(PDFs of full articles are available upon request.  Contact Dr. Cooper for articles.)

Innocenti, F.I.*, Cooper, G.M.*, Stanaway, I.B., Gamazon, E.R., Smith, J.D., Mirkov, S., Ramirez, J., Liu, W., Lin, Y.S., Maloney, C., Aldred, S.F., Trinklein, N.D., Shuetz, E., Nickerson, D.A., Cox, N.J., Thummel, K.E., Rieder, M.J., Rettie, A.E., Ratain, M.J., and Brown, C.D. †  2011.  Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue.  PLoS Genetics 7 (5): e1002078. PMID: 21637794

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.

Ng, S.B.*, Bigham, A.W.*, Buckingham, K.J., Hannibal, M., McMillin, M., Gildersleeve, H., Beck, A.E., Tabor, H., Cooper, G.M., Mefford, H., Lee, C., Turner, E.H., Smith, J.D., Rieder, M.J., Yoshiura, K., Matsumoto, N., Ohta, T., Niikawa, N., 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.

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

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

Girirajan, S.*, Rosenfeld, J.A.*, Cooper, G.M, Antonacci, F., Kidd, J.M., Siswara, P., Itsara, A., Vives, L.,., …[49 authors]…, 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

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

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

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

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

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

Hannes, F.D., Sharp, A.J., Mefford, H.C., de Ravel, T., Ruivenkamp, C.A., Breuning, M.H., Fryns, J.P., Devriendt, K., Van Buggenhout, G., Vogels, A., Stewart, H.H, Hennekam, R.C., 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

Kidd, J.M., Cooper, G.M., …[42 authors]…, Smith, D.R., and Eichler, E.E.  2008.  Mapping and sequencing of structural variation from eight human genomes.  Nature 453:56-64.  PMID: 18451855

Reiner, A.P., Barber, M.J., Guan, Y., Ridker, P.M., Lange, L.A., Chasman, D.I., Walston, J.D., Cooper, G.M., Jenny, N.S., Rieder, M.J., Durda, J.P., Smith, J.D., Novembre, J., Tracy, R.P., Rotter, J.I., 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

Walsh T., McClellan J.M., McCarthy, S.E., Pierce, S.B., Cooper, G.M., …[28 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

Sharp, A.J., Mefford, H., … [25 authors]… Cooper, G.M., Knight, S.J., Romano, C., Zuffardi, O., Chen, C., 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

Kathiresan, S., Melander, O., Guiducci, C., Surti, A., Burtt, N.P., Rieder, M.J., Cooper, G.M., … [17 authors] …, 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

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

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

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

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

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

Margulies, E.H.*, Cooper, G.M.*, Asimenos G.*, Thomas D.J.*, Dewey C.N.*, … [34 authors] …, 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

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

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

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

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

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

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

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

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

Reviews and Perspectives

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

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.  PMID: 17597777

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.  PMID: 16124857

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

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.  PMID: 14638322

* – equal contributions
corresponding author