Alan Moses' Computational Biology Lab
2017

Nguyen Ba AN, Strome B, Osman S, Legere EA, Zarin T, Moses AM. Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments.
PLoS Genetics 2017 Apr 14;13(4). Link to paper on PLoS Genetics - PDF mirror - Link to pubmed abstract

Zarin T, Tsai CN, Nguyen Ba AN, Moses AM. Selection maintains signaling function of a highly diverged intrinsically disordered region.
PNAS 2017 Feb 21;114(8). Link to paper on PNAS - PDF mirror - Link to pubmed abstract

Youn JY, Friesen H, Nguyen Ba AN, Liang W, Messier V, Cox MJ, Moses AM, Andrews B. Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library.
G3 2017 Mar 10;7(3):911-921. Link to paper on G3 - PDF mirror - Link to pubmed abstract

2016

Kompella PS, Moses AM, Peisajovich SG Introduction of Premature Stop Codons as an Evolutionary Strategy to Rescue Signaling Network Function
ACS Synth Biol. 2016 Dec 9. Link to paper on ACS Synthetic Biology - PDF mirror - Link to pubmed abstract

Moses AM Statistical Modeling and Machine Learning for Molecular Biology
CRC Press Taylor & Francis Group 2016 Dec.12 link to book on CRC press

Lu AX, Moses AM An Unsupervised kNN Method to Systematically Detect Changes in Protein Localization in High-Throughput Microscopy Images.
PLoS One 2016 Jul 21;11(7):e0158712 Link to paper on PLoS One - PDF mirror - Link to pubmed abstract

Austin RS, Hiu S, Waese J, Ierullo M, Pasha A, Wang TT, Fan J, Foong C, Breit R, Desveaux D, Moses A, Provart NJ. New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana
Plant J. 2016 Nov;88(3):490-504. Link to paper on Plant Journal - PDF mirror - Link to pubmed abstract

Douglas GM, Wilson MD, Moses AM Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration
Mol. Biol. Evol. 2016 Feb 16 Link to paper on Molecular Biology and Evolution - PDF mirror - Link to pubmed abstract

2015

Davey NE, Cyert MS, Moses AM Short linear motifs--ex nihilo evolution of protein regulation
Cell Comm. Sig. 2015 Nov 21 Link to paper on Cell Communication and Signaling - PDF mirror - Link to pubmed abstract

Wong KC, Li Y, Peng C, Moses AM, Zhang Z Computational learning on specificity-determining residue-nucleotide interactions
Nucleic Acids Res. 2015 Dec 2 Link to paper on Nucleic Acids Research - PDF mirror - Link to pubmed abstract

Khan T, Douglas GM, Patel P, Nguyen Ba AN, Moses AM. Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions.
Genome Biol Evol. 2015 Jun 4 Link to paper on Genome Biology and Evolution - PDF mirror - Link to pubmed abstract

Koh JL, Chong YT, Friesen H, Moses A, Boone C, Andrews BJ, Moffat J. CYCLoPs: A Comprehensive Database Constructed from Automated Analysis of Protein Abundance and Subcellular Localization Patterns in Saccharomyces cerevisiae.
G3 2015 Apr 15 Link to paper on G3 - PDF mirror - Link to pubmed abstract

Chong YT, Koh JL, Friesen H, Duffy K, Cox MJ, Moses A, Moffat J, Boone C, Andrews BJ. Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis.
Cell 2015 Jun 4 Link to paper on Cell - PDF mirror - Link to pubmed abstract

Gógl G, Schneider KD, Yeh BJ, Alam N, Nguyen Ba AN, Moses AM, Hetényi C, Reményi A, Weiss EL. The Structure of an NDR/LATS Kinase-Mob Complex Reveals a Novel Kinase-Coactivator System and Substrate Docking Mechanism.
PLoS Biol. 2015 May 12 Link to paper on PLoS Biology - PDF mirror - Link to pubmed abstract

2014

Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR, Moses AM. Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences.
PLoS Comput Biol. 2014 Dec 4;10(12):e1003977 Link to paper on PLoS Computational Biology - PDF mirror - Link to Pubmed abstract

Handfield LF, Strome B, Chong YT, Moses AM. Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images
Bioinformatics 2014 Nov 14 [Epub] Link to paper on Bioinformatics - PDF mirror - Link to Pubmed abstract

Nguyen Ba AN. Molecular Evolution of Posttranslational regulation in disordered regions
PhD Thesis, University of Toronto 2014 Link to thesis

Landry CR, Freschi L, Zarin T, Moses AM. Turnover of protein phosphorylation evolving under stabilizing selection.
Front Genet. 2014 Jul 23;5:245. Link to paper on Frontiers in Genetics - PDF mirror - Link to Pubmed abstract

Lumba S, Toh S, Handfield LF, Swan M, Liu R, Youn JY, Cutler SR, Subramaniam R, Provart N, Moses A, Desveaux D, McCourt P. A mesoscale abscisic acid hormone interactome reveals a dynamic signaling landscape in Arabidopsis.
Dev Cell.
2014 May 12;29(3):360-72. Link to paper on Developmental Cell - PDF mirror - Link to Pubmed abstract

Handfield LF Automated Image Analysis for Systematic and Quantitative Comparison of Protein Expression within Cell Populations.
PhD Thesis, University of Toronto 2014 Link to thesis

Zarin T, Moses AM. Insights into molecular evolution from yeast genomics.
Yeast. 2014 Apr 24. Link to paper on Yeast - PDF mirror - Link to Pubmed abstract

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. A high-definition view of functional genetic variation from natural yeast genomes.
Mol Biol Evol. 2014 Apr;31(4):872-88. Link to paper on MBE - PDF mirror - Link to Pubmed abstract

Safi M Computational Modeling of Drug Resistance: Structural and Evolutionary Models.
PhD Thesis, University of Toronto 2014 Link to thesis

2013

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. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.
Nat Genet. 2013 Jun 30 Link to paper on Nature Genetics - PDF mirror - Link to Pubmed abstract

Handfield LF, Chong YT, Simmons J, Andrews BJ, Moses AM. Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins.
PLoS Comput Biol. 2013 Jun;9(6):e1003085. Link to paper on PLoS computational biology - PDF mirror - Link to Pubmed abstract

Khoshraftar S, Hung S, Khan S, Gong Y, Tyagi V, Parkinson J, Sain M, Moses AM, Christendat D. Sequencing and annotation of the Ophiostoma ulmi genome.
BMC Genomics 2013 Mar 12;14:162. Link to paper on BMC Genomics - PDF mirror - Link to Pubmed abstract

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. High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome
BMC Genomics 2013 Jan 31;14:69. Link to paper on BMC Genomics - PDF mirror - Link to Pubmed abstract

2012

Zia A, Moses AM. Towards a theoretical understanding of false positives in DNA motif finding.
BMC Bioinformatics 2012 Jun 27;13:151. Link to paper on BMC Bioinformatics - PDF mirror - Link to Pubmed abstract

Nguyen Ba AN, Yeh BJ, van Dyk D, Davidson AR, Andrews BJ, Weiss EL, Moses AM. Proteome-wide discovery of evolutionary conserved sequences in disordered regions.
Sci Signal 2012,Mar 13;5(215):rs1.  Link to paper on Science Signaling - PDF mirror - Link to Pubmed abstract

Lai AC, Nguyen Ba AN, Moses AM. Predicting Kinase Substrates using Conservation of Local Motif Density.
Bioinformatics 2012,Feb 1[Epub]  Link to paper on Bioinformatics - PDF mirror - Link to Pubmed abstract

2011

Zia A, Moses AM. Ranking insertion, deletion and nonsense mutations based on their effect on genetic information.
BMC Bioinformatics 2011,Jul 22;12(1):299. Link to paper on BMC Bioinformatics - PDF mirror - Link to Pubmed abstract

Warringer J, Zorgo E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses A, Blomberg A. Trait variation in yeast is defined by population history.
PLoS Genet. 2011,Jun;7(6):e1002111. Link to paper on PLoS Genetics - PDF mirror - Link to Pubmed abstract

Moses AM, Davidson AR. In vitro evolution goes deep
Proc Natl Acad Sci U S A. 2011,May 17;108(20):8071-2 Link to paper on PNAS - PDF mirror - Link to Pubmed abstract

Sharifpoor S, Nguyen Ba AN, Youn JY, van Dyk D, Friesen H, Douglas AC, Kurat CF, Chong YT, Founk K, Moses AM, Andrews BJ: A quantitative literature-curated gold standard for kinase-substrate pairs
Genome Biol. 2011,Apr 14;12(4):R39 Link to paper on Genome Biology - PDF mirror - Link to Pubmed abstract

Parts L, Cubillos F, Warringer J, Jain K, Salinas F, Bumpstead SJ, Molin M, Zia A, Simpson JT, Quail MA, Moses AM, Louis EJ, Durbin R, Liti G: Revealing the genetic structure of a trait by sequencing a population under selection
Genome Res. 2011,Mar 21;In Press Link to paper on Genome Research - PDF mirror - Link to Pubmed abstract

Josephides C, Moses AM: Modeling the evolution of a classic genetic switch
BMC Syst Biol. 2011,Feb 5;5:24 Link to paper on BMC Systems Biology - PDF mirror - Link to Pubmed abstract

Gonsalves SE, Moses AM, Razak Z, Robert F, Westwood JT: Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster
PLoS One 2011,Jan 14;6(1):e15934 Link to paper on PLoS One - PDF mirror - Link to Pubmed abstract

Cutter AD, Moses AM: Polymorphism, divergence and the role of recombination in Saccharomyces cerevisiae genome evolution
Mol. Biol. Evol. 2011,28(5):1745-1754 Link to paper on MBE - PDF mirror - Link to Pubmed abstract

2010

Moses AM, Landry CR: Moving from transcriptional to phospho-evolution: generalizing regulatory evolution?
Trends in Genetics 2010,Sept. 1 Link to paper on Trends In Genetics - PDF mirror - Link to Pubmed abstract

Nguyen Ba AN, Moses AM: Evolution of characterized phosphorylation sites in budding yeast.
Mol. Biol. Evol. 2010,27:9 Link to paper on Molecular Biology and Evolution - PDF mirror - Link to Pubmed abstract

Fraser HB, Moses AM, Schadt EE: Evidence for widespread adaptive evolution of gene expression in budding yeast.
Proc Natl Acad Sci U S A. 2010,107:7 Link to paper on PNAS - PDF mirror - Link to Pubmed abstract

2009

Moses AM: Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites
BMC Evol Biol. 2009,9:28 Link to paper on BMC Evolutionary Biology - PDF mirror - Link to Pubmed abstract

Moses AM, Sinha S: Regulatory Motif Analysis
Bioinformatics: Tools and Applications (Edwards D, Stajich J,Hansen D)Springer Biomedical and Life Sciences collection. 2009 Link to section

Nguyen Ba AN, Pogoutse A, Provart N, Moses A: NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction
BMC Bioinformatics 2009,10:202 Link to paper on BMC bioinformatics - PDF mirror - Link to Pubmed abstract

Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen Ba AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ: Population genomics of domestic and wild yeasts
Nature 2009,458:337-41 Link to paper on Nature - PDF mirror - Link to Pubmed abstract

Moses AM, Durbin R: Inferring selection on amino acid preference in protein domains.
Mol Biol Evol. 2009,26:527-36 Link to paper on Molecular Biology and Evolution - PDF mirror - Link to Pubmed abstract

2008

Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Durbin R.: TreeFam: 2008 Update.
Nucleic Acids Res. 2008,36:D735-40 Link to paper on Nucleic Acids Research - PDF mirror - Link to Pubmed abstract

2007

Shultzaberger RK, Chiang DY, Moses AM, Eisen MB: Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis.
PLoS ONE 2007,2:e1199 Link to paper on PLoS ONE - PDF mirror - Link to Pubmed abstract

Moses AM, Liku ME, Li JJ, Durbin R: Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites.
Proc Natl Acad Sci U S A. 2007,104:17713-8 Link to paper on PNAS - PDF mirror - Link to Pubmed abstract

Moses AM, Hériché JK, Durbin R: Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.
Genome Biol. 2007,8:R23 Link to paper on Genome Biology - PDF mirror - Link to Pubmed abstract

2006

Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM: In vivo enhancer analysis of human conserved non-coding sequences.
Nature 2006,444:499-502 Link to paper on Nature - PDF mirror - Link to Pubmed abstract

Moses AM, Pollard D, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB: Large-scale turnover of functional transcription factor binding sites in Drosophila.
PLoS Comput Biol. 2006,2:e130 Link to paper on PLoS Comput Biol. - PDF mirror - Link to Pubmed abstract

Pollard D, Iyer VN, Moses AM, Eisen MB: Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting
PLoS Genetics. 2006,2:e130 Link to paper on PLoS Genetics - PDF mirror - Link to Pubmed abstract

Pollard DA, Moses AM, Iyer VN, Eisen MB: Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
BMC Bioinformatics. 2006,7:376 Link to paper on BMC Bioinformatics - PDF mirror - Link to Pubmed abstract

Wang QF, Prabhakar S, Wang Q, Moses A, Chanan S, Brown M, Eisen M, Cheng JF, Rubin E, Boffelli D: Primate-Specific Evolution of an LDLR Enhancer.
Genome Biol. 2006,7:R68 Link to paper on Genome Biology - PDF mirror - Link to Pubmed abstract

2005 and before

Moses AM: Molecular evolution of transcriptional regulation.
PHD thesis 2005,University of California:Berkeley. Link to thesis

Moses AM, Chiang DY, Pollard DA, Iyer VN and Eisen MB: MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
Genome Biol. 2004,5:R98 Link to paper on Genome Biology - PDF mirror - Link to Pubmed abstract

Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB: Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi.
PLoS Biol. 2004,2:e398 Link to paper on PLoS Biology - PDF mirror - Link to Pubmed abstract

Moses AM, Chiang DY, Eisen MB: Phylogenetic Motif Detection by Expectation Maximization on Evolutionary Mixtures.
Pacific Symposium on Biocomputing 2004,9:324-335 Link to paper - PDF mirror - Link to Pubmed abstract

Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB: Position specific variation in the rate of evolution in transcription factor binding sites: Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi.
BMC Evolutionary Biology 2003,3:19 Link to paper on BMC Evolutionary Biology - PDF mirror - Link to Pubmed abstract

Chiang DY, Moses AM, Kellis M, Lander ES and Eisen MB: Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts.
Genome Biology 2003,4:R43 Link to paper on Genome Biology - PDF mirror - Link to Pubmed abstract



Alan Moses' Lab, Copyright 2009.