Publications for Vanathi Gopalakrishnan, PhD
2020
Balasubramanian JB, Boes RD, Gopalakrishnan V. A novel approach to modeling multifactorial diseases using Ensemble Bayesian Rule classifiers. Journal of Biomedical Informatics 020 Jul;107:103455. doi: 10.1016/j.jbi.2020.103455. PMID: 32497685

2019
Y Liu, J Manners, Y Bittar, SHY Chou, V Gopalakrishnan. Towards precision critical care management of blood pressure in hemorrhagic stroke patients using dynamic linear models. PLoS One 2019;14(8): e0220283.

2018
Ceschin R, Zahner A, Reynolds W, Gaesser J, Zuccoli G, Lo CW, Gopalakrishnan V, Panigrahy A. A computational framework for the detection of subcortical brain dysmaturation in neonatal MRI using 3D Convolutional Neural Networks. Neuroimage. 2018 Sep;178:183-197. doi: 10.1016/j.neuroimage.2018.05.049. Epub 2018 May 21. PMID: 29793060.
Balasubramanian JB, Gopalakrishnan V. Tunable structure priors for Bayesian rule learning for knowledge integrated biomarker discovery.World J Clin Oncol. 2018 Sep 14;9(5): 89-109. doi: 10.5306/wjco.v9.i5.98. PMID: 30254965. PMC ID: PMC6153126.
2017
Liu Y, Gopalakrishnan V. An Overview and Evaluation of Recent Machine Learning Imputation Methods Using Cardiac Imaging Data. Data 2017, 2(1), 8; doi: 10.3390/data2010008.

Lustgarten JL, Balasubramanian JB, Visweswaran S, Gopalakrishnan V, Learning Parsimonious Classification Rules from Gene Expression Data Using Bayesian Networks with Local Structure. Data (Basel). 2017 Mar;2(1). pii: 5. Epub 2017 Jan 18. PMID: 28331847. PMCID: PMC5358670. DOI: 10.3390/data2010005.

2016
Pineda AL, Ogoe HA, Balasubramanian JB, Rangel Escareño C, Visweswaran S, Herman JG, Gopalakrishnan V. On Predicting lung cancer subtypes using 'omic' data from tumor and tumor-adjacent histologically-normal tissue. BMC Cancer. 2016 Mar 4;16:184. doi: 10.1186/s12885-016-2223-3. PMID: 26944944 PMCID: PMC4778315 DOI: 10.1186/s12885-016-2223-3.
2015
Ogoe, HA, Visweswaran, S, Lu, X, Gopalakrishnan, V. (2015) Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. BMC Bioinformatics 16:226 (designated as a Highly Accessed paper) PMID: 26202217 PMCID: PMC4512094
R. Ceschin, A. Panigrahy, and V. Gopalakrishnan, “Sfdm: Open-source software for temporal analysis and visualization of brain tumor diffusion mr using serial functional diffusion mapping,” Cancer Inform., vol. 14, pp. 1–9, 2015. PMID: 25673970 PMCID: PMC4315050 DOI: 10.4137/CIN.S17293

Pineda, AL, Gopalakrishnan, V. Novel Application of Junction Trees to the Interpretation of Epigenetic Differences among Lung Cancer Subtypes. Proceedings of the AMIA Translational Bioinformatics Summit. March 21-23, 2015. PMID: 26306226 Winner of the Marco Ramoni Distinguished Paper Award.
2014
Dutta-Moscato J, Gopalakrishnan V, Lotze MT, Becich MJ. Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics. J Pathol Inform. 2014 Mar 28;5(1):12. doi: 10.4103/2153-3539.129448. eCollection 2014. PMID: 24860688. PMCID: PMC4030307.

Avali VR, Cooper GF, Gopalakrishnan V. Application of Bayesian logistic regression to mining biomedical data. In: Proceedings of the Fall Symposium of the American Medical Informatics Association (2014) Nov 14;2014:266-73. PMID: 25954328 PMC4419893

Zaidi, A.H, Gopalakrishnan, V., Kasi, P. M., Zeng, X., Malhotra, U., Balasubramanian, J., Visweswaran, S., Sun, M., Flint, M. S., Davison, J. M., Hood, B. L., Conrads, T. P., Bergman, J.J., Bigbee, W. L., Jobe, B. A. Evaluation of a 4-protein serum biomarker panel – biglycan, annexin-A6, myeloperoxidase and protein S100-A9 (B-AMP©) – for the detection of esophageal adenocarcinoma. Cancer. 2014 Aug 5. PMID: 25100294. PMCID: PMC4441619 (Impact Factor = 5.201).
Jordan, R, Visweswaran, S, Gopalakrishnan, V. Semi-automated literature mining to identify putative biomarkers of disease from multiple biofluids. J Clin Bioinformatics. 2014, 4:13. PMID: 25379168 PMCID: PMC4215335.
2013
Grover H, Wallstrom G, Wu CC, Gopalakrishnan V. Context-Sensitive Markov Models for Peptide Scoring and Identification from Tandem Mass Spectrometry. Omics : a journal of integrative biology. 2013 Feb;17(2):94-105. doi: 10.1089/omi.2012.0073. Epub 2013 Jan 5 PMID: 23289783 PMCID: PMC3567622 [Available on 2014/2/1]
2012
Liu, G., Kong, L., Gopalakrishnan, V. A Partitioning Based Adaptive Method for Robust Removal of Irrelevant Features from High-dimensional Biomedical Datasets. In Proceedings of the 2012 AMIA Summit on Translational Bioinformatics. San Francisco, March 19-23, 2012. Pages 52-61. PMCID: PMC3392052
Bigbee, W. L*., Gopalakrishnan, V*, Weissfeld J, L., Wilson, D. O., Dacic, S. Lokshin, A. E., Siegfried, J. M. A Multiplexed Serum Biomarker Immunoassay Panel Discriminates Clinical Lung Cancer Patients from High-Risk Individuals Found to be Cancer-Free by CT Screening. J Thorac Oncol. 2012 Apr;7(4):698-708. (*These authors contributed equally to the study). PMID: 22425918 PMCID: PMC3308353
2011
Li, X., LeBlanc, J., Truong, A., Vuthoori, R., Chen, S. S., Lustgarten, J. L., Roth, B., Allard, J., Andrew Ippoliti, A., Presley, L.L., Borneman, J., Bigbee, W.L., Gopalakrishnan, V., Graeber, T.G., Elashoff, D., Braun, J., Goodglick, L. A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface. 2011. PLoS ONE 6(11): e26542. PMCID:PMC3221670
Ganchev, P., Malehorn, D., Bigbee, W. L., Gopalakrishnan, V. Transfer Learning of Classification Rules for Biomarker Discovery and Verification from Molecular Profiling Studies. J Biomed Inform. 2011 Dec;44 Suppl 1:S17-23. Epub 2011 May 6. (Won a Distinguished Paper Award at AMIA 2011 - Translational Bioinformatics) PMID: 21571094
Zeng X, Hood BL, Zhao T, Conrads TP, Sun M, Gopalakrishnan V, Grover H, Day RS, Weissfeld JL, Siegfried JM, Bigbee WL. Lung Cancer Serum Biomarker Discovery Using Label Free Liquid Chromatography-Tandem Mass Spectrometry. J Thorac Oncol. 2011 Apr;6(4):725-34. PMCID:PMC3104087.
Lustgarten JL, Visweswaran S, Gopalakrishnan V, Cooper GF. Application of an efficient Bayesian discretization method to biomedical data. BMC Bioinformatics 12 (2011) 309 http://www.biomedcentral.com/1471-2105/12/309. PMID: 21798039 PMC3162539

2010
Ryberg, H., An, J., Darko, S, Lustgarten, J.L., Jaffa, M., Gopalakrishnan, V., Lacomis, D, Cudkowicz, M, E., Bowser, R. Discovery and Verification of Amyotrophic Lateral Sclerosis Biomarkers by Proteomics. Muscle & nerve. 2010;42(1):104-11. PMID: 20583124
Gopalakrishnan V, Lustgarten JL, Visweswaran S, Cooper GF. Bayesian rule learning for biomedical data mining. Bioinformatics 26 (2010) 668-675. Doi:10.1093/bioinformatics/btq005. PMID: 20080512. PMC2852212.

2009
Lustgarten JL, Visweswaran S, Hogan WR, Gopalakrishnan V. Knowledge Based Variable Selection for Learning Rules from Proteomic Data. BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S16. PMID: 19761570 PMCID: PMC2745687.
Lustgarten JL, Gopalakrishnan V, Visweswaran S. Measuring stability of feature selection in biomedical datasets. In: Proceedings of the Fall Symposium of the American Medical Informatics Association (Nov 2009). 406-10. PMID: 20351889 PMCID: PMC2815476
2005
Ranganathan, S., Williams, E., Ganchev, P., Gopalakrishnan, V., Urbinelli, L., Newhall, K., Cudkowicz, M.E., Brown, R.H. Jr., Bowser, R. Proteomic Profiling of Cerebrospinal Fluid Identifies Biomarkers for Amyotrophic Lateral Sclerosis, J Neurochem. 2005 Dec;95(5):1461-71. PMID: 16313519 PMCID: PMC1540444. (Cited 170 times as per google scholar on 10/17/2014).
2004
Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B., Rosenberg, J.M. Machine-Learning Techniques for Macromolecular Crystallization Data, Acta Crystallogr D Biol Crystallogr 60 (2004)1705-1716. PMID:15388916
Lu, X., Zhai, C., Gopalakrishnan, V., and Buchanan, B.G. (2004) Automatic annotation of protein motif function with Gene Ontology terms. BMC Bioinformatics 5:122. PMID: 15345032
2002
2000
Gopalakrishnan V, Buchanan BG, Rosenberg JM. Intelligent Aids for Parallel Experiment Planning and Macromolecular Crystallization. In: Proceedings of the Eight International Conference on Intelligent Systems for Molecular Biology (2000) 171-180. PMID: 10977078