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Alan Moses, Ph.D. - Publications

Affiliations: 
Cells & Systems Biology University of Toronto, Toronto, ON, Canada 
Website:
http://www.moseslab.csb.utoronto.ca/
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Singh 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 Research. PMID 33712417 DOI: 10.1101/gr.272468.120  0.333
2020 Kuzmin 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, ... Moses A, et al. Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. Science (New York, N.Y.). 368. PMID 32586993 DOI: 10.1126/Science.Aaz5667  0.351
2018 Lu AX, Handfield LF, Moses AM. Extracting and Integrating Protein Localization Changes from Multiple Image Screens of Yeast Cells. Bio-Protocol. 8: e3022. PMID 34395810 DOI: 10.21769/BioProtoc.3022  0.682
2018 Lu 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 protein subcellular localization change. Elife. 7. PMID 29620521 DOI: 10.7554/Elife.31872  0.684
2018 Lu A, Handfield L, Moses A. Extracting and Integrating Protein Localization Changes from Multiple Image Screens of Yeast Cells Bio-Protocol. 8. DOI: 10.21769/BIOPROTOC.3022  0.664
2016 Austin RS, Hiu S, Waese J, Ierullo M, Pasha A, Wang T, 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. The Plant Journal : For Cell and Molecular Biology. PMID 27401965 DOI: 10.1111/Tpj.13261  0.321
2016 Douglas GM, Wilson MD, Moses AM. Decreased transcription factor binding levels nearby primate pseudogenes suggests regulatory degeneration. Molecular Biology and Evolution. PMID 26882985 DOI: 10.1093/Molbev/Msw030  0.301
2015 Davey NE, Cyert MS, Moses AM. Short linear motifs - ex nihilo evolution of protein regulation. Cell Communication and Signaling : Ccs. 13: 43. PMID 26589632 DOI: 10.1186/S12964-015-0120-Z  0.304
2015 Koh JL, Chong YT, Friesen H, Moses A, Boone C, Andrews BJ, Moffat J. CYCLoPs: A Comprehensive Database Constructed from Automated Analysis of Protein Abundance and Subcellular Localization Patterns in Saccharomyces cerevisiae. G3 (Bethesda, Md.). 5: 1223-32. PMID 26048563 DOI: 10.1534/G3.115.017830  0.388
2015 Chong YT, Koh JL, Friesen H, Duffy K, Cox MJ, Moses A, Moffat J, Boone C, Andrews BJ. Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis. Cell. 161: 1413-24. PMID 26046442 DOI: 10.1016/J.Cell.2015.04.051  0.372
2015 Handfield LF, Strome B, Chong YT, Moses AM. Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images. Bioinformatics (Oxford, England). 31: 940-7. PMID 25398614 DOI: 10.1093/Bioinformatics/Btu759  0.658
2014 Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR, Moses AM. Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. Plos Computational Biology. 10: e1003977. PMID 25474245 DOI: 10.1371/Journal.Pcbi.1003977  0.327
2014 Lumba S, Toh S, Handfield LF, Swan M, Liu R, Youn JY, Cutler SR, Subramaniam R, Provart N, Moses A, Desveaux D, McCourt P. A mesoscale abscisic acid hormone interactome reveals a dynamic signaling landscape in Arabidopsis. Developmental Cell. 29: 360-72. PMID 24823379 DOI: 10.1016/J.Devcel.2014.04.004  0.672
2013 Handfield LF, Chong YT, Simmons J, Andrews BJ, Moses AM. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins. Plos Computational Biology. 9: e1003085. PMID 23785265 DOI: 10.1371/Journal.Pcbi.1003085  0.684
2011 Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ, Molin M, Zia A, Simpson JT, Quail MA, Moses A, Louis EJ, Durbin R, Liti G. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Research. 21: 1131-8. PMID 21422276 DOI: 10.1101/Gr.116731.110  0.304
2011 Gonsalves SE, Moses AM, Razak Z, Robert F, Westwood JT. Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster. Plos One. 6: e15934. PMID 21264254 DOI: 10.1371/Journal.Pone.0015934  0.31
2008 Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, et al. TreeFam: 2008 Update. Nucleic Acids Research. 36: D735-40. PMID 18056084 DOI: 10.1093/Nar/Gkm1005  0.309
2007 Shultzaberger RK, Chiang DY, Moses AM, Eisen MB. Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. Plos One. 2: e1199. PMID 18030333 DOI: 10.1371/Journal.Pone.0001199  0.593
2007 Moses AM, Liku ME, Li JJ, Durbin R. Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. Proceedings of the National Academy of Sciences of the United States of America. 104: 17713-8. PMID 17978194 DOI: 10.1073/Pnas.0700997104  0.307
2006 Pollard DA, Iyer VN, Moses AM, Eisen MB. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. Plos Genetics. 2: e173. PMID 17132051 DOI: 10.1371/Journal.Pgen.0020173  0.726
2006 Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 444: 499-502. PMID 17086198 DOI: 10.1038/Nature05295  0.548
2006 Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB. Large-scale turnover of functional transcription factor binding sites in Drosophila. Plos Computational Biology. 2: e130. PMID 17040121 DOI: 10.1371/Journal.Pcbi.0020130  0.75
2006 Pollard DA, Moses AM, Iyer VN, Eisen MB. Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. Bmc Bioinformatics. 7: 376. PMID 16904011 DOI: 10.1186/1471-2105-7-376  0.748
2006 Wang QF, Prabhakar S, Wang Q, Moses AM, Chanan S, Brown M, Eisen MB, Cheng JF, Rubin EM, Boffelli D. Primate-specific evolution of an LDLR enhancer. Genome Biology. 7: R68. PMID 16884525 DOI: 10.1186/Gb-2006-7-8-R68  0.557
2004 Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB. MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biology. 5: R98. PMID 15575972 DOI: 10.1186/Gb-2004-5-12-R98  0.746
2004 Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB. Conservation and evolution of cis-regulatory systems in ascomycete fungi. Plos Biology. 2: e398. PMID 15534694 DOI: 10.1371/Journal.Pbio.0020398  0.697
2004 Moses AM, Chiang DY, Eisen MB. Phylogenetic motif detection by expectation-maximization on evolutionary mixtures. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 324-35. PMID 14992514  0.594
2003 Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB. Position specific variation in the rate of evolution in transcription factor binding sites. Bmc Evolutionary Biology. 3: 19. PMID 12946282 DOI: 10.1186/1471-2148-3-19  0.608
2003 Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB. Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biology. 4: R43. PMID 12844359 DOI: 10.1186/Gb-2003-4-7-R43  0.613
2003 Chiang DY, Moses AM, Kamvysselis M, Lander ES, Eisen MB. Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 84-93.  0.506
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