Pratap Venepally, PhD

Sr. Bioinformatics Engineer

As a member of the Core Informatics team at JCVI since 2004, Pratap Venepally provided data processing and analysis support to various research projects involving both prokaryotic and eukaryotic organisms. Most significant contributions have been in the areas of analyses pertaining to transcriptomics, sequence assembly, genotyping and SNP identification and proteomics. He is very experienced in areas of computer programming (Perl, Python, Unix & SQL), data analysis using R programming, various sequence analysis tools, NextGen sequencing software and platforms. Additionally, he has a strong Biological research background with a PhD in Molecular Biology and active contributions to several published research articles.

Research Priorities

  • Transcriptomics & RNA-Seq
  • Sequence assembly
  • Genotyping and SNP identification
  • Proteomics


Diagnostic microbiology and infectious disease. 2021-02-01; 99.2: 115242.
A comprehensive and contemporary "snapshot" of β-lactamases in carbapenem resistant Acinetobacter baumannii
Hujer AM, Hujer KM, Leonard DA, Powers RA, Wallar BJ, Mack AR, Taracila MA, Rather PN, Higgins PG, Prati F, Caselli E, Marshall SH, Clarke T, Greco C, Venepally P, Brinkac L, Kreiswirth BN, Fouts DE, Bonomo RA, Antibacterial Resistance Leadership Group (ARLG)
PMID: 33248392
Bioinformatics (Oxford, England). 2017-06-01; 33.11: 1725-1726.
LOCUST: a custom sequence locus typer for classifying microbial isolates
Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G
PMID: 28130240
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2017-01-01; 22.564-575.
Aevermann B, McCorrison J, Venepally P, Hodge R, Bakken T, Miller J, Novotny M, Tran DN, Diezfuertes F, Christiansen L, Zhang F, Steemers F, Lasken RS, Lein ED, Schork N, Scheuermann RH
PMID: 27897007
Scientific reports. 2016-08-10; 6.31291.
Transcriptomic evidence for modulation of host inflammatory responses during febrile Plasmodium falciparum malaria
Tran TM, Jones MB, Ongoiba A, Bijker EM, Schats R, Venepally P, Skinner J, Doumbo S, Quinten E, Visser LG, Whalen E, Presnell S, O'Connell EM, Kayentao K, Doumbo OK, Chaussabel D, Lorenzi H, Nutman TB, Ottenhoff TH, Haks MC, Traore B, Kirkness EF, Sauerwein RW, Crompton PD
PMID: 27506615
Nature communications. 2016-04-19; 7.11022.
Nuclear RNA-seq of single neurons reveals molecular signatures of activation
Lacar B, Linker SB, Jaeger BN, Krishnaswami S, Barron J, Kelder M, Parylak S, Paquola A, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin J, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH
PMID: 27090946
Nature protocols. 2016-03-01; 11.3: 499-524.
Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons
Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS
PMID: 26890679
PLoS pathogens. 2015-04-24; 11.4: e1004834.
Genetic Analysis Using an Isogenic Mating Pair of Aspergillus fumigatus Identifies Azole Resistance Genes and Lack of MAT Locus's Role in Virulence
Losada L, Sugui JA, Eckhaus MA, Chang YC, Mounaud S, Figat A, Joardar V, Pakala SB, Pakala S, Venepally P, Fedorova N, Nierman WC, Kwon-Chung KJ
PMID: 25909486
BMC bioinformatics. 2014-11-19; 15.357.
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly
McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA
PMID: 25407910
Bioinformatics (Oxford, England). 2014-05-15; 30.10: 1469-70.
PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
Tovchigrechko A, Venepally P, Payne SH
PMID: 24470574
Proceedings of the National Academy of Sciences of the United States of America. 2013-12-03; 110.49: 19802-7.
RNA-sequencing from single nuclei
Grindberg RV, Yee-Greenbaum JL, McConnell MJ, Novotny M, O'Shaughnessy AL, Lambert GM, Araúzo-Bravo MJ, Lee J, Fishman M, Robbins GE, Lin X, Venepally P, Badger JH, Galbraith DW, Gage FH, Lasken RS
PMID: 24248345
Nucleic acids research. 2012-11-01; 40.20: 10375-83.
Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast
Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews-Pfannkoch C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA
PMID: 22941652
BMC genomics. 2011-08-25; 12.433.
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium
Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN
PMID: 21867535
PloS one. 2011-01-10; 6.1: e15950.
Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains
Pandya GA, McEllistrem MC, Venepally P, Holmes MH, Jarrahi B, Sanka R, Liu J, Karamycheva SA, Bai Y, Fleischmann RD, Peterson SN
PMID: 21264340
Nucleic acids research. 2007-01-01; 35.Database issue: e148.
A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform
Pandya GA, Holmes MH, Sunkara S, Sparks A, Bai Y, Verratti K, Saeed K, Venepally P, Jarrahi B, Fleischmann RD, Peterson SN
PMID: 18006572

Research Priorities

  • Transcriptomics & RNA-Seq
  • Sequence assembly
  • Genotyping and SNP identification
  • Proteomics
Collaborator Release

Scientists identify a new kind of human brain cell

‘Rosehip’ neurons not found in rodents, may be involved in fine-level control between regions of the human brain