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Indresh K. Singh is director of informatics, leading Informatics Core Services (ICS) at the J. Craig Venter Institute (JCVI). He has been working on development and support of pipelines for processing and analyzing genome sequencing data for thousands of samples on JCVI High-throughput compute facility and AWS cloud. He is managing hundreds of terabytes of sequencing and analysis data, and he is helping JCVI Faculty and external collaborators with novel tools development and analysis for web technologies, database development, data mining, data visualization, machine learning, annotation. He has also contributed to the genomics data processing and analysis of Genomic Center for Infectious Diseases (GCID), Human Microbiome project (HMP) and CEIRS Data Processing and Coordinating Center (DPCC)
Since joining JCVI in 2003, Indresh and his team have won several awards for their innovative use of Java platform technology in a genomics environment. Previously, at Celera Genomics, Indresh developed a LIMS for genomics and proteomics applications. Indresh earned his MS in Computer Science and Engineering from Johns Hopkins University.
Research Priorities
- Software architecture, Software design, Large scale high performance compute infrastructure.
- Cloud (AWS, Google and Azure) Technologies
- Ontology based metadata tracking and data management.
- Development of data analysis tools and pipelines for genome analysis.
- Machine learning, annotation, database development, data mining, web technologies and statistical analysis.
Publications
Nucleic acids research. 2023-01-06; 51.D1: D678-D689.
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR
Virus research. 2021-10-15; 304.198545.
Novel isoforms of influenza virus PA-X and PB1-F2 indicated by automatic annotation
Nature communications. 2020-06-16; 11.1: 3132.
Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection
Nature communications. 2020-05-21; 11.1: 2537.
Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection
Antimicrobial agents and chemotherapy. 2020-04-21; 64.5:
ARGONAUT II Study of the In Vitro Activity of Plazomicin against Carbapenemase-Producing Klebsiella pneumoniae
The Journal of infectious diseases. 2019-07-19; 220.4: 666-676.
Ceftazidime-Avibactam in Combination With Fosfomycin: A Novel Therapeutic Strategy Against Multidrug-Resistant Pseudomonas aeruginosa
BMC bioinformatics. 2019-01-07; 20.1: 8.
OMeta: an ontology-based, data-driven metadata tracking system
BMC bioinformatics. 2014-11-19; 15.357.
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly
PloS one. 2014-06-17; 9.6: e99979.
Standardized metadata for human pathogen/vector genomic sequences
Nature. 2012-06-13; 486.7402: 215-21.
A framework for human microbiome research
Nature. 2012-06-13; 486.7402: 207-14.
Structure, function and diversity of the healthy human microbiome
Genome biology. 2011-10-17; 12.10: R100.
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
Research Priorities
- Software architecture, Software design, Large scale high performance compute infrastructure.
- Cloud (AWS, Google and Azure) Technologies
- Ontology based metadata tracking and data management.
- Development of data analysis tools and pipelines for genome analysis.
- Machine learning, annotation, database development, data mining, web technologies and statistical analysis.
DNA Barcode Deconvolution
This is a software library to run the JCVI barcode deconvolution pipeline using Sun Grid Engine, or optionally without the use of a grid.
Elvira
Collection of Java, Perl, and PHP tools supporting high-throughput sample sequencing, metadata, analysis, and reports for viral projects.
JCVI Primer Designer
High throughput PCR primer design software.
Jillion
Java framework for reading, writing, analyzing and manipulating sequence and assembly data.
VIGOR
Homology-based viral gene finder, predicting both proteins and mature peptides.
VIGOR
Homology-based viral gene finder, predicting both proteins and mature peptides.