Publications

YearPublication
2017Nguyen 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).
PLoS Genetics Link PDF Mirror PubMed Abstract Article
Saccharomyces cerevisiae Evolutionary genetics Molecular evolution Natural selection Gene duplication Fungal evolution Green fluorescent protein Sequence motif analysis
2017Zarin 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).
PNAS Link PDF Mirror PubMed Abstract Article
Evolution Intrinsically disordered Quantitative trait Phylogenetic comparative method Stabilizing selection
2017Youn 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.
G3 Link PDF Mirror PubMed Abstract Article
Yeast genetics Genetic interactions Kinase Transcription factor Genetic networks
2016Kompella 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.
ACS Synthetic Biology Link PDF Mirror PubMed Abstract Article
Evolution Premature stop codon Signaling network
2016Moses AM. Statistical Modeling and Machine Learning for Molecular Biology. CRC Press Taylor & Francis Group 2016 Dec.12.
CRC Press Link Book
Molecular biology Statistics Machine learning
2016Lu 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.
PLoS One Link PDF Mirror PubMed Abstract Article
Imaging techniques Cell cycle and cell division Genetic screens Subcellular localization Image analysis Saccharomyces cerevisiae Green fluorescent protein Perception
2016Austin 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.
Plant Journal Link PDF Mirror PubMed Abstract Article
Coexpression analysis Cis-element prediction Gene expression markers Reporter constructs Promoter analysis Arabidopsis thaliana Technical advance
2016Douglas GM, Wilson MD, Moses AM. Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration. Mol. Biol. Evol. 2016 Feb 16.
Molecular Biology and Evolution Link PDF Mirror PubMed Abstract Article
Pseudoenhancer Regulatory evolution ChIP-seq Neutral evolution Histone modifications
2015Davey NE, Cyert MS, Moses AM. Short linear motifs–ex nihilo evolution of protein regulation. Cell Comm. Sig. 2015 Nov 21.
Cell Communication and Signaling Link PDF Mirror PubMed Abstract Article
Motifs Short linear motifs SLiMs Cis-regulatory elements RNA motifs Evolution Modularity Protein evolution
2015Wong KC, Li Y, Peng C, Moses AM, Zhang Z. Computational learning on specificity-determining residue-nucleotide interactions. Nucleic Acids Res. 2015 Dec 2.
Nucleic Acids Research Link PDF Mirror PubMed Abstract Article
Protein-nucleic acid interaction Computational methods
2015Khan 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.
Genome Biology and Evolution Link PDF Mirror PubMed Abstract Article
Negative Selection Indels SNP Intrinsically Disordered Protein
2015Koh JL, Chong YT, Friesen H, Moses AM, 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.
G3 Link PDF Mirror PubMed Abstract Article
GFP Imaging Microscopy Subcellular localization CYCLoPs Database
2015Chong YT, Koh JL, Friesen H, Duffy K, Cox MJ, Moses AM, Moffat J, Boone C, Andrews BJ. Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis. Cell 2015 Jun 4.
Cell Link PDF Mirror PubMed Abstract Article
Proteomics Imaging GFP Microscopy CYCLoPs Database
2015Gógl 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.
PLoS Biology Link PDF Mirror PubMed Abstract Article
Phosphorylation Sequence motif analysis Crystal structure Saccharomyces cerevisiae Molecular dynamics Protein kinase signaling cascade Fungal evolution Protein structure
2014Nguyen 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.
PLoS Computational Biology Link PDF Mirror PubMed Abstract Article
Sequence motif analysis Fungal evolution Molecular evolution Gene duplication Saccharomyces cerevisiae Evolutionary genetics Sequence alignment Statistical distributions
2014Handfield 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.
Bioinformatics Link PDF Mirror PubMed Abstract Article
Bioinformatics Statistics Microscopy Imaging Subcellular localization Cell-to-cell variability
2014Nguyen Ba AN. Molecular Evolution of Posttranslational regulation in disordered regions. University of Toronto 2014.
Thesis Link PhD thesis
Molecular evolution Posttranslational Regulation Disordered regions
2014Landry CR, Freschi L, Zarin T, Moses AM. Turnover of protein phosphorylation evolving under stabilizing selection. Front Genet. 2014 Jul 23;5:245.
Frontiers in Genetics Link PDF Mirror PubMed Abstract Article
Protein phosphorylation Evolutionary turnover Molecular switches Molecular rheostats Protein evolution Molecular evolution Cell signaling
2014Lumba S, Toh S, Handfield LF, Swan M, Liu R, Youn JY, Cutler SR, Subramaniam R, Provart N, Moses AM, 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.
Developmental Cell Link PDF Mirror PubMed Abstract Article
Interactome ABA network Signaling Coexpression Arabidopsis thaliana
2014Handfield LF. Automated Image Analysis for Systematic and Quantitative Comparison of Protein Expression within Cell Populations. University of Toronto 2014.
Thesis Link PhD thesis
Imaging Microscopy Image analysis Protein expression
2014Zarin T, Moses AM. Insights into molecular evolution from yeast genomics. Yeast. 2014 Apr 24.
Yeast Link PDF Mirror PubMed Abstract Article
Molecular evolution Comparative genomics Experimental evolution Complex phenotypes Population genomics Gene duplication Gene order Regulatory evolution Functional synthesis Functional genomics
2014Bergström 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.
Molecular Biology and Evolution Link PDF Mirror PubMed Abstract Article
Population genomics Functional variation Genome evolution Yeast Subtelomeres Loss-of-function variants
2014Safi M. Computational Modeling of Drug Resistance: Structural and Evolutionary Models. University of Toronto 2014.
Thesis Link PhD thesis
Drug resistance Computational modeling Evolution Structural models
2013Haudry 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.
Nature Genetics Link PDF Mirror PubMed Abstract Article
Genomics Plant genetics Sequence annotation Regulatory regions
2013Handfield 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.
PLoS Computational Biology Link PDF Mirror PubMed Abstract Article
Ellipses Protein expression Cell cycle and cell division Subcellular localization Permutation Normal distribution Protein domains Fluorescence imaging
2013Khoshraftar 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.
BMC Genomics Link PDF Mirror PubMed Abstract Article
Sequencing Annotation Ophiostoma ulmi Genome
2013Liti 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.
BMC Genomics Link PDF Mirror PubMed Abstract Article
Sequencing Assembly Saccharomyces arboricolus Genome
2012Zia A, Moses AM. Towards a theoretical understanding of false positives in DNA motif finding. BMC Bioinformatics 2012 Jun 27;13:151.
BMC Bioinformatics Link PDF Mirror PubMed Abstract Article
Bioinformatics Sequence motif analysis False positive motifs DNA motif finding
2012Nguyen 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.
Science Signaling Link PDF Mirror PubMed Abstract Article
Proteomics Evolution Sequence conservation Disordered regions
2012Lai AC, Nguyen Ba AN, Moses AM. Predicting Kinase Substrates using Conservation of Local Motif Density. Bioinformatics 2012,Feb 1.
Bioinformatics Link PDF Mirror PubMed Abstract Article
Kinase Sequence conservation Motif density Sequence motif analysis
2011Zia A, Moses AM. Ranking insertion, deletion and nonsense mutations based on their effect on genetic information. BMC Bioinformatics 2011,Jul 22;12(1):299.
BMC Bioinformatics Link PDF Mirror PubMed Abstract Article
Mutation Indels Genetic information Nonsense mutation
2011Warringer J, Zorgo E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses AM, Blomberg A. Trait variation in yeast is defined by population history. PLoS Genet. 2011,Jun;7(6):e1002111.
PLoS Genetics Link PDF Mirror PubMed Abstract Article
Saccharomyces cerevisiae Galactose Genetic polymorphism Genetic drift Mutant genotypes Phenotypes Population genetics Evolutionary genetics
2011Moses AM, Davidson AR. In vitro evolution goes deep. Proc Natl Acad Sci U S A. 2011,May 17;108(20):8071-2.
PNAS Link PDF Mirror PubMed Abstract Article
Evolution Experimental evolution In vitro EMPIRIC
2011Sharifpoor 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.
Genome Biology Link PDF Mirror PubMed Abstract Article
Kinase Kinase interaction KID Database
2011Parts 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.
Genome Research Link PDF Mirror PubMed Abstract Article
QTL mapping Artificial selection Complex traits Genetics
2011Josephides C, Moses AM. Modeling the evolution of a classic genetic switch. BMC Syst Biol. 2011,Feb 5;5:24.
BMC Systems Biology Link PDF Mirror PubMed Abstract Article
Evolution Genetic switch Computational modeling Gene duplication
2011Gonsalves 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.
PLoS One Link PDF Mirror PubMed Abstract Article
DNA transcription Larvae Drosophila melanogaster Cell binding Gene regulation Introns Invertebrate genomics Binding analysis
2011Cutter AD, Moses AM. Polymorphism, divergence and the role of recombination in Saccharomyces cerevisiae genome evolution. Mol. Biol. Evol. 2011,28(5):1745-1754.
Molecular Biology and Evolution Link PDF Mirror PubMed Abstract Article
Genetic hitchhiking Background selection Recombination rate Mutagenic recombination Budding yeast Nucleotide polymorphism
2010Moses AM, Landry CR. Moving from transcriptional to phospho-evolution: generalizing regulatory evolution? Trends in Genetics 2010,Sept. 1.
Trends in Genetics Link PDF Mirror PubMed Abstract Article
Evolution Regulatory networks Transcriptional regulation Kinase
2010Nguyen Ba AN, Moses AM. Evolution of characterized phosphorylation sites in budding yeast. Mol. Biol. Evol. 2010,27:9.
Molecular Biology and Evolution Link PDF Mirror PubMed Abstract Article
Phosphorylation sites Evolution Prediction Saccharomyces cerevisiae
2010Fraser 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.
PNAS Link PDF Mirror PubMed Abstract Article
Gene expression Evolution Adaptation Saccharomyces cerevisiae
2009Moses AM. Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites. BMC Evol Biol. 2009,9:28.
BMC Evolutionary Biology Link PDF Mirror PubMed Abstract Article
Natural selection Regulatory regions Transcription factor Statistics
2009Moses AM, Sinha S. Regulatory Motif Analysis. Bioinformatics: Tools and Applications (Edwards D, Stajich J, Hansen D). Springer Biomedical and Life Sciences collection. 2009.
PDF Mirror Book chapter
Sequence motif analysis Regulatory Informatics Prediction Statistics
2009Nguyen Ba AN, Pogoutse A, Provart N, Moses AM. NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics 2009,10:202.
BMC Bioinformatics Link PDF Mirror PubMed Abstract Article
Nuclear localization signal Markov Model Prediction NLStradamus
2009Liti 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.
Nature Link PDF Mirror PubMed Abstract Article
Saccharomyces cerevisiae Population genetics Evolution Phenotypic variation
2009Moses AM, Durbin R. Inferring selection on amino acid preference in protein domains. Mol Biol Evol. 2009,26:527-36.
Molecular Biology and Evolution Link PDF Mirror PubMed Abstract Article
Weakly selected variants Protein domains Polymorphism McDonald–Kreitman test Deleterious Advantageous
2008Ruan 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.
Nucleic Acids Research Link PDF Mirror PubMed Abstract Article
Genes Genomes Phylogenetic trees TreeFam Database
2007Shultzaberger RK, Chiang DY, Moses AM, Eisen MB. Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS ONE 2007,2:e1199.
PLoS One Link PDF Mirror PubMed Abstract Article
Gene regulation Microarrays Gene expression Sulfur Transcription factors DNA-binding proteins Binding analysis Saccharomyces cerevisiae
2007Moses 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.
PNAS Link PDF Mirror PubMed Abstract Article
Evolution Regulatory regions Cyclin-dependent kinase Phosphorylation sites Saccharomyces cerevisiae
2007Moses 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.
Genome Biology Link PDF Mirror PubMed Abstract Article
Clustering Regulatory regions Cyclin-dependent kinase Phosphorylation sites Saccharomyces cerevisiae
2006Pennacchio 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.
Nature Link PDF Mirror PubMed Abstract Article
Enhancer analysis Sequence conservation In vivo Regulatory regions
2006Moses 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.
PLoS Computational Biology Link PDF Mirror PubMed Abstract Article
Drosophila melanogaster Sequence alignment Binding analysis Multiple alignment calculation Invertebrate genomics Evolutionary genetics Transcription factors Genome evolution
2006Pollard 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.
PLoS Genetics Link PDF Mirror PubMed Abstract Article
Phylogenetic analysis Comparative genomics Phylogenetics Invertebrate genomics Drosophila melanogaster Evolutionary genetics Speciation Drosophila
2006Pollard 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.
BMC Bioinformatics Link PDF Mirror PubMed Abstract Article
Sequence alignment Sequence conservation CisEvolver Binding sites
2006Wang 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.
Genome Biology Link PDF Mirror PubMed Abstract Article
Evolution LDLR enhancer Lipoprotein receptor
2005Moses AM. Molecular evolution of transcriptional regulation. University of California, Berkeley 2005.
Thesis Link PhD thesis
Molecular evolution Transcriptional regulation Evolution
2004Moses 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.
Genome Biology Link PDF Mirror PubMed Abstract Article
Sequence conservation Sequence alignment Evolution Binding site MONKEY
2004Gasch 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.
PLoS Biology Link PDF Mirror PubMed Abstract Article
Saccharomyces cerevisiae Sequence motif analysis Gene regulation Candida albicans Proteasomes DNA-binding proteins Fungal evolution Fungal genetics
2004Moses AM, Chiang DY, Eisen MB. Phylogenetic Motif Detection by Expectation Maximization on Evolutionary Mixtures. Pacific Symposium on Biocomputing 2004,9:324-335.
Pacific Symposium Link PDF Mirror PubMed Abstract Article
Sequence conservation Motif discovery Evolution Binding site
2003Moses 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.
BMC Evolutionary Biology Link PDF Mirror PubMed Abstract Article
Transcription factor Position specific variation Evolution Binding site
2003Chiang 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.
Genome Biology Link PDF Mirror PubMed Abstract Article
Sequence conservation Phylogenetics Gene expression Binding site Saccharomyces