2010). Identification of functional elements and regulatory circuits in Drosophila modENCODE. Science. +Co-first authors.
  • S. Roy, D. Martinez, H. Platero, T. Lane, M. Werner-Washburne (2009). Exploiting Amino Acid Composition for Predicting Protein-protein Interactions. PLoS ONE.
  • S. Roy, T. Lane, M. Werner-Washburne (2009). Learning structurally consistent undirected probabilistic graphical models. Proceedings of the 26th International Conference on Machine Learning.
  • S. Roy, S. Plis, M. Werner-Washburne, T. Lane (2009). Scalable learning of large networks. q-bio 2008 Special Issue for IET Systems Biology.
  • S. Roy, T. Lane, M. Werner-Washburne and D. Martinez (2009). Inference of functional networks of condition-specific response – A case study of quiescence in yeast. Pacific Symposium of Biocomputing.
  • S. Roy, M. Werner-Washburne, and T. Lane (2008). A system for generating transcription regulatory networks with combinatorial control of transcription. Bioinformatics, 24(10).
  • A.D. Aragon, A. L. Rodriguez, O. Meirelles, S. Roy>, G. S. Davidson, P. H. Tapia, C. Allen, R. Joe, D. Benn, and M. Werner-Washburne (2008). Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-phase cultures. Mol. Biol. Cell, 19(3).
  • A. Stark, M. F. Lin, P. Kheradpour, J. S. Pedersen, L. Parts, J. W. Carlson, M. A. Crosby, M. D. Rasmussen, S. Roy, A. N. Deoras, J. G. Ruby, J. Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, E. Hodges, A. S. Hinrichs, A. Caspi, B. Paten, S. Park, M. V. Han, M. L. Maeder, B. J. Polansky, B. E. Robson, S. Aerts, J. Helden, B. Hassan, D. G. Gilbert, D. A. Eastman, M. Rice, M. Weir, M. W. Hahn, Y. Park, C. N. Dewey, L. Pachter, W. J. Kent, D. Haussler, E. C. Lai, D. P. Bartel, G. J. Hannon, T. C. Kaufman, M. B. Eisen, A. G. Clark, D. Smith, S. E. Celniker, W. M. Gelbart, and M. Kellis (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature, 450.
  • P. Kheradpour, A. Stark, S. Roy, M. Kellis (2007). Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Research, 17.
  • S. Roy, T. Lane, C. Allen, A. D. Aragon, M. Werner-Washburne (2006). A Hidden-state Markov Model for Cell Population Deconvolution. Journal of Computational Biology, 13(10).
  • P. D. Wentzell, T. K. Karakach, S. Roy, M. J. Martinez, C. P. Allen, M. Werner-Washburne (2006). Multivariate curve resolution of time course microarray data. BMC Bioinformatics, 7(343).
  • A. D. Aragon, G. A. Quinones, E. V. Thomas, S. Roy, G. S. Davidson, and M. Werner-Washburne (2006). 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).
  • A. D. Aragon, G. A. Quinones, C. Allen, J. Thomas, S. Roy, G. S. Davidson, P. D. Wentzell, B. Millier, J. E. Jaetao, A. L. Rodriguez, and M. Werner-Washburne (2005). An Automated, Pressure-Driven Sampling Device for Harvesting from Liquid Cultures for Genomic and Biochemical Analyses. Journal of Biochemical Analysis, 65(2).
  • M. J. Martinez, S. Roy, A. B. Archueletta, P. D. Wentzell, S. A. Anna-Arriola, A. L. Rodriguez, A. D. Aragon, G. A. Quinones, C. Allen, M. Werner-Washburne (2004). Analysis of Stationary Phase and Exit in Saccharomyces cerevisiae: Gene Expression and Identification of Novel Essential Genes. Molecular Biology of the Cell, 15.

Technical Reports

  • S. Roy, T. Lane, M. Werner-Washburne (2009). Learning Probabilistic Networks of Condition-Specific Response: Digging Deep in Yeast Stationary Phase. UNM Computer Science Technical Report, TR-CS-2009-07.
  • S. Roy, T. Lane, M. Werner-Washburne (2008). Learning structurally consistent undirected probabilistic graphical models. UNM Computer Science Technical Report, TR-CS-2008-14.
  • S. Roy, T. Lane, M. Werner-Washburne (2007). A Simulation Framework for Modeling Combinatorial Control in Transcription Regulatory Networks. UNM Computer Science Technical Report, TR-CS-2007-06.
  • S. Roy, T. Lane, C. Allen, A. D. Aragon, M. Werner-Washburne (2004). A Sequential Monte Carlo Sampling Approach for Cell Population Deconvolution from Microarray Data.

Posters and Workshops

  • Reconstruction and analysis of evolutionary history of condition-specific transcriptional programs of multiple species. Talk at Cold Spring Harbour Laboratory meeting on Genome Informatics, 2011.
  • Re-constructing the structural and functional components of genome-wide regulatory networks. Talk at Cold Spring Harbour Laboratory meeting on Systems Biology: Networks meeting, 2011.
  • Inferring predictive regulatory networks in Drosophila melanogaster by large-scale data integration. Poster presentation at the CSHL Biology of Genomes meeting, 2011.
  • S. Roy, C. A. Bristow, J. Konieczka, P. Kheradpour, A. Regev, M. Kellis. A Mixture of Experts model for predicting expression from sequence (2010). Intelligent Systems in Molecular Biology.
  • S. Roy, T. Lane, M. Werner-Washburne (2009). Learning condition-specific networks. Third Annual q-bio Conference on Cellular Information Processing. Santa Fe. New Mexico, USA.
  • S. Roy, S. Plis, M. Werner-Washburne (2008). Scalable learning of large networks. Second Annual q-bio Conference on Cellular Information Processing. Santa Fe. New Mexico, USA.
  • S. Roy, A. Stark, P. Kheradpour, M. Kellis, M. Werner-Washburne, T. Lane (2008). A relational framework for predicting tissues and links in the Drosophila regulatory network. Poster at RECOMB Satellite on Regulatory Genom ics and Systems Biology.
  • S. Roy, T. Lane, M. Werner-Washburne (2008). Integrative Construction and Analysis of Condition-specific Biological Network. Thirteenth AAAI Doctoral Consortium. Chicago. Illinois, USA
  • S. Roy, T. Lane, M. Werner-Washburne (2007). Intergative construction and analysis of condition-specific biological networks. AAAI Student Abstract and Poster Program. Vancouver, Canada.
  • S. Roy, T. Lane, M. Werner-Washburne (2006). Predicting protein-protein interactions using amino-acid composition. Second Annual RECOMB Satellite Workshop on Systems Biology. S.Roy, T. Lane, C. Allen, A. D. Aragon, M. Werner-Washburne (2006). Cell population deconvolution using particle filter. Poster presentation at the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB).
  • S. Roy, T. Lane, C. Allen, A. D. Aragon, M. Werner-Washburne (2005). A Datamining approach to cell population deconvolution from gene expressions using particle filters. Fifth ACM SIGKDD Workshop on Data Mining in Bioinformatics.

Dissertation

Learning condition-specific networks (2009). UNM PhD Dissertation.

Master’s thesis

A Machine Learning Approach for Information Extraction (2005). UNM Master’s thesis.