Publications

Publications

Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A, BSMN Consortium. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data 2023 Nov 20, 10(1), 813     pmid:37985666

Anderson FM, Visser ND, Amses KR, Hodgins-Davis A, Weber AM, Metzner KM, McFadden MJ, Mills RE, O'Meara MJ, James TY, O'Meara TR. Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease. PLoS Biol 2023 May, 21(5), e3001822     pmid:37205709

Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, McConnell MJ, Brain Somatic Mosaicism Network. Mapping the Complex Genetic Landscape of Human Neurons. bioRxiv 2023 Mar 7, , N/A     pmid:36945473

Zhou W, Karan KR, Gu W, Klein HU, Sturm G, De Jager PL, Bennett DA, Hirano M, Picard M, Mills RE. Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts. bioRxiv 2023 Apr 21, , N/A     pmid:36778249

Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD Jr, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA Jr, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S, Gleeson JG, Focal Cortical Dysplasia Neurogenetics Consortium, Brain Somatic Mosaicism Network. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet 2023 Feb, 55(2), 209-220     pmid:36635388

Gu W, Bhangale A, Heft Neal ME, Smith JD, Brummel C, McHugh JB, Spector ME, Mills RE, Brenner JC. Analysis of Human Papilloma Virus Content and Integration in Mucoepidermoid Carcinoma. Viruses 2022 Oct 26, 14(11), N/A     pmid:36366450

Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Paul Flicek, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC, Human Genome Structural Variation Consortium. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 2022 Sep 1, 185(18), 3426-3440.e19     pmid:36055201

Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban AE, Leckman JF, Weinberger DR, Vaccarino FM, Abyzov A, Brain Somatic Mosaicism Network section sign. Analysis of somatic mutations in 131 human brains reveals aging- associated hypermutability. Science 2022 Jul 29, 377(6605), 511-517     pmid:35901164

Breuss MW, Yang X, Schlachetzki JCM, Antaki D, Lana AJ, Xu X, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, O'Brien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Van Der Kraan L, Ding Y, Glass CK, Gleeson JG, NIMH Brain Somatic Mosaicism Network. Somatic mosaicism reveals clonal distributions of neocortical development. Nature 2022 Apr, 604(7907), 689-696     pmid:35444276

Bao Y, Wadden J, Erb-Downward JR, Ranjan P, Zhou W, McDonald TL, Mills RE, Boyle AP, Dickson RP, Blaauw D, Welch JD. SquiggleNet: real-time, direct classification of nanopore signals. Genome Biol 2021 Oct 27, 22(1), 298     pmid:34706748

Cao Y, Haring CT, Brummel C, Bhambhani C, Aryal M, Lee C, Heft Neal M, Bhangale A, Gu W, Casper K, Malloy K, Sun Y, Shuman A, Prince ME, Spector ME, Chinn S, Shah J, Schonewolf C, McHugh JB, Mills RE, Tewari M, Worden FP, Swiecicki PL, Mierzwa M, Brenner JC. Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma. Clin Cancer Res 2022 Jan 15, 28(2), 350-359     pmid:34702772

Shi X, Radhakrishnan S, Wen J, Chen JY, Chen J, Lam BA, Mills RE, Stranger BE, Lee C, Setlur SR. Association of CNVs with methylation variation. NPJ Genom Med 2020 Sep 24, 5(1), 41     pmid:34556651

Lin J, Yang X, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Zhang C, Lee C, Devine SE, Eichler EE, Ye K, Human Genome Structural Variation Consortium. Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants. Genomics Proteomics Bioinformatics 2022 Feb, 20(1), 205-218     pmid:34224879

Pinatti LM, Gu W, Wang Y, Elhossiny A, Bhangale AD, Brummel CV, Carey TE, Mills RE, Brenner JC. SearcHPV: A novel approach to identify and assemble human papillomavirus- host genomic integration events in cancer. Cancer 2021 Oct 1, 127(19), 3531-3540     pmid:34160069

McDonald TL, Zhou W, Castro CP, Mumm C, Switzenberg JA, Mills RE, Boyle AP. Cas9 targeted enrichment of mobile elements using nanopore sequencing. Nat Commun 2021 Jun 11, 12(1), 3586     pmid:34117247

Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, Gerstein MB, Devine SE, Marschall T, Korbel JO, Eichler EE, Chaisson MJP, Lee C, Mills RE, Brand H, Talkowski ME, Human Genome Structural Variation Consortium. Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. Am J Hum Genet 2021 May 6, 108(5), 919-928     pmid:33789087

Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marques-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A, Brain Somatic Mosaicism Network. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol 2021 Mar 29, 22(1), 92     pmid:33781308

Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Hops W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 2021 Apr 2, 372(6537), N/A     pmid:33632895

Dayama G, Zhou W, Prado-Martinez J, Marques-Bonet T, Mills RE. Characterization of nuclear mitochondrial insertions in the whole genomes of primates. NAR Genom Bioinform 2020 Dec, 2(4), lqaa089     pmid:33575633

Oleksyk TK, Wolfsberger WW, Weber AM, Shchubelka K, Oleksyk OT, Levchuk O, Patrus A, Lazar N, Castro-Marquez SO, Hasynets Y, Boldyzhar P, Neymet M, Urbanovych A, Stakhovska V, Malyar K, Chervyakova S, Podoroha O, Kovalchuk N, Rodriguez-Flores JL, Zhou W, Medley S, Battistuzzi F, Liu R, Hou Y, Chen S, Yang H, Yeager M, Dean M, Mills RE, Smolanka V. Genome diversity in Ukraine. Gigascience 2021 Jan 13, 10(1), N/A     pmid:33438729

Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS, Mariani J, Petrov D, Barres BA, Duncan L, Abyzov A, Vogel H, Moran JV, Vaccarino FM, Tamminga CA, Levinson DF, Urban AE, Brain Somatic Mosaicism Network. Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. Nat Neurosci 2021 Feb, 24(2), 186-196     pmid:33432196

Rodin RE, Dou Y, Kwon M, Sherman MA, D'Gama AM, Doan RN, Rento LM, Girskis KM, Bohrson CL, Kim SN, Nadig A, Luquette LJ, Gulhan DC, Park PJ, Walsh CA, Brain Somatic Mosaicism Network. The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing. Nat Neurosci 2021 Feb, 24(2), 176-185     pmid:33432195

Shi X, Radhakrishnan S, Wen J, Chen JY, Chen J, Lam BA, Mills RE, Stranger BE, Lee C, Setlur SR. Association of CNVs with methylation variation. NPJ Genom Med 2020, 5, 41     pmid:33062306

Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol 2020 Nov, 38(11), 1347-1355     pmid:32541955

Shanta O, Noor A, Sebat J, Human Genome Structural Variation Consortium (HGSVC). The effects of common structural variants on 3D chromatin structure. BMC Genomics 2020 Jan 30, 21(1), 95     pmid:32000688

Sun C, Li H, Mills RE, Guan Y. Prognostic model for multiple myeloma progression integrating gene expression and clinical features. Gigascience 2019 Dec 1, 8(12), N/A     pmid:31886876

Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE. Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. Nucleic Acids Res 2020 Feb 20, 48(3), 1146-1163     pmid:31853540

Ho SS, Urban AE, Mills RE. Structural variation in the sequencing era. Nat Rev Genet 2020 Mar, 21(3), 171-189     pmid:31729472

Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA, Warren WC, Pollen AA, Chaisson MJP, Eichler EE, Human Genome Structural Variation Consortium. Human-specific tandem repeat expansion and differential gene expression during primate evolution. Proc Natl Acad Sci U S A 2019 Nov 12, 116(46), 23243-23253     pmid:31659027

Moldovan JB, Wang Y, Shuman S, Mills RE, Moran JV. RNA ligation precedes the retrotransposition of U6/LINE-1 chimeric RNA. Proc Natl Acad Sci U S A 2019 Oct 8, 116(41), 20612-20622     pmid:31548405

Rodriguez CM, Chun SY, Mills RE, Todd PK. Translation of upstream open reading frames in a model of neuronal differentiation. BMC Genomics 2019 May 20, 20(1), 391     pmid:31109297

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stutz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun 2019 Apr 16, 10(1), 1784     pmid:30992455

Ferrer-Torres D, Nancarrow DJ, Steinberg H, Wang Z, Kuick R, Weh KM, Mills RE, Ray D, Ray P, Lin J, Chang AC, Reddy RM, Orringer MB, Canto MI, Shaheen NJ, Kresty LA, Chak A, Wang TD, Rubenstein JH, Beer DG. Constitutively Higher Level of GSTT2 in Esophageal Tissues From African Americans Protects Cells Against DNA Damage. Gastroenterology 2019 Apr, 156(5), 1404-1415     pmid:30578782

Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A. FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods. Genome Biol 2018 Mar 20, 19(1), 38     pmid:29559002

Hovelson DH, Liu CJ, Wang Y, Kang Q, Henderson J, Gursky A, Brockman S, Ramnath N, Krauss JC, Talpaz M, Kandarpa M, Chugh R, Tuck M, Herman K, Grasso CS, Quist MJ, Feng FY, Haakenson C, Langmore J, Kamberov E, Tesmer T, Husain H, Lonigro RJ, Robinson D, Smith DC, Alva AS, Hussain MH, Chinnaiyan AM, Tewari M, Mills RE, Morgan TM, Tomlins SA. Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy. Oncotarget 2017 Oct 27, 8(52), 89848-89866     pmid:29163793

Zhao X, Weber AM, Mills RE. A recurrence-based approach for validating structural variation using long-read sequencing technology. Gigascience 2017 Aug 1, 6(8), 1-9     pmid:28873962

Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, Devine SE, 1000 Genomes Project Consortium. The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. Genome Res 2017 Nov, 27(11), 1916-1929     pmid:28855259

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), N/A     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 1, 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 1, 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 2, 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 4, 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 9, 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 8, 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 7, 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 1, 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 4, 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 8, 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 3, 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 9, 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 1, 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

Sherman,Marcus,D, Mills,Ryan,E. BAMnostic: an OS-agnostic toolkit for genomic sequence analysis The Journal of Open Source Science 2018 08 09, 3(28), 826     pmid: