Harinder Singh

Harinder Singh, PhD

Adjunct Scientist
301-795-7684

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.

Publications

Scientific reports. 2024-11-12; 14.1: 27637.

Major alteration of lung microbiome and the host responses in critically ill COVID-19 patients with high viral load

Bustos IG, Wiscovitch-Russo R, Singh H, Sievers BL, Matsuoka M, Freire M, Tan GS, Cala MP, Guerrero JL, Martin-Loeches I, Gonzalez-Juarbe N, Reyes LF
PMID: 39532981

PloS one. 2024-07-25; 19.7: e0304060.

Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia

Chekesa B, Singh H, Gonzalez-Juarbe N, Vashee S, Wiscovitch-Russo R, Dupont CL, Girma M, Kerro O, Gumi B, Ameni G
PMID: 39052555

Tuberculosis (Edinburgh, Scotland). 2024-07-01; 147.102399.

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

Microbial ecology. 2020-05-01; 79.4: 1034-1043.

Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy

Rajagopala SV, Singh H, Yu Y, Zabokrtsky KB, Torralba MG, Moncera KJ, Frank B, Pieper R, Sender L, Nelson KE
PMID: 31754744

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

Proteomes. 2018-12-09; 6.4:

Actinobaculum massiliense Proteome Profiled in Polymicrobial Urethral Catheter Biofilms

Yu Y, Tsitrin T, Singh H, Doerfert SN, Sizova MV, Epstein SS, Pieper R
PMID: 30544882

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

Improving Treatments for Urinary Tract Infections

Forensics Microbiome Database

Gut Microbiome Sysbiosis in Childhood Acute Lymphoblastic Leukemia (ALL) Patients

Biomarker Discovery and Systems Biology for Types 1 and 2 Diabetes and Healthy Aging

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). 

Human Hair Microbiota

Past Project
31-May-2016
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Unlocking the Mysteries of the Microbiome