T M. Murali - Publications

Affiliations: 
Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
Area:
Computer Science

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2020 Gallegos JE, Adames NR, Rogers MF, Kraikivski P, Ibele A, Nurzynski-Loth K, Kudlow E, Murali TM, Tyson JJ, Peccoud J. Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants. Npj Systems Biology and Applications. 6: 11. PMID 32376972 DOI: 10.1038/s41540-020-0134-z  0.44
2018 Tegge AN, Rodrigues RR, Larkin AL, Vu L, Murali TM, Rajagopalan P. Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models. Scientific Reports. 8: 11306. PMID 30054499 DOI: 10.1038/s41598-018-29455-x  0.4
2018 Pratapa A, Adames N, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, Murali TM, Berger B. CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models. Bioinformatics (Oxford, England). PMID 29432533 DOI: 10.1093/bioinformatics/bty072  0.44
2017 Bharadwaj A, Singh DP, Ritz A, Tegge AN, Poirel CL, Kraikivski P, Adames N, Luther K, Kale SD, Peccoud J, Tyson JJ, Murali TM. GraphSpace: stimulating interdisciplinary collaborations in network biology. Bioinformatics (Oxford, England). 33: 3134-3136. PMID 28957495 DOI: 10.1093/bioinformatics/btx382  0.92
2016 Ritz A, Poirel CL, Tegge AN, Sharp N, Simmons K, Powell A, Kale SD, Murali TM. Corrigendum: Pathway on demand: automated reconstruction of human signaling networks. Npj Systems Biology and Applications. 2: 16026. PMID 28731481 DOI: 10.1038/npjsba.2016.26  0.92
2016 Ritz A, Poirel CL, Tegge AN, Sharp N, Simmons K, Powell A, Kale SD, Murali TM. Pathways on demand: automated reconstruction of human signaling networks. Npj Systems Biology and Applications. 2: 16002. PMID 28725467 DOI: 10.1038/npjsba.2016.2  0.92
2016 Tegge AN, Sharp N, Murali TM. Xtalk: a path-based approach for identifying crosstalk between signaling pathways. Bioinformatics (Oxford, England). 32: 242-51. PMID 26400040 DOI: 10.1093/bioinformatics/btv549  1
2016 Rahman A, Jan S, Kim H, Prakash BA, Murali TM. Mining Unstable Communities from Network Ensembles Proceedings - 15th Ieee International Conference On Data Mining Workshop, Icdmw 2015. 508-515. DOI: 10.1109/ICDMW.2015.87  1
2015 Kraikivski P, Chen KC, Laomettachit T, Murali TM, Tyson JJ. From START to FINISH: computational analysis of cell cycle control in budding yeast. Npj Systems Biology and Applications. 1: 15016. PMID 28725464 DOI: 10.1038/npjsba.2015.16  0.44
2015 Adames NR, Schuck PL, Chen KC, Murali TM, Tyson JJ, Peccoud J. Experimental testing of a new integrated model of the budding yeast Start transition. Molecular Biology of the Cell. 26: 3966-84. PMID 26310445 DOI: 10.1091/mbc.E15-06-0358  1
2014 Ritz A, Tegge AN, Kim H, Poirel CL, Murali TM. Signaling hypergraphs. Trends in Biotechnology. 32: 356-62. PMID 24857424 DOI: 10.1016/j.tibtech.2014.04.007  1
2014 Estep C, Yi J, Ritz A, Murali TM. GraphSpace: Sharing and collaborating through networks on the web Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 631-632. DOI: 10.1145/2649387.2660809  1
2014 Ritz A, Murali TM. Pathway analysis with signaling hypergraphs Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 249-258. DOI: 10.1145/2649387.2649450  1
2013 Rahman A, Poirel CL, Badger DJ, Estep C, Murali TM. Reverse engineering molecular hypergraphs. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 1113-24. PMID 24384702 DOI: 10.1109/TCBB.2013.71  1
2013 Kidane YH, Lawrence C, Murali TM. Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions. Bmc Microbiology. 13: 224. PMID 24099000 DOI: 10.1186/1471-2180-13-224  1
2013 Lasher CD, Rajagopalan P, Murali TM. Summarizing cellular responses as biological process networks. Bmc Systems Biology. 7: 68. PMID 23895181 DOI: 10.1186/1752-0509-7-68  1
2013 Rajagopalan P, Kasif S, Murali TM. Systems biology characterization of engineered tissues. Annual Review of Biomedical Engineering. 15: 55-70. PMID 23862675 DOI: 10.1146/annurev-bioeng-071811-150120  1
2013 Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM. Top-down network analysis to drive bottom-up modeling of physiological processes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 409-18. PMID 23641868 DOI: 10.1089/cmb.2012.0274  1
2013 Larkin AL, Rodrigues RR, Murali TM, Rajagopalan P. Designing a multicellular organotypic 3D liver model with a detachable, nanoscale polymeric Space of Disse. Tissue Engineering. Part C, Methods. 19: 875-84. PMID 23556413 DOI: 10.1089/ten.TEC.2012.0700  1
2013 Kidane YH, Lawrence C, Murali TM. The landscape of host transcriptional response programs commonly perturbed by bacterial pathogens: towards host-oriented broad-spectrum drug targets. Plos One. 8: e58553. PMID 23516507 DOI: 10.1371/journal.pone.0058553  1
2013 Poirel CL, Rahman A, Rodrigues RR, Krishnan A, Addesa JR, Murali TM. Reconciling differential gene expression data with molecular interaction networks. Bioinformatics (Oxford, England). 29: 622-9. PMID 23314326 DOI: 10.1093/bioinformatics/btt007  1
2012 Rivera CG, Tyler BM, Murali TM. Sensitive detection of pathway perturbations in cancers. Bmc Bioinformatics. 13: S9. PMID 22536907 DOI: 10.1186/1471-2105-13-S3-S9  1
2012 Murali TM. Guest Editor's Introduction: Computationally driven experimental biology Computer. 45: 22-23. DOI: 10.1109/MC.2012.93  1
2011 Poirel CL, Owens CC, Murali TM. Network-based functional enrichment. Bmc Bioinformatics. 12: S14. PMID 22479706 DOI: 10.1186/1471-2105-12-S13-S14  1
2011 Murali TM, Dyer MD, Badger D, Tyler BM, Katze MG. Network-based prediction and analysis of HIV dependency factors. Plos Computational Biology. 7: e1002164. PMID 21966263 DOI: 10.1371/journal.pcbi.1002164  1
2011 Dyer MD, Murali TM, Sobral BW. Supervised learning and prediction of physical interactions between human and HIV proteins. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 917-23. PMID 21382517 DOI: 10.1016/J.Meegid.2011.02.022  1
2011 Lasher CD, Rajagopalan P, Murali TM. Discovering networks of perturbed biological processes in hepatocyte cultures. Plos One. 6: e15247. PMID 21245926 DOI: 10.1371/journal.pone.0015247  1
2010 Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, Bassaganya-Riera J, Murali TM, Sobral BW. The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. Plos One. 5: e12089. PMID 20711500 DOI: 10.1371/Journal.Pone.0012089  1
2010 Kim Y, Lasher CD, Milford LM, Murali TM, Rajagopalan P. A comparative study of genome-wide transcriptional profiles of primary hepatocytes in collagen sandwich and monolayer cultures. Tissue Engineering. Part C, Methods. 16: 1449-60. PMID 20412007 DOI: 10.1089/ten.tec.2010.0012  1
2009 Driscoll T, Dyer MD, Murali TM, Sobral BW. PIG--the pathogen interaction gateway. Nucleic Acids Research. 37: D647-50. PMID 18984614 DOI: 10.1093/nar/gkn799  1
2009 Owens CC, Murali TM, Ramakrishnan N. Capturing truthiness: Mining truth tables in binary datasets Proceedings of the Acm Symposium On Applied Computing. 1467-1474. DOI: 10.1145/1529282.1529609  1
2009 Rivera CG, Murali TM. Identifying evolutionarily conserved protein interaction modules using graphhopper Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5462: 67-78. DOI: 10.1007/978-3-642-00727-9_9  1
2008 Murali TM, Rivera CG. Network legos: building blocks of cellular wiring diagrams. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 829-44. PMID 18707557 DOI: 10.1089/cmb.2007.0139  1
2008 Ruscio JZ, Kumar D, Shukla M, Prisant MG, Murali TM, Onufriev AV. Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin. Proceedings of the National Academy of Sciences of the United States of America. 105: 9204-9. PMID 18599444 DOI: 10.1073/Pnas.0710825105  1
2008 Dyer MD, Murali TM, Sobral BW. The landscape of human proteins interacting with viruses and other pathogens. Plos Pathogens. 4: e32. PMID 18282095 DOI: 10.1371/Journal.Ppat.0040032  1
2008 Jin Y, Murali TM, Ramakrishnan N. Compositional mining of multirelational biological datasets Acm Transactions On Knowledge Discovery From Data. 2. DOI: 10.1145/1342320.1342322  1
2007 Shoja V, Murali TM, Zhang L. Expression divergence of tandemly arrayed genes in human and mouse. Comparative and Functional Genomics. 60964. PMID 18273387 DOI: 10.1155/2007/60964  1
2007 Dyer MD, Murali TM, Sobral BW. Computational prediction of host-pathogen protein-protein interactions. Bioinformatics (Oxford, England). 23: i159-66. PMID 17646292 DOI: 10.1093/bioinformatics/btm208  1
2006 Murali TM, Wu CJ, Kasif S. The art of gene function prediction. Nature Biotechnology. 24: 1474-5; author reply. PMID 17160037 DOI: 10.1038/nbt1206-1474  1
2006 Grothaus GA, Mufti A, Murali TM. Automatic layout and visualization of biclusters. Algorithms For Molecular Biology : Amb. 1: 15. PMID 16952321 DOI: 10.1186/1748-7188-1-15  1
2006 Li P, Sioson A, Mane SP, Ulanov A, Grothaus G, Heath LS, Murali TM, Bohnert HJ, Grene R. Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field. Plant Molecular Biology. 62: 593-609. PMID 16941220 DOI: 10.1007/S11103-006-9041-Y  1
2006 Massjouni N, Rivera CG, Murali TM. VIRGO: computational prediction of gene functions. Nucleic Acids Research. 34: W340-4. PMID 16845022 DOI: 10.1093/nar/gkl225  1
2006 Pati A, Vasquez-Robinet C, Heath LS, Grene R, Murali TM. XcisClique: analysis of regulatory bicliques. Bmc Bioinformatics. 7: 218. PMID 16630346 DOI: 10.1186/1471-2105-7-218  1
2004 Wu CJ, Fu Y, Murali TM, Kasif S. Gene expression module discovery using gibbs sampling. Genome Informatics. International Conference On Genome Informatics. 15: 239-48. PMID 15712126  1
2004 Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proceedings of the National Academy of Sciences of the United States of America. 101: 2888-93. PMID 14981259 DOI: 10.1073/Pnas.0307326101  1
2003 Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S. RankGene: Identification of diagnostic genes based on expression data Bioinformatics. 19: 1578-1579. PMID 12912841 DOI: 10.1093/Bioinformatics/Btg179  1
2003 Murali TM, Kasif S. Extracting conserved gene expression motifs from gene expression data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 77-88. PMID 12603019  1
2002 Efrat A, Guibas LJ, Har-Peled S, Mitchell JSB, Murali TM. New similarity measures between polylines with applications to morphing and polygon sweeping Discrete and Computational Geometry. 28: 535-569. DOI: 10.1007/S00454-002-2886-1  1
2002 Procopiuc CM, Jones M, Agarwal PK, Murali TM. A Monte Carlo algorithm for fast projective clustering Proceedings of the Acm Sigmod International Conference On Management of Data. 418-427.  1
2001 Efrat A, Har-Peled S, Guibas LJ, Murali TM. Morphing between polylines Proceedings of the Annual Acm-Siam Symposium On Discrete Algorithms. 680-689.  1
2000 Agarwal PK, Grove EF, Murali TM, Vitter JS. Binary space partitions for fat rectangles Siam Journal On Computing. 29: 1422-1448. DOI: 10.1137/S0097539797320578  1
2000 Agarwal PK, Guibas LJ, Murali TM, Vitter JS. Cylindrical static and kinetic binary space partitions Computational Geometry: Theory and Applications. 16: 103-127. DOI: 10.1016/S0925-7721(00)00005-5  1
1999 Grove EF, Murali TM, Vitter JS. The object complexity model for hidden-surface removal International Journal of Computational Geometry and Applications. 9: 207-217. DOI: 10.1142/S0218195999000145  1
1998 Agarwal PK, Arge L, Murali TM, Varadarajan KR, Vitter JS. I/O-efficient algorithms for contour-line extraction and planar graph blocking Proceedings of the Annual Acm-Siam Symposium On Discrete Algorithms. 117-126.  1
1998 Murali TM, Agarwal PK, Vitter JS. Constructing binary space partitions for orthogonal rectangles in practice Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1461: 211-222.  1
1997 Agarwal PK, Guibas LJ, Murali TM, Vitter JS. Cylindrical static and kinetic binary space partitions Proceedings of the Annual Symposium On Computational Geometry. 39-48.  1
1997 Agarwal PK, Murali TM, Vitter JS. Practical techniques for constructing Binary Space Partitions for orthogonal rectangles Proceedings of the Annual Symposium On Computational Geometry. 382-384.  1
1997 Murali TM, Funkhouser TA. Consistent solid and boundary representations from arbitrary polygonal data Proceedings of the Symposium On Interactive 3d Graphics. 155-162.  1
1996 Agarwal PK, Grove EF, Murali TM, Vitter JS. Binary space partitions for fat rectangles Annual Symposium On Foundations of Computer Science - Proceedings. 482-491.  1
Show low-probability matches.