Publications

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2021
Baslan T, Kovaka S, Sedlazeck FJ, Zhang Y, Wappel R, Tian S, Lowe SW, Goodwin S, Schatz MC. High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Res. 2021 ;49(21):e124.
Smith LM, Ladner JT, Hodara VL, Parodi LM, Harris RA, Callery JE, Lai Z, Zou Y, Raveedran M, Rogers J, Giavedoni LD. Multiplexed Simian Immunodeficiency Virus-Specific Paired RNA-Guided Cas9 Nickases Inactivate Proviral DNA. J Virol. 2021 ;95(23):e0088221.
Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol. 2021 ;39(9):1129-1140.
2020
Luo W, Wang Y, Zhang L, Ren P, Zhang C, Li Y, Azares AR, Zhang M, Guo J, Ghaghada KB, Starosolski ZA, Rajapakshe K, Coarfa C, Li Y, Chen R, Fujiwara K, Abe J-I, Coselli JS, Milewicz DM, LeMaire SA, Shen YH. Critical Role of Cytosolic DNA and Its Sensing Adaptor STING in Aortic Degeneration, Dissection, and Rupture. Circulation. 2020 ;141(1):42-66.
Lee I, Razaghi R, Gilpatrick T, Molnar M, Gershman A, Sadowski N, Sedlazeck FJ, Hansen KD, Simpson JT, Timp W. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat Methods. 2020 ;17(12):1191-1199.
2019
Greenwald WW, Li H, Benaglio P, Jakubosky D, Matsui H, Schmitt A, Selvaraj S, D'Antonio M, D'Antonio-Chronowska A, Smith EN, Frazer KA. Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression. Nat Commun. 2019 ;10(1):1054.
2018
Greytak SR, Engel KB, Zmuda E, Casas-Silva E, Guan P, Hoadley KA, Mungall AJ, Wheeler DA, Doddapaneni H, Moore HM. National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue. Biopreserv Biobank. 2018 ;16(4):247-250.
2017
Bainbridge MNeil, Li L, Tan Y, Cheong BY, Marian AJ. Identification of established arrhythmogenic right ventricular cardiomyopathy mutation in a patient with the contrasting phenotype of hypertrophic cardiomyopathy. BMC Med Genet. 2017 ;18(1):24.
Dharmat R, Liu W, Ge Z, Sun Z, Yang L, Li Y, Wang K, Thomas K, Sui R, Chen R. IFT81 as a Candidate Gene for Nonsyndromic Retinal Degeneration. Invest Ophthalmol Vis Sci. 2017 ;58(5):2483-2490.
2014
Wang F, Li H, Xu M, Li H, Zhao L, Yang L, Zaneveld JE, Wang K, Li Y, Sui R, Chen R. A homozygous missense mutation in NEUROD1 is associated with nonsyndromic autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2014 ;56(1):150-5.
Wang F, Wang Y, Zhang B, Zhao L, Lyubasyuk V, Wang K, Xu M, Li Y, Wu F, Wen C, Bernstein PS, Lin D, Zhu S, Wang H, Zhang K, Chen R. A missense mutation in HK1 leads to autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2014 ;55(11):7159-64.
2013
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 2013 ;23(2):341-51.
2012
Mubiru JN, Cavazos N, Hemmat P, Garcia-Forey M, Shade RE, Rogers J. Androgen receptor CAG repeat polymorphism in males of six non-human primate species. J Med Primatol. 2012 ;41(1):67-70.
Campeau PM, Lu JT, Dawson BC, Fokkema IFAC, Robertson SP, Gibbs RA, Lee BH. The KAT6B-related disorders genitopatellar syndrome and Ohdo/SBBYS syndrome have distinct clinical features reflecting distinct molecular mechanisms. Hum Mutat. 2012 ;33(11):1520-5.
2011
Bressler J, Shimmin LC, Boerwinkle E, Hixson JE. Global DNA methylation and risk of subclinical atherosclerosis in young adults: the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study. Atherosclerosis. 2011 ;219(2):958-62.
2010
McGuire AL, Majumder MA, Halpern SD, Swindell JS, Yaeger LV, Gibbs RA, Wheeler TM. Taking DNA from the dead. Nat Rev Genet. 2010 ;11(5):318.
2009
Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CLG, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny DM, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJM, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 ;19(12):2324-33.
Lin J, Kennedy SH, Svarovsky T, Rogers J, Kemnitz JW, Xu A, Zondervan KT. High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil. Anal Biochem. 2009 ;395(2):265-7.
Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, S Sahinalp C, Gibbs RA, Eichler EE. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet. 2009 ;41(10):1061-7.
2008
Persampieri J, Ritter DI, Lees D, Lehoczky J, Li Q, Guo S, Chuang JH. cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation. Bioinformatics. 2008 ;24(20):2418-9.
2007
Wu W, Stupi BP, Litosh VA, Mansouri D, Farley D, Morris S, Metzker S, Metzker ML. Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates. Nucleic Acids Res. 2007 ;35(19):6339-49.
2006
Johnson ME, Cheng Z, V Morrison A, Scherer SE, Ventura M, Gibbs RA, Green ED, Eichler EE. Recurrent duplication-driven transposition of DNA during hominoid evolution. Proc Natl Acad Sci U S A. 2006 ;103(47):17626-31.
Sodergren E, Shen Y, Song X, Zhang L, Gibbs RA, Weinstock GM. Shedding genomic light on Aristotle's lantern. Dev Biol. 2006 ;300(1):2-8.
2005
Price MG, Davis CF, Deng F, Burgess DL. The alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionate receptor trafficking regulator "stargazin" is related to the claudin family of proteins by Its ability to mediate cell-cell adhesion. J Biol Chem. 2005 ;280(20):19711-20.
Metzker ML. Emerging technologies in DNA sequencing. Genome Res. 2005 ;15(12):1767-76.