Dabburu, G. R., Jain, A., Subbarao, N., & Kumar, M. (2023). Designing dual inhibitors against potential drug targets of Plasmodium falciparum -M17 Leucyl Aminopeptidase and Plasmepsins. Journal of biomolecular structure & dynamics, 41(16), 8026–8041. https://doi.org/10.1080/07391102.2022.2129452

Jain, A., Singhal, N., & Kumar, M. (2023). AFRbase: a database of protein mutations responsible for antifungal resistance. Bioinformatics (Oxford, England), 39(11), btad677. https://doi.org/10.1093/bioinformatics/btad677

Aswal, M., Singhal, N., & Kumar, M. (2023). Genomic analysis of phylogroup D Escherichia coli strains using novel de-novo reference-based guided assembly. Scientific data, 10(1), 573. https://doi.org/10.1038/s41597-023-02444-0

Aswal, M., Singhal, N., & Kumar, M. (2023). Comprehensive genomic analysis of hypocholesterolemic probiotic Enterococcus faecium LR13 reveals unique proteins involved in cholesterol-assimilation. Frontiers in nutrition, 10, 1082566. https://doi.org/10.3389/fnut.2023.1082566

Ray, N., Kumar Vishwakarma, R., Jain, A., Kumar, M., & Goel, M. (2023). ProSeqAProDB: Prosequence Assisted Protein Database. Journal of molecular biology, 435(14), 168022. https://doi.org/10.1016/j.jmb.2023.168022

Garg, A., Dabburu, G. R., Singhal, N., & Kumar, M. (2022). Investigating the disordered regions (MoRFs, SLiMs and LCRs) and functions of mimicry proteins/peptides in silico. PloS one, 17(4), e0265657. https://doi.org/10.1371/journal.pone.0265657

Singh, N. S., Singhal, N., Kumar, M., & Virdi, J. S. (2022). Public health implications of plasmid-mediated quinolone and aminoglycoside resistance genes in Escherichia coli inhabiting a major anthropogenic river of India. Epidemiology and infection, 150, 1–21. Advance online publication. https://doi.org/10.1017/S095026882200053X

Pandey, D., Kumari, B., Singhal, N., & Kumar, M. (2022). BacARscan: an in silico resource to discern diversity in antibiotic resistance genes. Biology methods & protocols, 7(1), bpac031. https://doi.org/10.1093/biomethods/bpac031

Garg, A., Singhal, N., & Kumar, M. (2022). Investigating the eukaryotic host-like SLiMs in microbial mimitopes and their potential as novel drug targets for treating autoimmune diseases. Frontiers in microbiology, 13, 1039188. https://doi.org/10.3389/fmicb.2022.1039188

Zaidi, S., Aswal, M., Kumar, M., Rashid, F., & Khan, A. U. (2022). Protein expression profiling, in silico classification and pathway analysis of cariogenic bacteria Streptococcus mutans under bacitracin stress conditions. Journal of medical microbiology, 71(8), 10.1099/jmm.0.001572. https://doi.org/10.1099/jmm.0.001572

Garg, A., Singhal, N., & Kumar, M. (2021). Discerning novel drug targets for treating Mycobacterium avium ss. paratuberculosis-associated autoimmune disorders: an in silico approach. Briefings in bioinformatics, 22(3), bbaa195. https://doi.org/10.1093/bib/bbaa195

Singhal, N., Sharma, A., Aswal, M., Singh, N., Kumar, M., & Goel, M. (2021). Identification of Binding Partners of CsaA - An Archaeal Chaperonic Protein of Picrophilus torridus. Protein and peptide letters, 28(6), 675–679. https://doi.org/10.2174/0929866527999201126205131

Deeksha Pandey, Bandana Kumari, Neelja Singhal et al. Protocol for detection of bacterial proteins involved in efflux mediated antibiotic resistance (ARE) and their sub-families, 03 March 2021, PROTOCOL (Version 1) available at Protocol Exchange [https://doi.org/10.21203/rs.3.pex-1371/v1]

Singh, N. S., Singhal, N., Kumar, M., & Virdi, J. S. (2021). High Prevalence of Drug Resistance and Class 1 Integrons in Escherichia coli Isolated From River Yamuna, India: A Serious Public Health Risk. Frontiers in microbiology, 12, 621564. https://doi.org/10.3389/fmicb.2021.621564

Singh, N. S., Singhal, N., Kumar, M., & Virdi, J. S. (2021). Exploring the genetic mechanisms underlying amoxicillin-clavulanate resistance in waterborne Escherichia coli. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 90, 104767. https://doi.org/10.1016/j.meegid.2021.104767

Singhal, N., Singh, N. S., Mohanty, S., Kumar, M., & Virdi, J. S. (2021). Rhizospheric Lactobacillus plantarum (Lactiplantibacillus plantarum) strains exhibit bile salt hydrolysis, hypocholestrolemic and probiotic capabilities in vitro. Scientific reports, 11(1), 15288. https://doi.org/10.1038/s41598-021-94776-3

Singhal, N., Garg, A., Singh, N., Gulati, P., Kumar, M., & Goel, M. (2021). Efficacy of signal peptide predictors in identifying signal peptides in the experimental secretome of Picrophilous torridus, a thermoacidophilic archaeon. PloS one, 16(8), e0255826. https://doi.org/10.1371/journal.pone.0255826

Pandey, D., Singhal, N., & Kumar, M. (2021). Investigating the OXA Variants of ESKAPE Pathogens. Antibiotics (Basel, Switzerland), 10(12), 1539. https://doi.org/10.3390/antibiotics10121539

Aswal, M., Garg, A., Singhal, N., & Kumar, M. (2020). Comparative in-silico proteomic analysis discerns potential granuloma proteins of Yersinia pseudotuberculosis. Scientific reports, 10(1), 3036. https://doi.org/10.1038/s41598-020-59924-1

Garg, A., Singhal, N., Kumar, R., & Kumar, M. (2020). mRNALoc: a novel machine-learning based in-silico tool to predict mRNA subcellular localization. Nucleic acids research, 48(W1), W239–W243. https://doi.org/10.1093/nar/gkaa385

Pandey, D., Kumari, B., Singhal, N., & Kumar, M. (2020). BacEffluxPred: A two-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins. Scientific reports, 10(1), 9287. https://doi.org/10.1038/s41598-020-65981-3

Singhal, N., Sharma, A., Kumari, S., Garg, A., Rai, R., Singh, N., Kumar, M., & Goel, M. (2020). Biophysical and Biochemical Characterization of Nascent Polypeptide-Associated Complex of Picrophilus torridus and Elucidation of Its Interacting Partners. Frontiers in microbiology, 11, 915. https://doi.org/10.3389/fmicb.2020.00915

Singhal, N., Sharma, D., Kumar, M., Bisht, D., & Virdi, J. S. (2020). Comparative Proteomics of Commensal and Pathogenic Strains of Escherichia coli. Protein and peptide letters, 27(11), 1171–1177. https://doi.org/10.2174/0929866527666200517104154

Garg, A., Kumari, B., Singhal, N., & Kumar, M. (2019). Using molecular-mimicry-inducing pathways of pathogens as novel drug targets. Drug discovery today, 24(9), 1943–1952. https://doi.org/10.1016/j.drudis.2018.10.010

Singhal, N., Pandey, D., Singh, N. S., Kumar, M., & Virdi, J. S. (2019). ampD homologs in biotypes of Yersinia enterocolitica: Implications in regulation of chromosomal AmpC-type cephalosporinases. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 69, 211–215. https://doi.org/10.1016/j.meegid.2019.01.033

Kumari, B., Kumar, R., & Kumar, M. (2019). Identifying residues that determine palmitoylation using association rule mining. Bioinformatics (Oxford, England), 35(17), 2887–2890. https://doi.org/10.1093/bioinformatics/btz003

Sharma, D., Garg, A., Kumar, M., & Khan, A. U. (2019). Proteome profiling of carbapenem-resistant K. pneumoniae clinical isolate (NDM-4): Exploring the mechanism of resistance and potential drug targets. Journal of proteomics, 200, 102–110. https://doi.org/10.1016/j.jprot.2019.04.003

Singhal, N., Pandey, D., Kumar, M., & Virdi, J. S. (2019). Molecular analysis of ampR and ampD to understand variability in inducible expression of "BlaB-like" cephalosporinase in Yersinia enterocolitica biotype 1A. Gene, 704, 25–30. https://doi.org/10.1016/j.gene.2019.04.031

Singhal, N., Pandey, D., Somendro Singh, N., Kumar, M., & Virdi, J. S. (2019). Molecular Characteristics of "BlaB-Like" Chromosomal Inducible Cephalosporinase of Yersinia enterocolitica Biotype 1A Strains. Microbial drug resistance (Larchmont, N.Y.), 25(6), 824–829. https://doi.org/10.1089/mdr.2018.0282

Singhal, N., Maurya, A. K., Singh, N. S., Kumar, M., & Virdi, J. S. (2019). Antimicrobial resistance and its relationship with biofilm production and virulence-related factors in Yersinia enterocolitica biotype 1A. Heliyon, 5(5), e01777. https://doi.org/10.1016/j.heliyon.2019.e01777

Singhal, N., Maurya, A. K., Mohanty, S., Kumar, M., & Virdi, J. S. (2019). Evaluation of Bile Salt Hydrolases, Cholesterol-Lowering Capabilities, and Probiotic Potential of Enterococcus faecium Isolated From Rhizosphere. Frontiers in microbiology, 10, 1567. https://doi.org/10.3389/fmicb.2019.01567

Srivastava, A., & Kumar, M. (2018). Prediction of zinc binding sites in proteins using sequence derived information. Journal of biomolecular structure & dynamics, 36(16), 4413–4423. https://doi.org/10.1080/07391102.2017.1417910

Kumar, R., Kumari, B., & Kumar, M. (2018). Proteome-wide prediction and annotation of mitochondrial and sub-mitochondrial proteins by incorporating domain information. Mitochondrion, 42, 11–22. https://doi.org/10.1016/j.mito.2017.10.004

Garg, A., Kumari, B., Kumar, M. (2018). Emerging Role of HSP70 in Human Diseases. In: Asea, A., Kaur, P. (eds) HSP70 in Human Diseases and Disorders. Heat Shock Proteins, vol 14. Springer, Cham. https://doi.org/10.1007/978-3-319-89551-2_15

Srivastava, A., Kumar, R., & Kumar, M. (2018). BlaPred: Predicting and classifying β-lactamase using a 3-tier prediction system via Chou's general PseAAC. Journal of theoretical biology, 457, 29–36. https://doi.org/10.1016/j.jtbi.2018.08.030

Kumari, B., Kumar, R., & Kumar, M. (2018). Prediction of Rare Palmitoylation Events in Proteins. Journal of computational biology : a journal of computational molecular cell biology, 25(9), 997–1008. https://doi.org/10.1089/cmb.2017.0069

Kumari, B., Kumar, R., Chauhan, V., & Kumar, M. (2018). Comparative functional analysis of proteins containing low-complexity predicted amyloid regions. PeerJ, 6, e5823. https://doi.org/10.7717/peerj.5823

Kumar, R., Kumari, B., & Kumar, M. (2017). Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine. PeerJ, 5, e3561. https://doi.org/10.7717/peerj.3561

Garg, A., Kumari, B., Kumar, R., & Kumar, M. (2017). miPepBase: A Database of Experimentally Verified Peptides Involved in Molecular Mimicry. Frontiers in microbiology, 8, 2053. https://doi.org/10.3389/fmicb.2017.02053

Singhal, N., Kumar, M., & Virdi, J. S. (2016). MALDI-TOF MS in clinical parasitology: applications, constraints and prospects. Parasitology, 143(12), 1491–1500. https://doi.org/10.1017/S0031182016001189

Singhal, N., Kumar, M., & Virdi, J. S. (2016). Resistance to amoxicillin-clavulanate and its relation to virulence-related factors in Yersinia enterocolitica biovar 1A. Indian journal of medical microbiology, 34(1), 85–87. https://doi.org/10.4103/0255-0857.174125

Singhal, N., Kumar, M., Sharma, D., & Bisht, D. (2016). Comparative Protein Profiling of Intraphagosomal Expressed Proteins of Mycobacterium bovis BCG. Protein and peptide letters, 23(1), 51–54. https://doi.org/10.2174/0929866523666151106123121

Kumar, R., Kumari, B., & Kumar, M. (2016). PredHSP: Sequence Based Proteome-Wide Heat Shock Protein Prediction and Classification Tool to Unlock the Stress Biology. PloS one, 11(5), e0155872. https://doi.org/10.1371/journal.pone.0155872

Singhal, N., Kumar, M., Kanaujia, P. K., & Virdi, J. S. (2015). MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Frontiers in microbiology, 6, 791. https://doi.org/10.3389/fmicb.2015.00791

Kumari, B., Kumar, R., & Kumar, M. (2014). PalmPred: an SVM based palmitoylation prediction method using sequence profile information. PloS one, 9(2), e89246. https://doi.org/10.1371/journal.pone.0089246

Srivastava, A., Singhal, N., Goel, M., Virdi, J. S., & Kumar, M. (2014). Identification of family specific fingerprints in β-lactamase families. TheScientificWorldJournal, 2014, 980572. https://doi.org/10.1155/2014/980572

Kumar, R., Jain, S., Kumari, B., & Kumar, M. (2014). Protein sub-nuclear localization prediction using SVM and Pfam domain information. PloS one, 9(6), e98345. https://doi.org/10.1371/journal.pone.0098345

Kumar, R., Srivastava, A., Kumari, B., & Kumar, M. (2015). Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine. Journal of theoretical biology, 365, 96–103. https://doi.org/10.1016/j.jtbi.2014.10.008

Kumar, R., Kumari, B., Srivastava, A., & Kumar, M. (2014). NRfamPred: a proteome-scale two level method for prediction of nuclear receptor proteins and their sub-families. Scientific reports, 4, 6810. https://doi.org/10.1038/srep06810

Srivastava, A., Singhal, N., Goel, M., Virdi, J. S., & Kumar, M. (2014). CBMAR: a comprehensive β-lactamase molecular annotation resource. Database : the journal of biological databases and curation, 2014, bau111. https://doi.org/10.1093/database/bau111

Kumari, B., Kumar, R., & Kumar, M. (2015). Low complexity and disordered regions of proteins have different structural and amino acid preferences. Molecular bioSystems, 11(2), 585–594. https://doi.org/10.1039/c4mb00425f

Singhal, N., Sharma, P., Kumar, M., Joshi, B., & Bisht, D. (2012). Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates. Proteome science, 10(1), 14. https://doi.org/10.1186/1477-5956-10-14

Kumar, M., Gromiha, M. M., & Raghava, G. P. (2011). SVM based prediction of RNA-binding proteins using binding residues and evolutionary information. Journal of molecular recognition : JMR, 24(2), 303–313. https://doi.org/10.1002/jmr.1061

Kumar, M., & Raghava, G. P. (2009). Prediction of nuclear proteins using SVM and HMM models. BMC bioinformatics, 10, 22. https://doi.org/10.1186/1471-2105-10-22

Arora, P. K., Kumar, M., Chauhan, A., Raghava, G. P., & Jain, R. K. (2009). OxDBase: a database of oxygenases involved in biodegradation. BMC research notes, 2, 67. https://doi.org/10.1186/1756-0500-2-67

Ahmed, F., Kumar, M., & Raghava, G. P. (2009). Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies. In silico biology, 9(3), 135–148.https://doi.org/10.3233/ISB-2009-0395

Kumar, M., Gromiha, M. M., & Raghava, G. P. (2008). Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins, 71(1), 189–194. https://doi.org/10.1002/prot.21677

Kumar, M., Thakur, V., & Raghava, G. P. (2008). COPid: composition based protein identification. In silico biology, 8(2), 121–128.

Mishra, N. K., Kumar, M., & Raghava, G. P. (2007). Support vector machine based prediction of glutathione S-transferase proteins. Protein and peptide letters, 14(6), 575–580. https://doi.org/10.2174/092986607780990046