Publications

YearPublication
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)
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="NeurIPS link" link="https://papers.nips.cc/paper/8461-the-cells-out-of-sample-coos-dataset-and-benchmarks-for-measuring-out-of-sample-generalization-of-image-classifiers" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Lu_Moses_NeurIPS_2019.pdf" linkrel="" class="publication-buttons"] [label class="publication-types"]Book Chapter[/label]
[label class="publication-tags"]Deep Learning[/label] [label class="publication-tags"]Covariate shift[/label] [label class="publication-tags"]Image analysis[/label] [label class="publication-tags"]Subcellular localization[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Comp. Bio link" link="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007348" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Lu_Moses_PLoS_Comp_Bio_2019.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/31479439" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Deep Learning[/label] [label class="publication-tags"]Self-Supervised[/label] [label class="publication-tags"]Image analysis[/label] [label class="publication-tags"]Subcellular localization[/label]
2019Pritišanac I, Vernon RM, Moses AM, Forman-Kay JD Entropy and Information within Intrinsically Disordered Protein Regions . Entropy 2019 21(7), 662
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Entropy link" link="https://www.mdpi.com/1099-4300/21/7/662" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Pritisanac_Forman-Kay_Entropy_2019.pdf" linkrel="" class="publication-buttons"] [label class="publication-types"]Review[/label]
[label class="publication-tags"]Information theory[/label] [label class="publication-tags"]Biophysics[/label] [label class="publication-tags"]Intrinsically disordered[/label] [label class="publication-tags"]Evolution[/label]
2019Zarin T Sequence-function relationships in intrinsically disordered regions through the lens of evolution.
University of Toronto 2019 [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="Thesis Link" link="http://www.moseslab.csb.utoronto.ca/Zarin_Taraneh_201905_Phd_thesis.pdf" linkrel="" class="publication-buttons"] [label type="label-danger" class="publication-types"]PhD thesis[/label]
[label class="publication-tags"]Molecular evolution[/label] [label class="publication-tags"]Intrinsically disordered[/label] [label class="publication-tags"]Sequence divergence[/label][label class="publication-tags"]Biological function[/label]
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
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Elife link" link="https://elifesciences.org/articles/46883" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Zarin_Moses_Elife_2019.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/31264965" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Sequence analysis[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Intrinsically disordered[/label] [label class="publication-tags"]Evolution[/label]
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
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Bioinformatics link" link="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz402/5490207" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Lu_Moses_Bioinformatics_2019.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/31095270" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Image analysis[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]CNN[/label] [label class="publication-tags"]Machine Learning[/label]
2019Mehdi TF, Singh G, Mitchell JA, Moses AM. Variational Infinite Heterogeneous Mixture Model for Semi-supervised Clustering of Heart Enhancers. Bioinformatics 2019 Feb 7
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Bioinformatics link" link="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz064/5308600" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Mehdi_Moses_Bioinformatics_2019.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/30753279" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Regulatory networks[/label] [label class="publication-tags"]Transcription factors[/label] [label class="publication-tags"]Genomics[/label] [label class="publication-tags"]Machine Learning[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="G3 link" link="http://www.g3journal.org/content/9/2/561.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Hsu_Moses_G3_2019.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/30573469" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Regulatory networks[/label] [label class="publication-tags"]Subcellular localization[/label] [label class="publication-tags"]Time lapse microscopy[/label] [label class="publication-tags"]Cell signaling[/label]
2018Kompella PS Quantitatively Assessing the Effects of Mutations on Signaling Pathway Function University of Toronto 2019.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="Thesis Link" link="http://www.moseslab.csb.utoronto.ca/Kompella_Purnima_S_201906_PhD_thesis.pdf" linkrel="" class="publication-buttons"] [label type="label-danger" class="publication-types"]PhD thesis[/label]
[label class="publication-tags"]Molecular evolution[/label] [label class="publication-tags"]Posttranslational Regulation[/label] [label class="publication-tags"]Signalling[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Bio-protocol link" link="https://bio-protocol.org/e3022" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Lu_Moses_Bio-protocol_2018.pdf" linkrel="" class="publication-buttons"]
[label class="publication-tags"]Image analysis[/label] [label class="publication-tags"]Subcellular localization[/label] [label class="publication-tags"]Microscopy screens[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Systems Biology Link" link="https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-018-0597-3" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Strome_Moses_BMC_Sys_Bio_201.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/29970070" linkrel="" class="publication-buttons"][label class="publication-types"]Article[/label]
[label class="publication-tags"]Cell signaling[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Mitogen-activated kinases[/label] [label class="publication-tags"]Intrinsically disordered regions[/label] [label class="publication-tags"]Short linear motifs[/label] [label class="publication-tags"]High osmotic glycerol pathway[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="eLife Link" link="https://elifesciences.org/articles/31872" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Lu_Moses_eLife_2018.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/29620521" linkrel="" class="publication-buttons"][label class="publication-types"]Article[/label]
[label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Image analysis[/label] [label class="publication-tags"]Subcellular localization[/label] [label class="publication-tags"]Microscopy screens[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Bioinformatics Link" link="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2076-7" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Liku_Moses_BMC_Bioinformatics_2018.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/29482494" linkrel="" class="publication-buttons"][label class="publication-types"]Article[/label]
[label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Subcellular localization[/label] [label class="publication-tags"]Sequence motif analysis[/label]
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).
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Genetics Link" link="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006735" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/NguyenBa_Moses_PLoS_Genetics_2017.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/28410373" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Evolutionary genetics[/label] [label class="publication-tags"]Molecular evolution[/label] [label class="publication-tags"]Natural selection[/label] [label class="publication-tags"]Gene duplication[/label] [label class="publication-tags"]Fungal evolution[/label] [label class="publication-tags"]Green fluorescent protein[/label] [label class="publication-tags"]Sequence motif analysis[/label]
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).
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PNAS Link" link="http://www.pnas.org/content/114/8/E1450.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Zarin_Moses_PNAS_2017.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/28167781" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Intrinsically disordered[/label] [label class="publication-tags"]Quantitative trait[/label] [label class="publication-tags"]Phylogenetic comparative method[/label] [label class="publication-tags"]Stabilizing selection[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="G3 Link" link="http://www.g3journal.org/content/7/3/911.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Youn_Andrews_G3_2017.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/28122947" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Yeast genetics[/label] [label class="publication-tags"]Genetic interactions[/label] [label class="publication-tags"]Kinase[/label] [label class="publication-tags"]Transcription factor[/label] [label class="publication-tags"]Genetic networks[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="ACS Synthetic Biology Link" link="http://pubs.acs.org/doi/abs/10.1021/acssynbio.6b00142" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Kompella_Peisajovich_ACS_Synth_Bio_2016.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/27935292" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Premature stop codon[/label] [label class="publication-tags"]Signaling network[/label]
2016Moses AM. Statistical Modeling and Machine Learning for Molecular Biology. CRC Press Taylor & Francis Group 2016 Dec.12.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="CRC Press Link" link="https://www.crcpress.com/Statistical-Modeling-and-Machine-Learning-for-Molecular-Biology/Moses/p/book/9781482258592" linkrel="" class="publication-buttons"] [label type="label-success" class="publication-types"]Book[/label]
[label class="publication-tags"]Molecular biology[/label] [label class="publication-tags"]Statistics[/label] [label class="publication-tags"]Machine learning[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS One Link" link="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158712" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Lu_Moses_PLoS_One_2016.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/27442431" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Imaging techniques[/label] [label class="publication-tags"]Cell cycle and cell division[/label] [label class="publication-tags"]Genetic screens[/label] [label class="publication-tags"]Subcellular localization[/label] [label class="publication-tags"]Image analysis[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Green fluorescent protein[/label] [label class="publication-tags"]Perception[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Plant Journal Link" link="http://onlinelibrary.wiley.com/wol1/doi/10.1111/tpj.13261/abstract" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Austin_Provart_Plant_J_2016.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="https://www.ncbi.nlm.nih.gov/pubmed/27401965" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Coexpression analysis[/label] [label class="publication-tags"]Cis-element prediction[/label] [label class="publication-tags"]Gene expression markers[/label] [label class="publication-tags"]Reporter constructs[/label] [label class="publication-tags"]Promoter analysis[/label] [label class="publication-tags"]Arabidopsis thaliana[/label] [label class="publication-tags"]Technical advance[/label]
2016Douglas GM, Wilson MD, Moses AM. Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration. Mol. Biol. Evol. 2016 Feb 16.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Molecular Biology and Evolution Link" link="http://mbe.oxfordjournals.org/content/early/2016/03/07/molbev.msw030.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Douglas_Moses_MBE_2016.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/26882985" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Pseudoenhancer[/label] [label class="publication-tags"]Regulatory evolution[/label] [label class="publication-tags"]ChIP-seq[/label] [label class="publication-tags"]Neutral evolution[/label] [label class="publication-tags"]Histone modifications[/label]
2015Davey NE, Cyert MS, Moses AM. Short linear motifs–ex nihilo evolution of protein regulation. Cell Comm. Sig. 2015 Nov 21.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Cell Communication and Signaling Link" link="http://biosignaling.biomedcentral.com/articles/10.1186/s12964-015-0120-z" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Davey_Moses_CellCommSig_2015.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/26589632" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Motifs[/label] [label class="publication-tags"]Short linear motifs[/label] [label class="publication-tags"]SLiMs[/label] [label class="publication-tags"]Cis-regulatory elements[/label] [label class="publication-tags"]RNA motifs[/label] [label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Modularity[/label] [label class="publication-tags"]Protein evolution[/label]
2015Wong KC, Li Y, Peng C, Moses AM, Zhang Z. Computational learning on specificity-determining residue-nucleotide interactions. Nucleic Acids Res. 2015 Dec 2.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Nucleic Acids Research Link" link="http://nar.oxfordjournals.org/content/43/21/10180.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Wong_Zhang_NAR_2015.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/26527718" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Protein-nucleic acid interaction[/label] [label class="publication-tags"]Computational methods[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Genome Biology and Evolution Link" link="http://gbe.oxfordjournals.org/content/early/2015/06/04/gbe.evv105.abstract" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Khan_Moses_GBE_2015.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/26047845" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Negative Selection[/label] [label class="publication-tags"]Indels[/label] [label class="publication-tags"]SNP[/label] [label class="publication-tags"]Intrinsically Disordered Protein[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="G3 Link" link="http://www.g3journal.org/content/early/2015/06/05/g3.115.017830.abstract" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Koh_Moffat_G3_2015.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/26048563" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]GFP[/label] [label class="publication-tags"]Imaging[/label] [label class="publication-tags"]Microscopy[/label] [label class="publication-tags"]Subcellular localization[/label] [label class="publication-tags"]CYCLoPs[/label] [label class="publication-tags"]Database[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Cell Link" link="http://www.sciencedirect.com/science/article/pii/S0092867415005267" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Chong_Andrews_Cell_2015.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/26046442" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Proteomics[/label] [label class="publication-tags"] Imaging[/label] [label class="publication-tags"]GFP[/label] [label class="publication-tags"]Microscopy[/label] [label class="publication-tags"]CYCLoPs[/label] [label class="publication-tags"]Database[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Biology Link" link="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002146" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Gogl_Weiss_PLoS_Biol_2015.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/25966461" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Phosphorylation[/label] [label class="publication-tags"]Sequence motif analysis[/label] [label class="publication-tags"]Crystal structure[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Molecular dynamics[/label] [label class="publication-tags"]Protein kinase signaling cascade[/label] [label class="publication-tags"]Fungal evolution[/label] [label class="publication-tags"]Protein structure[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Computational Biology Link" link="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003977" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Nguyen_PLOS_COMP_2014.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/25474245" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Sequence motif analysis[/label] [label class="publication-tags"]Fungal evolution[/label] [label class="publication-tags"]Molecular evolution[/label] [label class="publication-tags"]Gene duplication[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Evolutionary genetics[/label] [label class="publication-tags"]Sequence alignment[/label] [label class="publication-tags"]Statistical distributions[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Bioinformatics Link" link="http://bioinformatics.oxfordjournals.org/content/early/2014/12/09/bioinformatics.btu759.abstract?keytype=ref&ijkey=PR1MELZehSTHz6X" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Handfield_Bioinformatics_2014.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/25398614" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Bioinformatics[/label] [label class="publication-tags"]Statistics[/label] [label class="publication-tags"]Microscopy[/label] [label class="publication-tags"]Imaging[/label] [label class="publication-tags"]Subcellular localization[/label] [label class="publication-tags"]Cell-to-cell variability[/label]
2014Nguyen Ba AN. Molecular Evolution of Posttranslational regulation in disordered regions. University of Toronto 2014.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="Thesis Link" link="http://www.moseslab.csb.utoronto.ca/NguyenBa_PhD_Thesis_2014.pdf" linkrel="" class="publication-buttons"] [label type="label-danger" class="publication-types"]PhD thesis[/label]
[label class="publication-tags"]Molecular evolution[/label] [label class="publication-tags"]Posttranslational[/label] [label class="publication-tags"]Regulation[/label] [label class="publication-tags"]Disordered regions[/label]
2014Landry CR, Freschi L, Zarin T, Moses AM. Turnover of protein phosphorylation evolving under stabilizing selection. Front Genet. 2014 Jul 23;5:245.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Frontiers in Genetics Link" link="http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00245/full" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Landry_Moses_FIG_2014.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/25101120" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Protein phosphorylation[/label] [label class="publication-tags"]Evolutionary turnover[/label] [label class="publication-tags"]Molecular switches[/label] [label class="publication-tags"]Molecular rheostats[/label] [label class="publication-tags"]Protein evolution[/label] [label class="publication-tags"]Molecular evolution[/label] [label class="publication-tags"]Cell signaling[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Developmental Cell Link" link="http://www.cell.com/developmental-cell/abstract/S1534-5807%2814%2900203-2" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Lumba_McCourt_Dev_Cell_2014.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/24823379" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Interactome[/label] [label class="publication-tags"]ABA network[/label] [label class="publication-tags"]Signaling[/label] [label class="publication-tags"]Coexpression[/label] [label class="publication-tags"]Arabidopsis thaliana[/label]
2014Handfield LF. Automated Image Analysis for Systematic and Quantitative Comparison of Protein Expression within Cell Populations. University of Toronto 2014.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="Thesis Link" link="http://www.moseslab.csb.utoronto.ca/Handfield_PhD_Thesis_2014.pdf" linkrel="" class="publication-buttons"] [label type="label-danger" class="publication-types"]PhD thesis[/label]
[label class="publication-tags"]Imaging[/label] [label class="publication-tags"]Microscopy[/label] [label class="publication-tags"]Image analysis[/label] [label class="publication-tags"]Protein expression[/label]
2014Zarin T, Moses AM. Insights into molecular evolution from yeast genomics. Yeast. 2014 Apr 24.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Yeast Link" link="http://onlinelibrary.wiley.com/doi/10.1002/yea.3018/abstract" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Zarin_Moses_Yeast_2014.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/24760744" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Molecular evolution[/label] [label class="publication-tags"]Comparative genomics[/label] [label class="publication-tags"]Experimental evolution[/label] [label class="publication-tags"]Complex phenotypes[/label] [label class="publication-tags"]Population genomics[/label] [label class="publication-tags"]Gene duplication[/label] [label class="publication-tags"]Gene order[/label] [label class="publication-tags"]Regulatory evolution[/label] [label class="publication-tags"]Functional synthesis[/label] [label class="publication-tags"]Functional genomics[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Molecular Biology and Evolution Link" link="https://academic.oup.com/mbe/article/31/4/872/1103434/A-High-Definition-View-of-Functional-Genetic" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Bergstrom_Liti_MBE_2014.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/24425782" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Population genomics[/label] [label class="publication-tags"]Functional variation[/label] [label class="publication-tags"]Genome evolution[/label] [label class="publication-tags"]Yeast[/label] [label class="publication-tags"]Subtelomeres[/label] [label class="publication-tags"]Loss-of-function variants[/label]
2014Safi M. Computational Modeling of Drug Resistance: Structural and Evolutionary Models. University of Toronto 2014.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="Thesis Link" link="http://www.moseslab.csb.utoronto.ca/Safi_PhD_Thesis_2014.pdf" linkrel="" class="publication-buttons"] [label type="label-danger" class="publication-types"]PhD thesis[/label]
[label class="publication-tags"]Drug resistance[/label] [label class="publication-tags"]Computational modeling[/label] [label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Structural models[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Nature Genetics Link" link="http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.2684.html" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Haudry_Blanchette_Nat_Genetics_2013.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/23817568" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Genomics[/label] [label class="publication-tags"]Plant genetics[/label] [label class="publication-tags"]Sequence annotation[/label] [label class="publication-tags"]Regulatory regions[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Computational Biology Link" link="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003085" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Handfield_Moses_PLoS_Comp_Biol_2013.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/23785265" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Ellipses[/label] [label class="publication-tags"]Protein expression[/label] [label class="publication-tags"]Cell cycle and cell division[/label] [label class="publication-tags"]Subcellular localization[/label] [label class="publication-tags"]Permutation[/label] [label class="publication-tags"]Normal distribution[/label] [label class="publication-tags"]Protein domains[/label] [label class="publication-tags"]Fluorescence imaging[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Genomics Link" link="http://www.biomedcentral.com/1471-2164/14/162" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Khoshraftar_Christendat_BMC_Genomics_2013.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/23496816" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Sequencing[/label] [label class="publication-tags"]Annotation[/label] [label class="publication-tags"]Ophiostoma ulmi[/label] [label class="publication-tags"]Genome[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Genomics Link" link="http://www.biomedcentral.com/1471-2164/14/69" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Liti_Nieduszynski_BMC_genomics_2013.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/23368932" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Sequencing[/label] [label class="publication-tags"]Assembly[/label] [label class="publication-tags"]Saccharomyces arboricolus[/label] [label class="publication-tags"]Genome[/label]
2012Zia A, Moses AM. Towards a theoretical understanding of false positives in DNA motif finding. BMC Bioinformatics 2012 Jun 27;13:151.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Bioinformatics Link" link="http://www.biomedcentral.com/1471-2105/13/151" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Zia_Moses_BMC_Bioinf_2012.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/22738169" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Bioinformatics[/label] [label class="publication-tags"]Sequence motif analysis[/label] [label class="publication-tags"]False positive motifs[/label] [label class="publication-tags"]DNA motif finding[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Science Signaling Link" link="http://stke.sciencemag.org/cgi/content/full/sigtrans;5/215/rs1?ijkey=6kN7zziDsmx86&keytype=ref&siteid=sigtrans" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/NguenBa_Moses_Science_Sig_2012_supp.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/22416277" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Proteomics[/label] [label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Sequence conservation[/label] [label class="publication-tags"]Disordered regions[/label]
2012Lai AC, Nguyen Ba AN, Moses AM. Predicting Kinase Substrates using Conservation of Local Motif Density. Bioinformatics 2012,Feb 1.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Bioinformatics Link" link="http://bioinformatics.oxfordjournals.org/content/early/2012/02/01/bioinformatics.bts060.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Lai_Moses_Bioinf_2012.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/22302575" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Kinase[/label] [label class="publication-tags"]Sequence conservation[/label] [label class="publication-tags"]Motif density[/label] [label class="publication-tags"]Sequence motif analysis[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Bioinformatics Link" link="http://www.biomedcentral.com/1471-2105/12/299" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Zia_Moses_BMC_Bioinf_2011.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/21781308" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Mutation[/label] [label class="publication-tags"]Indels[/label] [label class="publication-tags"]Genetic information[/label] [label class="publication-tags"]Nonsense mutation[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Genetics Link" link="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002111" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Warringer_Blomberg_PLoS_Gen_2011.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/21698134" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Galactose[/label] [label class="publication-tags"]Genetic polymorphism[/label] [label class="publication-tags"]Genetic drift[/label] [label class="publication-tags"]Mutant genotypes[/label] [label class="publication-tags"]Phenotypes[/label] [label class="publication-tags"]Population genetics[/label] [label class="publication-tags"]Evolutionary genetics[/label]
2011Moses AM, Davidson AR. In vitro evolution goes deep. Proc Natl Acad Sci U S A. 2011,May 17;108(20):8071-2.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PNAS Link" link="http://www.pnas.org/content/108/20/8071.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_Davidson_PNAS_2011.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/21551096" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Experimental evolution[/label] [label class="publication-tags"]In vitro[/label] [label class="publication-tags"]EMPIRIC[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Genome Biology Link" link="http://genomebiology.com/2011/12/4/R39/abstract" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Sharifpoor_Andrews_Genome_Biol_2011.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/21492431" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Kinase[/label] [label class="publication-tags"]Kinase interaction[/label] [label class="publication-tags"]KID[/label] [label class="publication-tags"]Database[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Genome Research Link" link="http://genome.cshlp.org/content/early/2011/03/18/gr.116731.110.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Parts_Liti_Genome_Res_2011.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/21422276" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]QTL mapping[/label] [label class="publication-tags"]Artificial selection[/label] [label class="publication-tags"]Complex traits[/label] [label class="publication-tags"]Genetics[/label]
2011Josephides C, Moses AM. Modeling the evolution of a classic genetic switch. BMC Syst Biol. 2011,Feb 5;5:24.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Systems Biology Link" link="http://www.biomedcentral.com/1752-0509/5/24" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Josephides_Moses_BMC_Sys_Bio_2011.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/21294912" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Genetic switch[/label] [label class="publication-tags"]Computational modeling[/label] [label class="publication-tags"]Gene duplication[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS One Link" link="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015934" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Gonsalves_Westwood_PLoS_One_2011.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/21264254" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]DNA transcription[/label] [label class="publication-tags"]Larvae[/label] [label class="publication-tags"]Drosophila melanogaster[/label] [label class="publication-tags"]Cell binding[/label] [label class="publication-tags"]Gene regulation[/label] [label class="publication-tags"]Introns[/label] [label class="publication-tags"]Invertebrate genomics[/label] [label class="publication-tags"]Binding analysis[/label]
2011Cutter AD, Moses AM. Polymorphism, divergence and the role of recombination in Saccharomyces cerevisiae genome evolution. Mol. Biol. Evol. 2011,28(5):1745-1754.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Molecular Biology and Evolution Link" link="http://mbe.oxfordjournals.org/content/early/2011/01/03/molbev.msq356?keytype=ref&ijkey=0Qm7gqJBhghouEh" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Cutter_Moses_MBE_2011.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/21199893" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Genetic hitchhiking[/label] [label class="publication-tags"]Background selection[/label] [label class="publication-tags"]Recombination rate[/label] [label class="publication-tags"]Mutagenic recombination[/label] [label class="publication-tags"]Budding yeast[/label] [label class="publication-tags"]Nucleotide polymorphism[/label]
2010Moses AM, Landry CR. Moving from transcriptional to phospho-evolution: generalizing regulatory evolution? Trends in Genetics 2010,Sept. 1.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Trends in Genetics Link" link="http://www.cell.com/trends/genetics/abstract/S0168-9525%2810%2900150-2" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_Landry_TIG_2010.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/20817339" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Regulatory networks[/label] [label class="publication-tags"]Transcriptional regulation[/label] [label class="publication-tags"]Kinase[/label]
2010Nguyen Ba AN, Moses AM. Evolution of characterized phosphorylation sites in budding yeast. Mol. Biol. Evol. 2010,27:9.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Molecular Biology and Evolution Link" link="http://mbe.oxfordjournals.org/content/27/9/2027.abstract" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/NguyenBa_Moses_MBE_2010.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/20368267" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Phosphorylation sites[/label] [label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Prediction[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PNAS Link" link="http://www.pnas.org/content/107/7/2977.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Fraser_Schadt_PNAS_2010.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/20133628" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Gene expression[/label] [label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Adaptation[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Evolutionary Biology Link" link="http://www.biomedcentral.com/1471-2148/9/286" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_BMC_Evol_Biol_2009.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/19995462" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Natural selection[/label] [label class="publication-tags"]Regulatory regions[/label] [label class="publication-tags"]Transcription factor[/label] [label class="publication-tags"]Statistics[/label]
2009Moses AM, Sinha S. Regulatory Motif Analysis. Bioinformatics: Tools and Applications (Edwards D, Stajich J, Hansen D). Springer Biomedical and Life Sciences collection. 2009.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_Sinha_Bioinf_Tools_apps_2009.pdf" linkrel="" class="publication-buttons"] [label type="label-info" class="publication-types"]Book chapter[/label]
[label class="publication-tags"]Sequence motif analysis[/label] [label class="publication-tags"]Regulatory Informatics[/label] [label class="publication-tags"]Prediction[/label] [label class="publication-tags"]Statistics[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Bioinformatics Link" link="http://www.biomedcentral.com/1471-2105/10/202" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/NguyenBa_Moses_BMC_Bioinf_2009.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/19563654" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Nuclear localization signal[/label] [label class="publication-tags"]Markov Model[/label] [label class="publication-tags"] Prediction[/label] [label class="publication-tags"]NLStradamus[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Nature Link" link="http://www.nature.com/nature/journal/v458/n7236/full/nature07743.html" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Liti_Louis_Nature_2009.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/19212322" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Population genetics[/label] [label class="publication-tags"] Evolution[/label] [label class="publication-tags"]Phenotypic variation[/label]
2009Moses AM, Durbin R. Inferring selection on amino acid preference in protein domains. Mol Biol Evol. 2009,26:527-36.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Molecular Biology and Evolution Link" link="http://mbe.oxfordjournals.org/cgi/content/full/26/3/527" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_Durbin_MBE_2008.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/19095755" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Weakly selected variants[/label] [label class="publication-tags"]Protein domains[/label] [label class="publication-tags"]Polymorphism[/label] [label class="publication-tags"]McDonald–Kreitman test[/label] [label class="publication-tags"]Deleterious[/label] [label class="publication-tags"]Advantageous[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Nucleic Acids Research Link" link="http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D735" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Ruan_Durbin_NAR_2008.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/18056084" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Genes[/label] [label class="publication-tags"]Genomes[/label] [label class="publication-tags"]Phylogenetic trees[/label] [label class="publication-tags"]TreeFam[/label] [label class="publication-tags"]Database[/label]
2007Shultzaberger RK, Chiang DY, Moses AM, Eisen MB. Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS ONE 2007,2:e1199.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS One Link" link="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001199" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Shulzaberger_Eisen_PLoS_One_2007.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/18030333" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Gene regulation[/label] [label class="publication-tags"]Microarrays[/label] [label class="publication-tags"]Gene expression[/label] [label class="publication-tags"]Sulfur[/label] [label class="publication-tags"]Transcription factors[/label] [label class="publication-tags"]DNA-binding proteins[/label] [label class="publication-tags"]Binding analysis[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PNAS Link" link="http://www.pnas.org/content/104/45/17713.long" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_Durbin_PNAS_2007.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/17978194" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Regulatory regions[/label] [label class="publication-tags"]Cyclin-dependent kinase[/label] [label class="publication-tags"]Phosphorylation sites[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Genome Biology Link" link="http://genomebiology.com/2007/8/2/R23" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_Durbin_Genome_biol_2007.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/17316440" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Clustering[/label] [label class="publication-tags"]Regulatory regions[/label] [label class="publication-tags"]Cyclin-dependent kinase[/label] [label class="publication-tags"]Phosphorylation sites[/label] [label class="publication-tags"]Saccharomyces cerevisiae[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Nature Link" link="http://www.nature.com/nature/journal/v444/n7118/abs/nature05295.html" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Pennacchio_Rubin_Nature_2006.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/17086198" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Enhancer analysis[/label] [label class="publication-tags"]Sequence conservation[/label] [label class="publication-tags"]In vivo[/label] [label class="publication-tags"]Regulatory regions[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Computational Biology Link" link="http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0020130" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_Eisen_PLoS_Comp_Biol_2006.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/17040121" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Drosophila melanogaster[/label] [label class="publication-tags"]Sequence alignment[/label] [label class="publication-tags"]Binding analysis[/label] [label class="publication-tags"]Multiple alignment calculation[/label] [label class="publication-tags"]Invertebrate genomics[/label] [label class="publication-tags"]Evolutionary genetics[/label] [label class="publication-tags"]Transcription factors[/label] [label class="publication-tags"]Genome evolution[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Genetics Link" link="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020173" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Pollard_Eisen_PLoS_Genetics_2006.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/17132051" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Phylogenetic analysis[/label] [label class="publication-tags"]Comparative genomics[/label] [label class="publication-tags"]Phylogenetics[/label] [label class="publication-tags"]Invertebrate genomics[/label] [label class="publication-tags"]Drosophila melanogaster[/label] [label class="publication-tags"]Evolutionary genetics[/label] [label class="publication-tags"]Speciation[/label] [label class="publication-tags"]Drosophila[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Bioinformatics Link" link="http://www.biomedcentral.com/1471-2105/7/376" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Pollard_Eisen_MBC_Bioinf_2006.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/16904011" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Sequence alignment[/label] [label class="publication-tags"]Sequence conservation[/label] [label class="publication-tags"]CisEvolver[/label] [label class="publication-tags"]Binding sites[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Genome Biology Link" link="http://genomebiology.com/2006/7/8/R68" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Wang_Boffelli_Genome_Biol_2006.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/16884525" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Evolution[/label] [label class="publication-tags"]LDLR enhancer[/label] [label class="publication-tags"]Lipoprotein receptor[/label]
2005Moses AM. Molecular evolution of transcriptional regulation. University of California, Berkeley 2005.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="Thesis Link" link="http://labs.eeb.utoronto.ca/moses/Moses_PhD_Thesis_2005.pdf" linkrel="" class="publication-buttons"] [label type="label-danger" class="publication-types"]PhD thesis[/label]
[label class="publication-tags"]Molecular evolution[/label] [label class="publication-tags"]Transcriptional regulation[/label] [label class="publication-tags"]Evolution[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Genome Biology Link" link="http://genomebiology.com/2004/5/12/R98" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_Eisen_Genome_Biol_2004.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/15575972" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Sequence conservation[/label] [label class="publication-tags"]Sequence alignment[/label] [label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Binding site[/label] [label class="publication-tags"] MONKEY[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PLoS Biology Link" link="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020398" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Gasch_Eisen_PLoS_Biol_2004.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/15534694" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Saccharomyces cerevisiae[/label] [label class="publication-tags"]Sequence motif analysis[/label] [label class="publication-tags"]Gene regulation[/label] [label class="publication-tags"]Candida albicans[/label] [label class="publication-tags"]Proteasomes[/label] [label class="publication-tags"]DNA-binding proteins[/label] [label class="publication-tags"]Fungal evolution[/label] [label class="publication-tags"]Fungal genetics[/label]
2004Moses AM, Chiang DY, Eisen MB. Phylogenetic Motif Detection by Expectation Maximization on Evolutionary Mixtures. Pacific Symposium on Biocomputing 2004,9:324-335.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Pacific Symposium Link" link="http://psb.stanford.edu/psb-online/proceedings/psb04/moses.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_PSB_2004.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/14992514" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Sequence conservation[/label] [label class="publication-tags"]Motif discovery[/label] [label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Binding site[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="BMC Evolutionary Biology Link" link="http://www.biomedcentral.com/1471-2148/3/19" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Moses_BMC_evol_biol_2003.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/12946282" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Transcription factor[/label] [label class="publication-tags"]Position specific variation[/label] [label class="publication-tags"]Evolution[/label] [label class="publication-tags"]Binding site[/label]
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.
[button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="Genome Biology Link" link="http://genomebiology.com/2003/4/7/R43" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-download-alt" align="left" type="link" target="true" title="PDF Mirror" link="http://www.moseslab.csb.utoronto.ca/Chiang_genome_biol_2003.pdf" linkrel="" class="publication-buttons"] [button style="btn-default btn-sm" icon="glyphicon glyphicon-share" align="left" type="link" target="true" title="PubMed Abstract" link="http://www.ncbi.nlm.nih.gov/pubmed/12844359" linkrel="" class="publication-buttons"] [label class="publication-types"]Article[/label]
[label class="publication-tags"]Sequence conservation[/label] [label class="publication-tags"]Phylogenetics[/label] [label class="publication-tags"]Gene expression[/label] [label class="publication-tags"]Binding site[/label] [label class="publication-tags"] Saccharomyces[/label]