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    Varghese, Neha

    TitleSoftware Developer 3
    SchoolLawrence Berkeley National Lab
    DepartmentJoint Genome Institute
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5696
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Daligault H, Davenport K, Erkkila T, Goodwin LA, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woolbert M, Gunde-Cimerman N, Wolf YI, Grebenc T, Gostincar C, Daly MJ. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Stand Genomic Sci. 2017; 12:46. PMID: 28775794.
        View in: PubMed
      2. Miroshnikov KK, Didriksen A, Naumoff DG, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Mukherjee S, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Dedysh SN, Svenning MM. Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil. Genome Announc. 2017 Jun 15; 5(24). PMID: 28619793.
        View in: PubMed
      3. Mukherjee S, Seshadri R, Varghese N, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat Biotechnol. 2017 Jul; 35(7):676-683. PMID: 28604660.
        View in: PubMed
      4. Rice MC, Norton JM, Stein LY, Kozlowski J, Bollmann A, Klotz MG, Sayavedra-Soto L, Shapiro N, Goodwin LA, Huntemann M, Clum A, Pillay M, Varghese N, Mikhailova N, Palaniappan K, Ivanova N, Mukherjee S, Reddy TB, Yee Ngan C, Daum C, Kyrpides N, Woyke T. Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters. Genome Announc. 2017 Mar 16; 5(11). PMID: 28302769.
        View in: PubMed
      5. Reeve W, van Berkum P, Ardley J, Tian R, Gollagher M, Marinova D, Elia P, Reddy TBK, Pillay M, Varghese N, Seshadri R, Ivanova N, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr. Stand Genomic Sci. 2017; 12:26. PMID: 28270909.
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      6. Patil Y, Müller N, Schink B, Whitman WB, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Junghare M. High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698). Stand Genomic Sci. 2017; 12:24. PMID: 28250895.
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      7. Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science. 2017 01 20; 355(6322):294-298. PMID: 28104891.
        View in: PubMed
      8. Hutt LP, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Boden R. Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria. Stand Genomic Sci. 2017; 12:10. PMID: 28127420.
        View in: PubMed
      9. Klonowska A, López-López A, Moulin L, Ardley J, Gollagher M, Marinova D, Tian R, Huntemann M, Reddy TB, Varghese N, Woyke T, Markowitz V, Ivanova N, Seshadri R, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W. High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia. Stand Genomic Sci. 2017; 12:7. PMID: 28116041.
        View in: PubMed
      10. Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J, Andersen E, Huntemann M, Varghese N, Hadjithomas M, Tennessen K, Nielsen T, Ivanova NN, Kyrpides NC. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 2017 Jan 04; 45(D1):D507-D516. PMID: 27738135.
        View in: PubMed
      11. Nouioui I, Gtari M, Göker M, Ghodhbane-Gtari F, Tisa LS, Fernandez MP, Normand P, Huntemann M, Clum A, Pillay M, Varghese N, Reddy TB, Ivanova N, Woyke T, Kyrpides NC, Klenk HP. Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales. Genome Announc. 2016 May 26; 4(3). PMID: 27231368; PMCID: PMC4882949.
      12. Varghese N, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 2015 Aug 18; 43(14):6761-71. PMID: 26150420; PMCID: PMC4538840.
      13. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2014 Jan; 42(Database issue):D560-7. PMID: 24165883; PMCID: PMC3965111.
      14. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res. 2014 Jan; 42(Database issue):D568-73. PMID: 24136997; PMCID: PMC3964948.
      15. Rishishwar L, Varghese N, Tyagi E, Harvey SC, Jordan IK, McCarty NA. Relating the disease mutation spectrum to the evolution of the cystic fibrosis transmembrane conductance regulator (CFTR). PLoS One. 2012; 7(8):e42336. PMID: 22879944; PMCID: PMC3413703.
      16. Jordan IK, Conley AB, Antonov IV, Arthur RA, Cook ED, Cooper GP, Jones BL, Knipe KM, Lee KJ, Liu X, Mitchell GJ, Pande PR, Petit RA, Qin S, Rajan VN, Sarda S, Sebastian A, Tang S, Thapliyal R, Varghese N, Ye T, Katz LS, Wang X, Rowe L, Frace M, Mayer LW. Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus. J Bacteriol. 2011 Oct; 193(20):5879-80. PMID: 21952546; PMCID: PMC3187195.
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