Cofactor Genomics

Cofactor Member Papers

Cofactor Genomics is a young team of scientists with a history of 17 publications in the last 10 years. These range from the original sequencing of the AML cancer, platypus, macaque, and human genomes to applications such as whole-genome resequencing, transcriptome and traditional EST analysis, assembly, and plant-microbe and plant-herbicide interactions.

Romanov MN, Tuttle EM, Houck ML, Modi WS, Chemnick LG, Korody ML, Mork EM,
Otten CA, Renner T, Jones KC, Dandekar S, Papp JC, Da Y; NISC Comparative
Sequencing Program, Green ED, Magrini V, Hickenbotham MT, Glasscock J, McGrath S,
Mardis ER, Ryder OA. The value of avian genomics to the conservation of wildlife.
BMC Genomics. 2009 Jul 14;10 Suppl 2:S10. PubMed PMID: 19607652; PubMed Central
PMCID: PMC2709253.

Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D,
Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt
DC, Pohl C, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Miner T, Fulton L,
Magrini V, Wylie T, Glasscock J, Conyers J, Sander N, Shi X, Osborne JR, Minx P,
Gordon D, Chinwalla A, Zhao Y, Ries RE, Payton JE, Westervelt P, Tomasson MH,
Watson M, Baty J, Ivanovich J, Heath S, Shannon WD, Nagarajan R, Walter MJ, Link
DC, Graubert TA, DiPersio JF, Wilson RK. DNA sequencing of a cytogenetically
normal acute myeloid leukaemia genome. Nature. 2008 Nov 6;456(7218):66-72. PubMed
PMID: 18987736; PubMed Central PMCID: PMC2603574.

Zhu J, Patzoldt WL, Shealy RT, Vodkin LO, Clough SJ, Tranel PJ. Transcriptome 
response to glyphosate in sensitive and resistant soybean. J Agric Food Chem.
2008 Aug 13;56(15):6355-63. Epub 2008 Jul 18. PubMed PMID: 18636734.

Zody MC, Jiang Z, Fung HC, Antonacci F, Hillier LW, Cardone MF, Graves TA,
Kidd JM, Cheng Z, Abouelleil A, Chen L, Wallis J, Glasscock J, Wilson RK, Reily
AD, Duckworth J, Ventura M, Hardy J, Warren WC, Eichler EE. Evolutionary toggling
of the MAPT 17q21.31 inversion region. Nat Genet. 2008 Aug 10.
[Epub ahead of print] PubMed PMID: 18690220.

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F,
Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P,
Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS,
López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A,
Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA,
Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS,
Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A,
Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP,
Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R,
Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M,
Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita
Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison
R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y,
Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl
CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK.
Genome analysis of the platypus reveals unique signatures of evolution. Nature.
2008 May 8;453(7192):175-83. Erratum in: Nature. 2008 Sep 11;455(7210):256.
Nefedov, Mikhail [added]; de Jong, Pieter J [added]. PubMed PMID: 18464734.

Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P,
Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart
DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER. Whole-genome
sequencing and variant discovery in C. elegans. Nat Methods. 2008 Feb;5(2):183-8.
Epub 2008 Jan 20. PubMed PMID: 18204455.

Schmidt CJ, Romanov M, Ryder O, Magrini V, Hickenbotham M, Glasscock J,
McGrath S, Mardis E, Stein LD. Gallus GBrowse: a unified genomic database for the
chicken. Nucleic Acids Res. 2008 Jan;36(Database issue):D719-23. Epub 2007 Oct
11. PubMed PMID: 17933775; PubMed Central PMCID: PMC2238981.

Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER,
Dangl JL, Jones CD. Extending assembly of short DNA sequences to handle error.
Bioinformatics. 2007 Nov 1;23(21):2942-4. Epub 2007 Sep 24. PubMed PMID:
17893086.

Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J,
Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL,
Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC,
Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T,
Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding
Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC,
Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness
EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth
LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers
YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek
AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern
AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E,
Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein
JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR,
Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K,
Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro
JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J,
Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby
A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R,
Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H,
Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R,
Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K,
Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP,
Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Evolutionary and
biomedical insights from the rhesus macaque genome. Science. 2007 Apr
13;316(5822):222-34. PubMed PMID: 17431167.

Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A,
Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra
MA, Jones SJ. Analysis of the prostate cancer cell line LNCaP transcriptome using
a sequencing-by-synthesis approach. BMC Genomics. 2006 Sep 29;7:246. PubMed PMID:
17010196; PubMed Central PMCID: PMC1592491.

Giannakis M, Stappenbeck TS, Mills JC, Leip DG, Lovett M, Clifton SW,
Ippolito JE, Glasscock JI, Arumugam M, Brent MR, Gordon JI. Molecular properties
of adult mouse gastric and intestinal epithelial progenitors in their niches. J
Biol Chem. 2006 Apr 21;281(16):11292-300. Epub 2006 Feb 7. PubMed PMID: 16464855.
Zou J, Rodriguez-Zas S, Aldea M, Li M, Zhu J, Gonzalez DO, Vodkin LO, DeLucia
E, Clough SJ. Expression profiling soybean response to Pseudomonas syringae
reveals new defense-related genes and rapid HR-specific downregulation of
photosynthesis. Mol Plant Microbe Interact. 2005 Nov;18(11):1161-74. PubMed PMID:
16353551.

Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D,
Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L,
Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C,
Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M,
Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K,
Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea  E, Hou S, Levy A,
Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S,
Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M,
Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM,
Maupin R, Latreille  P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N,
Nelson  JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL,
Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J,
Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC,
Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I,  Furey TS, Miller W, Eichler EE, Bork P Suyama M,
Torrents D, Waterston RH, Wilson RK. Generation and annotation of the DNA sequences of human
chromosomes 2  and 4. Nature. 2005 Apr 7;434(7034):724-31. PubMed PMID: 15815621.

Messina DN, Glasscock J, Gish W, Lovett M. An ORFeome-based analysis of human
transcription factor genes and the construction of a microarray to interrogate their
expression. Genome Res. 2004 Oct;14(10B):2041-7. PubMed PMID: 15489324; PubMed Central
PMCID: PMC528918.

Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M,
Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL. Viral discovery and sequence
recovery using DNA microarrays. PLoS Biol. 2003 Nov;1(2):E2. Epub 2003 Nov 17. PubMed
PMID: 14624234; PubMed Central PMCID: PMC261870.

Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J,
Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA,
Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J,
Andrews S, Isak A, Vanbrunt A, Nguyen C,  Du F, Lamar B, Courtney L, Kalicki J, Ozersky P,
Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S,
Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R,
Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR,
Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT,
Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E,
Gillett W,  Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R,
Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME,
Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH,
Wilson RK. The DNA sequence of human chromosome 7. Nature. 2003 Jul 10;424(6945):157-64.
PubMed PMID: 12853948.

Kan Z, Gish W, Rouchka E, Glasscock J, States D. UTR reconstruction and analysis using
genomically aligned EST sequences. Proc Int Conf Intell Syst Mol Biol. 2000;8:218-27. PubMed PMID: 10977083.