List of Publications
(*Equal contribution; #Corresponding Author)
In-Press
50. Neelja Singhal, Archana Sharma, Shobha Kumari, Anjali Garg, Ruchica Rai, Nirpendra Singh, Manish Kumar, Manisha Goel. Biophysical and biochemical characterization of nascent polypeptide associated complex of Picrophilus torridus and elucidation of its interacting partners. Frontiers in Microbiology, section Biology of Archaea
2020
49. Ashwal, 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.
2019
48. Sharma, D., Garg, A., Kumar, M., Khan, A.U. (2019). Down-Regulation of Flagellar, Fimbriae, and Pili Proteins in Carbapenem-Resistant Klebsiella pneumoniae (NDM-4) Clinical Isolates: A Novel Linkage to Drug Resistance. Frontiers in Microbiology, section Antimicrobial Resistance As a Global Public Health Problem: How Can We Address It? 10:2865.
47. Singhal N, Maurya AK, Mohanty S, Kumar M, Virdi JS. (2019) Evaluation of bile salt hydrolases, cholesterol-lowering capabilities and probiotic potential of Enterococcus faecium isolated from rhizosphere. Frontiers in Microbiology, section Food Microbiology. 10:1567.
46. Singhal N, Maurya AK, Singh NS, Kumar M, Virdi JS. (2019) Antimicrobial resistance and its relationship with biofilm production and virulence-related factors in Yersinia enterocolitica biotype 1A. Heliyon. 5(5):e01777.
45. 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. J Proteomics. 200:102-110.
44. Singhal, N., Pandey, D., Kumar, M. and 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.
43. Singhal, N., Pandey, D., Singh, N.S., Kumar, M. and Virdi, J. S. (2019). ampD homologs in biotypes of Yersinia enterocolitica: Implications in regulation of chromosomal AmpC-type cephalosporinases. Infection, Genetics and Evolution. 69:211-215.
42. Singhal, N., Pandey, D., Kumar, M. and Virdi, J. S. (2019). Molecular Characteristics of “BlaB-like” Chromosomal Inducible Cephalosporinase of Yersinia enterocolitica Biotype 1A Strains. Microbial Drug Resistance. 25(6):824-829.
41. Kumari, B., Kumar, R. and Kumar, M. (2019). Identifying residues that determine palmitoylation using association rule mining. Bioinformatics. 35(17):2887-2890.
40. Kumari, B., Kumar, R. and Kumar, M. (2018). Comparative functional analysis of proteins containing low-complexity predicted amyloid regions. Peer J. 25(6):824-829.
39. Garg A, Kumari B, Singhal N, Kumar M. (2018) Using molecular-mimicry-inducing pathways of pathogens as novel drug targets. Drug Discovery Today. 24(9):1943-1952.
2018
38. Garg, A., Kumari, B., and Kumar M.#. Emerging Role of HSP70 in Human Diseases. Heat Shock Proteins, Vol. 14, Alexzander A. A. Asea and Punit Kaur (Eds): HSP70 in Human Diseases and Disorders. Link
37. Kumari B, Kumar R and Kumar M#. Prediction of rare palmitoylation events in proteins. Journal of Computational Biology 2017 25(9):997-1008.
36. Srivastava A and Kumar M#. Prediction of Zinc Binding Sites in Proteins using Sequence Derived Information. Journal of Biomolecular Structure & Dynamics 2018 doi: 10.1080/07391102.2017.1417910
35. Srivastava A, Kumar R and Kumar M#. BlaPred: predicting and classifying beta-lactamase using a 3-tier prediction system via Chou's general PseAAC. Journal of Theoretical Biology 2018 457:29-36.
2017
34.# Garg A, Kumari B, Kumar R and Kumar M. miPepBase: A database of experimentally verified peptides involved in molecular mimicry. Frontiers in Microbiology, section Microbial Immunology 8:2053. doi: 10.3389/fmicb.2017.02053.
33. Kumar R, Kumari B and Kumar M#. Proteome-wide prediction and annotation of mitochondrial and sub-mitochondrial proteins by incorporating domain information. Mitochondrion 2017 (In Press)
32. Kumar R, Kumari B and Kumar M#. Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine. Peer J 2017; 5:e3561.
2016
31. Singhal N, Kumar M, and Virdi, JS MALDI-TOP MS in clinical parasitology: applications, constrains and prospects. Parasitology 2016;143(12):1491-500.
30. Kumar R, Kumari B and Kumar M#. PredHSP: Sequence Based Proteome-Wide Heat Shock Protein Prediction and Classification Tool to Unlock the Stress Biology. PLoS One. 11(5):e0155872.
29. Rani S, Srivastava A, Kumar M and Goel M A Database of Annotated Chaperone Repertoire in Archaeal Genomes. FEMS Microbiology Letters 2016 Mar;363(6).
28. Singhal N, Kumar M, and Virdi JS Resistance to amoxicillin-clavulanate and its relation to virulence-related factors in Yersinia enterocolitica biovar 1A. Indian Journal of Medical Microbiology 2016 Jan-Mar;34(1):8.
27. Singhal N, Kumar M, Sharma, P. and Bisht, D. Comparative Protein Profiling of Intraphagosomal Expressed Proteins of Mycobacterium bovis BCG. Protein & Peptide Letters 2016;23(1):51-4.
2015
26. Singhal N, Kumar M, Kanaujia, P.K. and Virdi JS. MALDI-TOF mass spectrometry: An emerging technology for microbial identification and diagnosis. Plos One 2015 Aug 5;6:791.
25. Singhal N, Srivastava A, Kumar M, Virdi JS. Structural variabilities in Beta-lactamase (blaA) of different biovars of Yersinia enterocolitica: implications for Beta-lactam antibiotic and Beta-lactamase inhibitor susceptibilities. Plos One 2015 10(4):e0123564.
24. Kumar R*, Srivastava A*, Kumari B and Kumar M#. Prediction of Beta-lactamase and its Class by Chou's Pseudo-amino Acid Composition and Support Vector Machine. Journal of Theoritical Biology. 2015 Jan 21;365:96-103.
23. Kumari B, Kumar R and Kumar M#. Low complexity and disordered regions of proteins have different structural and amino acid preferences. Molecular Biosystems. 2015 Feb;11(2):585-94.
2014
22. Srivastava A, Singhal N, Goel M, Virdi JS and Kumar M#. CBMAR: A Comprehensive Beta-Lactamase Molecular Annotation Resource. Database. 2014 Dec 3;2014:bau111.
21. Kumar R*, Kumari B*, Srivastava A and Kumar M#. NRfamPred: A proteome-scale two level method for prediction of nuclear receptor proteins and their sub-families. Scientific Reports. 4:5270.
20. Singhal N, Kumar M, Virdi JS. Molecular Analysis of Beta-Lactamase Genes to Understand their Differential Expression in Strains of Yersinia enterocolitica Biotype 1A. (2014) Scientific Reports 4:5270.
19. Kumar R, Jain S, Kumari B, Kumar M#. Protein Sub-Nuclear Localization Prediction Using SVM and Pfam Domain Information. PLoS One. 2014 Jun 4;9(6):e98345.
18. Srivastava A, Singhal N, Goel M, Virdi JS and Kumar M#. Identification of Family Specific Fingerprints in Beta-lactamase Families. The Scentific World Journal 2014:980572.
17. Kumari B*, Kumar R* and Kumar M#. PalmPred: An SVM based Palmitoylation Prediction Method using Sequence Profile Information. PLos One 9(2):e89246.
2012
16. Singhal N, Sharma P, Kumar M, Joshi B, Bisht D. Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates. (2012) Proteome Sci. 10:14
15. Harbi D, Parthiban M, Gendoo DM, Ehsani S, Kumar M, Schmitt-Ulms G, Sowdhamini R, Harrison PM. PrionHome: a database of prions and other sequences relevant to prion phenomena (2012) PLos One. 7:e31785.x
2011
14. Harbi D, Kumar M, Harrison PM. LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase. (2011) Database 7:e31785.x
13. Kumar M, Gromiha MM, Raghava GPS. SVM based prediction of RNA-binding proteins using binding residues and evolutionary information (2011) J Mol Recognit.24(2):303-13.
2010
12. Harrison PM, Khachane A, Kumar M. Genomic assessment of the evolution of the prion protein gene family in vertebrates.(2010) Genomics 95:268-77.
2009
11. Ahmed F, Kumar M, Raghava GPS. Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies.(2009) In Silico Biol. 9:135-48.
10. Rashid M, Singla D, Sharma A, Kumar M, Raghava GPS. Hmrbase: a database of hormones and their receptors.(2009) BMC Genomics.9;10:307.
9. Arora PK, Kumar M, Chauhan A, Raghava GPS, Jain RK. OxDBase: a database of oxygenases involved in biodegradation. (2009) BMC Res Notes. 2:67.
8. Kumar M, Raghava GPS. Prediction of nuclear proteins using SVM and HMM models. (2009) BMC Bioinformatics. 10:22.
2008
7. Kumar M, Thakur V, Raghava GPS. COPid: composition based protein identification. (2008) In Silico Biol. 8:121-8.
6. Kalita MK, Nandal UK, Pattnaik A, Sivalingam A, Ramasamy G, Kumar M, Raghava GPS, Gupta D. CyclinPred: a SVM-based method for predicting cyclin protein sequences. (2008) PLoS One. 3(7):e2605.
5. Kumar M, Gromiha MM, Raghava GPS. Prediction of RNA-binding sites in a protein using SVM and PSSM profile. (2008) Proteins. 71:189-94.
2007
4. Kumar M, Gromiha MM, Raghava GPS. Identification of DNA-binding proteins using support vector machines and evolutionary profiles. (2007) BMC Bioinformatics 8:463.
3. Mishra NK, Kumar M, Raghava GPS. Supprot vector machine based prediction of glutathione S-transferase proteins. (2007) Protein Pept Lett. 14(6):575-80.
2006
2. Kumar M, Verma R, Raghava GPS. Prediction of mitochondrial proteins using support vector machine and hidden Markov model. (2006) J Biol Chem. 3;281(9):5357-63.
2005
1. Kumar M, Bhasin M, Natt NK, Raghava GPS. BhairPred: prediction of beta-hairpins in a protein from multiple alignment information using ANN and SVM techniques. (2005) Nucleic Acids Res 33:W154-9.
