pvenepally

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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

Projects

Select Publications

LOCUST: a custom sequence locus typer for classifying microbial isolates.
Bioinformatics (Oxford, England). 2017-06-01; 33.11: 1725-1726.
PMID: 28130240
Nuclear RNA-seq of single neurons reveals molecular signatures of activation.
Nature communications. 2016-04-19; 7.11022.
PMID: 27090946
PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2016-01-01; 22.564-575.
PMID: 27897007
Genetic Analysis Using an Isogenic Mating Pair of Aspergillus fumigatus Identifies Azole Resistance Genes and Lack of MAT Locus's Role in Virulence.
PLoS pathogens. 2015-04-01; 11.4: e1004834.
PMID: 25909486
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.
BMC bioinformatics. 2014-11-19; 15.357.
PMID: 25407910
PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.
Bioinformatics (Oxford, England). 2014-05-15; 30.10: 1469-70.
PMID: 24470574
RNA-sequencing from single nuclei.
Proceedings of the National Academy of Sciences of the United States of America. 2013-12-03; 110.49: 19802-7.
PMID: 24248345
Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast.
Nucleic acids research. 2012-11-01; 40.20: 10375-83.
PMID: 22941652
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium.
BMC genomics. 2011-08-25; 12.433.
PMID: 21867535
Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains.
PloS one. 2011-01-10; 6.1: e15950.
PMID: 21264340
A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform.
Nucleic acids research. 2007-01-01; 35.Database issue: e148.
PMID: 18006572