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Gregory Cooper, Ph.D. - Publications

Affiliations: 
Genome Sciences University of Washington, Seattle, Seattle, WA 
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60 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
2024 Hiatt SM, Lawlor JM, Handley LH, Latner DR, Bonnstetter ZT, Finnila CR, Thompson ML, Boston LB, Williams M, Rodriguez-Nunez I, Jenkins J, Kelley WV, Bebin EM, Lopez MA, Hurst AC, ... ... Cooper GM, et al. Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders. Genome Research. PMID 39299904 DOI: 10.1101/gr.279227.124  0.402
2024 Anderson AG, Moyers BA, Loupe JM, Rodriguez-Nunez I, Felker SA, Lawlor JMJ, Bunney WE, Bunney BG, Cartagena PM, Sequeira A, Watson S, Akil H, Mendenhall EM, Cooper GM, Myers RM. Allele specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs. Genome Research. PMID 39152038 DOI: 10.1101/gr.278601.123  0.302
2024 Hiatt SM, Lawlor JM, Handley LH, Latner DR, Bonnstetter ZT, Finnila CR, Thompson ML, Boston LB, Williams M, Rodriguez Nunez I, Jenkins J, Kelley WV, Bebin EM, Lopez MA, Hurst AC, ... ... Cooper GM, et al. Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders. Medrxiv : the Preprint Server For Health Sciences. PMID 38585854 DOI: 10.1101/2024.03.22.24304633  0.405
2023 Rahman MA, Cai C, Bo N, McNamara DM, Ding Y, Cooper GF, Lu X, Liu J. An individualized Bayesian method for estimating genomic variants of hypertension. Bmc Genomics. 23: 863. PMID 37936055 DOI: 10.1186/s12864-023-09757-9  0.359
2023 Moyers BA, Loupe JM, Felker SA, Lawlor JMJ, Anderson AG, Rodriguez-Nunez I, Bunney WE, Bunney BG, Cartagena PM, Sequeira A, Watson SJ, Akil H, Mendenhall EM, Cooper GM, Myers RM. Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs. Biorxiv : the Preprint Server For Biology. PMID 37873117 DOI: 10.1101/2023.10.06.561245  0.311
2023 Felker SA, Lawlor JM, Hiatt SM, Thompson ML, Latner DR, Finnila CR, Bowling KM, Bonnstetter ZT, Bonini KE, Kelly NR, Kelley WV, Hurst AC, Rashid S, Kelly MA, Nakouzi G, ... ... Cooper GM, et al. Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 100884. PMID 37161864 DOI: 10.1016/j.gim.2023.100884  0.365
2023 Felker SA, Lawlor JM, Hiatt SM, Thompson ML, Latner DR, Finnila CR, Bowling KM, Bonnstetter ZT, Bonini KE, Kelly NR, Kelley WV, Hurst AC, Kelly MA, Nakouzi G, Hendon LG, ... ... Cooper GM, et al. Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. Biorxiv : the Preprint Server For Biology. PMID 36711854 DOI: 10.1101/2023.01.12.523654  0.37
2022 Hiatt SM, Trajkova S, Sebastiano MR, Partridge EC, Abidi FE, Anderson A, Ansar M, Antonarakis SE, Azadi A, Bachmann-Gagescu R, Bartuli A, Benech C, Berkowitz JL, Betti MJ, Brusco A, ... ... Cooper GM, et al. Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype. American Journal of Human Genetics. PMID 36586412 DOI: 10.1016/j.ajhg.2022.12.007  0.359
2022 Bowling KM, Thompson ML, Kelly MA, Scollon S, Slavotinek AM, Powell BC, Kirmse BM, Hendon LG, Brothers KB, Korf BR, Cooper GM, Greally JM, Hurst ACE. Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing. Genome Medicine. 14: 131. PMID 36414972 DOI: 10.1186/s13073-022-01139-2  0.309
2021 Hiatt SM, Lawlor JMJ, Handley LH, Ramaker RC, Rogers BB, Partridge EC, Boston LB, Williams M, Plott CB, Jenkins J, Gray DE, Holt JM, Bowling KM, Bebin EM, Grimwood J, ... ... Cooper GM, et al. Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders. Hgg Advances. 2. PMID 33937879 DOI: 10.1016/j.xhgg.2021.100023  0.398
2020 Scott TM, Guo H, Eichler EE, Rosenfeld JA, Pang K, Liu Z, Lalani S, Weimin B, Yang Y, Bacino CA, Streff H, Lewis AM, Koenig MK, Thiffault I, Bellomo A, ... ... Cooper GM, et al. BAZ2B haploinsufficiency as a cause of developmental delay, intellectual disability and autism spectrum disorder. Human Mutation. PMID 31999386 DOI: 10.1002/Humu.23992  0.423
2019 Carapito R, Ivanova EL, Morlon A, Meng L, Molitor A, Erdmann E, Kieffer B, Pichot A, Naegely L, Kolmer A, Paul N, Hanauer A, Tran Mau-Them F, Jean-Marçais N, Hiatt SM, ... Cooper GM, et al. ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder. American Journal of Human Genetics. PMID 31879022 DOI: 10.1016/j.ajhg.2019.11.014  0.479
2019 Cochran JN, McKinley EC, Cochran M, Amaral MD, Moyers BA, Lasseigne BN, Gray DE, Lawlor JMJ, Prokop JW, Geier EG, Holt JM, Thompson ML, Newberry JS, Yokoyama JS, Worthey EA, ... ... Cooper GM, et al. Genome sequencing for early-onset or atypical dementia: high diagnostic yield and frequent observation of multiple contributory alleles. Cold Spring Harbor Molecular Case Studies. 5. PMID 31836585 DOI: 10.1101/mcs.a003491  0.361
2019 Hiatt SM, Thompson ML, Prokop JW, Lawlor JMJ, Gray DE, Bebin EM, Rinne T, Kempers M, Pfundt R, van Bon BW, Mignot C, Nava C, Depienne C, Kalsner L, Rauch A, ... ... Cooper GM, et al. Deleterious Variation in BRSK2 Associates with a Neurodevelopmental Disorder. American Journal of Human Genetics. PMID 30879638 DOI: 10.1016/j.ajhg.2019.02.002  0.419
2019 Zweier M, Begemann A, McWalter K, Cho MT, Abela L, Banka S, Behring B, Berger A, Brown CW, Carneiro M, Chen J, Cooper GM, Finnila CR, Guillen Sacoto MJ, et al. Spatially clustering de novo variants in CYFIP2, encoding the cytoplasmic FMRP interacting protein 2, cause intellectual disability and seizures. European Journal of Human Genetics : Ejhg. PMID 30664714 DOI: 10.1038/s41431-018-0331-z  0.329
2018 Carapito R, Ivanova EL, Morlon A, Meng L, Molitor A, Erdmann E, Kieffer B, Pichot A, Naegely L, Kolmer A, Paul N, Hanauer A, Tran Mau-Them F, Jean-Marçais N, Hiatt SM, ... Cooper GM, et al. ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder. American Journal of Human Genetics. PMID 30639322 DOI: 10.1016/j.ajhg.2018.12.007  0.571
2018 Claassen D, Boals M, Bowling KM, Cooper GM, Cox J, Hershfield M, Lewis S, Wlodarski M, Weiss MJ, Estepp JH. Complexities of genetic diagnosis illustrated by an atypical case of congenital hypoplastic anemia. Cold Spring Harbor Molecular Case Studies. 4. PMID 30559313 DOI: 10.1101/mcs.a003384  0.324
2018 Carvill GL, Engel KL, Ramamurthy A, Cochran JN, Roovers J, Stamberger H, Lim N, Schneider AL, Hollingsworth G, Holder DH, Regan BM, Lawlor J, Lagae L, Ceulemans B, Bebin EM, ... ... Cooper GM, et al. Aberrant Inclusion of a Poison Exon Causes Dravet Syndrome and Related SCN1A-Associated Genetic Epilepsies. American Journal of Human Genetics. 103: 1022-1029. PMID 30526861 DOI: 10.1016/J.Ajhg.2018.10.023  0.602
2018 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research. PMID 30371827 DOI: 10.1093/Nar/Gky1016  0.371
2018 Mulhern MS, Stumpel C, Stong N, Brunner HG, Bier L, Lippa N, Riviello J, Rouhl RPW, Kempers M, Pfundt R, Stegmann APA, Kukolich MK, Telegrafi A, Lehman A, ... ... Cooper GM, et al. NBEA: developmental disease gene with early generalized epilepsy phenotypes. Annals of Neurology. PMID 30269351 DOI: 10.1002/ana.25350  0.526
2018 Gilbert JR, Losee JE, Mooney MP, Cray JJ, Gustafson J, Cunningham ML, Cooper GM. Genetic associations and phenotypic heterogeneity in the craniosynostotic rabbit. Plos One. 13: e0204086. PMID 30235265 DOI: 10.1371/journal.pone.0204086  0.395
2018 Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZC, Lewis AM, Sutton VR, ... ... Cooper GM, et al. Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies. American Journal of Human Genetics. PMID 29656860 DOI: 10.1016/J.Ajhg.2018.03.004  0.539
2017 Sanghvi RV, Buhay CJ, Powell BC, Tsai EA, Dorschner MO, Hong CS, Lebo MS, Sasson A, Hanna DS, McGee S, Bowling KM, Cooper GM, Gray DE, Lonigro RJ, Dunford A, et al. Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 29144510 DOI: 10.1038/Gim.2017.192  0.317
2017 Bowling KM, Thompson ML, Amaral MD, Finnila CR, Hiatt SM, Engel KL, Cochran JN, Brothers KB, East KM, Gray DE, Kelley WV, Lamb NE, Lose EJ, Rich CA, Simmons S, ... ... Cooper GM, et al. Genomic diagnosis for children with intellectual disability and/or developmental delay. Genome Medicine. 9: 43. PMID 28554332 DOI: 10.1186/S13073-017-0433-1  0.335
2017 Manolio TA, Fowler DM, Starita LM, Haendel MA, MacArthur DG, Biesecker LG, Worthey E, Chisholm RL, Green ED, Jacob HJ, McLeod HL, Roden D, Rodriguez LL, Williams MS, Cooper GM, et al. Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research. Cell. 169: 6-12. PMID 28340351 DOI: 10.1016/J.Cell.2017.03.005  0.338
2015 Cooper GM. Parlez-vous VUS? Genome Research. 25: 1423-6. PMID 26430151 DOI: 10.1101/gr.190116.115  0.377
2015 Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, Murray ML, Tokita MJ, Gallego CJ, Kim DS, Bennett JT, Crosslin DR, Ranchalis J, Jones KL, Rosenthal EA, ... ... Cooper GM, et al. Actionable exomic incidental findings in 6503 participants: challenges of variant classification. Genome Research. 25: 305-15. PMID 25637381 DOI: 10.1101/Gr.183483.114  0.782
2014 MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, et al. Guidelines for investigating causality of sequence variants in human disease. Nature. 508: 469-76. PMID 24759409 DOI: 10.1038/Nature13127  0.386
2014 Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genetics. 46: 310-5. PMID 24487276 DOI: 10.1038/Ng.2892  0.684
2013 Gallo PH, Cray JJ, Durham EL, Mooney MP, Cooper GM, Kathju S. Molecular Analysis of Twist1 and FGF Receptors in a Rabbit Model of Craniosynostosis: Likely Exclusion as the Loci of Origin. International Journal of Genomics. 2013: 305971. PMID 23738319 DOI: 10.1155/2013/305971  0.326
2013 Lorente-Galdos B, Bleyhl J, Santpere G, Vives L, Ramírez O, Hernandez J, Anglada R, Cooper GM, Navarro A, Eichler EE, Marques-Bonet T. Accelerated exon evolution within primate segmental duplications. Genome Biology. 14: R9. PMID 23360670 DOI: 10.1186/Gb-2013-14-1-R9  0.652
2011 Cooper GM, Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews. Genetics. 12: 628-40. PMID 21850043 DOI: 10.1038/Nrg3046  0.402
2011 Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V, Abdel-Hamid H, Bader P, McCracken E, Niyazov D, Leppig K, et al. A copy number variation morbidity map of developmental delay. Nature Genetics. 43: 838-46. PMID 21841781 DOI: 10.1038/Ng.909  0.757
2011 Cooper GM, Mefford HC. Detection of copy number variation using SNP genotyping. Methods in Molecular Biology (Clifton, N.J.). 767: 243-52. PMID 21822880 DOI: 10.1007/978-1-61779-201-4_18  0.592
2010 Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nature Genetics. 42: 790-3. PMID 20711175 DOI: 10.1038/Ng.646  0.585
2010 Cooper GM, Goode DL, Ng SB, Sidow A, Bamshad MJ, Shendure J, Nickerson DA. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nature Methods. 7: 250-1. PMID 20354513 DOI: 10.1038/Nmeth0410-250  0.425
2010 Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P, Itsara A, Vives L, Walsh T, McCarthy SE, Baker C, Mefford HC, Kidd JM, Browning SR, Browning BL, Dickel DE, et al. A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nature Genetics. 42: 203-9. PMID 20154674 DOI: 10.1038/Ng.534  0.71
2010 Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A. Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Research. 20: 301-10. PMID 20067941 DOI: 10.1101/Gr.102210.109  0.428
2010 Zerr T, Cooper GM, Eichler EE, Nickerson DA. Targeted interrogation of copy number variation using SCIMMkit. Bioinformatics (Oxford, England). 26: 120-2. PMID 19846438 DOI: 10.1093/Bioinformatics/Btp606  0.502
2009 Mefford HC, Cooper GM, Zerr T, Smith JD, Baker C, Shafer N, Thorland EC, Skinner C, Schwartz CE, Nickerson DA, Eichler EE. A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease. Genome Research. 19: 1579-85. PMID 19506092 DOI: 10.1101/Gr.094987.109  0.72
2009 Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, Krauss RM, Myers RM, Ridker PM, Chasman DI, Mefford H, Ying P, Nickerson DA, Eichler EE. Population analysis of large copy number variants and hotspots of human genetic disease. American Journal of Human Genetics. 84: 148-61. PMID 19166990 DOI: 10.1016/J.Ajhg.2008.12.014  0.759
2009 Hannes FD, Sharp AJ, Mefford HC, de Ravel T, Ruivenkamp CA, Breuning MH, Fryns JP, Devriendt K, Van Buggenhout G, Vogels A, Stewart H, Hennekam RC, Cooper GM, Regan R, Knight SJ, et al. Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant. Journal of Medical Genetics. 46: 223-32. PMID 18550696 DOI: 10.1136/jmg.2007.055202  0.735
2008 Cooper GM, Zerr T, Kidd JM, Eichler EE, Nickerson DA. Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nature Genetics. 40: 1199-203. PMID 18776910 DOI: 10.1038/Ng.236  0.662
2008 Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 453: 56-64. PMID 18451855 DOI: 10.1038/Nature06862  0.794
2008 Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, et al. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science (New York, N.Y.). 320: 539-43. PMID 18369103 DOI: 10.1126/Science.1155174  0.475
2008 Sharp AJ, Mefford HC, Li K, Baker C, Skinner C, Stevenson RE, Schroer RJ, Novara F, De Gregori M, Ciccone R, Broomer A, Casuga I, Wang Y, Xiao C, Barbacioru C, ... ... Cooper GM, et al. A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nature Genetics. 40: 322-8. PMID 18278044 DOI: 10.1038/Ng.93  0.715
2008 Bovee D, Zhou Y, Haugen E, Wu Z, Hayden HS, Gillett W, Tuzun E, Cooper GM, Sampas N, Phelps K, Levy R, Morrison VA, Sprague J, Jewett D, Buckley D, et al. Closing gaps in the human genome with fosmid resources generated from multiple individuals. Nature Genetics. 40: 96-101. PMID 18157130 DOI: 10.1038/Ng.2007.34  0.543
2007 Mefford HC, Clauin S, Sharp AJ, Moller RS, Ullmann R, Kapur R, Pinkel D, Cooper GM, Ventura M, Ropers HH, Tommerup N, Eichler EE, Bellanne-Chantelot C. Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy. American Journal of Human Genetics. 81: 1057-69. PMID 17924346 DOI: 10.1086/522591  0.701
2007 Clark TG, Andrew T, Cooper GM, Margulies EH, Mullikin JC, Balding DJ. Functional constraint and small insertions and deletions in the ENCODE regions of the human genome Genome Biology. 8. PMID 17784950 DOI: 10.1186/gb-2007-8-9-r180  0.376
2007 Cooper GM, Nickerson DA, Eichler EE. Mutational and selective effects on copy-number variants in the human genome. Nature Genetics. 39: S22-9. PMID 17597777 DOI: 10.1038/Ng2054  0.593
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Cooper GM, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.31
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, 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  0.325
2005 Stone EA, Cooper GM, Sidow A. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annual Review of Genomics and Human Genetics. 6: 143-64. PMID 16124857 DOI: 10.1146/annurev.genom.6.080604.162146  0.317
2005 Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Research. 15: 901-13. PMID 15965027 DOI: 10.1101/Gr.3577405  0.313
2004 Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I. Automated whole-genome multiple alignment of rat, mouse, and human. Genome Research. 14: 685-92. PMID 15060011 DOI: 10.1101/Gr.2067704  0.303
2004 Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Research. 14: 539-48. PMID 15059994 DOI: 10.1101/Gr.2034704  0.313
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Cooper GM, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  0.644
2004 Cooper GM, Sidow A. Genomic regulatory regions: insights from comparative sequence analysis. Current Opinion in Genetics & Development. 13: 604-10. PMID 14638322 DOI: 10.1016/j.gde.2003.10.001  0.34
2003 Cooper GM, Brudno M, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Research. 13: 813-20. PMID 12727901 DOI: 10.1101/Gr.1064503  0.349
2003 Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Research. 13: 721-31. PMID 12654723 DOI: 10.1101/Gr.926603  0.349
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