个人简介

Ph.D. University of California, Berkeley 2005 B.A. Columbia University 2000

研究领域

Bioinformatics & Computational Biology Comparative Genomics Evolutionary Biology Microbiology Molecular Biology Proteomics Systems Biology

Consider the incredible diversity of cells and tissues in our own bodies: an information transmitting nerve cell and a bacteria-hunting white blood cell look and act nothing alike, yet they are specified by the same genome. This feat – phenotypic diversity without genetic diversity – is accomplished by genes that turn on and off other genes in a so-called ‘regulatory network’. We seek to understand how are these regulatory networks are encoded in genome sequences. How is information in the genome converted into regulatory interactions between proteins? One of the important components of this ‘regulatory code’ has been discovered: ‘regulatory motifs’ in the sequences of DNA, RNA and proteins. One of the major aims of our research is to develop computational and statistical tools to identify these motifs. Just as differential gene activity can explain cellular and physiological diversity within a single organism (nerve cell vs. white blood cell with same genes), it has also been proposed as explanation for physiological and morphological differences between closely related organisms (chimpanzee vs. human with very similar genes). We seek to understand how regulatory networks are sculpted by evolution. Can genetic changes in regulatory interactions explain evolutionary changes in function and form? We focus on the evolution of regulatory motifs because, by mediating the regulatory interactions, they specify the connections in regulatory networks. Our goal is to translate the evolutionary differences in regulatory motifs to quantitative differences in regulatory networks, and ultimately, to their impact on organismal fitness.

近期论文

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Turnover of protein phosphorylation evolving under stabilizing selection.Landry CR, Freschi L, Zarin T, Moses AM.Front Genet 2014;5:245 pubmed Insights into molecular evolution from yeast genomics.Zarin T, Moses AM.Yeast 2014 Jul;31(7):233-41 pubmed A high-definition view of functional genetic variation from natural yeast genomes.Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.Mol. Biol. Evol. 2014 Apr;31(4):872-88 pubmed An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandáková T, Lysak MA, van den Bergh E, Schranz ME, Harrison PM, Moses AM, Bureau TE, Wright SI, Blanchette M.Nat. Genet. 2013 Aug;45(8):891-8 pubmed Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.Handfield LF, Chong YT, Simmons J, Andrews BJ, Moses AM.PLoS Comput. Biol. 2013;9(6):e1003085 pubmed High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome.Liti G, Nguyen Ba AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, Nieduszynski CA.BMC Genomics 2013;14:69 pubmed Towards a theoretical understanding of false positives in DNA motif finding.Zia A, Moses AM.BMC Bioinformatics 2012;13:151 pubmed Proteome-wide discovery of evolutionary conserved sequences in disordered regions.Nguyen Ba AN, Yeh BJ, van Dyk D, Davidson AR, Andrews BJ, Weiss EL, Moses AM.Sci Signal 2012 Mar;5(215):rs1 pubmed Predicting kinase substrates using conservation of local motif density.Lai AC, Nguyen Ba AN, Moses AM.Bioinformatics 2012 Apr;28(7):962-9 pubmed Ranking insertion, deletion and nonsense mutations based on their effect on genetic information.Zia A, Moses AM.BMC Bioinformatics 2011;12:299 pubmed In vitro evolution goes deep.Moses AM, Davidson AR.Proc. Natl. Acad. Sci. U.S.A. 2011 May;108(20):8071-2 pubmed A quantitative literature-curated gold standard for kinase-substrate pairs.Sharifpoor S, Nguyen Ba AN, Youn JY, Young JY, van Dyk D, Friesen H, Douglas AC, Kurat CF, Chong YT, Founk K, Moses AM, Andrews BJ.Genome Biol. 2011;12(4):R39 pubmed