Grantee Research Project Results
Publications Details for Grant Number R835737C005
Pathway Analysis Core
RFA:
Organotypic Culture Models for Predictive Toxicology Center (2013)
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| Reference Type | Citation | Progress Report Year | Document Sources |
|---|---|---|---|
| Book Chapter | Siahpirani AF, Chasman D, Roy S. Integrative approaches for inference of genome-scale gene regulatory networks. In:Sanguinetti G, Huynh-Thu V, ed. Gene Regulatory Networks 2019. New York, NY:Humana Press, 2019, pp. 161-194. |
R835737C005 (Final) |
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| Journal Article | 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 Biology2016;12(7):e1005013. |
R835737 (2015) R835737 (2016) R835737 (2017) R835737C005 (2015) |
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| Journal Article | Chasman D, Fotuhi Siahpirani A, Roy S. Network-based approaches for analysis of complex biological systems. Current Opinion in Biotechnology 2016;39:157-166. |
R835737 (2015) R835737 (2016) R835737 (2017) R835737C005 (2015) |
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| Journal Article | Chasman D, Roy S. Inference of cell type specific regulatory networks on mammalian lineages. Current Opinion in Systems Biology 2017;2:130-139. |
R835737 (2017) R835737C004 (2017) R835737C005 (2016) R835737C005 (2017) |
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| Journal Article | Garcia K, Chasman D, Roy S, Ane J-M. Physiological responses and gene co-expression network of mycorrhizal roots under K+ deprivation. Plant Physiology 2017;173(3):1811-1823. |
R835737 (2017) R835737C004 (2017) R835737C005 (2017) |
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| Journal Article | Roy S, Sridharan R. Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes. Genome Research 2017;27(7):1250-1262. |
R835737C004 (2017) R835737C005 (2017) |
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| Journal Article | Siahpirani A, Roy S. A prior-based integrative framework for functional transcriptional regulatory network inference. Nucleic Acids Research 2017;45(4):e21 (22 pp.). |
R835737C005 (2017) |
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| Journal Article | Wheeler HE, Ploch SA, Barberia AN, Bonazzola R, Andaleon A, Fotuhi S, 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 2019. |
R835737C005 (Final) |
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| Journal Article | Roy S, Sridharan R. Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes. Genome Research 2017;27(7):1250-1262. |
R835737 (2017) R835737C005 (2016) |
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| Presentation | Chasman D, Roy S. Network-based integration of transcriptomic and proteomic data to dissect mammalian cellular response to external perturbations. Poster presented at the 56th Annual Meeting of the Society of Toxicology, Baltimore, MD, March 12-16, 2017. |
R835737 (2016) R835737 (2017) R835737C005 (2016) R835737C005 (2017) |
not available |
| Presentation | Chasman D, Fotuhi Siahpirani A, Estevez-Silva MC, Ashton RS, Roy S. Characterizing expression state dynamics and regulatory networks in early neural development. Poster presented at the Great Lakes Bioinformatics Conference (GLBIO), Chicago, IL, May 15-17, 2017. |
R835737 (2017) R835737C004 (2017) R835737C005 (2017) |
not available |
| Presentation | Chasman D, Iyer N, Fotuhi Siahpirani A, Estevez Silva M, Lippman E, McIntosh B, Thomson J, Ashton RS, Roy S. Inference of regulatory network dynamics in early neural development. Presented at the 13th Cold Spring Harbor Conference Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor, NY, March 20-23, 2018. |
R835737 (2017) R835737C001 (2017) R835737C004 (2017) R835737C005 (2017) |
not available |
| Presentation | Lee DI, Roy S. A graph-regularized non-negative matrix factorization method to discover organizational units of chromosomes. Presented at Intelligent Systems for Molecular Biology (ISMB), Chicago, IL, July 7, 2018. |
R835737C005 (Final) |
not available |
| Presentation | Roy S. Integrative inference of functional transcriptional gene regulatory networks. Presented at the Great Lakes Bioinformatics Conference (GLBIO), Chicago, IL, May 15-17, 2017 (invited). |
R835737 (2017) R835737C004 (2017) R835737C005 (2017) |
not available |
| Presentation | Baur B, Zhang S, Chasman D, Roy S. In silico prediction of high-resolution chromosomal contact counts in multiple cell lines. Presented at Intelligent Systems for Molecular Biology (ISMB), Chicago, IL, July 2018. |
R835737C005 (Final) |
not available |
| Presentation | Chasman, Siahpirani AF, Sridharan R, Roy S. Dynamic regulatory module networks for integrative interference of cell-type specific regulatory programs. Presented at Intelligent Systems for Molecular Biology (ISMB), Chicago, IL, July 7, 2018. |
R835737C005 (Final) |
not available |
| Presentation | Roy S. Network-based approaches to dissect complex systems: from network reconstruction to interpretation. Presented at the 3rd Annual STAR Organotypic Culture Models (OCM) for Predictive Toxicology Research Centers Progress Review Meeting, Research Triangle Park, NC, May 22, 2018. |
R835737C005 (Final) |
not available |
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.