Alan Michael Moses - Publications

2005 University of California, Berkeley, Berkeley, CA, United States 

58 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  0.403
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  0.406
2019 Pritišanac I, Vernon RM, Moses AM, Forman Kay JD. Entropy and Information within Intrinsically Disordered Protein Regions. Entropy (Basel, Switzerland). 21. PMID 33267376 DOI: 10.3390/E21070662  0.371
2019 Zarin 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. 8. PMID 31264965 DOI: 10.7554/Elife.46883  0.326
2019 Mehdi TF, Singh G, Mitchell JA, Moses AM. Variational Infinite Heterogeneous Mixture Model for Semi-supervised Clustering of Heart Enhancers. Bioinformatics (Oxford, England). PMID 30753279 DOI: 10.1093/Bioinformatics/Btz064  0.352
2018 Liku 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. 19: 65. PMID 29482494 DOI: 10.1186/S12859-018-2076-7  0.325
2017 Nguyen Ba AN, Strome B, Osman S, Legere EA, Zarin T, Moses AM. Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments. Plos Genetics. 13: e1006735. PMID 28410373 DOI: 10.1371/Journal.Pgen.1006735  0.388
2017 Zarin T, Tsai CN, Nguyen Ba AN, Moses AM. Selection maintains signaling function of a highly diverged intrinsically disordered region. Proceedings of the National Academy of Sciences of the United States of America. PMID 28167781 DOI: 10.1073/Pnas.1614787114  0.35
2017 Youn JY, Friesen H, Nguyen Ba AN, Liang W, Messier V, Cox MJ, Moses AM, Andrews B. Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library. G3 (Bethesda, Md.). PMID 28122947 DOI: 10.1534/G3.116.038471  0.303
2016 Kompella PS, Moses AM, Peisajovich SG. Introduction of Premature Stop Codons as an Evolutionary Strategy to Rescue Signaling Network Function. Acs Synthetic Biology. PMID 27935292 DOI: 10.1021/Acssynbio.6B00142  0.301
2016 Lu AX, Moses AM. An Unsupervised kNN Method to Systematically Detect Changes in Protein Localization in High-Throughput Microscopy Images. Plos One. 11: e0158712. PMID 27442431 DOI: 10.1371/Journal.Pone.0158712  0.304
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  0.376
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  0.494
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  0.462
2015 Wong KC, Li Y, Peng C, Moses AM, Zhang Z. Computational learning on specificity-determining residue-nucleotide interactions. Nucleic Acids Research. PMID 26527718 DOI: 10.1093/Nar/Gkv1134  0.385
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  0.304
2015 Gógl G, Schneider KD, Yeh BJ, Alam N, Nguyen Ba AN, Moses AM, Hetényi C, Reményi A, Weiss EL. The Structure of an NDR/LATS Kinase-Mob Complex Reveals a Novel Kinase-Coactivator System and Substrate Docking Mechanism. Plos Biology. 13: e1002146. PMID 25966461 DOI: 10.1371/Journal.Pbio.1002146  0.33
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  0.479
2014 Landry CR, Freschi L, Zarin T, Moses AM. Turnover of protein phosphorylation evolving under stabilizing selection. Frontiers in Genetics. 5: 245. PMID 25101120 DOI: 10.3389/Fgene.2014.00245  0.337
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  0.313
2014 Zarin T, Moses AM. Insights into molecular evolution from yeast genomics. Yeast (Chichester, England). 31: 233-41. PMID 24760744 DOI: 10.1002/Yea.3018  0.397
2014 Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G. A high-definition view of functional genetic variation from natural yeast genomes. Molecular Biology and Evolution. 31: 872-88. PMID 24425782 DOI: 10.1093/Molbev/Msu037  0.373
2013 Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, ... ... Moses AM, et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature Genetics. 45: 891-8. PMID 23817568 DOI: 10.1038/Ng.2684  0.475
2013 Khoshraftar S, Hung S, Khan S, Gong Y, Tyagi V, Parkinson J, Sain M, Moses AM, Christendat D. Sequencing and annotation of the Ophiostoma ulmi genome. Bmc Genomics. 14: 162. PMID 23496816 DOI: 10.1186/1471-2164-14-162  0.407
2013 Liti G, Nguyen Ba AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, Nieduszynski CA. High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. Bmc Genomics. 14: 69. PMID 23368932 DOI: 10.1186/1471-2164-14-69  0.416
2012 Zia A, Moses AM. Towards a theoretical understanding of false positives in DNA motif finding. Bmc Bioinformatics. 13: 151. PMID 22738169 DOI: 10.1186/1471-2105-13-151  0.382
2012 Nguyen Ba AN, Yeh BJ, van Dyk D, Davidson AR, Andrews BJ, Weiss EL, Moses AM. Proteome-wide discovery of evolutionary conserved sequences in disordered regions. Science Signaling. 5: rs1. PMID 22416277 DOI: 10.1126/Scisignal.2002515  0.363
2012 Lai AC, Nguyen Ba AN, Moses AM. Predicting kinase substrates using conservation of local motif density. Bioinformatics (Oxford, England). 28: 962-9. PMID 22302575 DOI: 10.1093/Bioinformatics/Bts060  0.31
2011 Zia A, Moses AM. Ranking insertion, deletion and nonsense mutations based on their effect on genetic information. Bmc Bioinformatics. 12: 299. PMID 21781308 DOI: 10.1186/1471-2105-12-299  0.315
2011 Warringer J, Zörgö E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses A, Blomberg A. Trait variation in yeast is defined by population history. Plos Genetics. 7: e1002111. PMID 21698134 DOI: 10.1371/Journal.Pgen.1002111  0.31
2011 Moses AM, Davidson AR. In vitro evolution goes deep. Proceedings of the National Academy of Sciences of the United States of America. 108: 8071-2. PMID 21551096 DOI: 10.1073/Pnas.1104843108  0.391
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  0.324
2011 Josephides C, Moses AM. Modeling the evolution of a classic genetic switch. Bmc Systems Biology. 5: 24. PMID 21294912 DOI: 10.1186/1752-0509-5-24  0.314
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  0.495
2011 Cutter AD, Moses AM. Polymorphism, divergence, and the role of recombination in Saccharomyces cerevisiae genome evolution. Molecular Biology and Evolution. 28: 1745-54. PMID 21199893 DOI: 10.1093/Molbev/Msq356  0.364
2010 Moses AM, Landry CR. Moving from transcriptional to phospho-evolution: generalizing regulatory evolution? Trends in Genetics : Tig. 26: 462-7. PMID 20817339 DOI: 10.1016/J.Tig.2010.08.002  0.408
2010 Nguyen Ba AN, Moses AM. Evolution of characterized phosphorylation sites in budding yeast. Molecular Biology and Evolution. 27: 2027-37. PMID 20368267 DOI: 10.1093/Molbev/Msq090  0.414
2010 Fraser HB, Moses AM, Schadt EE. Evidence for widespread adaptive evolution of gene expression in budding yeast. Proceedings of the National Academy of Sciences of the United States of America. 107: 2977-82. PMID 20133628 DOI: 10.1073/Pnas.0912245107  0.673
2010 Fraser HB, Moses AM, Schadt EE. Reply to Jensen and Rando: Population size change does not account for widespread gene expression adaptation in yeast Proceedings of the National Academy of Sciences of the United States of America. 107: E111. DOI: 10.1073/Pnas.1006152107  0.645
2009 Moses AM. Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites. Bmc Evolutionary Biology. 9: 286. PMID 19995462 DOI: 10.1186/1471-2148-9-286  0.45
2009 Nguyen Ba AN, Pogoutse A, Provart N, Moses AM. NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. Bmc Bioinformatics. 10: 202. PMID 19563654 DOI: 10.1186/1471-2105-10-202  0.345
2009 Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, et al. Population genomics of domestic and wild yeasts. Nature. 458: 337-41. PMID 19212322 DOI: 10.1038/Nature07743  0.381
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  0.342
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  0.762
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  0.432
2007 Moses AM, Hériché JK, Durbin R. Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. Genome Biology. 8: R23. PMID 17316440 DOI: 10.1186/Gb-2007-8-2-R23  0.347
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  0.734
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  0.638
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  0.768
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  0.767
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  0.639
2005 Pollard D, Iyer VN, Moses AM, Eisen MB. Whole Genome Phylogeny of the Drosophila melanogaster Species Subgroup: Widespread Discordance with Species Tree & Evidence for Incomplete Lineage Sorting Plos Genetics. DOI: 10.1371/Journal.Pgen.0020173.Eor  0.715
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  0.771
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  0.78
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  0.788
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  0.797
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  0.811
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.  0.74
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