Publications

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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.
Matejková P, Strouhal M, Smajs D, Norris SJ, Palzkill T, Petrosino JF, Sodergren E, Norton JE, Singh J, Richmond TA, Molla MN, Albert TJ, Weinstock GM. Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol. 2008 ;8:76.
Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, Wang JD, Chen R. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 2008 ;4(8):e1000139.
Reid JG, Nagaraja AK, Lynn FC, Drabek RB, Muzny DM, Shaw CA, Weiss MK, Naghavi AO, Khan M, Zhu H, Tennakoon J, Gunaratne GH, Corry DB, Miller J, McManus MT, German MS, Gibbs RA, Matzuk MM, Gunaratne PH. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genome Res. 2008 ;18(10):1571-81.
Liu S, Ballian N, Belaguli NS, Patel S, Li M, Templeton NSmyth, Gingras M-C, Gibbs R, Fisher W, F Brunicardi C. PDX-1 acts as a potential molecular target for treatment of human pancreatic cancer. Pancreas. 2008 ;37(2):210-20.
McGuire AL, Caulfield T, Cho MK. Research ethics and the challenge of whole-genome sequencing. Nat Rev Genet. 2008 ;9(2):152-6.
2007
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Pond SLKosakovs, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, W Kent J. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007 ;17(12):1797-808.
Lin H, Doddapaneni HV, Takahashi Y, M Walker A. Comparative analysis of ESTs involved in grape responses to Xylella fastidiosa infection. BMC Plant Biol. 2007 ;7:8.
Marshall V, Parks T, Bagni R, Wang CDian, Samols MA, Hu J, Wyvil KM, Aleman K, Little RF, Yarchoan R, Renne R, Whitby D. Conservation of virally encoded microRNAs in Kaposi sarcoma--associated herpesvirus in primary effusion lymphoma cell lines and in patients with Kaposi sarcoma or multicentric Castleman disease. J Infect Dis. 2007 ;195(5):645-59.
Shimmin LC, Natarajan S, Ibarguen H, Montasser M, Kim D-K, Hanis CL, Boerwinkle E, Wadhwa PD, Hixson JE. Corticotropin releasing hormone (CRH) gene variation: comprehensive resequencing for variant and molecular haplotype discovery in monosomic hybrid cell lines. DNA Seq. 2007 ;18(6):434-44.
Daniel A, Bonnen PE, Fischetti VA. First complete genome sequence of two Staphylococcus epidermidis bacteriophages. J Bacteriol. 2007 ;189(5):2086-100.
Aronstein KA, Murray KD, de León JH, Qin X, Weinstock GM. High mobility group (HMG-box) genes in the honeybee fungal pathogen Ascosphaera apis. Mycologia. 2007 ;99(4):553-61.
Wang M, Vikis HG, Wang Y, Jia D, Wang D, Bierut LJ, Bailey-Wilson JE, Amos CI, Pinney SM, Petersen GM, de Andrade M, Yang P, Wiest JS, Fain PR, Schwartz AG, Gazdar A, Minna J, Gaba C, Rothschild H, Mandal D, Kupert E, Seminara D, Liu Y, Viswanathan A, Govindan R, Anderson MW, You M. Identification of a novel tumor suppressor gene p34 on human chromosome 6q25.1. Cancer Res. 2007 ;67(1):93-9.
Pannu H, Tran-Fadulu V, Papke CL, Scherer SE, Liu Y, Presley C, Guo D, Estrera AL, Safi HJ, Brasier AR, G Vick W, Marian AJ, Raman CS, L Buja M, Milewicz DM. MYH11 mutations result in a distinct vascular pathology driven by insulin-like growth factor 1 and angiotensin II. Hum Mol Genet. 2007 ;16(20):2453-62.
Highlander SK, Hultén KG, Qin X, Jiang H, Yerrapragada S, Mason EO, Shang Y, Williams TM, Fortunov RM, Liu Y, Igboeli O, Petrosino J, Tirumalai M, Uzman A, Fox GE, Cardenas AMaria, Muzny DM, Hemphill L, Ding Y, Dugan S, Blyth PR, Buhay CJ, Dinh HH, Hawes AC, Holder M, Kovar CL, Lee SL, Liu W, Nazareth LV, Wang Q, Zhou J, Kaplan SL, Weinstock GM. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol. 2007 ;7:99.
Hotopp JCDunning, Clark ME, Oliveira DCSG, Foster JM, Fischer P, Torres MCMuñoz, Giebel JD, Kumar N, Ishmael N, Wang S, Ingram J, Nene RV, Shepard J, Tomkins J, Richards S, Spiro DJ, Ghedin E, Slatko BE, Tettelin H, Werren JH. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science. 2007 ;317(5845):1753-6.
2006
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.
Elsik CG, Worley KC, Zhang L, Milshina NV, Jiang H, Reese JT, Childs KL, Venkatraman A, C Dickens M, Weinstock GM, Gibbs RA. Community annotation: procedures, protocols, and supporting tools. Genome Res. 2006 ;16(11):1329-33.
Childers CP, Newkirk HL, Honeycutt DA, Ramlachan N, Muzny DM, Sodergren E, Gibbs RA, Weinstock GM, Womack JE, Skow LC. Comparative analysis of the bovine MHC class IIb sequence identifies inversion breakpoints and three unexpected genes. Anim Genet. 2006 ;37(2):121-9.
Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, R Harris A, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZMohid, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song X-Z, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, M Ansari-Lari A, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen B-V, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJH, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK-S, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. The DNA sequence, annotation and analysis of human chromosome 3. Nature. 2006 ;440(7088):1194-8.
Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, R Harris A, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZMohid, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Montgomery KT, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song X-Z, Steffen D, Lovering RC, Wheeler DA, Worley KC, Yuan Y, Zhang Z, Adams CQ, M Ansari-Lari A, Ayele M, Brown MJ, Chen G, Chen Z, Clerc-Blankenburg KP, Davis C, Delgado O, Dinh HH, Draper H, Gonzalez-Garay ML, Havlak P, Jackson LR, Jacob LS, Kelly SH, Li L, Li Z, Liu J, Liu W, Lu J, Maheshwari M, Nguyen B-V, Okwuonu GO, Pasternak S, Perez LM, Plopper FJH, Santibanez J, Shen H, Tabor PE, Verduzco D, Waldron L, Wang Q, Williams GA, Zhang J, Zhou J, Allen CC, Amin AG, Anyalebechi V, Bailey M, Barbaria JA, Bimage KE, Bryant NP, Burch PE, Burkett CE, Burrell KL, Calderon E, Cardenas V, Carter K, Casias K, Cavazos I, Cavazos SR, Ceasar H, Chacko J, Chan SN, Chavez D, Christopoulos C, Chu J, Cockrell R, Cox CD, Dang M, Dathorne SR, David R, Davis CMon'Et, Davy-Carroll L, Deshazo DR, Donlin JE, D'Souza L, Eaves KA, Egan A, Emery-Cohen AJ, Escotto M, Flagg N, Forbes LD, Gabisi AM, Garza M, Hamilton C, Henderson N, Hernandez O, Hines S, Hogues ME, Huang M, Idlebird DVG, Johnson R, Jolivet A, Jones S, Kagan R, King LM, Leal B, Lebow H, Lee S, LeVan JM, Lewis LC, London P, Lorensuhewa LM, Loulseged H, Lovett DA, Lucier A, Lucier RL, Ma J, Madu RC, Mapua P, Martindale AD, Martinez E, Massey E, Mawhiney S, Meador MG, Mendez S, Mercado C, Mercado IC, Merritt CE, Miner ZL, Minja E, Mitchell T, Mohabbat F, Mohabbat K, Montgomery B, Moore N, Morris S, Munidasa M, Ngo RN, Nguyen NB, Nickerson E, Nwaokelemeh OO, Nwokenkwo S, Obregon M, Oguh M, Oragunye N, Oviedo RJ, Parish BJ, Parker DN, Parrish J, Parks KL, Paul HA, Payton BA, Perez A, Perrin W, Pickens A, Primus EL, Pu L-L, Puazo M, Quiles MM, Quiroz JB, Rabata D, Reeves K, Ruiz SJuana, Shao H, Sisson I, Sonaike T, Sorelle RP, Sutton AE, Svatek AF, Svetz LAnne, Tamerisa KS, Taylor TR, Teague B, Thomas N, Thorn RD, Trejos ZY, Trevino BK, Ukegbu ON, Urban JB, Vasquez LI, Vera VA, Villasana DM, Wang L, Ward-Moore S, Warren JT, Wei X, White F, Williamson AL, Wleczyk R, Wooden HS, Wooden SH, Yen J, Yoon L, Yoon V, Zorrilla SE, Nelson D, Kucherlapati R, Weinstock G, Gibbs RA. The finished DNA sequence of human chromosome 12. Nature. 2006 ;440(7082):346-51.
Mamun AAmar MAl, Gautam S, M Humayun Z. Hypermutagenesis in mutA cells is mediated by mistranslational corruption of polymerase, and is accompanied by replication fork collapse. Mol Microbiol. 2006 ;62(6):1752-63.
Chen SL, Hung C-S, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, Bieri T, Meyer RR, Ozersky P, Armstrong JR, Fulton RS, J Latreille P, Spieth J, Hooton TM, Mardis ER, Hultgren SJ, Gordon JI. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci U S A. 2006 ;103(15):5977-82.
Fernández-Valdivia R, Zhang Y, Pai S, Metzker ML, Schumacher A. l7Rn6 encodes a novel protein required for clara cell function in mouse lung development. Genetics. 2006 ;172(1):389-99.