| 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 |
0.548 |
|
| 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 |
0.598 |
|
| 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 |
0.323 |
|
| 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 |
0.408 |
|
| 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 |
0.637 |
|
| 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 |
0.396 |
|
| 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 |
0.592 |
|
| 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 |
0.687 |
|
| 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 |
0.551 |
|
| 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 |
0.599 |
|
| 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 |
0.59 |
|
| 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 |
0.577 |
|
| 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 |
0.637 |
|
| 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 |
0.758 |
|
| 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 |
0.789 |
|
| 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 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2016 |
Siahpirani AF, Roy S. A prior-based integrative framework for functional transcriptional regulatory network inference. Nucleic Acids Research. PMID 27899626 DOI: 10.1093/nar/gkw1160 |
0.296 |
|
| 2020 |
Shin J, Marx H, Richards A, Vaneechoutte D, Jayaraman D, Maeda J, Chakraborty S, Sussman M, Vandepoele K, Ané JM, Coon J, Roy S. A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies. Nucleic Acids Research. PMID 33219668 DOI: 10.1093/nar/gkaa1041 |
0.296 |
|
| 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 |
0.295 |
|
| 2023 |
McCalla SG, Siahpirani AF, Li J, Pyne S, Stone M, Periyasamy V, Shin J, Roy S. Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data. G3 (Bethesda, Md.). PMID 36626328 DOI: 10.1093/g3journal/jkad004 |
0.293 |
|
| 2018 |
Khan H, Roy S, Anshu A, Kittipongdaja W, Schieke SM. Abstract 2178: Single cell dynamics maintain an intrinsic drug resistant state in T cell leukemia and lymphoma Cancer Research. 78: 2178-2178. DOI: 10.1158/1538-7445.Am2018-2178 |
0.284 |
|
| 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 |
0.284 |
|
| 2024 |
Pereira WJ, Boyd J, Conde D, Triozzi PM, Balmant KM, Dervinis C, Schmidt HW, Boaventura-Novaes C, Chakraborty S, Knaack SA, Gao Y, Feltus FA, Roy S, Ané JM, Frugoli J, et al. The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula. Cell Reports. 43: 113747. PMID 38329875 DOI: 10.1016/j.celrep.2024.113747 |
0.277 |
|
| 2001 |
Rossetti S, Strmecki L, Gamble V, Burton S, Sneddon V, Peral B, Roy S, Bakkaloglu A, Komel R, Winearls CG, Harris PC. Mutation Analysis of the Entire PKD1 Gene: Genetic and Diagnostic Implications American Journal of Human Genetics. 68: 46-63. PMID 11115377 DOI: 10.1086/316939 |
0.276 |
|
| 2022 |
Mehta TK, Penso-Dolfin L, Nash W, Roy S, Di-Palma F, Haerty W. Evolution of miRNA binding sites and regulatory networks in cichlids. Molecular Biology and Evolution. PMID 35748824 DOI: 10.1093/molbev/msac146 |
0.271 |
|
| 2021 |
Lee DI, Roy S. GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization. Genome Biology. 22: 164. PMID 34034791 DOI: 10.1186/s13059-021-02378-z |
0.259 |
|
| 2021 |
Huang K, Wu Y, Shin J, Zheng Y, Siahpirani AF, Lin Y, Ni Z, Chen J, You J, Keles S, Wang D, Roy S, Lu Q. Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. Plos Genetics. 17: e1009309. PMID 33539344 DOI: 10.1371/journal.pgen.1009309 |
0.249 |
|
| 2019 |
Khan H, Anshu A, Prasad A, Roy S, Jeffery J, Kittipongdaja W, Yang DT, Schieke SM. Metabolic Rewiring in Response to Biguanides Is Mediated by mROS/HIF-1a in Malignant Lymphocytes. Cell Reports. 29: 3009-3018.e4. PMID 31801069 DOI: 10.1016/J.Celrep.2019.11.007 |
0.246 |
|
| 2021 |
Saha K, Sontheimer EJ, Brooks PJ, Dwinell MR, Gersbach CA, Liu DR, Murray SA, Tsai SQ, Wilson RC, Anderson DG, Asokan A, Banfield JF, Bankiewicz KS, Bao G, Bulte JWM, ... ... Roy S, ... ... Roy S, et al. The NIH Somatic Cell Genome Editing program. Nature. 592: 195-204. PMID 33828315 DOI: 10.1038/s41586-021-03191-1 |
0.245 |
|
| 2018 |
Schieke S, Khan H, Roy S, Xiao T, Anshu A. Single-cell variability drives phenotypic heterogeneity and intrinsic drug-resistance in cutaneous T-cell lymphoma European Journal of Cancer. 101. DOI: 10.1016/J.Ejca.2018.07.154 |
0.243 |
|
| 2017 |
Azencott CA, Aittokallio T, Roy S, Norman T, Friend S, Stolovitzky G, Goldenberg A. The inconvenience of data of convenience: computational research beyond post-mortem analyses. Nature Methods. 14: 937-938. PMID 28960198 DOI: 10.1038/Nmeth.4457 |
0.236 |
|
| 2022 |
Conde D, Triozzi PM, Pereira WJ, Schmidt HW, Balmant KM, Knaack SA, Redondo-López A, Roy S, Dervinis C, Kirst M. Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus. Development (Cambridge, England). PMID 36178121 DOI: 10.1242/dev.200632 |
0.234 |
|
| 1997 |
Sampson JR, Maheshwar MM, Aspinwall R, Thompson P, Cheadle JP, Ravine D, Roy S, Haan E, Bernstein J, Harris PC. Renal cystic disease in tuberous sclerosis: role of the polycystic kidney disease 1 gene American Journal of Human Genetics. 61: 843-851. PMID 9382094 DOI: 10.1086/514888 |
0.233 |
|
| 2018 |
Schieke S, Roy S, Khan H, Nihal A, Buethe P. Metabolic dynamics control invasion and dissemination of cutaneous T-cell lymphoma European Journal of Cancer. 101. DOI: 10.1016/J.Ejca.2018.07.155 |
0.22 |
|
| 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 |
0.213 |
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| 2023 |
Floy ME, Shabnam F, Givens SE, Patil VA, Ding Y, Li G, Roy S, Raval AN, Schmuck EG, Masters KS, Ogle BM, Palecek SP. Identifying molecular and functional similarities and differences between human primary cardiac valve interstitial cells and ventricular fibroblasts. Frontiers in Bioengineering and Biotechnology. 11: 1102487. PMID 37051268 DOI: 10.3389/fbioe.2023.1102487 |
0.209 |
|
| 2023 |
Baur B, Roy S. Predicting patient-specific enhancer-promoter interactions. Cell Reports Methods. 3: 100594. PMID 37751694 DOI: 10.1016/j.crmeth.2023.100594 |
0.208 |
|
| 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 |
0.178 |
|
| 2022 |
Iyer NR, Shin J, Cuskey S, Tian Y, Nicol NR, Doersch TE, Seipel F, McCalla SG, Roy S, Ashton RS. Modular derivation of diverse, regionally discrete human posterior CNS neurons enables discovery of transcriptomic patterns. Science Advances. 8: eabn7430. PMID 36179024 DOI: 10.1126/sciadv.abn7430 |
0.176 |
|
| 2016 |
Punwani D, Kawahara M, Yu J, Sanford U, Roy S, Patel K, Carbonaro DA, Karlen AD, Khan S, Cornetta KG, Rothe M, Schambach A, Kohn DB, Malech HL, McIvor RS, et al. Lentivirus Mediated Correction of Artemis-deficient Severe Combined Immunodeficiency. Human Gene Therapy. PMID 27611239 DOI: 10.1089/Hum.2016.064 |
0.163 |
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| 2022 |
Irving TB, Chakraborty S, Maia LGS, Knaack S, Conde D, Schmidt HW, Triozzi PM, Simmons CH, Roy S, Kirst M, Ané JM. An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp. Plant Physiology. PMID 35929094 DOI: 10.1093/plphys/kiac356 |
0.156 |
|
| 2006 |
Rubenstein JL, Kadoch C, Karch J, Josephson A, Issa S, Becker C, Schulman H, Damon L, Shuman MA, Roy S. Identification of CSF Biomarkers for the Diagnosis of CNS Lymphoma. Blood. 108: 2036-2036. DOI: 10.1182/Blood.V108.11.2036.2036 |
0.149 |
|
| 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 |
0.142 |
|
| 2023 |
Schmuck EG, Roy S, Zhou T, Wille D, Reeves SM, Conklin J, Raval AN. Human left ventricular cardiac fibroblasts undergo a dynamic shift in secretome and gene expression toward a cardiac myofibroblast phenotype during early passage in typical culture expansion conditions. Cytotherapy. PMID 37930292 DOI: 10.1016/j.jcyt.2023.10.001 |
0.137 |
|
| 1999 |
Rosenbaum DM, Roy S, Hecht MH. Screening combinatorial libraries of de Novo proteins by hydrogen- deuterium exchange and electrospray mass spectrometry Journal of the American Chemical Society. 121: 9509-9513. DOI: 10.1021/Ja991843X |
0.132 |
|
| 2021 |
Baur B, Lee DI, Haag J, Chasman D, Gould M, Roy S. Deciphering the Role of 3D Genome Organization in Breast Cancer Susceptibility. Frontiers in Genetics. 12: 788318. PMID 35087569 DOI: 10.3389/fgene.2021.788318 |
0.131 |
|
| 2003 |
Wang W, Zhou H, Lin H, Roy S, Shaler TA, Hill LR, Norton S, Kumar P, Anderle M, Becker CH. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Analytical Chemistry. 75: 4818-26. PMID 14674459 DOI: 10.1021/Ac026468X |
0.109 |
|
| 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 |
0.109 |
|
| 2004 |
Anderle M, Roy S, Lin H, Becker C, Joho K. Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum. Bioinformatics (Oxford, England). 20: 3575-82. PMID 15284095 DOI: 10.1093/Bioinformatics/Bth446 |
0.106 |
|
| 2021 |
Schmuck EG, Roy S, Dhillon A, Walker S, Spinali K, Colevas S, Zhou T, Chhabra G, Liu Y, Kader Sagar MA, Childs CJ, Kink JA, Eliceiri KW, Hematti P, Raval AN. Cultured Cardiac Fibroblasts and Myofibroblasts Express Sushi Containing Domain 2 and Assemble a Unique Fibronectin Rich Matrix. Experimental Cell Research. 112489. PMID 33453237 DOI: 10.1016/j.yexcr.2021.112489 |
0.101 |
|
| 2019 |
Chen JC, Luu AR, Wise N, Angelis R, Agrawal V, Mangini L, Vincelette J, Handyside B, Sterling HJ, Lo MJ, Wong H, Galicia N, Pacheco G, Van Vleet J, Giaramita A, ... ... Roy SM, et al. Intracerebroventricular enzyme replacement therapy with Beta-Galactosidase reverses brain pathologies due to GM1 gangliosidosis in mice. The Journal of Biological Chemistry. PMID 31481471 DOI: 10.1074/Jbc.Ra119.009811 |
0.099 |
|
| 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 DOI: 10.1155/2006/670439 |
0.097 |
|
| 2015 |
Roy S, Shamsuzzaman S, Mamun K, Ahmed M, Halder S. Cultural Isolation and PCR Based Assay for Detection of flaA gene of Campylobacter jejuni from Acute Diarrheic Patients in Tertiary Care Hospital at Dhaka, Bangladesh British Microbiology Research Journal. 10: 1-9. DOI: 10.9734/bmrj/2015/19818 |
0.088 |
|
| 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 |
0.082 |
|
| 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 |
0.08 |
|
| 2012 |
Roy S, Javed S, Jain SK, Majumdar SS, Mukhopadhyay A. Donor hematopoietic stem cells confer long-term marrow reconstitution by self-renewal divisions exceeding to that of host cells. Plos One. 7: e50693. PMID 23227199 DOI: 10.1371/journal.pone.0050693 |
0.079 |
|
| 2009 |
Rossetti S, Kubly VJ, Consugar MB, Hopp K, Roy S, Horsley SW, Chauveau D, Rees L, Barratt TM, van't Hoff WG, Niaudet P, Niaudet WP, Torres VE, Harris PC. Incompletely penetrant PKD1 alleles suggest a role for gene dosage in cyst initiation in polycystic kidney disease. Kidney International. 75: 848-55. PMID 19165178 DOI: 10.1038/Ki.2008.686 |
0.079 |
|
| 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 |
0.068 |
|
| 2020 |
Roy S, Spinali K, Schmuck EG, Kink JA, Hematti P, Raval AN. Cardiac fibroblast derived matrix-educated macrophages express VEGF and IL-6, and recruit mesenchymal stromal cells. Journal of Immunology and Regenerative Medicine. 10. PMID 33564732 DOI: 10.1016/j.regen.2020.100033 |
0.067 |
|
| 2023 |
Singh CK, Mintie CA, Ndiaye MA, Chhabra G, Roy S, Sullivan R, Longley BJ, Schieke SM, Ahmad N. Protective effects of dietary grape against atopic dermatitis-like skin lesions in NC/NgaTndCrlj mice. Frontiers in Immunology. 13: 1051472. PMID 36741360 DOI: 10.3389/fimmu.2022.1051472 |
0.066 |
|
| 2007 |
Roy SM, Becker CH. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling. Methods in Molecular Biology (Clifton, N.J.). 359: 87-105. PMID 17484112 DOI: 10.1007/978-1-59745-255-7_6 |
0.066 |
|
| 2013 |
Hazir T, Begum K, El Arifeen S, Khan AM, Huque MH, Kazmi N, Roy S, Abbasi S, Rahman QS, Theodoratou E, Khorshed MS, Rahman KM, Bari S, Kaiser MM, Saha SK, et al. Measuring coverage in MNCH: a prospective validation study in Pakistan and Bangladesh on measuring correct treatment of childhood pneumonia. Plos Medicine. 10: e1001422. PMID 23667339 DOI: 10.1371/journal.pmed.1001422 |
0.064 |
|
| 2024 |
Raval AN, Schmuck EG, Roy S, Saito Y, Zhou T, Conklin J, Hacker TA, Koonce C, Boyer M, Stack K, Hebron E, Nagle SK, Hsieh PCH, Kamp TJ. Human iPSC-derived Committed Cardiac Progenitors Generate Cardiac Tissue Grafts in a Swine Ischemic Cardiomyopathy Model without Triggering Ventricular Arrhythmias. Biorxiv : the Preprint Server For Biology. PMID 38405927 DOI: 10.1101/2024.02.14.580375 |
0.062 |
|
| 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 |
0.061 |
|
| 2007 |
Pati AK, Parganiha A, Kar A, Soni R, Roy S, Choudhary V. Alterations of the characteristics of the circadian rest-activity rhythm of cancer in-patients. Chronobiology International. 24: 1179-97. PMID 18075806 DOI: 10.1080/07420520701800868 |
0.057 |
|
| 2022 |
Magat J, Jones S, Baridon B, Agrawal V, Wong H, Giaramita A, Mangini L, Handyside B, Vitelli C, Parker M, Yeung N, Zhou Y, Pungor E, Slabodkin I, Gorostiza O, ... ... Roy SM, et al. Intracerebroventricular dosing of N-sulfoglucosamine sulfohydrolase in mucopolysaccharidosis IIIA mice reduces markers of brain lysosomal dysfunction. The Journal of Biological Chemistry. 102625. PMID 36306823 DOI: 10.1016/j.jbc.2022.102625 |
0.051 |
|
| 2010 |
Wiesner C, Hannum C, Reckamp K, Figlin R, Dubridge R, Roy SM, Lin S, Becker CH, Jones T, Hiller J, Cheville JC, Wilson K. Consistency of a two clinical site sample collection: a proteomics study. Proteomics. Clinical Applications. 4: 726-38. PMID 21137090 DOI: 10.1002/prca.200900206 |
0.048 |
|
| 2008 |
Bhaumik SK, Singh M, Basu R, Bhaumik S, Roychoudhury K, Naskar K, Roy S, De T. Virulence attenuation of a UDP-galactose/N-acetylglucosamine beta1,4 galactosyltransferase expressing Leishmania donovani promastigote. Glycoconjugate Journal. 25: 459-72. PMID 18197475 DOI: 10.1007/s10719-007-9098-0 |
0.043 |
|
| 2017 |
Roy S, Ahmed MU, Uddin BMM, Ratan ZA, Rajawat M, Mehta V, Zaman SB. Evaluation of antibiotic susceptibility in wound infections: A pilot study from Bangladesh. F1000research. 6: 2103. PMID 29527295 DOI: 10.12688/f1000research.12887.1 |
0.041 |
|
| 2023 |
Ponty Y, Roy S. ISMB/ECCB 2023 proceedings. Bioinformatics (Oxford, England). 39: i1-i2. PMID 37387153 DOI: 10.1093/bioinformatics/btad319 |
0.01 |
|
| 2022 |
Dessimoz C, Roy S. ISMB 2022 proceedings. Bioinformatics (Oxford, England). 38: i8-i9. PMID 35758785 DOI: 10.1093/bioinformatics/btac305 |
0.01 |
|
| 2009 |
Rubenstein JL, Chen L, Kadoch C, Roy S, Becker C, Schulman H. Reply to H. Zetterberg et al Journal of Clinical Oncology. 27: 2303-2304. DOI: 10.1200/Jco.2008.20.0006 |
0.01 |
|
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