Harish Nagarajan - Publications

Affiliations: 
2012 Bioinformatics University of California, San Diego, La Jolla, CA 

22 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, ... ... Nagarajan H, et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Systems. 3: 434-443.e8. PMID 27883890 DOI: 10.1016/j.cels.2016.10.020  0.8
2016 Movahedi NS, Embree M, Nagarajan H, Zengler K, Chitsaz H. Efficient Synergistic Single-Cell Genome Assembly. Frontiers in Bioengineering and Biotechnology. 4: 42. PMID 27243002 DOI: 10.3389/fbioe.2016.00042  0.72
2015 Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, ... ... Nagarajan H, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284  0.8
2015 Sivashanmugam M, Nagarajan H, Vetrivel U, Ramasubban G, Therese KL, Narahari MH. In silico analysis and prioritization of drug targets in Fusarium solani. Medical Hypotheses. 84: 81-4. PMID 25555413 DOI: 10.1016/j.mehy.2014.12.015  0.6
2014 Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Molecular Systems Biology. 10: 737. PMID 24987116 DOI: 10.15252/msb.20145243  0.8
2014 Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. Plos Computational Biology. 10: e1003575. PMID 24762737 DOI: 10.1371/journal.pcbi.1003575  0.8
2014 Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho BK, Zengler K, Palsson B. Determining the control circuitry of redox metabolism at the genome-scale. Plos Genetics. 10: e1004264. PMID 24699140 DOI: 10.1371/journal.pgen.1004264  0.8
2014 Embree M, Qiu Y, Shieu W, Nagarajan H, O'Neil R, Lovley D, Zengler K. The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism. Applied and Environmental Microbiology. 80: 2918-27. PMID 24584254 DOI: 10.1128/AEM.03916-13  0.8
2014 Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. The Isme Journal. 8: 757-67. PMID 24152715 DOI: 10.1038/ismej.2013.187  0.8
2013 Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. Microbial Cell Factories. 12: 118. PMID 24274140 DOI: 10.1186/1475-2859-12-118  0.8
2013 Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nature Communications. 4: 2809. PMID 24264237 DOI: 10.1038/ncomms3809  0.8
2013 Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nature Biotechnology. 31: 759-65. PMID 23873082 DOI: 10.1038/nbt.2624  0.8
2013 Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, ... ... Nagarajan H, et al. MS/MS networking guided analysis of molecule and gene cluster families. Proceedings of the National Academy of Sciences of the United States of America. 110: E2611-20. PMID 23798442 DOI: 10.1073/pnas.1303471110  0.8
2013 Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee DH, Qiu Y, Zengler K. The genome organization of Thermotoga maritima reflects its lifestyle. Plos Genetics. 9: e1003485. PMID 23637642 DOI: 10.1371/journal.pgen.1003485  0.8
2013 Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K. Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nature Communications. 4: 1755. PMID 23612296 DOI: 10.1038/ncomms2743  0.8
2013 Nakatsuji T, Chiang HI, Jiang SB, Nagarajan H, Zengler K, Gallo RL. The microbiome extends to subepidermal compartments of normal skin. Nature Communications. 4: 1431. PMID 23385576 DOI: 10.1038/ncomms2441  0.8
2012 Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, et al. Proteomic analysis of Chinese hamster ovary cells. Journal of Proteome Research. 11: 5265-76. PMID 22971049 DOI: 10.1021/pr300476w  0.8
2012 Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. Plos Genetics. 8: e1002867. PMID 22912590 DOI: 10.1371/journal.pgen.1002867  0.8
2012 Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO. Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction. Plos One. 7: e33727. PMID 22470465 DOI: 10.1371/journal.pone.0033727  0.8
2012 Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nature Reviews. Microbiology. 10: 291-305. PMID 22367118 DOI: 10.1038/nrmicro2737  0.8
2011 Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, et al. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology. 29: 735-41. PMID 21804562 DOI: 10.1038/nbt.1932  0.8
2010 Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL. De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. Plos One. 5: e10922. PMID 20544019 DOI: 10.1371/journal.pone.0010922  0.8
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