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FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods.

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.

Genome Biol. 2018 Mar 20;19(1):38. doi: 10.1186/s13059-018-1404-6.


Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy.

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.

Oncotarget. 2017 Sep 22;8(52):89848-89866. doi: 10.18632/oncotarget.21163. eCollection 2017 Oct 27.


A recurrence-based approach for validating structural variation using long-read sequencing technology.

Zhao X, Weber AM, Mills RE.

Gigascience. 2017 Aug 1;6(8):1-9. doi: 10.1093/gigascience/gix061.


The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology.

Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE; 1000 Genomes Project Consortium, Devine SE.

Genome Res. 2017 Nov;27(11):1916-1929. doi: 10.1101/gr.218032.116. Epub 2017 Aug 30.


Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.

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.

Science. 2017 Apr 28;356(6336). pii: eaal1641. doi: 10.1126/science.aal1641. Epub 2017 Apr 27. Review.


Genetics of Combined Pituitary Hormone Deficiency: Roadmap into the Genome Era.

Fang Q, George AS, Brinkmeier ML, Mortensen AH, Gergics P, Cheung LY, Daly AZ, Ajmal A, Pérez Millán MI, Ozel AB, Kitzman JO, Mills RE, Li JZ, Camper SA.

Endocr Rev. 2016 Dec;37(6):636-675. Epub 2016 Nov 9. Review.


CodonShuffle: a tool for generating and analyzing synonymously mutated sequences.

Jorge DM, Mills RE, Lauring AS.

Virus Evol. 2015 Oct 2;1(1):vev012. eCollection 2015.


Resolving complex structural genomic rearrangements using a randomized approach.

Zhao X, Emery SB, Myers B, Kidd JM, Mills RE.

Genome Biol. 2016 Jun 10;17(1):126. doi: 10.1186/s13059-016-0993-1.


Defining the optimal formulation and schedule of a candidate toxoid vaccine against Clostridium difficile infection: A randomized Phase 2 clinical trial.

de Bruyn G, Saleh J, Workman D, Pollak R, Elinoff V, Fraser NJ, Lefebvre G, Martens M, Mills RE, Nathan R, Trevino M, van Cleeff M, Foglia G, Ozol-Godfrey A, Patel DM, Pietrobon PJ, Gesser R; H-030-012 Clinical Investigator Study Team.

Vaccine. 2016 Apr 27;34(19):2170-8. doi: 10.1016/j.vaccine.2016.03.028. Epub 2016 Mar 21.


An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz 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; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.


Unbiased modifier screen reveals that signal strength determines the regulatory role murine TLR9 plays in autoantibody production.

Mills RE, Lam VC, Tan A, Cresalia N, Oksenberg N, Zikherman J, Anderson M, Weiss A, Hermiston ML.

J Immunol. 2015 Apr 15;194(8):3675-86. doi: 10.4049/jimmunol.1500026. Epub 2015 Mar 13.


The genomic landscape of polymorphic human nuclear mitochondrial insertions.

Dayama G, Emery SB, Kidd JM, Mills RE.

Nucleic Acids Res. 2014 Nov 10;42(20):12640-9. doi: 10.1093/nar/gku1038. Epub 2014 Oct 27.


Increased genomic integrity of an improved protein-based mouse induced pluripotent stem cell method compared with current viral-induced strategies.

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.

Stem Cells Transl Med. 2014 May;3(5):599-609. doi: 10.5966/sctm.2013-0149. Epub 2014 Apr 24.


Primate genome architecture influences structural variation mechanisms and functional consequences.

Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15764-9. doi: 10.1073/pnas.1305904110. Epub 2013 Sep 6.


Does germ-line deletion of the PIP gene constitute a widespread risk for cancer?

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.

Eur J Hum Genet. 2014 Mar;22(3):307-9. doi: 10.1038/ejhg.2013.134. Epub 2013 Jun 19. No abstract available.


Copy number variation genotyping using family information.

Chu JH, Rogers A, Ionita-Laza I, Darvishi K, Mills RE, Lee C, Raby BA.

BMC Bioinformatics. 2013 May 9;14:157. doi: 10.1186/1471-2105-14-157.


CGG repeat-associated translation mediates neurodegeneration in fragile X tremor ataxia syndrome.

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.

Neuron. 2013 May 8;78(3):440-55. doi: 10.1016/j.neuron.2013.03.026. Epub 2013 Apr 18. Erratum in: Neuron. 2013 Jul 24;79(2):402.


Regulatory element copy number differences shape primate expression profiles.

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.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12656-61. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13.


Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration.

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.

Nat Genet. 2012 Mar 4;44(4):390-7, S1. doi: 10.1038/ng.2202.


Impact of the transition to ICD-10 on Medicare inpatient hospital payments.

Mills RE, Butler RR, McCullough EC, Bao MZ, Averill RF.

Medicare Medicaid Res Rev. 2011 Jun 6;1(2). doi: 10.5600/mmrr.001.02.a02.


Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis.

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.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):529-34. doi: 10.1073/pnas.1112163109. Epub 2011 Dec 27.


Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection.

Gokcumen O, Babb PL, Iskow RC, Zhu Q, Shi X, Mills RE, Ionita-Laza I, Vallender EJ, Clark AG, Johnson WE, Lee C.

Genome Biol. 2011;12(5):R52. doi: 10.1186/gb-2011-12-5-r52. Epub 2011 May 31.


Natural genetic variation caused by small insertions and deletions in the human genome.

Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS, Ponting CP, Webber C, Devine SE.

Genome Res. 2011 Jun;21(6):830-9. doi: 10.1101/gr.115907.110. Epub 2011 Apr 1.


Mapping copy number variation by population-scale genome sequencing.

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, Stütz 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.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.


Small insertions and deletions (INDELs) in human genomes.

Mullaney JM, Mills RE, Pittard WS, Devine SE.

Hum Mol Genet. 2010 Oct 15;19(R2):R131-6. doi: 10.1093/hmg/ddq400. Epub 2010 Sep 21. Review.


The junctional adhesion molecule JAML is a costimulatory receptor for epithelial gammadelta T cell activation.

Witherden DA, Verdino P, Rieder SE, Garijo O, Mills RE, Teyton L, Fischer WH, Wilson IA, Havran WL.

Science. 2010 Sep 3;329(5996):1205-10. doi: 10.1126/science.1192698.


Gammadelta T cells are reduced and rendered unresponsive by hyperglycemia and chronic TNFalpha in mouse models of obesity and metabolic disease.

Taylor KR, Mills RE, Costanzo AE, Jameson JM.

PLoS One. 2010 Jul 2;5(7):e11422. doi: 10.1371/journal.pone.0011422.


Natural mutagenesis of human genomes by endogenous retrotransposons.

Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE.

Cell. 2010 Jun 25;141(7):1253-61. doi: 10.1016/j.cell.2010.05.020.


Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

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.

Nat Genet. 2010 May;42(5):400-5. doi: 10.1038/ng.555. Epub 2010 Apr 4.


Expanding the definition of the classical bipartite nuclear localization signal.

Lange A, McLane LM, Mills RE, Devine SE, Corbett AH.

Traffic. 2010 Mar;11(3):311-23. doi: 10.1111/j.1600-0854.2009.01028.x. Epub 2009 Dec 15.


Assessment of organochlorine pesticides and metals in ring-tailed lemurs (Lemur catta) at Beza Mahafaly Special Reserve, Madagascar.

Rainwater TR, Sauther ML, Rainwater KA, Mills RE, Cuozzo FP, Zhang B, McDaniel LN, Abel MT, Marsland EJ, Weber MA, Youssouf Jacky IA, Platt SG, Cobb GP, Anderson TA.

Am J Primatol. 2009 Dec;71(12):998-1010. doi: 10.1002/ajp.20742.


A highly annotated whole-genome sequence of a Korean individual.

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.

Nature. 2009 Aug 20;460(7258):1011-5. doi: 10.1038/nature08211. Epub 2009 Jul 8.


T cell dependence on mTOR signaling.

Mills RE, Jameson JM.

Cell Cycle. 2009 Feb 15;8(4):545-8. Epub 2009 Feb 12. Review.


Active Alu retrotransposons in the human genome.

Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE.

Genome Res. 2008 Dec;18(12):1875-83. doi: 10.1101/gr.081737.108. Epub 2008 Oct 3.


Defects in skin gamma delta T cell function contribute to delayed wound repair in rapamycin-treated mice.

Mills RE, Taylor KR, Podshivalova K, McKay DB, Jameson JM.

J Immunol. 2008 Sep 15;181(6):3974-83.


A PY-NLS nuclear targeting signal is required for nuclear localization and function of the Saccharomyces cerevisiae mRNA-binding protein Hrp1.

Lange A, Mills RE, Devine SE, Corbett AH.

J Biol Chem. 2008 May 9;283(19):12926-34. doi: 10.1074/jbc.M800898200. Epub 2008 Mar 14.


Which transposable elements are active in the human genome?

Mills RE, Bennett EA, Iskow RC, Devine SE.

Trends Genet. 2007 Apr;23(4):183-91. Epub 2007 Feb 27. Review.


Classical nuclear localization signals: definition, function, and interaction with importin alpha.

Lange A, Mills RE, Lange CJ, Stewart M, Devine SE, Corbett AH.

J Biol Chem. 2007 Feb 23;282(8):5101-5. Epub 2006 Dec 14. Review.


An initial map of insertion and deletion (INDEL) variation in the human genome.

Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE.

Genome Res. 2006 Sep;16(9):1182-90. Epub 2006 Aug 10.


Recently mobilized transposons in the human and chimpanzee genomes.

Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE.

Am J Hum Genet. 2006 Apr;78(4):671-9. Epub 2006 Feb 2.


A system for cost and reimbursement control in hospitals. 1976.

Fetter RB, Thompson JD, Mills RE.

Yale J Biol Med. 2000 Jan-Dec;73(1-6):411-24. No abstract available.


Effects of dose and dose protraction on embryotoxicity of 14.1 MeV neutron irradiation in rats.

Beckman DA, Solomon HM, Buck SJ, Gorson RO, Mills RE, Brent RL.

Radiat Res. 1994 Jun;138(3):337-42.


Comparative effects of neutron irradiation and X irradiation on the embryonic development of the rat.

Solomon HM, Beckman DA, Buck SJ, Gorson RO, Mills RE, Brent RL.

Radiat Res. 1994 Feb;137(2):226-30.


Comment on "Relationship between Fröhlich and Davydov models of biological order"

Mills RE.

Phys Rev A. 1991 Mar 15;43(6):3176-3178. No abstract available.


Steady states in the extended Fröhlich model of far-from-equilibrium energy transport.

Mills RE.

Phys Rev A. 1990 Feb 15;41(4):2196-2199. No abstract available.


Comparison of X-ray and gamma-ray dose-response curves for pink somatic mutations in Tradescantia clone 02.

Underbrink AG, Kellerer AM, Mills RE, Sparrow AH.

Radiat Environ Biophys. 1976 Dec 23;13(4):295-303.


The application of diagnostic specific cost profiles to cost and reimbursement control in hospitals.

Fetter RB, Mills RE, Riedel DC, Thompson JD.

J Med Syst. 1977;1(2):137-49.


A system for cost and reimbursement control in hospitals.

Fetter RB, Thompson JD, Mills RE.

Yale J Biol Med. 1976 May;49(2):123-36.


Quantitative cinemorphology of the human brain displayed by means of mobile computer graphics.

Livingston RB, Wilson KR, Atkinson B, Tribble GL 3rd, Rempel DM, MacGregor JS 3rd, Mills RE, Edge TC, Pakan SD.

Trans Am Neurol Assoc. 1976;101:99-101. No abstract available.


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