Publications

1. Examining the dynamics of three-dimensional genome organization with multitask matrix factorization DI Lee, S Roy Genome Research 35 (5) 1179-1193 (2025)
2. Uncovering Functional Gene Regulatory Networks in Bulk and Single-Cell Data through Robust Transcription Factor Activity Estimation and Model-Guided Experimental Validation AF Siahpirani, SG McCalla, S Pyne, CM Dillingham, R Sridharan, S Roy bioRxiv, 2025.06. 09.658650 (2025)
3. Transcriptomic analysis reveals vector attraction to potato virus Y is mediated through temporal regulation of TERPENE SYNTHASE 1 (TPS1) CT Nihranz, P Garg, J Shin, M Dumas, SG McCalla, S Roy, CL Casteel Plant Stress, 16, 100862 (2025)
4. Perspective on recent developments and challenges in regulatory and systems genomics J Zeiltinger, S Roy, F Ay, A Mathelier, A Medina-Rivera, S Mahony, … Bioinformatics Advances 5 (1) vbaf106 (2025)
5. The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula WJ Pereira, J Boyd, D Conde, PM Triozzi, KM Balmant, C Dervinis, … Cell Reports 43 (2) (2024)
6. Current and future directions in network biology M Zitnik, MM Li, A Wells, K Glass, DM Gysi, A Krishnan, TM Murali, … Bioinformatics Advances 4 (1) vbae099 (2024)
7. Predicting patient-specific enhancer-promoter interactions B Baur, S Roy Cell Reports Methods 3 (9) (2023)
8. Benchmarking graph representation learning algorithms for detecting modules in molecular networks Z Song, B Baur, S Roy F1000Research 12, 941 (2023)
9. ISMB/ECCB 2023 proceedings Y Ponty, S Roy Bioinformatics 39 (Supplement_1), i1-i2 (2023)
10. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets S Zhang, S Pyne, S Pietrzak, S Halberg, SG McCalla, AF Siahpirani, … Nature Communications 14 (1), 3064 (2023)
11. A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen CC Carriel, S Pyne, SA Halberg-Spencer, SC Park, H Seo, A Schmidt, … bioRxiv, 2023.05. 11.538573 (2023)
12. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft MG Dozmorov, MA Marshall, NS Rashid, JM Grible, A Valentine, AL Olex, … Scientific Reports 13 (1), 5420 (2023)
13. Examining dynamics of three-dimensional genome organization with multi-task matrix factorization DI Lee, S Roy bioRxiv, 2023.08. 25.554883 (2023)
14. Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus D Conde, PM Triozzi, WJ Pereira, HW Schmidt, KM Balmant, SA Knaack, … Development 149 (21), dev200632 (2022)
15. An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp. TB Irving, S Chakraborty, LGS Maia, S Knaack, D Conde, HW Schmidt, … Plant Physiology 190 (3), 1699-1714 (2022)
16. Modular derivation of diverse, regionally discrete human posterior CNS neurons enables discovery of transcriptomic patterns NR Iyer, J Shin, S Cuskey, Y Tian, NR Nicol, TE Doersch, F Seipel, … Science Advances 8 (39), eabn7430 (2022)
17. Profiling Cell Type Specificity and Adverse Events of Genome Editing Nucleases in the Brain and Retina Using Single Cell Transcriptomics K Saha, K Gimse, J Shin, Y Wang, JM Metzger, K Mueller, E Capowski, … ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 63, 63-63 (2022)
18. ISMB 2022 proceedings C Dessimoz, S Roy Bioinformatics 38 (Supplement_1), i8-i9 (2022)
19. Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids TK Mehta, L Penso-Dolfin, W Nash, S Roy, F Di-Palma, W Haerty Molecular Biology and Evolution 39 (7), msac146 (2022)
20. Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE S Roy Yeast Functional Genomics: Methods and Protocols 2477 (2022)
21. Enabling studies of genome-scale regulatory network evolution in large phylogenies with MRTLE S Zhang, S Knaack, S Roy Yeast Functional Genomics: Methods and Protocols, 439-455 (2022)
22. Deciphering the role of 3D genome organization in breast cancer susceptibility B Baur, DI Lee, J Haag, D Chasman, M Gould, S Roy Frontiers in Genetics 12, 788318 (2022)
23. Additional file 2 of Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula SA Knaack, D Conde, S Chakraborty, KM Balmant, TB Irving, LGS Maia, … (2022)
24. Single-cell analysis resolves the genetic program of primary vascular system formation in hybrid poplar D Conde, PM Triozzi, WJ Pereira, HW Schmidt, KM Balmant, SA Knaack, … bioRxiv, 2021.12. 28.474348 (2022)
25. Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade WJ Pereira, S Knaack, S Chakraborty, D Conde, RA Folk, PM Triozzi, … New Phytologist 234 (2), 634-649 (2022)
26. GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization DI Lee, S Roy Genome biology 22 (1), 1-31 (2021)
27. Evolution of regulatory networks associated with traits under selection in cichlids TK Mehta, C Koch, W Nash, SA Knaack, P Sudhakar, M Olbei, … Genome Biology 22 (1), 1-28 (2021)
28. The NIH somatic cell genome editing program K Saha, EJ Sontheimer, PJ Brooks, MR Dwinell, CA Gersbach, DR Liu, … Nature 592 (7853), 195-204 (2021)
29. Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder K Huang, Y Wu, J Shin, Y Zheng, AF Siahpirani, Y Lin, Z Ni, J Chen, J You, … PLoS genetics 17 (2), e1009309 (2021)
30. A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies J Shin, H Marx, A Richards, D Vaneechoutte, D Jayaraman, J Maeda, … Nucleic Acids Research 49 (1), e3-e3 (2021)
31. Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula SA Knaack, D Conde, KM Balmant, TB Irving, LG Maia, PM Triozzi, … bioRxiv (2021)
32. Modular Derivation and Unbiased Single-cell Analysis of Regional Human Hindbrain And Spinal Neurons Enables Discovery of Nuanced Transcriptomic Patterns along Developmental Axes NR Iyer, J Shin, S Cuskey, Y Tian, NR Nichol, TE Doersch, SG McCalla, … bioRxiv (2021)
33. Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation BA Baur, J Shin, J Schreiber, S Zhang, Y Zhang, M Manjunath, JS Song, … bioRxiv (2021)
34. Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data M Stone, SG McCalla, AF Siahpirani, V Periyasamy, J Shin, S Roy bioRxiv (2021)
35. Dynamic regulatory module networks for inference of cell type-specific transcriptional networks AF Siahpirani, S Knaack, D Chasman, M Seirup, R Sridharan, R Stewart, … bioRxiv, 2020.07. 18.210328 (2021)
36. Data integration for inferring context-specific gene regulatory networks B Baur, J Shin, S Zhang, S Roy Current opinion in systems biology 23, 38-46 (2020)
37. Identification of FMR1-regulated molecular networks in human neurodevelopment M Li, J Shin, RD Risgaard, MJ Parries, J Wang, D Chasman, S Liu, S Roy, … Genome Research 30 (3), 361-374 (2020)
38. Chromatin Accessibility Characterization of the Gene Regulatory Network Controlling Nodulation Factors Response in Medicago truncatula D Conde, S Knaack, K Balmant, L Maia, T Irving, C Dervinis, M Crook, … Plant and Animal Genome XXVIII Conference (January 11-15, 2020)
39. Simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization DI Lee, S Roy bioRxiv (2020)
40. ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants M Manjunath, Y Zhang, S Zhang, S Roy, P Perez-Pinera, JS Song Frontiers in genetics, 730 (2020)
41. In silico prediction of high-resolution Hi-C interaction matrices S Zhang, D Chasman, S Knaack, S Roy Nature Communications 10 (1), 1-18 (2019)
42. Imputed gene associations identify replicable trans‐acting genes enriched in transcription pathways and complex traits HE Wheeler, S Ploch, AN Barbeira, R Bonazzola, A Andaleon, … Genetic epidemiology 43 (6), 596-608 (2019)
43. Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency KA Tran, SJ Pietrzak, NZ Zaidan, AF Siahpirani, SG McCalla, AS Zhou, … Cell reports 27 (6), 1726-1741. e5 (2019)
44. The cancer-associated genetic variant Rs3903072 modulates immune cells in the tumor microenvironment Y Zhang, M Manjunath, J Yan, BA Baur, S Zhang, S Roy, JS Song Frontiers in genetics, 754 (2019)
45. Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks AF Siahpirani, D Chasman, S Roy Gene Regulatory Networks, 161-194 (2019)
46. Integrative genomic analysis discovers the causative regulatory mechanisms of a breast cancer-associated genetic variant Y Zhang, M Manjunath, S Zhang, D Chasman, S Roy, JS Song Cancer Research 78 (13 Supplement), 1220-1220 (2018)
47. Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer–associated genetic variant rs4415084 Y Zhang, M Manjunath, S Zhang, D Chasman, S Roy, JS Song Cancer research 78 (7), 1579-1591 (2018)
48. Can cancer GWAS variants modulate immune cells in the tumor microenvironment? Y Zhang, M Manjunath, J Yan, BA Baur, S Zhang, S Roy, JS Song bioRxiv, 493171 (2018)
49. Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes S Roy, R Sridharan Genome research 27 (7), 1250-1262 (2017)
50. Inference and evolutionary analysis of genome-scale regulatory networks in large phylogenies C Koch, J Konieczka, T Delorey, A Lyons, A Socha, K Davis, SA Knaack, … Cell systems 4 (5), 543-558. e8 (2017)
51. Physiological responses and gene co-expression network of mycorrhizal roots under K+ deprivation K Garcia, D Chasman, S Roy, JM Ané Plant physiology 173 (3), 1811-1823 (2017)
52. A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions A Fotuhi Siahpirani, F Ay, S Roy Genome biology 17 (1), 1-18 (2016)
53. A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium melilotiH Marx, CE Minogue, D Jayaraman, AL Richards, NW Kwiecien, … Nature biotechnology 34 (11), 1198-1205 (2016)
54. A prior-based integrative framework for functional transcriptional regulatory network inference AF Siahpirani, S Roy Nucleic acids research 45 (4), e21-e21 (2016)
55. Integrating transcriptomic and proteomic data using predictive regulatory network models of host response to pathogens D Chasman, KB Walters, TJS Lopes, AJ Eisfeld, Y Kawaoka, S Roy PLoS computational biology 12 (7), e1005013 (2016)
56. Network-based approaches for analysis of complex biological systems D Chasman, AF Siahpirani, S Roy Current opinion in biotechnology 39, 157-166 (2016)
57. A predictive modeling approach for cell line-specific long-range regulatory interactions S Roy, AF Siahpirani, D Chasman, S Knaack, F Ay, R Stewart, M Wilson, … Nucleic acids research 44 (4), 1977 (2016)
58. Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions Z Niu, D Chasman, AJ Eisfeld, Y Kawaoka, S Roy Bioinformatics 32 (10), 1509-1517 (2016)
59. Reconstruction and analysis of the evolution of modular transcriptional regulatory programs using Arboretum SA Knaack, DA Thompson, S Roy Yeast Functional Genomics, 375-389 (2016)
60. A predictive modeling approach for cell line-specific long-range regulatory interactions S Roy, AF Siahpirani, D Chasman, S Knaack, F Ay, R Stewart, M Wilson, … Nucleic acids research 43 (18), 8694-8712 (2015)
61. A predictive modeling approach for cell line-specific long-range regulatory interactions S Roy, AF Siahpirani, D Chasman, S Knaack, F Ay, R Stewart, M Wilson, … Nucleic acids research 43 (18), 8694-8712 (2015)
62. Comparative analysis of gene regulatory networks: from network reconstruction to evolution D Thompson, A Regev, S Roy Annu Rev Cell Dev Biol 31 (1), 399-428 (2015)
63. Deep sequencing of the Medicago truncatula root transcriptome reveals a massive and early interaction between nodulation factor and ethylene signals E Larrainzar, BK Riely, SC Kim, N Carrasquilla-Garcia, HJ Yu, HJ Hwang, … Plant Physiology 169 (1), 233-265 (2015)
64. SIRT3 mediates multi-tissue coupling for metabolic fuel switching KE Dittenhafer-Reed, AL Richards, J Fan, MJ Smallegan, AF Siahpirani, … Cell metabolism 21 (4), 637-646 (2015)
65. Collaborative rewiring of the pluripotency network by chromatin and signalling modulating pathways KA Tran, SA Jackson, ZPG Olufs, NZ Zaidan, N Leng, C Kendziorski, … Nature communications 6 (1), 1-14 (2015)
66. High-order interactions observed in multi-task intrinsic networks are dominant indicators of aberrant brain function in schizophrenia SM Plis, J Sui, T Lane, S Roy, VP Clark, VK Potluru, RJ Huster, A Michael, … Neuroimage 102, 35-48 (2014)
67. A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components SA Knaack, AF Siahpirani, S Roy Cancer informatics 13, CIN. S14058 (2014)
68. Integrated module and gene-specific regulatory inference implicates upstream signaling networks S Roy, S Lagree, Z Hou, JA Thomson, R Stewart, AP Gasch PLoS computational biology 9 (10), e1003252 (2013)
69. Correction: Evolutionary principles of modular gene regulation in yeasts DA Thompson, S Roy, M Chan, MP Styczynski, J Pfiffner, C French, … Elife 2, e01114 (2013)
70. Evolutionary principles of modular gene regulation in yeasts DA Thompson, S Roy, M Chan, MP Styczynsky, J Pfiffner, C French, … Elife 2, e00603 (2013)
71. Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules S Roy, I Wapinski, J Pfiffner, C French, A Socha, J Konieczka, N Habib, … Genome research 23 (6), 1039-1050 (2013)
72. Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome AS Hebert, KE Dittenhafer-Reed, W Yu, DJ Bailey, ES Selen, … Molecular cell 49 (1), 186-199 (2013)
73. A graph-based comparative analysis of three-dimensional organization of chromosomes in yeast and mammals. S Roy, R Atlas (2012)
74. 6.047/6.878 Lecture 18 Regulatory Networks: Inference, Analysis, Application S Roy, S Feizi (2012)
75. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks D Marbach, S Roy, F Ay, PE Meyer, R Candeias, T Kahveci, CA Bristow, … Genome research 22 (7), 1334-1349 (2012)
76. Predictive Regulatory Models in of Transcriptional Networks D Marbach, S Roy, F Ay, PE Meyer, R Candeias, T Kahveci, CA Bristow, … Cold Spring Harbor Laboratory Press (2012)
77. Comparative functional genomics of the fission yeasts N Rhind, Z Chen, M Yassour, DA Thompson, BJ Haas, N Habib, … Science 332 (6032), 930-936 (2011)
78. A multiple network learning approach to capture system-wide condition-specific responses S Roy, M Werner-Washburne, T LaneBioinformatics 27 (13), 1832-1838 (2011)
79. The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase culturesGS Davidson, RM Joe, S Roy, O Meirelles, CP Allen, MR Wilson, … Molecular biology of the cell 22 (7), 988-998 (2011)
80. Aging and the survival of quiescent and non-quiescent cells in yeast stationary-phase cultures M Werner-Washburne, S Roy, GS Davidson Aging research in yeast, 123-143 (2011)
81. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE modENCODE Consortium, S Roy, J Ernst, PV Kharchenko, P Kheradpour, … Science 330 (6012), 1787-1797 (2010)
82. Information-Theoretic Inference of Gene Networks Using Backward Elimination. P Meyer, D Marbach, S Roy, M Kellis BioComp, 700-705 (2010)
83. Exploiting amino acid composition for predicting protein-protein interactions S Roy, D Martinez, H Platero, T Lane, M Werner-Washburne PloS one 4 (11), e7813 (2009)
84. Scalable learning of large networks S Roy, S Plis, M Werner-Washburne, T Lane IET systems biology 3 (5), 404-413 (2009)
85. Learning structurally consistent undirected probabilistic graphical models S Roy, T Lane, M Werner-Washburne Proceedings of the 26th annual international conference on machine learning … (2009)
86. INFERENCE OF FUNCTIONAL NETWORKS OF CONDITION-SPECIFIC RESPONSE-A CASE STUDY OF QUIESCENCE IN YEAST S Roy, T Lane, M Werner-Washburne, D Martinez Biocomputing 2009, 51-62 (2009)
87. Learning condition-specific networks S Roy The University of New Mexico (2009)
88. A system for generating transcription regulatory networks with combinatorial control of transcription S Roy, M Werner-Washburne, T LaneBioinformatics 24 (10), 1318-1320 (2008)
89. Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-phase culture AD Aragon, AL Rodriguez, O Meirelles, S Roy, GS Davidson, PH Tapia, … Molecular biology of the cell 19 (3), 1271-1280 (2008)
90. Reliable prediction of regulator targets using 12 Drosophila genomes P Kheradpour, A Stark, S Roy, M Kellis Genome research 17 (12), 1919-1931 (2007)
91. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures A Stark, MF Lin, P Kheradpour, JS Pedersen, L Parts, JW Carlson, … Nature 450 (7167), 219 (2007)
92. Integrative Construction and Analysis of Condition-specific Biological Networks. S Roy, T Lane, M Werner-Washburne AAAI, 1898-1899 (2007)
93. A simulation framework for modeling combinatorial control in transcription regulatory networks S Roy, T Lane, M Werner-Washburne UNM Computer Science Technical Report, TR-CS-2007-06, 1-10 (2007)
94. Multivariate curve resolution of time course microarray data PD Wentzell, TK Karakach, S Roy, MJ Martinez, CP Allen, … BMC bioinformatics 7 (1), 1-19 (2006)
95. A hidden-state Markov model for cell population deconvolution S Roy, T Lane, C Allen, AD Aragon, M Werner-Washburne Journal of Computational Biology 13 (10), 1749-1774 (2006)
96. Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress AD Aragon, GA Quiñones, EV Thomas, S Roy, M Werner-Washburne Genome biology 7 (2), 1-13 (2006)
97. A datamining approach to cell population deconvolution from gene expressions using particle filters S Roy, T Lane, M Werner-Washburne Proceedings of the 5th international workshop on Bioinformatics, 46-53 (2005)
98. A genomic analysis of quiescence and exit from the quiescent state in S-cerevisiae. J Martinez, A Aragon, A Archuletta, A Rodriguez, S Roy, … Yeast 20, S343-S343 (2003)

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.

Master’s Thesis

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