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Journal Article
Malukiewicz J, Boere V, de Oliveira MAdélia Bo, D'arc M, Ferreira JVA, French J, Housman G, de Souza CIgayara, Jerusalinsky L, de Melo FR, Valença-Montenegro MM, Moreira SBahadian, Silva Ide Oliveir, Pacheco FSantos, Rogers J, Pissinatti A, Del Rosario RCH, Ross C, Ruiz-Miranda CR, Pereira LCM, Schiel N, da Silva Fde Fátima, Souto A, Šlipogor V, Tardif S. An Introduction to the Callithrix Genus and Overview of Recent Advances in Marmoset Research. ILAR J. 2020 ;61(2-3):110-138.
Richards S. It's more than stamp collecting: how genome sequencing can unify biological research. Trends Genet. 2015 ;31(7):411-21.
Chen R, Mardon G. Keeping an eye on the fly genome. Dev Biol. 2005 ;282(2):285-93.
Bourgogne A, Garsin DA, Qin X, Singh KV, Sillanpaa J, Yerrapragada S, Ding Y, Dugan-Rocha S, Buhay C, Shen H, Chen G, Williams G, Muzny DM, Maadani A, Fox KA, Gioia J, Chen L, Shang Y, Arias CA, Nallapareddy SR, Zhao M, Prakash VP, Chowdhury S, Jiang H, Gibbs RA, Murray BE, Highlander SK, Weinstock GM. Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol. 2008 ;9(7):R110.
Day FR, Ruth KS, Thompson DJ, Lunetta KL, Pervjakova N, Chasman DI, Stolk L, Finucane HK, Sulem P, Bulik-Sullivan B, Esko T, Johnson AD, Elks CE, Franceschini N, He C, Altmaier E, Brody JA, Franke LL, Huffman JE, Keller MF, McArdle PF, Nutile T, Porcu E, Robino A, Rose LM, Schick UM, Smith JA, Teumer A, Traglia M, Vuckovic D, Yao J, Zhao W, Albrecht E, Amin N, Corre T, Hottenga J-J, Mangino M, Smith AV, Tanaka T, Abecasis G, Andrulis IL, Anton-Culver H, Antoniou AC, Arndt V, Arnold AM, Barbieri C, Beckmann MW, Beeghly-Fadiel A, Benitez J, Bernstein L, Bielinski SJ, Blomqvist C, Boerwinkle E, Bogdanova NV, Bojesen SE, Bolla MK, Borresen-Dale A-L, Boutin TS, Brauch H, Brenner H, Brüning T, Burwinkel B, Campbell A, Campbell H, Chanock SJ, J Chapman R, Chen Y-DIda, Chenevix-Trench G, Couch FJ, Coviello AD, Cox A, Czene K, Darabi H, De Vivo I, Demerath EW, Dennis J, Devilee P, Dörk T, Dos-Santos-Silva I, Dunning AM, Eicher JD, Fasching PA, Faul JD, Figueroa J, Flesch-Janys D, Gandin I, Garcia ME, García-Closas M, Giles GG, Girotto GG, Goldberg MS, González-Neira A, Goodarzi MO, Grove ML, Gudbjartsson DF, Guénel P, Guo X, Haiman CA, Hall P, Hamann U, Henderson BE, Hocking LJ, Hofman A, Homuth G, Hooning MJ, Hopper JL, Hu FB, Huang J, Humphreys K, Hunter DJ, Jakubowska A, Jones SE, Kabisch M, Karasik D, Knight JA, Kolcic I, Kooperberg C, Kosma V-M, Kriebel J, Kristensen V, Lambrechts D, Langenberg C, Li J, Li X, Lindström S, Liu Y, Luan J'an, Lubinski J, Mägi R, Mannermaa A, Manz J, Margolin S, Marten J, Martin NG, Masciullo C, Meindl A, Michailidou K, Mihailov E, Milani L, Milne RL, Müller-Nurasyid M, Nalls M, Neale BM, Nevanlinna H, Neven P, Newman AB, Nordestgaard BG, Olson JE, Padmanabhan S, Peterlongo P, Peters U, Petersmann A, Peto J, Pharoah PDP, Pirastu NN, Pirie A, Pistis G, Polasek O, Porteous D, Psaty BM, Pylkäs K, Radice P, Raffel LJ, Rivadeneira F, Rudan I, Rudolph A, Ruggiero D, Sala CF, Sanna S, Sawyer EJ, Schlessinger D, Schmidt MK, Schmidt F, Schmutzler RK, Schoemaker MJ, Scott RA, Seynaeve CM, Simard J, Sorice R, Southey MC, Stöckl D, Strauch K, Swerdlow A, Taylor KD, Thorsteinsdottir U, Toland AE, Tomlinson I, Truong T, Tryggvadottir L, Turner ST, Vozzi D, Wang Q, Wellons M, Willemsen G, Wilson JF, Winqvist R, Wolffenbuttel BBHR, Wright AF, Yannoukakos D, Zemunik T, Zheng W, Zygmunt M, Bergmann S, Boomsma DI, Buring JE, Ferrucci L, Montgomery GW, Gudnason V, Spector TD, van Duijn CM, Alizadeh BZ, Ciullo M, Crisponi L, Easton DF, Gasparini PP, Gieger C, Harris TB, Hayward C, Kardia SLR, Kraft P, McKnight B, Metspalu A, Morrison AC, Reiner AP, Ridker PM, Rotter JI, Toniolo D, Uitterlinden AG, Ulivi S, Völzke H, Wareham NJ, Weir DR, Yerges-Armstrong LM, Price AL, Stefansson K, Visser JA, Ong KK, Chang-Claude J, Murabito JM, Perry JRB, Murray A. Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair. Nat Genet. 2015 ;47(11):1294-1303.
Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge M, White S, Salerno W, Buhay C, Yu F, Muzny DM, Daly R, Duyk G, Gibbs RA, Boerwinkle E. Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. BMC Bioinformatics. 2014 ;15:30.
Eldomery MK, Coban-Akdemir Z, Harel T, Rosenfeld JA, Gambin T, Stray-Pedersen A, Küry S, Mercier S, Lessel D, Denecke J, Wiszniewski W, Penney S, Liu P, Bi W, Lalani SR, Schaaf CP, Wangler MF, Bacino CA, Lewis RAlan, Potocki L, Graham BH, Belmont JW, Scaglia F, Orange JS, Jhangiani SN, Chiang T, Doddapaneni H, Hu J, Muzny DM, Xia F, Beaudet AL, Boerwinkle E, Eng CM, Plon SE, V Sutton R, Gibbs RA, Posey JE, Yang Y, Lupski JR. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med. 2017 ;9(1):26.
Hollister EB, Oezguen N, Chumpitazi BP, Luna RAnn, Weidler EM, Rubio-Gonzales M, Dahdouli M, Cope JL, Mistretta T-A, Raza S, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Heitkemper M, Savidge TC, Shulman RJ, Versalovic J. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. J Mol Diagn. 2019 ;21(3):449-461.
Creighton CJ. Making Use of Cancer Genomic Databases. Curr Protoc Mol Biol. 2018 ;121:19.14.1-19.14.13.
Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 ;467(7319):1061-73.
McGuire AL, Gibbs RA. Meeting the growing demands of genetic research. J Law Med Ethics. 2006 ;34(4):809-12.
Petrosino JF, Highlander S, Luna RAnn, Gibbs RA, Versalovic J. Metagenomic pyrosequencing and microbial identification. Clin Chem. 2009 ;55(5):856-66.
Wheeler DA, Takebe N, Hinoue T, Hoadley KA, Cardenas MF, Hamilton AM, Laird PW, Wang L, Johnson A, Dewal N, Miller V, Piñeyro D, de Moura MCastro, Esteller M, Shen H, Zenklusen JClaude, Tarnuzzer R, McShane LM, Tricoli JV, Williams PM, Lubensky I, O'Sullivan-Coyne G, Kohn EC, Little RF, White J, Malik S, Harris L, Weil C, Chen AP, Karlovich C, Rodgers B, Shankar L, Jacobs P, Nolan T, Hu J, Muzny DM, Doddapaneni H, Korchina V, Gastier-Foster J, Bowen J, Leraas K, Edmondson EF, Doroshow JH, Conley BA, S Ivy P, Staudt LM. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment. Cancer Cell. 2021 ;39(1):38-53.e7.
Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MReza, Stray-Pedersen A, Liu P, Wen S, Alcaraz W, Cui H, Walkiewicz M, Reid J, Bainbridge M, Patel A, Boerwinkle E, Beaudet AL, Lupski JR, Plon SE, Gibbs RA, Eng CM. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA. 2014 ;312(18):1870-9.
Chen F, Zhang Y, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny DM, Kang H, Lee J, Tamboli P, Reuter V, Shelley CSimon, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, A Hakimi A, Wheeler DA, Creighton CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep. 2016 ;14(10):2476-89.
Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biol. 2022 ;23(1):182.
Chin C-S, Behera S, Khalak A, Sedlazeck FJ, Sudmant PH, Wagner J, Zook JM. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nat Methods. 2023 ;20(8):1213-1221.
Luo R, Sedlazeck FJ, Lam T-W, Schatz MC. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nat Commun. 2019 ;10(1):998.
Pickering CR, Zhou JH, J Lee J, Drummond JA, S Peng A, Saade RE, Tsai KY, Curry JL, Tetzlaff MT, Lai SY, Yu J, Muzny DM, Doddapaneni H, Shinbrot E, Covington KR, Zhang J, Seth S, Caulin C, Clayman GL, El-Naggar AK, Gibbs RA, Weber RS, Myers JN, Wheeler DA, Frederick MJ. Mutational landscape of aggressive cutaneous squamous cell carcinoma. Clin Cancer Res. 2014 ;20(24):6582-92.
Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol. 2020 ;38(9):1044-1053.
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.
Venner E, Yi V, Murdock DR, Kalla SE, Wu T-J, Sabo A, Li S, Meng Q, Tian X, Murugan M, Cohen M, Kovar C, Wei W-Q, Chung WK, Weng C, Wiesner GL, Jarvik GP, Muzny DM, Gibbs RA. Neptune: an environment for the delivery of genomic medicine. Genet Med. 2021 ;23(10):1838-1846.
Sedlazeck FJ, Rescheneder P, von Haeseler A. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics. 2013 ;29(21):2790-1.
Baumert J, Huang J, McKnight B, Sabater-Lleal M, Steri M, Chu AY, Trompet S, Lopez LM, Fornage M, Teumer A, Tang W, Rudnicka AR, Mälarstig A, Hottenga J-J, Kavousi M, Lahti J, Tanaka T, Hayward C, Huffman JE, Morange P-E, Rose LM, Basu S, Rumley A, Stott DJ, Buckley BM, de Craen AJM, Sanna S, Masala M, Biffar R, Homuth G, Silveira A, Sennblad B, Goel A, Watkins H, Müller-Nurasyid M, Rückerl R, Taylor K, Chen M-H, de Geus EJC, Hofman A, Witteman JCM, de Maat MPM, Palotie A, Davies G, Siscovick DS, Kolcic I, Wild SH, Song J, McArdle WL, Ford I, Sattar N, Schlessinger D, Grotevendt A, Franzosi MGrazia, Illig T, Waldenberger M, Lumley T, Tofler GH, Willemsen G, Uitterlinden AG, Rivadeneira F, Räikkönen K, Chasman DI, Folsom AR, Lowe GD, Westendorp RGJ, P Slagboom E, Cucca F, Wallaschofski H, Strawbridge RJ, Seedorf U, Koenig W, Bis JC, Mukamal KJ, van Dongen J, Widen E, Franco OH, Starr JM, Liu K, Ferrucci L, Polasek O, Wilson JF, Oudot-Mellakh T, Campbell H, Navarro P, Bandinelli S, Eriksson J, Boomsma DI, Dehghan A, Clarke R, Hamsten A, Boerwinkle E, J Jukema W, Naitza S, Ridker PM, Völzke H, Deary IJ, Reiner AP, Trégouët D-A, O'Donnell CJ, Strachan DP, Peters A, Smith NL. No evidence for genome-wide interactions on plasma fibrinogen by smoking, alcohol consumption and body mass index: results from meta-analyses of 80,607 subjects. PLoS One. 2014 ;9(12):e111156.
Yuan B, Harel T, Gu S, Liu P, Burglen L, Chantot-Bastaraud S, Gelowani V, Beck CR, Carvalho CMB, Cheung SWai, Coe A, Malan V, Munnich A, Magoulas PL, Potocki L, Lupski JR. Nonrecurrent 17p11.2p12 Rearrangement Events that Result in Two Concomitant Genomic Disorders: The PMP22-RAI1 Contiguous Gene Duplication Syndrome. Am J Hum Genet. 2015 ;97(5):691-707.