Publications for Vanathi Gopalakrishnan, PhD

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

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.

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

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.

Menon PG, Morris L, Staines M, Lima J, Lee DC, Gopalakrishnan V. Novel MRI-derived quantitative biomarker for cardiac function applied to classifying ischemic cardiomyopathy within a Bayesian rule learning framework. Proceedings of the SPIE Medical Imaging 2014; February 15-20, 2014; San Diego, CA, USA. 2014.

Gopalakrishnan V, Menon PG, Madan S. A novel framework to enhance scientific knowledge of cardiovascular MRI biomarkers and their application to pediatric cardiomyopathy classification. Proceedings of the Second International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014); Granada, Spain. 2014. p. (8 pages). In Press.

Balasubramanian JB, Cooper GF, Visweswaran S, Gopalakrishnan V. Selective Model Averaging with Bayesian Rule Learning for Predictive Biomedicine. Proceedings of the AMIA 2014 Joint Summits in Translational Science (In Press); April 2014; San Francisco, CA, USA2014.

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 (CoSBBI). Journal of Pathology Informatics. 2014; In Press. PMC In Process.

McMillan A, Visweswaran S, Gopalakrishnan V. Machine Learning for Biomarker-based Classification of Alzheimer's Disease Progression Journal of Pathology Informatics. 2014; In Press.

Staines M, Morris L, Menon PG, Lima J, Lee DC, Gopalakrishnan V. Discovering Biomarkers for Cardiovascular Disease Using Rule Learning. Journal of Pathology Informatics. 2014; In Press.

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

Floudas, C. S., Balasubramanian, J, Romkes, M., Gopalakrishnan, V. An empirical workflow for genome-wide single nucleotide polymorphism-based predictive modeling. In the Proceedings of the AMIA Translational Bioinformatics Summit 2013, March 18-20, San Francisco, CA.

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

Grover, H., Gopalakrishnan, V. Efficient Processing of Models for Large-scale Shotgun Proteomics Data. In Proceedings of the International Workshop on Collaborative Big Data (C-Big 2012), Pittsburgh, PA, October 14, 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.

Bigbee, W.L., Gopalakrishnan, V., Dacic, .S., Hauskrecht, M., Weissfeld, J.L., Wilson, D.O., Siegfried, J.M., Lokshin, A.E. A Multiplexed Serum Biomarker Immunoassay Panel Discriminates Clinical Lung Cancer Patients from Cancer-Free High-Risk Subjects in a CT-Screened Cohort. AACR 2010. Late Breaking Abstract in AACR  2010 Proceedings.

2009

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

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.

Kolli, V. S. K., Seth, B., Weaver, L., Lustgarten, J. L., Gopalakrishnan, V., Malehorn, D.,  Bigbee, B, Mural, R. J., Shriver, C.D. MALDI-TOF Profiling of Breast Cancer Sera for Pattern Analysis. Human Proteome Organization HUPO 2009  Proceedings.

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

Gopalakrishnan V, Buchanan BG, Rosenberg JM. A Simple Simulator of Protein Crystallization, Journal of Applied Crystallography 35(6) (2002) 727-733.

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

1994

Hennessy D, Gopalakrishnan V, Buchanan BG, Subramanian D, Rosenberg JM. Induction of Rules for Biological Macromolecule Crystallization, In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (1994) 179-187. PMID: 7584388

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