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Dennis M. Vitkup, Ph.D. - Publications

Biomedical Informatics Columbia University, New York, NY 
 1999 Brandeis University, Waltham, MA, United States 
relationship of protein three-dimensional structure to chemical function

21 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 Mayers JR, Torrence ME, Danai LV, Papagiannakopoulos T, Davidson SM, Bauer MR, Lau AN, Ji BW, Dixit PD, Hosios AM, Muir A, Chin CR, Freinkman E, Jacks T, Wolpin BM, ... Vitkup D, et al. Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. Science (New York, N.Y.). 353: 1161-5. PMID 27609895 DOI: 10.1126/science.aaf5171  1
2015 Chang J, Gilman SR, Chiang AH, Sanders SJ, Vitkup D. Genotype to phenotype relationships in autism spectrum disorders. Nature Neuroscience. 18: 191-8. PMID 25531569 DOI: 10.1038/nn.3907  1
2015 Plata G, Henry CS, Vitkup D. Long-term phenotypic evolution of bacteria Nature. 517: 369-372. PMID 25363780 DOI: 10.1038/nature13827  1
2013 Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, ... ... Vitkup D, et al. The COMBREX project: design, methodology, and initial results. Plos Biology. 11: e1001638. PMID 24013487 DOI: 10.1371/journal.pbio.1001638  1
2013 Hu J, Locasale JW, Bielas JH, O'Sullivan J, Sheahan K, Cantley LC, Vander Heiden MG, Vitkup D. Heterogeneity of tumor-induced gene expression changes in the human metabolic network. Nature Biotechnology. 31: 522-9. PMID 23604282 DOI: 10.1038/nbt.2530  1
2013 Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, Sorger PK. Properties of cell death models calibrated and compared using Bayesian approaches. Molecular Systems Biology. 9: 644. PMID 23385484 DOI: 10.1038/msb.2012.69  1
2012 Gilman SR, Chang J, Xu B, Bawa TS, Gogos JA, Karayiorgou M, Vitkup D. Diverse types of genetic variation converge on functional gene networks involved in schizophrenia. Nature Neuroscience. 15: 1723-8. PMID 23143521 DOI: 10.1038/nn.3261  1
2011 Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, ... ... Vitkup D, et al. Verification of systems biology research in the age of collaborative competition. Nature Biotechnology. 29: 811-5. PMID 21904331 DOI: 10.1038/nbt.1968  1
2011 Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D. Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron. 70: 898-907. PMID 21658583 DOI: 10.1016/j.neuron.2011.05.021  1
2011 Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, ... ... Vitkup D, et al. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Research. 39: D11-4. PMID 21097892 DOI: 10.1093/nar/gkq1168  1
2010 Plata G, Gottesman ME, Vitkup D. The rate of the molecular clock and the cost of gratuitous protein synthesis. Genome Biology. 11: R98. PMID 20920270 DOI: 10.1186/gb-2010-11-9-r98  1
2010 Plata G, Hsiao TL, Olszewski KL, Llinás M, Vitkup D. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Molecular Systems Biology. 6: 408. PMID 20823846 DOI: 10.1038/msb.2010.60  1
2010 Chastanet A, Vitkup D, Yuan GC, Norman TM, Liu JS, Losick RM. Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 107: 8486-91. PMID 20404177 DOI: 10.1073/pnas.1002499107  1
2008 Hsiao TL, Vitkup D. Role of duplicate genes in robustness against deleterious human mutations Plos Genetics. 4. PMID 18369440 DOI: 10.1371/journal.pgen.1000014  1
2006 Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. Bmc Bioinformatics. 7: 177. PMID 16571130 DOI: 10.1186/1471-2105-7-177  1
2006 Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D. Multiple solvent crystal structures: probing binding sites, plasticity and hydration. Journal of Molecular Biology. 357: 1471-82. PMID 16488429 DOI: 10.1016/j.jmb.2006.01.039  1
2002 Vitkup D, Ringe D, Karplus M, Petsko GA. Why protein R-factors are so large: a self-consistent analysis. Proteins. 46: 345-54. PMID 11835510 DOI: 10.1002/prot.10035  1
2001 Vitkup D, Melamud E, Moult J, Sander C. Completeness in structural genomics Nature Structural Biology. 8: 559-565. PMID 11373627 DOI: 10.1038/88640  1
2000 Vitkup D, Ringe D, Petsko GA, Karplus M. Solvent mobility and the protein 'glass' transition. Nature Structural Biology. 7: 34-8. PMID 10625424 DOI: 10.1038/71231  1
1999 Zhou Y, Vitkup D, Karplus M. Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. Journal of Molecular Biology. 285: 1371-5. PMID 9917381 DOI: 10.1006/jmbi.1998.2374  1
1997 Vitkup D, Petsko GA, Karplus M. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Nature Structural Biology. 4: 202-8. PMID 9164461 DOI: 10.1038/nsb0397-202  1
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