Singh R, Xiao Y. One Health: Virtual Special Issue in the International Journal of Antimicrobial Agents. International journal of antimicrobial agents. 2025 Oct 20:107645. https://doi.org/10.1016/j.ijantimicag.2025.107645
Singh R, Kusalik A, Dillon JA. Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review. Briefings in Functional Genomics. 2022 Mar;21(2):78-89. https://doi.org/10.1093/bfgp/elab028
Single-Cell Sequencing in Human Genital Infections
Singh R. Single-cell sequencing in human genital infections. Single-cell Sequencing and Methylation: Methods and Clinical Applications. 2020:203-20. https://doi.org/10.1007/978-981-15-4494-1_17
Crits-Christoph A, Gangavarapu K, Pekar J, Moshiri N, Singh R, Levy J, Goldstein S, Suchard M, Popescu S, Robertson D, Lemey P. Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control.Zenodo. https://doi.org/10.5281/zenodo.7754299
Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Peacock TP, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F (2024). "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic." Cell. 187(19):5468–5482.e11. doi:10.1016/j.cell.2024.08.010
Singh R, Dillon JA, Jamieson F, Khan I, Long R, McDonald R, Minion J, Rea E, Richard-Greenblatt M, Kaushal Sharma M, Shokoples S. Utilizing whole genome sequencing to delineate relapse and reinfection tuberculosis on the Canadian prairies. Canadian Journal of Respiratory, Critical Care, and Sleep Medicine. 2024 Jul 3;8(4):168-78,doi:10.1080/24745332.2024.2366310
The protein kinases of Dictyostelia and their incorporation into a signalome
Kin K, Chen ZH, Forbes G, Lawal H, Schilde C, Singh R, Cole C, Barton GJ, Schaap P. The protein kinases of Dictyostelia and their incorporation into a signalome. Cellular Signalling. 2023 Aug 1;108:110714. doi.org/10.1016/j.cellsig.2023.110714
Sanderson H, Nnajide CR, McCarthy MC, Singh R, Rubin JE, Dillon JA, White AP. Hybrid genome assemblies of 245 avian and broiler barn environment-associated Escherichia coli strains isolated from Saskatchewan Broiler Farms. Microbiology resource announcements. 2023 May 17;12(5):e00110-23.10.1128/mra.00110-23
Singh R, Yarmovich T, Kusalik A, Dillon JA. Gen2EpiGUI: User-Friendly Pipeline for Analyzing Whole-Genome Sequencing Data for Epidemiological Studies of Neisseria gonorrhoeae. Sexually Transmitted Diseases. 2020 Oct 1;47(10):e42-4.10.1097/OLQ.0000000000001206
Parmar NR, Singh R, Martin I, Perera SR, Demczuk W, Kusalik A, Minion J, Dillon JA. Genomic analysis reveals antibiotic-susceptible clones and emerging resistance in Neisseria gonorrhoeae in Saskatchewan, Canada. Antimicrobial agents and chemotherapy. 2020 Aug 20;64(9):10-128.10.1128/aac.02514-19
Singh R, Dillon JA, Demczuk W, Kusalik A. Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae. BMC Genomics 20, 165 (2019). 10.1186/s12864-019-5542-3
Singh R, Perera SR, Katselis GS, Chumala P, Martin I, Kusalik A, Mitzel KM, Dillon JA. A β-lactamase-producing plasmid from Neisseria gonorrhoeae carrying a unique 6 bp deletion in bla TEM-1 encoding a truncated 24 kDa TEM-1 penicillinase that hydrolyses ampicillin slowly. Journal of Antimicrobial Chemotherapy. 2019 Oct 1;74(10):2904-12.10.1093/jac/dkz306
Improved Annotation with de novo Transcriptome Assembly in Four Social Amoeba Species
Singh R, Lawal HM, Schilde C, Glöckner G, Barton GJ, Schaap P, Cole C. Improved annotation with de novo transcriptome assembly in four social amoeba species. BMC genomics. 2017 Dec;18:1-7.10.1186/s12864-017-3505-0
Chen ZH, Singh R, Cole C, Lawal HM, Schilde C, Febrer M, Barton GJ, Schaap P. Adenylate cyclase A acting on PKA mediates induction of stalk formation by cyclic diguanylate at the Dictyostelium organizer. Proceedings of the National Academy of Sciences. 2017 Jan 17;114(3):516-21.10.1073/pnas.1608393114
Singh R, Schilde C, Schaap P. A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group. BMC Evolutionary Biology. 2016 Dec;16:1-1.10.1186/s12862-016-0825-7
The multicellularity genes of dictyostelid social amoebas
Glöckner G, Lawal HM, Felder M, Singh R, Singer G, Weijer CJ, Schaap P. The multicellularity genes of dictyostelid social amoebas. Nature communications. 2016 Jun 30;7(1):12085.10.1038/ncomms12085
Pauline Schaap, Israel Barrantes, Pat Minx, Narie Sasaki, Roger W. Anderson, Marianne Bénard, Kyle K. Biggar, Nicolas E. Buchler, Ralf Bundschuh, Xiao Chen, Catrina Fronick, Lucinda Fulton, Georg Golderer, Niels Jahn, Volker Knoop, Laura F. Landweber, Chrystelle Maric, Dennis Miller, Angelika A. Noegel, Rob Peace, Gérard Pierron, Taeko Sasaki, Mareike Schallenberg-Rüdinger, Michael Schleicher, Reema Singh, Thomas Spaller, Kenneth B. Storey, Takamasa Suzuki, Chad Tomlinson, John J. Tyson, Wesley C. Warren, Ernst R. Werner, Gabriele Werner-Felmayer, Richard K. Wilson, Thomas Winckler, Jonatha M. Gott, Gernot Glöckner, Wolfgang Marwan. The Physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling. Genome Biology and Evolution. 2016 Jan 1;8(1):109-25.10.1093/gbe/evv237
Parmar N, Singh R, Martin I, Perera S, Demczuk W, Kusalik A, Minion J, Dillon JA (2019). P644 Analyzing the genomes of Neisseria gonorrhoeae isolates using a novel integrated bioinformatics pipeline: Gen2Epi. Sex Transm Infect 95:A284.
Hariprasad G, Singh R (2014). Group III phospholipase A2: collective unity amidst structural and functional diversity. The FASEB Journal 28,769.1.
Singh R, Arora S, Singh H (2008). DLact: an antimicrobial resistance gene database. Genomic Med 2:217–240.