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Harinder Singh, PhD is a Staff Scientist in the Infectious Disease Department at the J. Craig Venter Institute (JCVI). Dr. Singh's area of research is mostly focused on various data analysis, data mining, development of prediction algorithm and databases and bioinformatics pipelines for the scientific community. Dr. Singh has significant experience in analyzing proteomics, metabolomics, expression, microbiome and metagenomics datasets using various bioinformatics pipelines. Dr. Singh's interest lies in understanding the long-term effects of diabetes and predict bio-signature with the progression of diabetes using meta-omics dataset and system biology. Dr. Singh received his PhD from CSIR-Institute of Microbial Technology in Bioinformatics and obtained his master’s degree in biotechnology from Thapar University, INDIA.
Research Priorities
Analysis of microbiomes using metagenomics
- Understanding human disease diagnosis and progression due to changes in the microbiome.
- Prediction of geo-location based on the personal microbiome.
Understanding diabetes and chronic kidney diseases
- Protein biomarkers for diagnosis and progression of diabetes and chronic kidney disease.
Development of Bioinformatics tools
- Pipeline for analyzing different ‘omics data.
- Development of prediction methods for understanding complex datasets.
- Management and development of databases and web-based applications.
Publications
Tuberculosis (Edinburgh, Scotland). 2023-08-24; 102399.
Predictive biomarkers for latent Mycobacterium tuberculosis infection
Singh H, Gonzalez-Juarbe N, Pieper R, Yu Y, Vashee S
PMID: 37648595
Heliyon. 2023-07-04; 9.7: e17958.
Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19
Jang H, Choudhury S, Yu Y, Sievers BL, Gelbart T, Singh H, Rawlings SA, Proal A, Tan GS, Qian Y, Smith D, Freire M
PMID: 37483779
Microorganisms. 2023-04-29; 11.5:
MPrESS: An R-Package for Accurately Predicting Power for Comparisons of 16S rRNA Microbiome Taxa Distributions including Simulation by Dirichlet Mixture Modeling
Clarke TH, Greco C, Brinkac L, Nelson KE, Singh H
PMID: 37317139
Critical care (London, England). 2023-04-20; 27.1: 155.
Major adverse cardiovascular events are associated with necroptosis during severe COVID-19
Wiscovitch-Russo R, Ibáñez-Prada ED, Serrano-Mayorga CC, Sievers BL, Engelbride MA, Padmanabhan S, Tan GS, Vashee S, Bustos IG, Pachecho C, Mendez L, Dube PH, Singh H, Reyes LF, Gonzalez-Juarbe N
PMID: 37081485
Scientific reports. 2022-12-20; 12.1: 22013.
Author Correction: Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes
Clarke T, Brinkac L, Greco C, Alleyne AT, Carrasco P, Inostroza C, Tau T, Wisitrasameewong W, Torralba MG, Nelson K, Singh H
PMID: 36539474
Frontiers in microbiology. 2022-12-12; 13.946779.
Gut and lung microbiome profiles in pregnant mice
Wiscovitch-Russo R, Taal AM, Kuelbs C, Oldfield LM, Ramar M, Singh H, Fedulov AV, Gonzalez-Juarbe N
PMID: 36578567
Scientific reports. 2022-11-03; 12.1: 18547.
Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes
Clarke T, Brinkac L, Greco C, Alleyne AT, Carrasco P, Inotroza C, Inostroza C, Tau T, Wisitrasameewong W, Torralba MG, Nelson K, Singh H
PMID: 36329122
PloS one. 2022-04-05; 17.4: e0265891.
An optimized approach for processing of frozen lung and lavage samples for microbiome studies
Wiscovitch-Russo R, Singh H, Oldfield LM, Fedulov AV, Gonzalez-Juarbe N
PMID: 35381030
Amyotrophic lateral sclerosis & frontotemporal degeneration. 2022-02-01; 23.1-2: 91-99.
Gut microbiome differences between amyotrophic lateral sclerosis patients and spouse controls
Hertzberg VS, Singh H, Fournier CN, Moustafa A, Polak M, Kuelbs CA, Torralba MG, Tansey MG, Nelson KE, Glass JD
PMID: 33818222
Journal of virology. 2021-09-27; 95.20: e0101021.
Kinetic Multi-omic Analysis of Responses to SARS-CoV-2 Infection in a Model of Severe COVID-19
Cantwell AM, Singh H, Platt M, Yu Y, Lin YH, Ikeno Y, Hubbard G, Xiang Y, Gonzalez-Juarbe N, Dube PH
PMID: 34319784
Frontiers in medicine. 2021-06-23; 8.667462.
Urethral Catheter Biofilms Reveal Plasticity in Bacterial Composition and Metabolism and Withstand Host Immune Defenses in Hypoxic Environment
Yu Y, Singh H, Tsitrin T, Bekele S, Lin YH, Sikorski P, Moncera KJ, Torralba MG, Morrow L, Wolcott R, Nelson KE, Pieper R
PMID: 34249966
Frontiers in cellular and infection microbiology. 2021-06-04; 11.595554.
Protein and Microbial Biomarkers in Sputum Discern Acute and Latent Tuberculosis in Investigation of Pastoral Ethiopian Cohort
HaileMariam M, Yu Y, Singh H, Teklu T, Wondale B, Worku A, Zewude A, Mounaud S, Tsitrin T, Legesse M, Gobena A, Pieper R
PMID: 34150670
GeroScience. 2021-04-01; 43.2: 593-606.
Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort
Yu Y, Singh H, Kwon K, Tsitrin T, Petrini J, Nelson KE, Pieper R
PMID: 32974878
Frontiers in microbiology. 2021-03-23; 12.644861.
Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing
Singh H, Clarke T, Brinkac L, Greco C, Nelson KE
PMID: 33833745
Microorganisms. 2020-09-03; 8.9:
Gut Microbial Changes in Diabetic db/db Mice and Recovery of Microbial Diversity upon Pirfenidone Treatment
Singh H, Miyamoto S, Darshi M, Torralba MG, Kwon K, Sharma K, Pieper R
PMID: 32899353
ACS infectious diseases. 2020-08-14; 6.8: 2120-2129.
Predictive Signatures of 19 Antibiotic-Induced Escherichia coli Proteomes
Yu Y, O'Rourke A, Lin YH, Singh H, Eguez RV, Beyhan S, Nelson KE
PMID: 32673475
Gut microbes. 2020-05-03; 11.3: 265-275.
Intestinal and hepatic microbiota changes associated with chronic ethanol administration in mice
Bluemel S, Wang L, Kuelbs C, Moncera K, Torralba M, Singh H, Fouts DE, Schnabl B
PMID: 30982395
Journal of immunology (Baltimore, Md. : 1950). 2020-02-15; 204.4: 796-809.
Type II but Not Type I IFN Signaling Is Indispensable for TLR7-Promoted Development of Autoreactive B Cells and Systemic Autoimmunity
Chodisetti SB, Fike AJ, Domeier PP, Singh H, Choi NM, Corradetti C, Kawasawa YI, Cooper TK, Caricchio R, Rahman ZSM
PMID: 31900342
GeroScience. 2019-12-01; 41.6: 907-921.
Gastro-intestinal and oral microbiome signatures associated with healthy aging
Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE, Pieper R
PMID: 31620923
Journal of proteome research. 2019-04-05; 18.4: 1907-1915.
Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery
Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Goliusinski W, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y
PMID: 30848925
Scientific reports. 2018-03-12; 8.1: 4333.
Microbial metagenome of urinary tract infection
Moustafa A, Li W, Singh H, Moncera KJ, Torralba MG, Yu Y, Manuel O, Biggs W, Venter JC, Nelson KE, Pieper R, Telenti A
PMID: 29531289
Forensic science international. Genetics. 2017-09-01; 30.141-147.
Integrating the microbiome as a resource in the forensics toolkit
Clarke TH, Gomez A, Singh H, Nelson KE, Brinkac LM
PMID: 28728057
Theranostics. 2017-07-07; 7.10: 2704-2717.
Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function
Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R
PMID: 28819457
Biology direct. 2015-03-25; 10.10.
QSAR based model for discriminating EGFR inhibitors and non-inhibitors using Random forest
Singh H, Singh S, Singla D, Agarwal SM, Raghava GP
PMID: 25880749
PloS one. 2014-01-01; 9.10: e105667.
Evaluation of protein dihedral angle prediction methods
Singh H, Singh S, Raghava GP
PMID: 25166857
PloS one. 2013-01-01; 8.12: e62216.
Improved method for linear B-cell epitope prediction using antigen's primary sequence
Singh H, Ansari HR, Raghava GP
PMID: 23667458
Nucleic acids research. 2012-01-01; 40.Database issue: D486-9.
ccPDB: compilation and creation of data sets from Protein Data Bank
Singh H, Chauhan JS, Gromiha MM, Open Source Drug Discovery Consortium, Raghava GP
PMID: 22139939
Research Priorities
Analysis of microbiomes using metagenomics
- Understanding human disease diagnosis and progression due to changes in the microbiome.
- Prediction of geo-location based on the personal microbiome.
Understanding diabetes and chronic kidney diseases
- Protein biomarkers for diagnosis and progression of diabetes and chronic kidney disease.
Development of Bioinformatics tools
- Pipeline for analyzing different ‘omics data.
- Development of prediction methods for understanding complex datasets.
- Management and development of databases and web-based applications.
Genomics and Proteomics Approaches to T1D
This study addresses the complex interactions between the host and environmental factors as they relate to the development of Type I Diabetes (T1D).
31-May-2016
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