Moses Lab

Publications

yearpublication
2024Lu AX, Moses AM. Using Dimensionality Reduction to Visualize Phenotypic Changes in High-Throughput Microscopy. Methods Mol Biol. 2800:217-229.
Methods in Molecular Biology Link PDF Mirror PubMed Abstract
2024Duncan AG, Mitchell JA, Moses AM. Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation. Bioinformatics Mar 29;40(4):btae190.
Bioinformatics Link PDF Mirror PubMed Abstract
2023Alderson TR, Pritišanac I, Kolarić Đ, Moses AM, Forman-Kay JD.
Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2. PNAS Oct 31;120(44):e2304302120
PNAS Link PDF Mirror PubMed Abstract
2023Millar SR, Huang JQ, Schreiber KJ, Tsai YC, Won J, Zhang J, Moses AM, Youn JY. A New Phase of Networking: The Molecular Composition and Regulatory Dynamics of Mammalian Stress Granules. Chem Rev. Jul 26;123(14):9036-9064
Chemical Reviews Link PDF Mirror PubMed Abstract
2022Duffy EE, Finander B, Choi G, Carter AC, Pritisanac I, Alam A, Luria V, Karger A, Phu W, Sherman MA, Assad EG, Pajarillo N, Khitun A, Crouch EE, Ganesh S, Chen J, Berger B, Sestan N, O’Donnell-Luria A, Huang EJ, Griffith EC, Forman-Kay JD, Moses AM, Kalish BT, Greenberg ME. Developmental dynamics of RNA translation in the human brain. Nat Neurosci. Oct;25(10):1353-1365.
Nature Neuroscience Link PDF Mirror PubMed Abstract
2022Nursimulu N, Moses AM, Parkinson J. Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation. PLoS Comput Biol. Sep 8;18(9)
PLoS Comp. Bio. Link PDF Mirror PubMed Abstract
2022Sangster AG, Zarin T, Moses AM. Evolution of short linear motifs and disordered proteins Topic: yeast as model system to study evolution. Curr Opin Genet Dev Oct;76:101964
Curr Opin Genet Dev Link PDF Mirror PubMed Abstract
2022Lu AX, Lu AX, Pritišanac I, Zarin T, Forman-Kay JD, Moses AM.
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning. PLoS Comput Biol. Jun 29;18(6)
PLoS Comp. Bio. Link PDF Mirror PubMed Abstract
2021Hua SBZ, Lu AX, Moses AM. CytoImageNet: A large-scale pretraining dataset for bioimage transfer learning Learning Meaningful Representations of Life (LMRL 2021)
arxiv Link PDF Mirror
2021Hsu IS, Strome B, Lash E, Robbins N, Cowen LE, Moses AM. A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling PLoS Genet. 2021 Sep 10; 17(9):e1009629
PLoS Genetics Link PDF Mirror PubMed Abstract
2021Hsu IS Quantitative Experimental and Mathematical Approaches to Extract Information about Transcription Factor Pulsing University of Toronto 2021 Thesis Link PhD thesis
Thesis Link
2021Lu AX Unsupervised machine learning for hypothesis discovery and representation learning in biological image and sequence analysis University of Toronto 2021 Thesis Link PhD thesis
Thesis Link
2021Singh G, Mullany S, Moorthy SD, Zhang R, Mehdi T, Tian R, Duncan AG, Moses AM, Mitchell JA. A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells Genome Res. 2021 Apr;31(4):564-575
Genome Research Link PDF Mirror PubMed Abstract
2021Zarin T, Strome B, Peng G, Pritišanac I, Forman-Kay JD, Moses AM.
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions. Elife. 2021 Feb 22;10:e60220
Elife Link PDF Mirror PubMed Abstract
2021Hsu IS, Moses AM Stochastic models for single-cell data: Current challenges and the way forward. FEBS J. Feb 11 2021
FEBS J. Link PDF Mirror PubMed Abstract
2020Tsang B, Pritišanac I, Scherer SW, Moses AM, Forman-Kay JD Phase separation as a missing mechanism for interpretation of disease mutations Cell 2020 Dec 23
Cell Press Link PDF Mirror PubMed Abstract
2020Lu AX, Lu AX, Moses A Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning 15th Machine Learning in Computational Biology (MLCB 2020)
arXiv Link PDF Mirror
2020Lu AX, Zhang H, Ghassemi M, Moses A Self-Supervised Contrastive Learning of Protein Representations By Mutual Information Maximization 15th Machine Learning in Computational Biology (MLCB 2020)
biorxiv Link PDF Mirror
2020 Pritišanac I, Zarin T, Forman-Kay JD, Moses AM Whence Blobs? Phylogenetics of functional protein condensates Biochem Soc Trans. 2020 Sep 28
Biochem Soc Trans. Link PDF Mirror PubMed Abstract
2020Kuzmin E, VanderSluis B, Nguyen Ba AN, Wang W, Koch EN, Usaj M, Khmelinskii A, Usaj MM, van Leeuwen J, Kraus O, Tresenrider A, Pryszlak M, Hu MC, Varriano B, Costanzo M, Knop M, Moses A, Myers CL, Andrews BJ, Boone C. Exploring whole-genome duplicate gene retention with complex genetic interaction analysis Science. 2020 Jun 26;368(6498):eaaz5667
Science Link PDF Mirror PubMed Abstract
2020Iserman C, Desroches Altamirano C, Jegers C, Friedrich U, Zarin T, Fritsch AW, Mittasch M, Domingues A, Hersemann L, Jahnel M, Richter D, Guenther UP, Hentze MW, Moses AM, Hyman AA, Kramer G, Kreysing M, Franzmann TM, Alberti S Condensation of Ded1p Promotes a Translational Switch from Housekeeping to Stress Protein Production Cell. 2020 May 14;181(4):818-831.e19.
Cell Press Link PDF Mirror PubMed Abstract
2020Michowski W, Chick JM, Chu C, Kolodziejczyk A, Wang Y, Suski JM, Abraham B, Anders L, Day D, Dunkl LM, Li Cheong Man M, Zhang T, Laphanuwat P, Bacon NA, Liu L, Fassl A, Sharma S, Otto T, Jecrois E, Han R, Sweeney KE, Marro S, Wernig M, Geng Y, Moses A, Li C, Gygi SP, Young RA, Sicinski P Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells Mol Cell. 2020 May 7;78(3):459-476.e13
Cell Press Link PDF Mirror PubMed Abstract
2019 Moses AM, Lu AX, Lu AX, Ghassemi M Transfer Learning vs. Batch Effects: what can we expect from neural networks in computational biology? 14th Machine Learning in Computational Biology (MLCB 2019)
MLCB link PDF Mirror
2019 Lu AX, Lu AX, Schormann W, Ghassemi M, Andrews DW, Moses AM The Cells Out of Sample (COOS) dataset and benchmarks for measuring out-of-sample generalization of image classifiers Advances in Neural Information Processing Systems 32 (NeurIPS 2019)
NeurIPS link PDF Mirror
2019Lu AX, Kraus OZ, Cooper S, Moses AM. Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting. PLoS Comput Biol. 2019 Sep 3;15(9):e1007348.
PLoS Comp. Bio link PDF Mirror PubMed Abstract
2019Pritišanac I, Vernon RM, Moses AM, Forman-Kay JD Entropy and Information within Intrinsically Disordered Protein Regions . Entropy 2019 21(7), 662
Entropy link PDF Mirror
2019Zarin T Sequence-function relationships in intrinsically disordered regions through the lens of evolution.
University of Toronto 2019 Thesis Link PhD thesis
Thesis Link
2019Zarin T, Strome B, Nguyen Ba AN, Alberti S, Forman-Kay JD, Moses AM. Proteome-wide signatures of function in highly diverged intrinsically disordered regions. Elife 2019 Jul 2;8
Elife link PDF Mirror PubMed Abstract
2019Lu AX, Zarin T, Hsu IS, Moses AM. YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells. Bioinformatics 2019 May 16
Bioinformatics link PDF Mirror PubMed Abstract
2019Mehdi TF, Singh G, Mitchell JA, Moses AM. Variational Infinite Heterogeneous Mixture Model for Semi-supervised Clustering of Heart Enhancers. Bioinformatics 2019 Feb 7
Bioinformatics link PDF Mirror PubMed Abstract
2019Hsu IS, Strome B, Plotnikov S, Moses AM. A Noisy Analog-to-Digital Converter Connects Cytosolic Calcium Bursts to Transcription Factor Nuclear Localization Pulses in Yeast. G3 2019 Feb 7;9(2):561-570.
G3 link PDF Mirror PubMed Abstract
2018Kompella PS Quantitatively Assessing the Effects of Mutations on Signaling Pathway Function University of Toronto 2019.
Thesis Link
2018Lu AX, Handfield LF, Moses AM. Extracting and Integrating Protein Localization Changes from Multiple Image Screens of Yeast Cells. Bio-protocol Vol 8, Iss 18, Sep 20, 2018.
Bio-protocol link PDF Mirror
2018Strome B, Hsu IS, Li Cheong Man M, Zarin T, Nguyen Ba A, Moses AM. Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity. BMC Syst Biol. 2018 Jul 3;12(1):75.
BMC Systems Biology Link PDF Mirror PubMed Abstract
2018Lu AX, Chong YT, Hsu IS, Strome B, Handfield LF, Kraus O, Andrews BJ, Moses AM. Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins. eLife 2018;7:e31872.
eLife Link PDF Mirror PubMed Abstract
2018Liku ME, Legere EA, Moses AM NoLogo: a new statistical model highlights the diversity and suggests new classes of Crm1-dependent nuclear export signals. BMC Bioinformatics. 2018 7:Feb 27;19(1):65.
BMC Bioinformatics Link PDF Mirror PubMed Abstract
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
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
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
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
2016Moses AM. Statistical Modeling and Machine Learning for Molecular Biology. CRC Press Taylor & Francis Group 2016 Dec.12.
CRC Press Link
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
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
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
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
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
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
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
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
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
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
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
2014Nguyen Ba AN. Molecular Evolution of Posttranslational regulation in disordered regions. University of Toronto 2014.
Thesis Link
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
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
2014Handfield LF. Automated Image Analysis for Systematic and Quantitative Comparison of Protein Expression within Cell Populations. University of Toronto 2014.
Thesis Link
2014Zarin T, Moses AM. Insights into molecular evolution from yeast genomics. Yeast. 2014 Apr 24.
Yeast Link PDF Mirror PubMed Abstract
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
2014Safi M. Computational Modeling of Drug Resistance: Structural and Evolutionary Models. University of Toronto 2014.
Thesis Link
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
2005Moses AM. Molecular evolution of transcriptional regulation. University of California, Berkeley 2005.
Thesis Link
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
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
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
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
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