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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.


Serial Quantification of Urinary Protein Biomarkers to Predict Drug-induced Acute Kidney Injury.

Da Y, Akalya K, Murali T, Vathsala A, Tan CS, Low S, Lim HN, Teo BW, Lau T, Ong L, Chua HR.

Curr Drug Metab. 2019;20(8):656-664. doi: 10.2174/1389200220666190711114504.


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.


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.


Genome-based taxonomic classification.

Paul B, Dixit G, Murali TS, Satyamoorthy K.

Genome. 2019 Feb;62(2):45-52. doi: 10.1139/gen-2018-0072. Epub 2019 Jan 16.


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.


Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky.

Liu J, Murali T, Yu T, Liu C, Sivakumaran TA, Moseley HNB, Zhulin IB, Weiss HL, Durbin EB, Ellingson SR, Liu J, Huang B, Hallahan BJ, Horbinski CM, Hodges K, Napier DL, Bocklage T, Mueller J, Vanderford NL, Fardo DW, Wang C, Arnold SM.

Cancer Epidemiol Biomarkers Prev. 2019 Feb;28(2):348-356. doi: 10.1158/1055-9965.EPI-17-0984. Epub 2018 Oct 30.


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.


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.


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.


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.


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.


Severity of drug resistance and co-existence of Enterococcus faecalis in diabetic foot ulcer infections.

Shettigar K, Bhat DV, Satyamoorthy K, Murali TS.

Folia Microbiol (Praha). 2018 Jan;63(1):115-122. doi: 10.1007/s12223-017-0547-2. Epub 2017 Sep 9.


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.


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.


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.


Virulence determinants in clinical Staphylococcus aureus from monomicrobial and polymicrobial infections of diabetic foot ulcers.

Shettigar K, Jain S, Bhat DV, Acharya R, Ramachandra L, Satyamoorthy K, Murali TS.

J Med Microbiol. 2016 Dec;65(12):1392-1404. doi: 10.1099/jmm.0.000370. Epub 2016 Oct 19.


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.


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.


Bodyweight-supported treadmill training for retraining gait among chronic stroke survivors: A randomized controlled study.

Srivastava A, Taly AB, Gupta A, Kumar S, Murali T.

Ann Phys Rehabil Med. 2016 Sep;59(4):235-41. doi: 10.1016/ Epub 2016 Apr 20.


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.


Modulation of genetic clusters for synthesis of bioactive molecules in fungal endophytes: A review.

Deepika VB, Murali TS, Satyamoorthy K.

Microbiol Res. 2016 Jan;182:125-40. doi: 10.1016/j.micres.2015.10.009. Epub 2015 Oct 29. Review.


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.


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.


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.


Genome Sequence of a Burkholderia pseudomallei Clinical Isolate from a Patient with Community-Acquired Pneumonia and Septicemia.

Mukhopadhyay C, Vandana KE, Chaitanya TA, Shaw T, Bhat HV, Chakrabarty S, Paul B, Mallya S, Murali TS, Satyamoorthy K.

Genome Announc. 2015 Aug 20;3(4). pii: e00915-15. doi: 10.1128/genomeA.00915-15.


Rehabilitation interventions to improve locomotor outcome in chronic stroke survivors: A prospective, repeated-measure study.

Srivastava A, Taly AB, Gupta A, Murali T.

Neurol India. 2015 May-Jun;63(3):347-52. doi: 10.4103/0028-3886.158202.


A search for antiplasmodial metabolites among fungal endophytes of terrestrial and marine plants of southern India.

Kaushik NK, Murali TS, Sahal D, Suryanarayanan TS.

Acta Parasitol. 2014 Oct;59(4):745-57. doi: 10.2478/s11686-014-0307-2. Epub 2014 Sep 20.


Modified technique of continuous ambulatory peritoneal dialysis catheter insertion in the pediatric population.

Ravichandran R, Vikram HN, Murali TR, Sampathkumar K.

J Pediatr Urol. 2014 Dec;10(6):1277-9. doi: 10.1016/j.jpurol.2014.07.001. Epub 2014 Jul 10.


Characteristics of microbial drug resistance and its correlates in chronic diabetic foot ulcer infections.

Murali TS, Kavitha S, Spoorthi J, Bhat DV, Prasad AS, Upton Z, Ramachandra L, Acharya RV, Satyamoorthy K.

J Med Microbiol. 2014 Oct;63(Pt 10):1377-85. doi: 10.1099/jmm.0.076034-0. Epub 2014 Jul 18.


Integrating the interactome and the transcriptome of Drosophila.

Murali T, Pacifico S, Finley RL Jr.

BMC Bioinformatics. 2014 Jun 10;15:177. doi: 10.1186/1471-2105-15-177.


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.


Genome Sequences of Four Clinical Staphylococcus aureus Strains with Diverse Drug Resistance Profiles Isolated from Diabetic Foot Ulcers.

Murali TS, Paul B, Parikh H, Singh RP, Kavitha S, Bhat MK, Satyamoorthy K.

Genome Announc. 2014 Mar 20;2(2). pii: e00204-14. doi: 10.1128/genomeA.00204-14.


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.


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.


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.


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.


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.


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.


Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito.

Mairiang D, Zhang H, Sodja A, Murali T, Suriyaphol P, Malasit P, Limjindaporn T, Finley RL Jr.

PLoS One. 2013;8(1):e53535. doi: 10.1371/journal.pone.0053535. Epub 2013 Jan 11.


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.


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.


Network-based functional enrichment.

Poirel CL, Owens CC 3rd, Murali TM.

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


Computationally Driven Experimental Biology.

Murali TM.

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


Assigning confidence scores to protein-protein interactions.

Yu J, Murali T, Finley RL Jr.

Methods Mol Biol. 2012;812:161-74. doi: 10.1007/978-1-61779-455-1_9.


Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling.

Friedman AA, Tucker G, Singh R, Yan D, Vinayagam A, Hu Y, Binari R, Hong P, Sun X, Porto M, Pacifico S, Murali T, Finley RL Jr, Asara JM, Berger B, Perrimon N.

Sci Signal. 2011 Oct 25;4(196):rs10. doi: 10.1126/scisignal.2002029.


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.


Optimization of subarachanoid block by oral pregabalin for hysterectomy.

Kohli M, Murali T, Gupta R, Khan P, Bogra J.

J Anaesthesiol Clin Pharmacol. 2011 Jan;27(1):101-5.


Genetic variation in genes involved in folate and drug metabolism in a south Indian population.

Rai PS, Murali TS, Vasudevan TG, Prasada SK, Bhagavath AK, Pai P, Gopinath PM, Satyamoorthy K.

Indian J Hum Genet. 2011 May;17 Suppl 1:S48-53. doi: 10.4103/0971-6866.80359.

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