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Hire Dr. Nitin K.

United Kingdom

USD 119 /hr

PhD in Bioinformatics | Expert in R & Python | 10+ years in Pathogen and Microbiome research

Profile Summary

Computational biologist with over 10 years of experience in bioinformatics, specializing in large-scale genomic data analysis, statistical analysis, and scientific writing. My main expertise are genomics (bacterial pangenome analysis, phylogneny) , transcriptomics and metagenomics (16S and shotgun). Experienced in delivering bioinformatics solutions across both academic and commercial settings, with a proven record of managing and completing complex projects to high standards within deadlines. Author of 30 peer-reviewed publications in high-impact international journals. Proficient in R programming and data visualization. I have presented my work in many national and international conferences.

Subject Matter Expertise

• ★ Computational Biology
• ★ Microbiome Research
• ★ Bioinformatics
• ☆ Evolutionary Biology
• ☆ Microbiology
• ☆ Biostatistics
• ☆ Molecular Biology
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Ecology
• ☆ Taxonomy/Classification
• ☆ Biological Taxonomy/Classification
• ☆ Phylogenetics
• ☆ Population Genetics
• ☆ R

Services

• Writing
• Research
• Consulting

Writing Medical Writing, Technical Writing, Copywriting, General Proofreading & Editing

Research Market Research, Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Work Experience

Bioinformatics Consultant

General Bioinformatics Ltd, UK

April 2022 - February 2024

Senior Bioinformatician

Wellcome Sanger Institute

May 2018 - March 2022

Postdoctoral Research Scientist

Wellcome Sanger Institute

January 2014 - April 2018

Education

PhD (Biology)

University of York

October 2010 - December 2013

M.Sc (Bioinformatics)

Jamia Millia Islamia

2007 - 2009

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA, et al. (2024). Genomic attributes of airway commensal bacteria and mucosa . Communications biology.

Crobach MJT, Hornung BVH, Verduin C, Vos MC, Hopman J, Kumar N, Harmanus C, Sanders I, Terveer EM, Stares MD, et al. (2023). Screening for Clostridioides difficile colonization at admission to the hospital: a multi-centre study . Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Forster SC, Clare S, Beresford-Jones BS, Harcourt K, Notley G, Stares MD, Kumar N, Soderholm AT, Adoum A, Wong H, et al. (2022). Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis . Nature microbiology.

Forster SC, Liu J, Kumar N, Gulliver EL, Gould JA, Escobar-Zepeda A, Mkandawire T, Pike LJ, Shao Y, Stares MD, et al. (2022). Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome . Nature communications.

Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, Boehmler DJ, Soderholm AT, Kumar N, Vervier K, et al. (2021). The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping . Cell host & microbe.

Vervier K, Moss S, Kumar N, Adoum A, Barne M, Browne H, Kaser A, Kiely CJ, Neville BA, Powell N, et al. (2021). Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet . Gut.

Browne HP, Almeida A, Kumar N, Vervier K, Adoum AT, Viciani E, Dawson NJR, Forster SC, Cormie C, Goulding D, et al. (2021). Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle . Genome biology.

Strobbe F, Bénard MV, Rossen NG, de Vos WM, Kumar N, Lawley TD, Zoetendal EG, Hugenholtz F, Ponsioen CY (2021). A novel technique capable of taking 'protected' biopsies for reliable assessment of the distribution of microbiota along the colonic mucosa . Journal of microbiological methods.

Costa D, Lévesque S, Kumar N, Fresia P, Ferrés I, Lawley TD, Iraola G (2021). Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts . Scientific reports.

Fitzpatrick Z, Frazer G, Ferro A, Clare S, Bouladoux N, Ferdinand J, Tuong ZK, Negro-Demontel ML, Kumar N, Suchanek O, et al. (2020). Gut-educated IgA plasma cells defend the meningeal venous sinuses . Nature.

Nitin Kumar, Kylie R. James, Tomas Gomes, Rasa Elmentaite, Emily L. Gulliver, Hamish W. King, Mark D. Stares, Bethany R. Bareham, John R. Ferdinand, Velislava N. Petrova, et al.(2020). Distinct microbial and immune niches of the human colon . Nature Immunology. 21. (3). p. 343--353. Springer Science and Business Media {LLC}

Shao Y, Forster SC, Tsaliki E, Vervier K, Strang A, Simpson N, Kumar N, Stares MD, Rodger A, Brocklehurst P, et al. (2019). Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth . Nature.

Kumar N, Browne HP, Viciani E, Forster SC, Clare S, Harcourt K, Stares MD, Dougan G, Fairley DJ, Roberts P, et al. (2019). Adaptation of host transmission cycle during Clostridium difficile speciation . Nature genetics.

Nitin Kumar, Marina Muñoz, Daniel Restrepo-Montoya, Gregorio Iraola, Milena Camargo, Diana Díaz-Arévalo, Nelly S. Roa-Molina, Mayra A. Tellez, Giovanny Herrera, Dora I. Ríos-Chaparro, et al. (2019). Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia . Scientific Reports.

Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, et al. (2019). A human gut bacterial genome and culture collection for improved metagenomic analyses . Nature biotechnology.

Fleurbaaij F, Henneman AA, Corver J, Knetsch CW, Smits WK, Nauta ST, Giera M, Dragan I, Kumar N, Lawley TD, et al. (2018). Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans . Scientific reports.

Thomas-White K, Forster SC, Kumar N, Van Kuiken M, Putonti C, Stares MD, Hilt EE, Price TK, Wolfe AJ, Lawley TD (2018). Culturing of female bladder bacteria reveals an interconnected urogenital microbiota . Nature communications.

Sharma C, Kumar R, Kumar N, Masih A, Gupta D, Chowdhary A (2018). Investigation of Multiple Resistance Mechanisms in Voriconazole-Resistant Aspergillus flavus Clinical Isolates from a Chest Hospital Surveillance in Delhi, India . Antimicrobial agents and chemotherapy.

Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP, Harmanus C, Sanders IM, Harris SR, Turner L, Morris T, et al. (2018). Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans . Journal of clinical microbiology.

Pike LJ, Viciani E, Kumar N (2018). Genome watch: Microbial diversity knows no borders . Nature reviews. Microbiology.

Iraola G, Forster SC, Kumar N, Lehours P, Bekal S, García-Peña FJ, Paolicchi F, Morsella C, Hotzel H, Hsueh PR, et al. (2017). Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota . Nature communications.

Kumar N, Forster SC (2017). Genome watch: Microbiota shuns the modern world . Nature reviews. Microbiology.

Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T, et al. (2017). DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome . Gastroenterology.

Sharma C, Kumar N, Pandey R, Meis JF, Chowdhary A (2016). Whole genome sequencing of emerging multidrug resistant Candida auris isolates in India demonstrates low genetic variation . New microbes and new infections.

Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, Goulding D, Lawley TD (2016). Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation . Nature.

Fung TC, Bessman NJ, Hepworth MR, Kumar N, Shibata N, Kobuley D, Wang K, Ziegler CGK, Goc J, Shima T, et al. (2016). Lymphoid-Tissue-Resident Commensal Bacteria Promote Members of the IL-10 Cytokine Family to Establish Mutualism . Immunity.

Kumar N, Miyajima F, He M, Roberts P, Swale A, Ellison L, Pickard D, Smith G, Molyneux R, Dougan G, et al. (2015). Genome-Based Infection Tracking Reveals Dynamics of Clostridium difficile Transmission and Disease Recurrence . Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Forster SC, Browne HP, Kumar N, Hunt M, Denise H, Mitchell A, Finn RD, Lawley TD (2015). HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes . Nucleic acids research.

Sharma C, Kumar N, Meis JF, Pandey R, Chowdhary A (2015). Draft Genome Sequence of a Fluconazole-Resistant Candida auris Strain from a Candidemia Patient in India . Genome announcements.

Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JP, Bailly X (2015). Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum . Open biology.

Bailly X, Giuntini E, Sexton MC, Lower RP, Harrison PW, Kumar N, Young JP (2011). Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates . The ISME journal.

Bhardwaj A, Bhartiya D, Kumar N, Open Source Drug Discovery Consortium, Scaria V (2009). TBrowse: an integrative genomics map of Mycobacterium tuberculosis . Tuberculosis (Edinburgh, Scotland).