Webb Miller - Publications

Center for Comparative Genomics and Bioinformatics Pennsylvania State University, State College, PA, United States 

109 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
2020 Fry E, Kim SK, Chigurapti S, Mika KM, Ratan A, Dammermann A, Mitchell BJ, Miller W, Lynch VJ. Functional architecture of deleterious genetic variants in the genome of a Wrangel Island mammoth. Genome Biology and Evolution. PMID 32031213 DOI: 10.1093/gbe/evz279  0.52
2019 Kitchen SA, Ratan A, Bedoya-Reina OC, Burhans R, Fogarty ND, Miller W, Baums IB. Genomic Variants Among Threatened Corals. G3 (Bethesda, Md.). PMID 30914426 DOI: 10.1534/g3.119.400125  0.52
2016 Agaba M, Ishengoma E, Miller WC, McGrath BC, Hudson CN, Bedoya Reina OC, Ratan A, Burhans R, Chikhi R, Medvedev P, Praul CA, Wu-Cavener L, Wood B, Robertson H, Penfold L, et al. Giraffe genome sequence reveals clues to its unique morphology and physiology. Nature Communications. 7: 11519. PMID 27187213 DOI: 10.1038/ncomms11519  0.36
2015 Fuller ZL, Niño EL, Patch HM, Bedoya-Reina OC, Baumgarten T, Muli E, Mumoki F, Ratan A, McGraw J, Frazier M, Masiga D, Schuster S, Grozinger CM, Miller W. Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools. Bmc Genomics. 16: 518. PMID 26159619 DOI: 10.1186/s12864-015-1712-0  0.52
2015 Lynch VJ, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W, Schuster SC. Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Reports. 12: 217-28. PMID 26146078 DOI: 10.1016/j.celrep.2015.06.027  0.52
2015 Ratan A, Olson TL, Loughran TP, Miller W. Identification of indels in next-generation sequencing data. Bmc Bioinformatics. 16: 42. PMID 25879703 DOI: 10.1186/s12859-015-0483-6  0.64
2015 Zhang Y, Aubry JF, Zhang J, Wang Y, Roy J, Mata JF, Miller W, Dumont E, Xie M, Lee K, Zuo Z, Wintermark M. Defining the optimal age for focal lesioning in a rat model of transcranial HIFU. Ultrasound in Medicine & Biology. 41: 449-55. PMID 25542495 DOI: 10.1016/j.ultrasmedbio.2014.09.029  0.6
2015 Kistler L, Ratan A, Godfrey LR, Crowley BE, Hughes CE, Lei R, Cui Y, Wood ML, Muldoon KM, Andriamialison H, McGraw JJ, Tomsho LP, Schuster SC, Miller W, Louis EE, et al. Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs. Journal of Human Evolution. 79: 45-54. PMID 25523037 DOI: 10.1016/j.jhevol.2014.06.016  0.64
2014 Kim HL, Ratan A, Perry GH, Montenegro A, Miller W, Schuster SC. Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history. Nature Communications. 5: 5692. PMID 25471224 DOI: 10.1038/ncomms6692  0.64
2014 Welch AJ, Bedoya-Reina OC, Carretero-Paulet L, Miller W, Rode KD, Lindqvist C. Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment Genome Biology and Evolution. 6: 433-450. PMID 24504087 DOI: 10.1093/gbe/evu025  0.64
2014 Giardine B, Borg J, Viennas E, Pavlidis C, Moradkhani K, Joly P, Bartsakoulia M, Riemer C, Miller W, Tzimas G, Wajcman H, Hardison RC, Patrinos GP. Updates of the HbVar database of human hemoglobin variants and thalassemia mutations Nucleic Acids Research. 42: D1063-D1069. PMID 24137000 DOI: 10.1093/nar/gkt911  0.64
2013 Bedoya-Reina OC, Ratan A, Burhans R, Kim HL, Giardine B, Riemer C, Li Q, Olson TL, Loughran TP, Vonholdt BM, Perry GH, Schuster SC, Miller W. Galaxy tools to study genome diversity. Gigascience. 2: 17. PMID 24377391 DOI: 10.1186/2047-217X-2-17  0.64
2013 Perry GH, Louis EE, Ratan A, Bedoya-Reina OC, Burhans RC, Lei R, Johnson SE, Schuster SC, Miller W. Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. Proceedings of the National Academy of Sciences of the United States of America. 110: 5823-8. PMID 23530231 DOI: 10.1073/pnas.1211990110  0.64
2013 Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC. Comparison of sequencing platforms for single nucleotide variant calls in a human sample. Plos One. 8: e55089. PMID 23405114 DOI: 10.1371/journal.pone.0055089  0.64
2012 Giardine BM, Riemer C, Burhans R, Ratan A, Miller W. Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit15.2. PMID 22948727 DOI: 10.1002/0471250953.bi1502s39  0.64
2012 Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G. Sequencing and analysis of a South Asian-Indian personal genome. Bmc Genomics. 13: 440. PMID 22938532 DOI: 10.1186/1471-2164-13-440  0.64
2012 Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, Tomsho LP, Ibarra-Laclette E, Herrera-Estrella L, Peacock E, Farley S, et al. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences of the United States of America. 109: E2382-90. PMID 22826254 DOI: 10.1073/pnas.1210506109  0.64
2012 Song G, Riemer C, Dickins B, Kim HL, Zhang L, Zhang Y, Hsu CH, Hardison RC, Nisc Comparative Sequencing Program, Green ED, Miller W. Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. Genome Biology and Evolution. 4: 586-601. PMID 22454131 DOI: 10.1093/gbe/evs032  0.64
2012 Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE, Pritchard JK, Mason CE, Gilad Y. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biology and Evolution. 4: 126-35. PMID 22155688 DOI: 10.1093/gbe/evr132  0.64
2011 Song G, Hsu CH, Riemer C, Zhang Y, Kim HL, Hoffmann F, Zhang L, Hardison RC, Green ED, Miller W. Conversion events in gene clusters. Bmc Evolutionary Biology. 11: 226. PMID 21798034 DOI: 10.1186/1471-2148-11-226  0.64
2011 Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, ... ... Miller W, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 21: 1659-71. PMID 21795386 DOI: 10.1101/gr.125088.111  0.64
2011 Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, et al. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences of the United States of America. 108: 12348-53. PMID 21709235 DOI: 10.1073/pnas.1102838108  0.64
2011 Giardine B, Borg J, Higgs DR, Peterson KR, Philipsen S, Maglott D, Singleton BK, Anstee DJ, Basak AN, Clark B, Costa FC, Faustino P, Fedosyuk H, Felice AE, Francina A, ... ... Miller W, et al. Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach. Nature Genetics. 43: 295-301. PMID 21423179 DOI: 10.1038/ng.785  0.64
2011 Song G, Hsu CH, Riemer C, Miller W. Evaluation of methods for detecting conversion events in gene clusters. Bmc Bioinformatics. 12: S45. PMID 21342577 DOI: 10.1186/1471-2105-12-S1-S45  0.64
2011 Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Miller W, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/nature09687  0.64
2010 Hsu CH, Zhang Y, Hardison RC, Green ED, Miller W. An effective method for detecting gene conversion events in whole genomes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1281-97. PMID 20874409 DOI: 10.1089/cmb.2010.0103  0.64
2010 Song G, Zhang L, Vinar T, Miller W. CAGE: Combinatorial Analysis of Gene-cluster Evolution. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1227-42. PMID 20874406 DOI: 10.1089/cmb.2010.0094  0.64
2010 Elnitski L, Burhans R, Riemer C, Hardison R, Miller W. MultiPipMaker: a comparative alignment server for multiple DNA sequences. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit10.4. PMID 20521245 DOI: 10.1002/0471250953.bi1004s30  0.64
2010 Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W. Calling SNPs without a reference sequence. Bmc Bioinformatics. 11: 130. PMID 20230626 DOI: 10.1186/1471-2105-11-130  0.64
2010 Lindqvist C, Schuster SC, Sun Y, Talbot SL, Qi J, Ratan A, Tomsho LP, Kasson L, Zeyl E, Aars J, Miller W, Ingólfsson O, Bachmann L, Wiig O. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proceedings of the National Academy of Sciences of the United States of America. 107: 5053-7. PMID 20194737 DOI: 10.1073/pnas.0914266107  0.64
2010 Tindall EA, Petersen DC, Nikolaysen S, Miller W, Schuster SC, Hayes VM. Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation. Bmc Research Notes. 3: 39. PMID 20175893 DOI: 10.1186/1756-0500-3-39  0.44
2010 Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/nature08795  0.64
2010 Miller W, Wright SJ, Zhang Y, Schuster SC, Hayes VM. Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 43-53. PMID 19908356  0.6
2009 Adamson P, Andreopoulos C, Arms KE, Armstrong R, Auty DJ, Ayres DS, Backhouse C, Barnes PD, Barr G, Barrett WL, Becker BR, Belias A, Bernstein RH, Betancourt M, Bhattacharya D, ... ... Miller WH, et al. Search for muon-neutrino to electron-neutrino transitions in MINOS. Physical Review Letters. 103: 261802. PMID 20366304 DOI: 10.1103/PhysRevLett.103.261802  0.52
2009 Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, et al. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Research. 19: 2172-84. PMID 19887574 DOI: 10.1101/gr.098921.109  0.64
2009 Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, ... ... Miller W, et al. Prepublication data sharing. Nature. 461: 168-70. PMID 19741685 DOI: 10.1038/461168a  0.32
2009 Zhang Y, Song G, Vinar T, Green ED, Siepel A, Miller W. Evolutionary history reconstruction for Mammalian complex gene clusters. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1051-70. PMID 19645598 DOI: 10.1089/cmb.2009.0040  0.64
2009 Willerslev E, Gilbert MT, Binladen J, Ho SY, Campos PF, Ratan A, Tomsho LP, da Fonseca RR, Sher A, Kuznetsova TV, Nowak-Kemp M, Roth TL, Miller W, Schuster SC. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. Bmc Evolutionary Biology. 9: 95. PMID 19432984 DOI: 10.1186/1471-2148-9-95  0.64
2009 Zhang Y, Song G, Hsu CH, Miller W. Simultaneous history reconstruction for complex gene clusters in multiple species. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 162-73. PMID 19209701  0.64
2009 Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MT, Dalén L, Arsuaga JL, Ericson PG, et al. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research. 19: 213-20. PMID 19139089 DOI: 10.1101/gr.082628.108  0.64
2009 Addo-Quaye C, Miller W, Axtell MJ. CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics (Oxford, England). 25: 130-1. PMID 19017659 DOI: 10.1093/bioinformatics/btn604  0.64
2008 Adamson P, Andreopoulos C, Arms KE, Armstrong R, Auty DJ, Ayres DS, Backhouse C, Baller B, Barr G, Barrett WL, Becker BR, Belias A, Bernstein RH, Bhattacharya D, Bishai M, ... ... Miller WH, et al. Search for active neutrino disappearance using neutral-current interactions in the MINOS long-baseline experiment. Physical Review Letters. 101: 221804. PMID 19113477 DOI: 10.1103/PhysRevLett.101.221804  0.52
2008 Chen H, Xu CF, Ma J, Eliseenkova AV, Li W, Pollock PM, Pitteloud N, Miller WT, Neubert TA, Mohammadi M. A crystallographic snapshot of tyrosine trans-phosphorylation in action. Proceedings of the National Academy of Sciences of the United States of America. 105: 19660-5. PMID 19060208 DOI: 10.1073/pnas.0807752105  0.52
2008 Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 456: 387-90. PMID 19020620 DOI: 10.1038/nature07446  0.64
2008 Adamson P, Andreopoulos C, Arms KE, Armstrong R, Auty DJ, Ayres DS, Baller B, Barr G, Barrett WL, Becker BR, Belias A, Bernstein RH, Bhattacharya D, Bishai M, Blake A, ... ... Miller WH, et al. Testing Lorentz invariance and CPT conservation with NuMI neutrinos in the MINOS near detector. Physical Review Letters. 101: 151601. PMID 18999585 DOI: 10.1103/PhysRevLett.101.151601  0.52
2008 Adamson P, Andreopoulos C, Arms KE, Armstrong R, Auty DJ, Ayres DS, Baller B, Barnes PD, Barr G, Barrett WL, Becker BR, Belias A, Bernstein RH, Bhattacharya D, Bishai M, ... ... Miller WH, et al. Measurement of neutrino oscillations with the MINOS detectors in the NuMI beam. Physical Review Letters. 101: 131802. PMID 18851439 DOI: 10.1103/PhysRevLett.101.131802  0.52
2008 Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar SA, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC. Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Research. 18: 1896-905. PMID 18818370 DOI: 10.1101/gr.083089.108  0.64
2008 Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. The infinite sites model of genome evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 14254-61. PMID 18787111 DOI: 10.1073/pnas.0805217105  0.64
2008 Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D. DUPCAR: reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 1007-27. PMID 18774902 DOI: 10.1089/cmb.2008.0069  0.64
2008 Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. Methods in Molecular Biology (Clifton, N.J.). 422: 171-84. PMID 18629667 DOI: 10.1007/978-1-59745-581-7_11  0.64
2008 Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. Methods in Molecular Biology (Clifton, N.J.). 422: 133-44. PMID 18629665 DOI: 10.1007/978-1-59745-581-7_9  0.64
2008 Gilbert MT, Drautz DI, Lesk AM, Ho SY, Qi J, Ratan A, Hsu CH, Sher A, Dalén L, Götherström A, Tomsho LP, Rendulic S, Packard M, Campos PF, Kuznetsova TV, ... ... Miller W, et al. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences of the United States of America. 105: 8327-32. PMID 18541911 DOI: 10.1073/pnas.0802315105  0.64
2008 Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 453: 175-83. PMID 18464734 DOI: 10.1038/nature06936  0.64
2008 Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biology. 9: R76. PMID 18447906 DOI: 10.1186/gb-2008-9-4-r76  0.64
2008 Buckley M, Walker A, Ho SY, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Koon H, Penkman K, Elsworth B, Ashford D, Solazzo C, Andrews P, Strahler J, ... ... Miller W, et al. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science (New York, N.Y.). 319: 33; author reply 33. PMID 18174420 DOI: 10.1126/science.1147046  0.64
2007 Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Comparative genomic analysis using the UCSC genome browser. Methods in Molecular Biology (Clifton, N.J.). 395: 17-34. PMID 17993665 DOI: 10.1385/1-59745-514-8:17  0.64
2007 Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17: 1797-808. PMID 17984227 DOI: 10.1101/gr.6761107  0.64
2007 Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ. Molecular and genomic data identify the closest living relative of primates. Science (New York, N.Y.). 318: 792-4. PMID 17975064 DOI: 10.1126/science.1147555  0.64
2007 Gilbert MT, Tomsho LP, Rendulic S, Packard M, Drautz DI, Sher A, Tikhonov A, Dalén L, Kuznetsova T, Kosintsev P, Campos PF, Higham T, Collins MJ, Wilson AS, Shidlovskiy F, ... ... Miller W, et al. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science (New York, N.Y.). 317: 1927-30. PMID 17901335 DOI: 10.1126/science.1146971  0.44
2007 Chen H, Ma J, Li W, Eliseenkova AV, Xu C, Neubert TA, Miller WT, Mohammadi M. A molecular brake in the kinase hinge region regulates the activity of receptor tyrosine kinases. Molecular Cell. 27: 717-30. PMID 17803937 DOI: 10.1016/j.molcel.2007.06.028  0.52
2007 Bird CP, Stranger BE, Liu M, Thomas DJ, Ingle CE, Beazley C, Miller W, Hurles ME, Dermitzakis ET. Fast-evolving noncoding sequences in the human genome. Genome Biology. 8: R118. PMID 17578567 DOI: 10.1186/gb-2007-8-6-r118  0.64
2007 Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Research. 17: 960-4. PMID 17568012 DOI: 10.1101/gr.5578007  0.64
2007 King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J, Chiaromonte F, Miller W, Hardison RC. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Research. 17: 775-86. PMID 17567996 DOI: 10.1101/gr.5592107  0.64
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Miller W, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/gr.6034307  0.64
2007 Han K, Konkel MK, Xing J, Wang H, Lee J, Meyer TJ, Huang CT, Sandifer E, Hebert K, Barnes EW, Hubley R, Miller W, Smit AF, Ullmer B, Batzer MA. Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome. Science (New York, N.Y.). 316: 238-40. PMID 17431169 DOI: 10.1126/science.1139462  0.64
2007 Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Miller W, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/science.1139247  0.64
2007 Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, ... ... Miller W, et al. PhenCode: connecting ENCODE data with mutations and phenotype. Human Mutation. 28: 554-62. PMID 17326095 DOI: 10.1002/humu.20484  0.64
2007 Giardine B, van Baal S, Kaimakis P, Riemer C, Miller W, Samara M, Kollia P, Anagnou NP, Chui DH, Wajcman H, Hardison RC, Patrinos GP. HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. Human Mutation. 28: 206. PMID 17221864 DOI: 10.1002/humu.9479  0.64
2007 Gilbert MT, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research. 35: 1-10. PMID 16920744 DOI: 10.1093/nar/gkl483  0.64
2006 Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, Chiaromonte F. ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Research. 16: 1596-604. PMID 17053093 DOI: 10.1101/gr.4537706  0.64
2006 Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, et al. Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Research. 16: 1480-92. PMID 17038566 DOI: 10.1101/gr.5353806  0.64
2006 Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. Reconstructing contiguous regions of an ancestral genome. Genome Research. 16: 1557-65. PMID 16983148 DOI: 10.1101/gr.5383506  0.64
2006 Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. Plos Computational Biology. 2: e33. PMID 16628248 DOI: 10.1371/journal.pcbi.0020033  0.64
2006 Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, Buigues B, Tikhonov A, Huson DH, Tomsho LP, Auch A, Rampp M, Miller W, Schuster SC. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science (New York, N.Y.). 311: 392-4. PMID 16368896 DOI: 10.1126/science.1123360  0.44
2005 Elnitski L, Riemer C, Burhans R, Hardison R, Miller W. MultiPipMaker: comparative alignment server for multiple DNA sequences. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit10.4. PMID 18428743 DOI: 10.1002/0471250953.bi1004s9  0.64
2005 Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Research. 15: 1451-5. PMID 16169926 DOI: 10.1101/gr.4086505  0.64
2005 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research. 15: 1034-50. PMID 16024819 DOI: 10.1101/gr.3715005  0.64
2005 King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Research. 15: 1051-60. PMID 16024817 DOI: 10.1101/gr.3642605  0.64
2005 Margulies EH, Vinson JP, Miller W, Jaffe DB, Lindblad-Toh K, Chang JL, Green ED, Lander ES, Mullikin JC, Clamp M. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proceedings of the National Academy of Sciences of the United States of America. 102: 4795-800. PMID 15778292 DOI: 10.1073/pnas.0409882102  0.64
2005 Elnitski L, Giardine B, Shah P, Zhang Y, Riemer C, Weirauch M, Burhans R, Miller W, Hardison RC. Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Research. 33: D466-70. PMID 15608239 DOI: 10.1093/nar/gki045  0.64
2005 Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, Stubbs L. Evolution and functional classification of vertebrate gene deserts. Genome Research. 15: 137-45. PMID 15590943 DOI: 10.1101/gr.3015505  0.64
2005 Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W. Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Research. 15: 184-94. PMID 15590941 DOI: 10.1101/gr.3007205  0.64
2004 Blanchette M, Green ED, Miller W, Haussler D. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Research. 14: 2412-23. PMID 15574820 DOI: 10.1101/gr.2800104  0.52
2004 Miller W, Makova KD, Nekrutenko A, Hardison RC. Comparative genomics. Annual Review of Genomics and Human Genetics. 5: 15-56. PMID 15485342 DOI: 10.1146/annurev.genom.5.061903.180057  0.64
2004 She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, ... Miller W, et al. The structure and evolution of centromeric transition regions within the human genome. Nature. 430: 857-64. PMID 15318213 DOI: 10.1038/nature02806  0.64
2004 Wang JP, Lindsay BG, Leebens-Mack J, Cui L, Wall K, Miller WC, dePamphilis CW. EST clustering error evaluation and correction. Bioinformatics (Oxford, England). 20: 2973-84. PMID 15189818 DOI: 10.1093/bioinformatics/bth342  0.64
2004 Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research. 14: 708-15. PMID 15060014 DOI: 10.1101/gr.1933104  0.64
2004 Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Research. 14: 517-27. PMID 15059992 DOI: 10.1101/gr.1984404  0.64
2004 Ovcharenko I, Loots GG, Hardison RC, Miller W, Stubbs L. zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome Research. 14: 472-7. PMID 14993211 DOI: 10.1101/gr.2129504  0.64
2004 Patrinos GP, Giardine B, Riemer C, Miller W, Chui DH, Anagnou NP, Wajcman H, Hardison RC. Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. Nucleic Acids Research. 32: D537-41. PMID 14681476 DOI: 10.1093/nar/gkh006  0.64
2003 Elnitski L, Riemer C, Schwartz S, Hardison R, Miller W. PipMaker: a World Wide Web server for genomic sequence alignments. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 10.2. PMID 18428692 DOI: 10.1002/0471250953.bi1002s00  0.64
2003 Farhadi HF, Lepage P, Forghani R, Friedman HC, Orfali W, Jasmin L, Miller W, Hudson TJ, Peterson AC. A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 23: 10214-23. PMID 14614079  0.64
2003 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences of the United States of America. 100: 11484-9. PMID 14500911 DOI: 10.1073/pnas.1932072100  0.64
2003 Florea L, McClelland M, Riemer C, Schwartz S, Miller W. EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae. Nucleic Acids Research. 31: 3527-32. PMID 12824359 DOI: 10.1093/nar/gkg551  0.64
2003 Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A, Green ED, Hardison RC, Miller W. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Research. 31: 3518-24. PMID 12824357 DOI: 10.1093/nar/gkg579  0.64
2003 Giardine B, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W, Hardison RC. GALA, a database for genomic sequence alignments and annotations. Genome Research. 13: 732-41. PMID 12671007 DOI: 10.1101/gr.603103  0.64
2003 Green P, Ewing B, Miller W, Thomas PJ, Green ED. Transcription-associated mutational asymmetry in mammalian evolution. Nature Genetics. 33: 514-7. PMID 12612582 DOI: 10.1038/ng1103  0.64
2003 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Research. 13: 103-7. PMID 12529312 DOI: 10.1101/gr.809403  0.64
2003 Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, Chiaromonte F. Distinguishing regulatory DNA from neutral sites. Genome Research. 13: 64-72. PMID 12529307 DOI: 10.1101/gr.817703  0.64
2003 Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, ... Miller W, et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13: 13-26. PMID 12529302 DOI: 10.1101/gr.844103  0.64
2002 Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics. 80: 681-90. PMID 12504859 DOI: 10.1006/geno.2002.7018  0.64
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Miller W, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/nature01262  0.52
2002 Maul JE, Lilly JW, Cui L, dePamphilis CW, Miller W, Harris EH, Stern DB. The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. The Plant Cell. 14: 2659-79. PMID 12417694 DOI: 10.1105/tpc.006155  0.64
2002 Molete JM, Petrykowska H, Sigg M, Miller W, Hardison R. Functional and binding studies of HS3.2 of the beta-globin locus control region. Gene. 283: 185-97. PMID 11867225 DOI: 10.1016/S0378-1119(01)00858-7  0.64
2002 Hardison RC, Chui DH, Giardine B, Riemer C, Patrinos GP, Anagnou N, Miller W, Wajcman H. HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server. Human Mutation. 19: 225-33. PMID 11857738 DOI: 10.1002/humu.10044  0.64
2002 Kurihara LJ, Semenova E, Miller W, Ingram RS, Guan XJ, Tilghman SM. Candidate genes required for embryonic development: a comparative analysis of distal mouse chromosome 14 and human chromosome 13q22. Genomics. 79: 154-61. PMID 11829485 DOI: 10.1006/geno.2002.6692  0.64
2002 Sumiyama K, Irvine SQ, Stock DW, Weiss KM, Kawasaki K, Shimizu N, Shashikant CS, Miller W, Ruddle FH. Genomic structure and functional control of the Dlx3-7 bigene cluster. Proceedings of the National Academy of Sciences of the United States of America. 99: 780-5. PMID 11792834 DOI: 10.1073/pnas.012584999  0.64
2002 DeSilva U, Elnitski L, Idol JR, Doyle JL, Gan W, Thomas JW, Schwartz S, Dietrich NL, Beckstrom-Sternberg SM, McDowell JC, Blakesley RW, Bouffard GG, Thomas PJ, Touchman JW, Miller W, et al. Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome. Genome Research. 12: 3-15. PMID 11779826 DOI: 10.1101/gr.214802  0.64
1997 Chen GQ, Shi XG, Tang W, Xiong SM, Zhu J, Cai X, Han ZG, Ni JH, Shi GY, Jia PM, Liu MM, He KL, Niu C, Ma J, Zhang P, ... ... Miller W, et al. Use of arsenic trioxide (As2O3) in the treatment of acute promyelocytic leukemia (APL): I. As2O3 exerts dose-dependent dual effects on APL cells. Blood. 89: 3345-53. PMID 9129041  0.52
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