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Barsh, G.S., Cooper, G.M., Copenhaver, G.P., Gibson, G., McCarthy, M.I., Tang, H., and Williams, S.M. 2015. PLOS Genetics data sharing policy: In pursuit of functional utility. PLOS Genetics 11(12): e1005716. PMID: 26655768. PDF

Savic, D., Roberts, B.S., Carleton, J.B., Partridge, E.C., White, M.A., Cohen, B.A., Cooper, G.M., Gertz, J., Myers, R.M.. 2015. Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein beta binding sites. Genome Research 25(12):1791-1800. PMID: 26486725. PDF

Cooper, G.M.. 2015. Parlez-vous VUS? Genome Research 25(12):1423-1426. PMID: 26430151. PDF

Cirulli, E.T.*, Lasseigne, B.N.*, Petrovski, S., … [65 additional authors] …, Cooper, G.M., Harris, T., Myers, R.M.*, and Goldstein, D.B.* 2015. Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways. Science 347 (6229): 1436-1441. PMID: 25700176. PDF

Amendola, L.M., Dorschner, M.O., Robertson, P.D., … [67 additional authors] …, Rehm, H., Nickerson, D.A., and Jarvik, G.P. 2015. Actionable exomic incidental findings in 6503 participants: challenges of variant classification. Genome Research 25(3):305-315. PMID: 25637381. PDF


MacArthur, D.G., Manolio, T.A., … [24 additional authors] …, Winckler, W., and Gunter, C. 2014. Guidelines for investigating causality of sequence variants in human disease. Nature 508(7497):469-76. PMID: 24759409. PDF

Kircher, M.*, Witten, D.M.*, Jain, P., O’Roak, B.J., Cooper, G.M., and Shendure, J. 2014. A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genetics 46(3):310-315. PMID: 24487276. PDF


Gertz, J., Savic, D., Varley, K.E., Partridge, E.C., Safi, A., Jain, P., Cooper, G.M., Reddy, T.E., Crawford, G.E., and Myers, R.M. 2013. Distinct properties of cell-type-specific and shared transcription factor binding sites. Molecular Cell 52(1):25-36 PMID: 24076218. PDF

Savic, D., Gertz, J., Jain, P., Cooper, G.M., and Myers, R.M. 2013. Mapping genome-wide transcription factor binding sites in frozen tissue. Epigenetics & Chromatin 6:30. PMID: 24279905. PDF

Lorente-Galdos, B., Bleyhl, J., Santpere, G., Vives, L., Ramirez, O., Hernandez, J., Anglada, R., Cooper, G.M., Navarro, A., Eichler, E.E., and Marques-Bonet, T. 2013. Accelerated exon evolution within primate segmental duplications. Genome Biology 14 (1):R9. PMID: 23360670. PDF


Kaelin, C.B.*, Xu, X.*, Hong, L.Z., … [17 additional authors] …, O’Brien, S.J., Barsh, G.S., and Menotti-Raymond, M. 2012. Specifying and sustaining pigmentation patterns in domestic and wild cats. Science 337 (6101): 1536-1541. PMID: 22997338. PDF

Patwardhan, R.P., Hiatt, J.B., Witten, D.M., Kim, M.J., Smith, R.P., May, D., Lee, C., Andrie, J.M., Lee, S.I., Cooper, G.M., Ahituv, N., Pennacchio, L.A., and Shendure, J.  2012.  Massively parallel functional dissection of mammalian enhancers in vivo.  Nature Biotechnology 30 (3): 265-270. PMID: 22371081. PDF


Cooper, G.M. and Shendure, J.  2011. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data.  Nature Reviews Genetics 12 (9): 628-640.  Review. PMID: 21850043. PDF

Cooper, G.M.*, Coe, B.P.*, Girirajan, S.J.*, … [21 additional authors] …, Shaffer, L., and Eichler, E.E.  2011.  A copy number variation morbidity map of developmental delay.  Nature Genetics 43(9): 838-846. PMID: 21841781. PDF

Innocenti, F.I.*, Cooper, G.M.*, Stanaway, I.B., … [15 additional authors] …, Ratain, M.J., and Brown, C.D.  2011.  Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue.  PLoS Genetics 7 (5): e1002078. PMID: 21637794. PDF

Cooper, G.M. and Mefford, H.C. 2011.  Detection of copy number variation using SNP genotyping.  Methods in Molecular Biology. 767: 243-252.  Review/Book Chapter. PMID: 21822880. PDF


Davydov, E., Goode, D.L., Sirota, M., Cooper, G.M., Sidow, A., and Batzoglou, S.  2010. Identifying a high fraction of the human genome to be under selective constraint using GERP++.  PLoS Computational Biology 6 (12): e1001025. PMID: 21152010. PDF

Ng, S.B.*, Bigham, A.W.*, … [16 additional authors] …, Nickerson, D.A., Bamshad, M.J., and Shendure, J.  2010.  Exome sequencing reveals that mutations in MLL2 cause Kabuki syndrome.  Nature Genetics 42 (9): 7990-7993.  PMID: 20711175. PDF

Cooper, G.M., Goode, D.L., Ng, S.B., Sidow, A., Bamshad, M., Shendure, J., and Nickerson, D.A.  2010.  Single-nucleotide evolutionary constraint scores highlight disease-causing mutations.  Nature Methods 7 (4): 250-251.  PMID: 20354513. PDF

Goode, D.L., Cooper, G.M., Schmutz, J., Dickson, M., Gonzales, E., Tsai, M., Davydov, E., Batzoglou, S., Myers, R.M., and Sidow, A.  2010.  Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Research 20 (3): 301-310.  PMID: 20067941. PDF

Girirajan, S.*, Rosenfeld, J.A.*, Cooper, G.M, … [53 additional authors] …, King, M.C., Shaffer, L.G., and Eichler, E.E.  2010.  A recurrent 16p12.1 microdeletion suggests a two-hit model for severe developmental delay.  Nature Genetics 42 (3): 203-209.  PMID: 20154674. PDF

Zerr, T., Cooper, G.M., Eichler, E.E., and Nickerson, D.A.  Targeted interrogation of copy number variation using SCIMMkit.  2010.  Bioinformatics 26 (1): 120-122.  PMID: 19846438. PDF


Mefford, H.C.*, Cooper, G.M.*, Zerr, T.*, Smith, J.D., Baker, C., Shafer, N., Thorland, E.C., Skinner, C., Schwartz, C.E., Nickerson, D.A., and Eichler, E.E.  2009.  A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease. Genome Research 19 (9): 1579-1585.  PMID: 19506092. PDF

Itsara, A.*, Cooper, G.M.*, Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R.M., Myers, R.M., Ridker, P.M., Chasman, D.I., Mefford, H., Ying, P., Nickerson, D.A., and Eichler, E.E.  2009. Population analysis of large copy number variants and hotspots of human genetic disease. American Journal of Human Genetics 84 (2): 148-161. PMID: 19166990. PDF


Cooper, G.M.*, Zerr, T.R.*, Kidd, J.M., Eichler, E.E., and Nickerson, D.A.  2008.  Systematic assessment of copy-number variant detection via genome-wide SNP genotyping.  Nature Genetics 40 (10): 1199-1203.  PMID: 18776910. PDF

Cooper, G.M., Johnson, J.A., Langaee, T.Y., Feng, H., Stanaway, I.B., Schwarz, U., Ritchie, M.D., Stein, C.M., Roden, D.M., Smith, J.D., Veenstra, D.L., Rettie, A.E., and Rieder, M.J.  2008.  A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose.  Blood 112 (4): 1022-1027.  PMID: 18535201. PDF

Hannes, F.D., Sharp, A.J., Mefford, H.C., … [9 additional authors] …, Cooper, G.M., Regan, R., Knight, S.J.L, Eichler, E.E., and Vermeesch, J.R.  2008.  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 (4): 223-232. PMID: 18550696. PDF

Kidd, J.M., Cooper, G.M., Donahue, W.F., … [39 additional authors] …, Olson, M.V., Kaul, R., Smith, D.R., and Eichler, E.E.  2008.  Mapping and sequencing of structural variation from eight human genomes.  Nature 453:56-64.  PMID: 18451855. PDF

Reiner, A.P., Barber, M.J., Guan, Y., … [12 additional authors] …, Stephens, M., Nickerson, D.A., and Krauss, R.M.  2008. Polymorphisms of the HNF1A gene encoding Hepatocyte Nuclear Factor-1a are associated with C-Reactive Protein.  American Journal of Human Genetics 82:1-9.  PMID: 18439552. PDF

Walsh, T., McClellan, J.M., McCarthy, S.E., Addington, A.M., Pierce, S.B., Cooper, G.M., … [28 additional authors] …, King, M.C., and Sebat, J.  2008.  Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia.  Science 320 (5875): 539-543.  PMID: 18369103. PDF

Sharp, A.J., Mefford, H., Li, K., … [29 additional authors] …, Schwartz, C.E., and Eichler, E.E.  2008.  A recurrent 15p13.3 microdeletion syndrome associated with mental retardation and seizures.  Nature Genetics 40 (3): 322-328.  PMID: 18278044. PDF

Cooper, G.M.* and Brown, C.D.*  2008.  Qualifying the relationship between sequence conservation and molecular function.  Genome Research 18 (2): 201-205.  Review/Perspective. PMID: 18245453. PDF

Kathiresan, S., Melander, O., Guiducci, C., … [20 additional authors] …, Groop, L., Altshuler, D.M., and Orho-Melander, M.  2008.  Genome-wide association analysis identifies six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, or triglycerides in humans.  Nature Genetics 40 (2): 189-197.  PMID: 18193044. PDF

Bovee, D., Zhou, Y., Haugen, E., Wu, Z., Hayden, H.S., Gillett, W., Tuzun, E., Cooper, G.M., Sampas, N., Phelps, K., Levy, R., Morrison, V.A., Sprague, J., Jewett, D., Buckley, D., Subramaniam, S., Chang, J., Smith, D.R, Olson, M.V., Eichler, E.E, and Kaul, R.  2008.  Closing gaps in the human genome with fosmid resources generated from multiple individuals.  Nature Genetics 40 (1): 96-101.  PMID: 18157130. PDF


Cooper, G.M., Nickerson, D.A., and Eichler, E.E.†  2007.  Mutational and selective effects on copy-number variants in the human genome.  Nature Genetics 39 (7 Suppl): S22-S29. Review. PMID: 17597777. PDF

Mefford, H.C., Clauin, S., Sharp, A.J., Moller, R.S., Ullmann, R., Kapur, R., Pinkel, D., Cooper, G.M., Ventura, M., Ropers, H.H., Tommerup, N., Eichler, E.E., and Bellanne-Chantelot, C.  2007.  Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy.  American Journal of Human Genetics 81 (5): 1057-1069.  PMID: 17924346. PDF

Clark, T.G. Andrew, T., Cooper, G.M., Margulies, E.H., Mullikin, J.C., and Balding, D.J.  2007.  Functional constraint and small insertions and deletions in the ENCODE regions of the human genome.  Genome Biology 8 (9): R180.  PMID: 17784950. PDF

Kaelin, C.B., Cooper, G.M., Sidow, A., and Barsh, G.S.  2007.  Mammalian comparative sequence analysis of the Agrp locus.  PLoS ONE 2 (8): e702.  PMID: 17684549. PDF

The ENCODE Project Consortium (including Cooper, G.M.).  2007.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (7146): 799-816.  PMID: 17571346. PDF

Margulies, E.H.*, Cooper, G.M.*, Asimenos G.*, Thomas D.J.*, Dewey C.N.*, … [67 additional authors] …, Haussler, D., Miller, W., Pachter, L., Green, E.D, and Sidow, A.  2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research 17 (6): 760-774.  PMID: 17567995. PDF


Stone, E.A., Cooper, G.M., and Sidow, A. 2005. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annual Review of Genomics and Human Genetics 6: 143-164.  Review. PMID: 16124857. PDF

Cooper, G.M., Stone, E.A., Asimenos, G., NISC Comparative Sequencing Program, Green, E.D., Batzoglou, S., and Sidow, A. 2005.  Distribution and intensity of constraint in mammalian genomic sequence.  Genome Research 15 (7): 978-986.  PMID: 15965027. PDF


Cooper, G.M., Singaravelu, S.A.G., and Sidow, A. 2004.  ABC: Software for interactive browsing of genomic multiple sequence alignment data.  BMC Bioinformatics 5: 192.  PMID: 15588288. PDF

Okun, A., Cooper, G.M., Bailer, A.J., Bena, J., and Stayner, L.  2004.  Trends in occupational lead exposure since the 1978 OSHA lead standard.  American Journal of Industrial Medicine 45 (6): 558-572.  PMID: 15164400. PDF

The ENCODE Project Consortium (including Cooper, G.M.).  2004.  The ENCODE (ENCyclopedia Of DNA Elements) Project.  Science 306 (5696): 636-640.  Review/Viewpoint. PMID: 15499007. PDF

Rat Genome Sequencing Project Consortium, including Cooper, G.M. (Co-Leader, Evolutionary Analysis Group).  2004. Genome sequence of the Brown Norway Rat yields insights into mammalian evolution.  Nature 428 (6982): 493-521.  PMID: 15057822. PDF

Cooper, G.M., Brudno, M., Stone, E.A., Dubchak, I., Batzoglou, S., and Sidow, A. 2004.  Characterization of evolutionary rates and constraints in three mammalian genomes.  Genome Research 14 (4): 539-548.  PMID: 15059994. PDF

Brudno, M., Poliakov, A., Salamov, A., Cooper, G.M., Sidow, A., Rubin, E.M., Solovyev, V., Batzoglou, S., and Dubchak, I. 2004. Automated whole-genome multiple alignment of rat, mouse, and human. Genome Research 14 (4): 685-692.  PMID: 15060011. PDF


Cooper, G.M. and Sidow, A.  2003.  Genomic regulatory regions: insights from comparative sequence analysis.  Current Opinion in Genetics and Development 13 (6): 604-610. Review. PMID: 14638322. PDF

Cooper, G.M., Brudno, M., NISC Comparative Sequencing Program, Green, E.D., Batzoglou, S., and Sidow, A.  2003. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.  Genome Research 13 (5): 813-820.  PMID: 12727901. PDF

Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., NISC Comparative Sequencing Program, Green, E.D., Sidow, A., and Batzoglou, S.  2003.  LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Research 13 (4): 721-731.  PMID: 12654723. PDF

* – equal contributions;  – corresponding author