Rajesh Chowdhary

Email: rajeshchowdhary-gmail-com
Web: rajeshchowdhary.com

 Short Bio

Rajesh Chowdhary is CSO of Insilicom LLC. His research interest lies in application of machine learning/AI approaches to biomedical problems. Rajesh has worked as a biomedical-informatics faculty scientist at Marshfield Clinic, WI, with an honorary position at School of Medicine and Public Health, University of Wisconsin, Madison. He was a research fellow in computational biology at Department of Statistics, Harvard University. Rajesh has a PhD from School of Computing, National University of Singapore, a Master's in Biomedical Engineering from Imperial College, and a Bachelor's in Civil Engineering from IIT Bombay.


Principal Investigator. Cell-line identification with DNA-replication timing fingerprints. NIH SBIR grant (1R43GM131546-01A1), Insilicom LLC, 05/2019.
Principal Investigator. Warfarin dose prediction using machine learning. NIH-Clinical and Translational Science Award (CTSA) - ICTR T1 pilot grant, 2013.
Principal Investigator. Modeling and risk profiling superficial vein thrombosis. Disease-specific competitive grant, Marshfield Clinic, 2013.
Principal Investigator. Characterization and modeling of promoters of asthma associated genes. Disease-specific competitive grant, Marshfield Clinic, 2012.
Principal Investigator. Mining textual data in EMR for prediction of Atrial Fibrillation/Flutter (AFF) through application of machine learning. Wisconsin Genomics Initiative (WGI) Demonstration Project competitive grant, 2012.


Journal publications
  1. Piatek MJ, Schramm MC, Burra DD, binShbreen A, Jankovic BR, Chowdhary R, Archer JAC, Bajic VB. Simplified Method for Predicting a Functional Class of Proteins in Transcription Factor Complexes. PLoS ONE 8(7):e68857, 2013.
  2. Chowdhary R, Zhang J, Tan SL, Osborne D, Bajic VB, Liu JS. PIMiner: a web tool for extracting protein interactions from Biological Text. International Journal of Data Mining and Bioinformatics (IJDMB) 7(4):450-62, 2013.
  3. Mora AM, Ashoor H, Awara K, Jankovic BR, Kamau A, Chowdhary R, Archer JAC, Bajic VB. Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. Bioinformatics 29(1):117-8, 2013.
  4. Chowdhary R, Tan SL, Zhang J, Karnik S, Bajic VB, Liu JS. Context-specific Protein Network Miner - a webserver to explore context-specific protein interaction network from literature. PLoS ONE, 2012.
  5. Chowdhary R, Tan SL, Pavesi G, Jin JJ, Dong D, Mathur SK, Burkart A, Narang V, Glurich I, Raby BA, Weiss ST, Wong L, Liu JS, Bajic VB. A database of annotated promoters of genes associated with common respiratory and related diseases. American Journal of Respiratory Cell and Molecular Biology (AJRCMB), 2012.
  6. Balaji S, Mcclendon C, Chowdhary R, Liu JS, Zhang J. IMID: Integrated molecular interaction database. Bioinformatics, 28(5):747-749, 2012.
  7. Kalkatawi M, Rangkuti F, Jankovic BR, Kamau A, Chowdhary R, Archer JAC, Bajic VB. Dragon Poly(A) Spotter: Predictor of poly(A) motifs within human genomic DNA sequences. Bioinformatics, 28(1):127-129, 2012.
  8. Bell L, Chowdhary R, Liu JS, Niu X and Zhang J. Integrated bio-entity network: a system for biological knowledge discovery. PLoS ONE, 6(6):e21474, 2011.
  9. Chowdhary R, Bajic V, Dong D, Wong L, Liu JS. Genome-wide analysis of regions similar to promoters of histone genes. BMC Systems Biology, 4(1):S4, 2010.
  10. Chowdhary R, Zhang J, Liu JSBayesian inference of protein-protein interactions from biological literature. Bioinformatics, 25(12):1536-1542, 2009
  11. Brahmachary M, Schonbach C, Yang L, Huang E, Tan SL, Chowdhary R, Krishnan SPT, Lin CY, Hume DA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB. Computational Promoter Analysis of Mouse, Rat and Human Antimicrobial Peptide-coding Genes. BMC Bioinformatics, 7(5):S8, 2006.
  12. Chowdhary R, Tan SL, Ali RA, Boerlage B, Wong L, Bajic VB. Dragon Promoter Mapper (DPM): a Bayesian framework for modeling promoter structures. Bioinformatics, 22(18):2310-2312, 2006.
  13. Chowdhary R, Wong L, Bajic VB. Finding functional promoter motifs by computational methods: a word of caution. International Journal of Bioinformatics Research and Applications (IJBRA), 2(3):282-288, 2006.
  14. Chowdhary R, Ali RA, Albig W, Doenecke D, Bajic VB. Promoter modeling: the case study of mammalian histone promoters, Bioinformatics, 21(11):2623-2628, 2005.
  15. Singh V, Chowdhary R, Chowdhary N. Does nasal breathing cause frictional trauma in allergic rhinitis? Journal of Association of Physicians of India (JAPI), 48(5):501-504, 2000.
  16. Singh V, Chowdhary R, Chowdhary N. The role of cough and hyperventilation in perpetuating airway inflammation in asthma. Journal of Association of Physicians of India (JAPI), 48(3):343-345, 2000.
  17. Chowdhary R, Singh V, Tattersfield AE, Sharma SD, Kar S, Gupta AB. Relationship of flow and cross-sectional area to frictional stress in airway models of asthma. J Asthma, 36(5):419-426, 1999.
Book Chapters
  1. Chowdhary R, Jankovic BR, Archer JAC, Zhang X, Gao X, Bajic VB. Automated mining of disease-specific networks of protein interactions based on biomedical literature. In Biological Data Mining and its Applications in Healthcare; published by World Scientific. In press 2013.
  2. Jankovic BR, Archer JAC, Chowdhary R, Schaefer U, Bajic VB. Promoter structures conserved between Homo sapiens, Mus musculus and Drosophila melanogaster. In Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances, 92-104, 2011.
  3. Ashoor H, Mora AM, Awara K, Jankovic BR, Chowdhary R, Archer JAC, Bajic VB. Recognition of translation initiation sites in Arabidopsis. In Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances, 105-116, 2011.
  4. Narang V, Chowdhary R, Mittal A, Sung WK. Bayesian network modeling of transcription factor binding sites, in Bayesian Network Technologies: Applications of Graphical Models, Idea Group Publishing, Pennsylvania, USA, 2006.
  5. Huang E, Yang L, Chowdhary R, Kassim A, Bajic VB. An algorithm for ab-initio DNA motif detection, in Information Processing and Living Systems, World Scientific, 611-614, 2005.
Conferences, Workshops, Symposiums, Meetings, et al.
  1. Karnik S, Tan SL, Berg B, Glurich I, Zhang J, Vidaillet HJ, Page CD, Chowdhary R. Predicting Atrial Fibrillation and Flutter using Electronic Health Records. In Annual International Conference of the IEEE: Engineering in Medicine and Biology Society (EMBC), 5562-5, 2012.
  2. Bell L, Chowdhary R, Liu JS, Niu X, Zhang J. IBN: a system for Biological Network-based Knowledge Discovery. In Annual International Conference of the IEEE: Engineering in Medicine and Biology Society (EMBC), Abstract 2012.
  3. Zhang C, Chowdhary R, Zhang J. Biological Pathway Discovery through Text mining and Data Integration. In Annual International Conference of the IEEE: Engineering in Medicine and Biology Society (EMBC), 2012.
  4. Belknap SM, Godinez-Puig V, Brannigan RE, Lin SM, Cashy J, Chowdhary R, Postelnick MJ, Fotis MA, Irwig M, Khan SA, Gradishar WJ, Garg V, Shen X, Raisch DW, Nardone B, Rosen ST, Edwards BJ, McKoy JM, Yarnold PR, West DP. Association of breast cancer in men with exposure to 5-alpha reductase inhibitors: A RADAR report. American Society of Clinical Oncology (ASCO) Annual Meeting 2012.
  5. Chowdhary R, Berg B, Tan SL, Mendonca EA, Karanjia PN, Glurich I, Montilla RG, Peissig PL, Vidaillet HJ, Page CD. Mining textual data in the EMR for prediction of Atrial Fibrillation/Flutter (AFF). Workshop on Learning from Unstructured Clinical Text, International Conference on Machine Learning (ICML), Bellevue USA, 2011.
  6. Chowdhary R, Zhang J, Tan SL, Osborne DE, Liu JS. BiotextMiner: a protein interaction extraction system. Upper Midwest Informatics CTSA Consortium Meeting, Madison, USA 2010.
  7. Chowdhary R, Ali RA, Bajic VB. Modeling 5' regions of histone genes using Bayesian networks. Asia-Pacific Bioinformatics Conference (APBC) 283-288, 2005.
  8. Singh V, Chowdhary R, Sharma SD, Gupta AB, Kar S. Mechanical shear trauma in models of asthma. American Review of Respiratory Diseases Conference (ARRD), 147:A832, 1993.

 Talks and Seminars
  1. Context-specific Protein Network Miner. Fourth Annual Wisconsin Science & Technology Symposium, University of Wisconsin, Whitewater, 2012.
  2. Data Mining Techniques. Wisconsin Network for Health Research (WiNHR) Advisory Committee Meeting and Educational Forum, 2011.
  3. Mining protein networks from literature. Greehey Children's Cancer Research Institute, San Antonio, Texas, 2011.
  4. Network/Integrative Biology. MCRF Scientist meeting, 2011.
  5. Asthma Genetics. Allergy Grand Rounds, Section of Allergy, Pulmonary and Critical Care, University of Wisconsin, Madison, 2010.
  6. Asthma Gene Regulation. BIRC Center meeting, 2010.
  7. Genome-wide analysis of Histone Gene Promoters. Computation and Informatics in Biology and Medicine (CIBM) Seminars, University of Wisconsin, Madison, 2009.
  8. Biological literature mining. MCRF Board of Trustees, 2009.
  9. PPI extraction from unstructured biological text. Department of Biostatistics, University of Wisconsin, Madison, 2009.
  10. Overview of Bayesian networks applications in Bioinformatics. Department of Biostatistics, Harvard School of Public Health, Harvard University, 2006.