Publications

Publications

McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM, Brain Somatic Mosaicism Network. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science 2017 Apr 28, 356(6336),      pmid:28450582

Chun SY, Rodriguez CM, Todd PK, Mills RE. SPECtre: a spectral coherence--based classifier of actively translated transcripts from ribosome profiling sequence data. BMC Bioinformatics 2016 Nov 25, 17(1), 482     pmid:27884106

Fang Q, George AS, Brinkmeier ML, Mortensen AH, Gergics P, Cheung LY, Daly AZ, Ajmal A, Perez Millan MI, Ozel AB, Kitzman JO, Mills RE, Li JZ, Camper SA. Genetics of Combined Pituitary Hormone Deficiency: Roadmap into the Genome Era. Endocr Rev 2016 Dec, 37(6), 636-675     pmid:27828722

Jorge DM, Mills RE, Lauring AS. CodonShuffle: a tool for generating and analyzing synonymously mutated sequences. Virus Evol 2015, 1(1), vev012     pmid:27774284

Zhao X, Emery SB, Myers B, Kidd JM, Mills RE. Resolving complex structural genomic rearrangements using a randomized approach. Genome Biol 2016 Jun 10, 17(1), 126     pmid:27287201

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stutz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO, 1000 Genomes Project Consortium. An integrated map of structural variation in 2,504 human genomes. Nature 2015 Oct 01, 526(7571), 75-81     pmid:26432246

Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR, 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 2015 Oct 01, 526(7571), 68-74     pmid:26432245

Delaneau O, Marchini J, 1000 Genomes Project Consortium, 1000 Genomes Project Consortium. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun 2014 Jun 13, 5, 3934     pmid:25653097

Dayama G, Emery SB, Kidd JM, Mills RE. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res 2014 Nov 10, 42(20), 12640-9     pmid:25348406

Brand H, Pillalamarri V, Collins RL, Eggert S, O'Dushlaine C, Braaten EB, Stone MR, Chambert K, Doty ND, Hanscom C, Rosenfeld JA, Ditmars H, Blais J, Mills R, Lee C, Gusella JF, McCarroll S, Smoller JW, Talkowski ME, Doyle AE. Cryptic and complex chromosomal aberrations in early-onset neuropsychiatric disorders. Am J Hum Genet 2014 Oct 02, 95(4), 454-61     pmid:25279985

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, 1000 Genomes Project Consortium. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol 2014 Jun 30, 15(6), R88     pmid:24980144

Park H, Kim D, Kim CH, Mills RE, Chang MY, Iskow RC, Ko S, Moon JI, Choi HW, Man Yoo PS, Do JT, Han MJ, Lee EG, Jung JK, Zhang C, Lanza R, Kim KS. Increased genomic integrity of an improved protein-based mouse induced pluripotent stem cell method compared with current viral-induced strategies. Stem Cells Transl Med 2014 May, 3(5), 599-609     pmid:24763686

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gumus ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M, 1000 Genomes Project Consortium. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 2013 Oct 04, 342(6154), 1235587     pmid:24092746

Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M, 1000 Genomes Project Consortium. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Res 2013 Dec, 23(12), 2042-52     pmid:24026178

Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stutz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO. Primate genome architecture influences structural variation mechanisms and functional consequences. Proc Natl Acad Sci U S A 2013 Sep 24, 110(39), 15764-9     pmid:24014587

Silva AG, Krepischi AC, Torrezan GT, Capelli LP, Carraro DM, D'Angelo CS, Koiffmann CP, Zatz M, Naslavsky MS, Masotti C, Otto PA, Achatz MI, Mills RE, Lee C, Pearson PL, Rosenberg C. Does germ-line deletion of the PIP gene constitute a widespread risk for cancer? Eur J Hum Genet 2014 Mar, 22(3), 307-9     pmid:23778870

Chu JH, Rogers A, Ionita-Laza I, Darvishi K, Mills RE, Lee C, Raby BA. Copy number variation genotyping using family information. BMC Bioinformatics 2013 May 09, 14, 157     pmid:23656838

Todd PK, Oh SY, Krans A, He F, Sellier C, Frazer M, Renoux AJ, Chen KC, Scaglione KM, Basrur V, Elenitoba-Johnson K, Vonsattel JP, Louis ED, Sutton MA, Taylor JP, Mills RE, Charlet-Berguerand N, Paulson HL. CGG repeat-associated translation mediates neurodegeneration in fragile X tremor ataxia syndrome. Neuron 2013 May 08, 78(3), 440-55     pmid:23602499

Rogers AJ, Chu JH, Darvishi K, Ionita-Laza I, Lehmann H, Mills R, Lee C, Raby BA. Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility. Clin Exp Allergy 2013 Apr, 43(4), 455-62     pmid:23517041

Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G, 1000 Genomes Project Consortium. The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res 2013 May, 23(5), 749-61     pmid:23478400

Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C, 1000 Genomes Project Consortium. Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet 2012 Dec 07, 91(6), 1022-32     pmid:23217326

Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 2012 Nov 01, 491(7422), 56-65     pmid:23128226

Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C. Regulatory element copy number differences shape primate expression profiles. Proc Natl Acad Sci U S A 2012 Jul 31, 109(31), 12656-61     pmid:22797897

Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, 1000 Genomes Project Consortium. The 1000 Genomes Project: data management and community access. Nat Methods 2012 Apr 27, 9(5), 459-62     pmid:22543379

Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, McLaughlan CJ, Bawden CS, Reid SJ, Faull RL, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, MacDonald ME, Gusella JF, Talkowski ME. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet 2012 Mar 04, 44(4), 390-7, S1     pmid:22388000

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C, 1000 Genomes Project Consortium. A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012 Feb 17, 335(6070), 823-8     pmid:22344438

Brown KH, Dobrinski KP, Lee AS, Gokcumen O, Mills RE, Shi X, Chong WW, Chen JY, Yoo P, David S, Peterson SM, Raj T, Choy KW, Stranger BE, Williamson RE, Zon LI, Freeman JL, Lee C. Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis. Proc Natl Acad Sci U S A 2012 Jan 10, 109(2), 529-34     pmid:22203992

Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project. The functional spectrum of low-frequency coding variation. Genome Biol 2011 Sep 14, 12(9), R84     pmid:21917140

Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, Bustamante CD, 1000 Genomes Project. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A 2011 Jul 19, 108(29), 11983-8     pmid:21730125

Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, 1000 Genomes Project. Variation in genome-wide mutation rates within and between human families. Nat Genet 2011 Jun 12, 43(7), 712-4     pmid:21666693

Gokcumen O, Babb PL, Iskow RC, Zhu Q, Shi X, Mills RE, Ionita-Laza I, Vallender EJ, Clark AG, Johnson WE, Lee C. Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection. Genome Biol 2011, 12(5), R52     pmid:21627829

Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, Macdonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith RS, Park JH, Hurles ME, Carter NP, Lee C, Scherer SW, Feuk L. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 2011 May 08, 29(6), 512-20     pmid:21552272

Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS, Ponting CP, Webber C, Devine SE. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res 2011 Jun, 21(6), 830-9     pmid:21460062

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stutz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature 2011 Feb 03, 470(7332), 59-65     pmid:21293372

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE, 1000 Genomes Project. Diversity of human copy number variation and multicopy genes. Science 2010 Oct 29, 330(6004), 641-6     pmid:21030649

Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA, 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 2010 Oct 28, 467(7319), 1061-73     pmid:20981092

Mullaney JM, Mills RE, Pittard WS, Devine SE. Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet 2010 Oct 15, 19(R2), R131-6     pmid:20858594

Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 2010 Jun 25, 141(7), 1253-61     pmid:20603005

Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, Yoo YJ, Shin JY, Kim HJ, Yavartanoo M, Chang YW, Ha JS, Chong W, Hwang GR, Darvishi K, Kim H, Yang SJ, Yang KS, Kim H, Hurles ME, Scherer SW, Carter NP, Tyler-Smith C, Lee C, Seo JS. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 2010 May, 42(5), 400-5     pmid:20364138

Lange A, McLane LM, Mills RE, Devine SE, Corbett AH. Expanding the definition of the classical bipartite nuclear localization signal. Traffic 2010 Mar, 11(3), 311-23     pmid:20028483

Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS. A highly annotated whole-genome sequence of a Korean individual. Nature 2009 Aug 20, 460(7258), 1011-5     pmid:19587683

Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. Active Alu retrotransposons in the human genome. Genome Res 2008 Dec, 18(12), 1875-83     pmid:18836035

Borodovsky M, Lomsadze A, Ivanov N, Mills R. Eukaryotic gene prediction using GeneMark.hmm. Curr Protoc Bioinformatics 2003 May, Chapter 4, Unit4.6     pmid:18428701

Borodovsky M, Mills R, Besemer J, Lomsadze A. Prokaryotic gene prediction using GeneMark and GeneMark.hmm. Curr Protoc Bioinformatics 2003 May, Chapter 4, Unit4.5     pmid:18428700

Lange A, Mills RE, Devine SE, Corbett AH. A PY-NLS nuclear targeting signal is required for nuclear localization and function of the Saccharomyces cerevisiae mRNA-binding protein Hrp1. J Biol Chem 2008 May 09, 283(19), 12926-34     pmid:18343812

Mills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet 2007 Apr, 23(4), 183-91     pmid:17331616

Lange A, Mills RE, Lange CJ, Stewart M, Devine SE, Corbett AH. Classical nuclear localization signals: definition, function, and interaction with importin alpha. J Biol Chem 2007 Feb 23, 282(8), 5101-5     pmid:17170104

Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 2006 Sep, 16(9), 1182-90     pmid:16902084

Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE. Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet 2006 Apr, 78(4), 671-9     pmid:16532396

Kattenhorn LM, Mills R, Wagner M, Lomsadze A, Makeev V, Borodovsky M, Ploegh HL, Kessler BM. Identification of proteins associated with murine cytomegalovirus virions. J Virol 2004 Oct, 78(20), 11187-97     pmid:15452238

Mills R, Rozanov M, Lomsadze A, Tatusova T, Borodovsky M. Improving gene annotation of complete viral genomes. Nucleic Acids Res 2003 Dec 01, 31(23), 7041-55     pmid:14627837

Perelygina L, Zhu L, Zurkuhlen H, Mills R, Borodovsky M, Hilliard JK. Complete sequence and comparative analysis of the genome of herpes B virus (Cercopithecine herpesvirus 1) from a rhesus monkey. J Virol 2003 Jun, 77(11), 6167-77     pmid:12743273