Publications

Lalani A-KA, Xie W, Martini DJ, Steinharter JA, Norton CK, Krajewski KM, Duquette A, Bossé D, Bellmunt J, Van Allen EM, McGregor BA, Creighton CJ, Harshman LC, Choueiri TK. Change in Neutrophil-to-lymphocyte ratio (NLR) in response to immune checkpoint blockade for metastatic renal cell carcinoma. J Immunother Cancer. 2018 ;6(1):5.

Dolzhenko E, English A, Dashnow H, Brandine GDe Sena, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KPin, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Züchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol. 2024 ;.

Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SWai, Wu L, Yu F. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat. 2017 ;38(6):669-677.

Tominaga A, Mahmoud MA, Mamun AA al, Mukaihara T. Characterization of cryptic flagellin genes in Shigella boydii and Shigella dysenteriae. Genes Genet Syst. 2001 ;76(2):111-20.

Qin X, Singh KV, Weinstock GM, Murray BE. Characterization of fsr, a regulator controlling expression of gelatinase and serine protease in Enterococcus faecalis OG1RF. J Bacteriol. 2001 ;183(11):3372-82.

Parfenov M, Pedamallu CSekhar, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, D Hayes N, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 ;111(43):15544-9.

Gelb BD, Worley KC, Griffin LD, Adams V, Chinault AC, McCabe ER. Characterization of human genomic yeast artificial chromosome inserts containing hexokinase 1 coding information on chromosome 10. Biochem Med Metab Biol. 1992 ;47(3):265-9.

Lee IS, Carvalho CMB, Douvaras P, Ho S-M, Hartley BJ, Zuccherato LW, Ladran IG, Siegel AJ, McCarthy S, Malhotra D, Sebat J, Rapoport J, Fossati V, Lupski JR, Levy DL, Brennand KJ. Characterization of molecular and cellular phenotypes associated with a heterozygous deletion using patient-derived hiPSC neural cells. NPJ Schizophr. 2015 ;1:15019-.

Fawcett GL, Raveendran M, Deiros DRio, Chen D, Yu F, Harris RAlan, Ren Y, Muzny DM, Reid JG, Wheeler DA, Worley KC, Shelton SE, Kalin NH, Milosavljevic A, Gibbs R, Rogers J. Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). BMC Genomics. 2011 ;12:311.

Palmieri M, Impey S, Kang H, di Ronza A, Pelz C, Sardiello M, Ballabio A. Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Hum Mol Genet. 2011 ;20(19):3852-66.

Hu J, Renne R. Characterization of the minimal replicator of Kaposi's sarcoma-associated herpesvirus latent origin. J Virol. 2005 ;79(4):2637-42.

Chew LJ, Yuan X, Scherer SE, Qie L, Huang F, Hayes WP, Gallo V. Characterization of the rat GRIK5 kainate receptor subunit gene promoter and its intragenic regions involved in neural cell specificity. J Biol Chem. 2001 ;276(45):42162-71.

Wilton PR, Sloan DB, Logsdon JM, Doddapaneni H, Neiman M. Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum). Mol Ecol Resour. 2013 ;13(2):289-94.

Tsukayama P, Boolchandani M, Patel S, Pehrsson EC, Gibson MK, Chiou KL, Jolly CJ, Rogers J, Phillips-Conroy JE, Dantas G. Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes. mSystems. 2018 ;3(3).

Lu JT, Wang Y, Gibbs RA, Yu F. Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms. Genome Biol. 2012 ;13(2):R15.

Wang QY, Song J, Gibbs RA, Boerwinkle E, Dong JF, Yu FL. Characterizing polymorphisms and allelic diversity of von Willebrand factor gene in the 1000 Genomes. J Thromb Haemost. 2013 ;11(2):261-9.

Sanghvi RV, Buhay CJ, Powell BC, Tsai EA, Dorschner MO, Hong CS, Lebo MS, Sasson A, Hanna DS, McGee S, Bowling KM, Cooper GM, Gray DE, Lonigro RJ, Dunford A, Brennan CA, Cibulskis C, Walker K, Carneiro MO, Sailsbery J, Hindorff LA, Robinson DR, Santani A, Sarmady M, Rehm HL, Biesecker LG, Nickerson DA, Hutter CM, Garraway L, Muzny DM, Wagle N. Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genet Med. 2018 ;20(8):855-866.

Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, Mardis ER, McPherson JD, Minna JD, Morgan MB, Nadel M, Orringer MB, Osborne JR, Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd F, Sougnez C, Spitz MR, Tsao M-S, Twomey D, Verhaak RGW, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S, Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis WD, Pao W, Rubin MA, Gabriel SB, Gibbs RA, Varmus HE, Wilson RK, Lander ES, Meyerson M. Characterizing the cancer genome in lung adenocarcinoma. Nature. 2007 ;450(7171):893-8.

Mistretta B, Rankothgedera S, Castillo M, Rao M, Holloway K, Bhardwaj A, Noafal MEl, Albarracin C, El-Zein R, Rezaei H, Su X, Akbani R, Shao XM, Czerniecki BJ, Karchin R, Bedrosian I, Gunaratne PH. Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front Immunol. 2023 ;14:1188831.

Gillentine MA, White JJ, Grochowski CM, Lupski JR, Schaaf CP, Calarge CA. CHRNA7 Deletions are Enriched in Risperidone-Treated Children and Adolescents. J Child Adolesc Psychopharmacol. 2017 ;27(10):908-915.

Grochowski CM, Krepischi ACV, Eisfeldt J, Du H, Bertola DR, Oliveira D, Costa SS, Lupski JR, Lindstrand A, Carvalho CMB. Chromoanagenesis Event Underlies a Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome. Front Genet. 2021 ;12:708348.

Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SRama Srida, Purushothaman K, Saju JM, Jiang J, Mbandi SKimbung, Jonas M, Tong AHin Yan, Mwangi S, Lau D, Ngoh SYan, Liew WChang, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin C-S, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Katneni VKumar, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet. 2016 ;12(4):e1005954.

Petrosino JF, Xiang Q, Karpathy SE, Jiang H, Yerrapragada S, Liu Y, Gioia J, Hemphill L, Gonzalez A, Raghavan TM, Uzman A, Fox GE, Highlander S, Reichard M, Morton RJ, Clinkenbeard KD, Weinstock GM. Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence. J Bacteriol. 2006 ;188(19):6977-85.

Natarajan P, Pampana A, Graham SE, Ruotsalainen SE, Perry JA, de Vries PS, Broome JG, Pirruccello JP, Honigberg MC, Aragam K, Wolford B, Brody JA, Antonacci-Fulton L, Arden M, Aslibekyan S, Assimes TL, Ballantyne CM, Bielak LF, Bis JC, Cade BE, Do R, Doddapaneni H, Emery LS, Hung Y-J, Irvin MR, Khan AT, Lange L, Lee J, Lemaitre RN, Martin LW, Metcalf GA, Montasser ME, Moon J-Y, Muzny DM, O'Connell JR, Palmer ND, Peralta JM, Peyser PA, Stilp AM, Tsai M, Wang FFei, Weeks DE, Yanek LR, Wilson JG, Abecasis G, Arnett DK, Becker LC, Blangero J, Boerwinkle E, Bowden DW, Chang Y-C, Chen Y-DI, Choi WJung, Correa A, Curran JE, Daly MJ, Dutcher SK, Ellinor PT, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, He J, Hveem K, Jarvik GP, Kaplan RC, Kardia SLR, Kenny E, Kim RW, Kooperberg C, Laurie CC, Lee S, Lloyd-Jones DM, Loos RJF, Lubitz SA, Mathias RA, Martinez KAViaud, McGarvey ST, Mitchell BD, Nickerson DA, North KE, Palotie A, Park CJoo, Psaty BM, Rao DC, Redline S, Reiner AP, Seo D, Seo J-S, Smith AV, Tracy RP, Vasan RS, Kathiresan S, L Cupples A, Rotter JI, Morrison AC, Rich SS, Ripatti S, Willer C, Peloso GM. Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices. Nat Commun. 2021 ;12(1):2182.

Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin C-S, Church GM, Li H. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol. 2021 ;39(3):309-312.