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Items: 50

1.

Reconstructing signaling pathways using regular language constrained paths.

Wagner MJ, Pratapa A, Murali TM.

Bioinformatics. 2019 Jul 15;35(14):i624-i633. doi: 10.1093/bioinformatics/btz360.

2.

Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01.

Gu Y, Wong YH, Liew CW, Chan CEZ, Murali TM, Yap J, Too CT, Purushotorman K, Hamidinia M, El Sahili A, Goh ATH, Teo RZC, Wood KJ, Hanson BJ, Gascoigne NRJ, Lescar J, Vathsala A, MacAry PA.

Nat Commun. 2019 Feb 21;10(1):893. doi: 10.1038/s41467-019-08790-1.

3.

Electronic health records accurately predict renal replacement therapy in acute kidney injury.

Low S, Vathsala A, Murali TM, Pang L, MacLaren G, Ng WY, Haroon S, Mukhopadhyay A, Lim SL, Tan BH, Lau T, Chua HR.

BMC Nephrol. 2019 Jan 31;20(1):32. doi: 10.1186/s12882-019-1206-4.

4.

Large-scale protein function prediction using heterogeneous ensembles.

Wang L, Law J, Kale SD, Murali TM, Pandey G.

F1000Res. 2018 Sep 28;7. pii: ISCB Comm J-1577. doi: 10.12688/f1000research.16415.1. eCollection 2018.

5.

Automating the PathLinker app for Cytoscape.

Huang LJ, Law JN, Murali TM.

F1000Res. 2018 Jun 12;7:727. doi: 10.12688/f1000research.14616.1. eCollection 2018.

6.

Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models.

Tegge AN, Rodrigues RR, Larkin AL, Vu L, Murali TM, Rajagopalan P.

Sci Rep. 2018 Jul 27;8(1):11306. doi: 10.1038/s41598-018-29455-x.

7.

CrossPlan: systematic planning of genetic crosses to validate mathematical models.

Pratapa A, Adames N, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, Murali TM.

Bioinformatics. 2018 Jul 1;34(13):2237-2244. doi: 10.1093/bioinformatics/bty072.

8.

Pathway Analysis with Signaling Hypergraphs.

Ritz A, Avent B, Murali TM.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct;14(5):1042-1055. doi: 10.1109/TCBB.2015.2459681.

9.

GraphSpace: stimulating interdisciplinary collaborations in network biology.

Bharadwaj A, Singh DP, Ritz A, Tegge AN, Poirel CL, Kraikivski P, Adames N, Luther K, Kale SD, Peccoud J, Tyson JJ, Murali TM.

Bioinformatics. 2017 Oct 1;33(19):3134-3136. doi: 10.1093/bioinformatics/btx382.

10.

Corrigendum: Pathway on demand: automated reconstruction of human signaling networks.

Ritz A, Poirel CL, Tegge AN, Sharp N, Simmons K, Powell A, Kale SD, Murali TM.

NPJ Syst Biol Appl. 2016 Nov 17;2:16026. doi: 10.1038/npjsba.2016.26. eCollection 2016.

11.

The PathLinker app: Connect the dots in protein interaction networks.

Gil DP, Law JN, Murali TM.

F1000Res. 2017 Jan 20;6:58. doi: 10.12688/f1000research.9909.1. eCollection 2017.

12.

Hyperlactatemia Predicts Citrate Intolerance With Regional Citrate Anticoagulation During Continuous Renal Replacement Therapy.

Tan JN, Haroon SWP, Mukhopadhyay A, Lau T, Murali TM, Phua J, Tan ZY, Lee N, Chua HR.

J Intensive Care Med. 2019 May;34(5):418-425. doi: 10.1177/0885066617701068. Epub 2017 Apr 4.

PMID:
28372501
13.

XTalkDB: a database of signaling pathway crosstalk.

Sam SA, Teel J, Tegge AN, Bharadwaj A, Murali TM.

Nucleic Acids Res. 2017 Jan 4;45(D1):D432-D439. doi: 10.1093/nar/gkw1037. Epub 2016 Nov 28.

14.

Aminoglycoside-associated acute kidney injury in elderly patients with and without shock.

Ong LZ, Tambyah PA, Lum LH, Low ZJ, Cheng I, Murali TM, Wan MQ, Chua HR.

J Antimicrob Chemother. 2016 Nov;71(11):3250-3257. Epub 2016 Aug 5.

PMID:
27494924
15.

Pathways on demand: automated reconstruction of human signaling networks.

Ritz A, Poirel CL, Tegge AN, Sharp N, Simmons K, Powell A, Kale SD, Murali TM.

NPJ Syst Biol Appl. 2016 Mar 3;2:16002. doi: 10.1038/npjsba.2016.2. eCollection 2016. Erratum in: NPJ Syst Biol Appl. 2016 Nov 17;2:16026.

16.

From START to FINISH: computational analysis of cell cycle control in budding yeast.

Kraikivski P, Chen KC, Laomettachit T, Murali TM, Tyson JJ.

NPJ Syst Biol Appl. 2015 Dec 10;1:15016. doi: 10.1038/npjsba.2015.16. eCollection 2015.

17.

Xtalk: a path-based approach for identifying crosstalk between signaling pathways.

Tegge AN, Sharp N, Murali TM.

Bioinformatics. 2016 Jan 15;32(2):242-51. doi: 10.1093/bioinformatics/btv549. Epub 2015 Sep 23.

18.

Experimental testing of a new integrated model of the budding yeast Start transition.

Adames NR, Schuck PL, Chen KC, Murali TM, Tyson JJ, Peccoud J.

Mol Biol Cell. 2015 Nov 5;26(22):3966-84. doi: 10.1091/mbc.E15-06-0358. Epub 2015 Aug 26.

19.

Signaling hypergraphs.

Ritz A, Tegge AN, Kim H, Poirel CL, Murali TM.

Trends Biotechnol. 2014 Jul;32(7):356-62. doi: 10.1016/j.tibtech.2014.04.007. Epub 2014 May 22.

20.

Reverse engineering molecular hypergraphs.

Rahman A, Poirel CL, Badger DJ, Estep C, Murali TM.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1113-24. doi: 10.1109/TCBB.2013.71.

21.
22.

Summarizing cellular responses as biological process networks.

Lasher CD, Rajagopalan P, Murali TM.

BMC Syst Biol. 2013 Jul 29;7:68. doi: 10.1186/1752-0509-7-68.

23.

Systems biology characterization of engineered tissues.

Rajagopalan P, Kasif S, Murali TM.

Annu Rev Biomed Eng. 2013;15:55-70. doi: 10.1146/annurev-bioeng-071811-150120. Review.

PMID:
23862675
24.

Top-down network analysis to drive bottom-up modeling of physiological processes.

Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM.

J Comput Biol. 2013 May;20(5):409-18. doi: 10.1089/cmb.2012.0274.

25.

Designing a multicellular organotypic 3D liver model with a detachable, nanoscale polymeric Space of Disse.

Larkin AL, Rodrigues RR, Murali TM, Rajagopalan P.

Tissue Eng Part C Methods. 2013 Nov;19(11):875-84. doi: 10.1089/ten.TEC.2012.0700. Epub 2013 Jun 22.

26.

The landscape of host transcriptional response programs commonly perturbed by bacterial pathogens: towards host-oriented broad-spectrum drug targets.

Kidane YH, Lawrence C, Murali TM.

PLoS One. 2013;8(3):e58553. doi: 10.1371/journal.pone.0058553. Epub 2013 Mar 13.

27.

Reconciling differential gene expression data with molecular interaction networks.

Poirel CL, Rahman A, Rodrigues RR, Krishnan A, Addesa JR, Murali TM.

Bioinformatics. 2013 Mar 1;29(5):622-9. doi: 10.1093/bioinformatics/btt007. Epub 2013 Jan 12.

28.

Sensitive detection of pathway perturbations in cancers.

Rivera CG, Tyler BM, Murali TM.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S9. doi: 10.1186/1471-2105-13-S3-S9.

29.

Network-based functional enrichment.

Poirel CL, Owens CC 3rd, Murali TM.

BMC Bioinformatics. 2011;12 Suppl 13:S14. Epub 2011 Nov 30.

30.

Computationally Driven Experimental Biology.

Murali TM.

Computer (Long Beach Calif). 2012 Mar;45(3):22-23.

31.

Network-based prediction and analysis of HIV dependency factors.

Murali TM, Dyer MD, Badger D, Tyler BM, Katze MG.

PLoS Comput Biol. 2011 Sep;7(9):e1002164. doi: 10.1371/journal.pcbi.1002164. Epub 2011 Sep 22.

32.

Supervised learning and prediction of physical interactions between human and HIV proteins.

Dyer MD, Murali TM, Sobral BW.

Infect Genet Evol. 2011 Jul;11(5):917-23. doi: 10.1016/j.meegid.2011.02.022. Epub 2011 Mar 5.

33.

Discovering networks of perturbed biological processes in hepatocyte cultures.

Lasher CD, Rajagopalan P, Murali TM.

PLoS One. 2011 Jan 5;6(1):e15247. doi: 10.1371/journal.pone.0015247.

34.

The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis.

Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, Bassaganya-Riera J, Murali TM, Sobral BW.

PLoS One. 2010 Aug 9;5(8):e12089. doi: 10.1371/journal.pone.0012089.

35.

A comparative study of genome-wide transcriptional profiles of primary hepatocytes in collagen sandwich and monolayer cultures.

Kim Y, Lasher CD, Milford LM, Murali TM, Rajagopalan P.

Tissue Eng Part C Methods. 2010 Dec;16(6):1449-60. doi: 10.1089/ten.TEC.2010.0012. Epub 2010 Jun 7.

36.

PIG--the pathogen interaction gateway.

Driscoll T, Dyer MD, Murali TM, Sobral BW.

Nucleic Acids Res. 2009 Jan;37(Database issue):D647-50. doi: 10.1093/nar/gkn799. Epub 2008 Nov 4.

37.

Network legos: building blocks of cellular wiring diagrams.

Murali TM, Rivera CG.

J Comput Biol. 2008 Sep;15(7):829-44. doi: 10.1089/cmb.2007.0139.

PMID:
18707557
38.

Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin.

Ruscio JZ, Kumar D, Shukla M, Prisant MG, Murali TM, Onufriev AV.

Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9204-9. doi: 10.1073/pnas.0710825105. Epub 2008 Jul 1.

39.

The landscape of human proteins interacting with viruses and other pathogens.

Dyer MD, Murali TM, Sobral BW.

PLoS Pathog. 2008 Feb 8;4(2):e32. doi: 10.1371/journal.ppat.0040032.

40.

Expression divergence of tandemly arrayed genes in human and mouse.

Shoja V, Murali TM, Zhang L.

Comp Funct Genomics. 2007:60964. doi: 10.1155/2007/60964.

41.

Computational prediction of host-pathogen protein-protein interactions.

Dyer MD, Murali TM, Sobral BW.

Bioinformatics. 2007 Jul 1;23(13):i159-66.

PMID:
17646292
42.

The art of gene function prediction.

Murali TM, Wu CJ, Kasif S.

Nat Biotechnol. 2006 Dec;24(12):1474-5; author reply 1475-6. No abstract available.

PMID:
17160037
43.

Automatic layout and visualization of biclusters.

Grothaus GA, Mufti A, Murali TM.

Algorithms Mol Biol. 2006 Sep 4;1:15.

44.

Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field.

Li P, Sioson A, Mane SP, Ulanov A, Grothaus G, Heath LS, Murali TM, Bohnert HJ, Grene R.

Plant Mol Biol. 2006 Nov;62(4-5):593-609. Epub 2006 Aug 29.

PMID:
16941220
45.

VIRGO: computational prediction of gene functions.

Massjouni N, Rivera CG, Murali TM.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W340-4.

46.

XcisClique: analysis of regulatory bicliques.

Pati A, Vasquez-Robinet C, Heath LS, Grene R, Murali TM.

BMC Bioinformatics. 2006 Apr 21;7:218.

47.

Gene expression module discovery using gibbs sampling.

Wu CJ, Fu Y, Murali TM, Kasif S.

Genome Inform. 2004;15(1):239-48.

PMID:
15712126
48.

Whole-genome annotation by using evidence integration in functional-linkage networks.

Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S.

Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2888-93. Epub 2004 Feb 23.

49.

RankGene: identification of diagnostic genes based on expression data.

Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S.

Bioinformatics. 2003 Aug 12;19(12):1578-9.

PMID:
12912841
50.

Extracting conserved gene expression motifs from gene expression data.

Murali TM, Kasif S.

Pac Symp Biocomput. 2003:77-88.

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