Brian Haas at The Broad Institute

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Creason A, Haan D, Dang K, Chiotti KE, Inkman M, Lamb A, Yu T, Hu Y, Norman TC, Buchanan A, van Baren MJ, Spangler R, Rollins MR, Spellman PT, Rozanov D, Zhang J, Maher CA, Caloian C, Watson JD, Uhrig S, Haas BJ, Jain M, Akeson M, Ahsen ME Cell Syst. 2021 Aug 18;12(8):827-838.e5. doi: 10.1016/j.cels.2021.05.021. Epub 2021 Jun 18. PMID: 34146471; PMCID: PMC8376800.

Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival. Gillani R, Seong BKA, Crowdis J, Conway JR, Dharia NV, Alimohamed S, Haas BJ, Han K, Park J, Dietlein F, He MX, Imamovic A, Ma C, Bassik MC, Boehm JS, Vazquez F, Gusev A, Liu D, Janeway KA, McFarland JM, Stegmaier K, Van Allen EM. Cancer Res. 2021 Aug 1;81(15):3971-3984. doi: 10.1158/0008-5472.CAN-21-0791. Epub 2021 Jun 7. PMID: 34099491; PMCID: PMC8338889.

Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology. Nair RR, Zabezhinsky D, Gelin-Licht R, Haas BJ, Dyhr MC, Sperber HS, Nusbaum C, Gerst JE. Elife. 2021 May 4;10:e66050. doi: 10.7554/eLife.66050. PMID: 33942720; PMCID: PMC8137142.

von Willebrand factor D and EGF domains is an evolutionarily conserved and required feature of blastemas capable of multitissue appendage regeneration. Leigh ND, Sessa S, Dragalzew AC, Payzin-Dogru D, Sousa JF, Aggouras AN, Johnson K, Dunlap GS, Haas BJ, Levin M, Schneider I, Whited JL. Evol Dev. 2020 Jul;22(4):297-311. doi: 10.1111/ede.12332. Epub 2020 Mar 12. PMID: 32163674; PMCID: PMC7390686.

Next-generation characterization of the Cancer Cell Line Encyclopedia. Ghandi M, Huang FW, Jane-Valbuena J, Kryukov GV, Lo CC, McDonald ER 3rd, Barretina J, Gelfand ET, Bielski CM, Li H, Hu K, Andreev-Drakhlin AY, Kim J, Hess JM, Haas BJ, Aguet F, Weir BA, Rothberg MV, Paolella BR, Lawrence MS, Akbani R, Lu Y, Tiv HL, Gokhale PC, de Weck A, Mansour AA, Oh C, Shih J, Hadi K, Rosen Y, Bistline J, Venkatesan K, Reddy A, Sonkin D, Liu M, Lehar J, Korn JM, Porter DA, Jones MD, Golji J, Caponigro G, Taylor JE, Dunning CM, Creech AL, Warren AC, McFarland JM, Zamanighomi M, Kauffmann A, Stransky N, Imielinski M, Maruvka YE, Cherniack AD, Tsherniak A, Vazquez F, Jaffe JD, Lane AA, Weinstock DM, Johannessen CM, Morrissey MP, Stegmeier F, Schlegel R, Hahn WC, Getz G, Mills GB, Boehm JS, Golub TR, Garraway LA, Sellers WR. Nature. 2019 May;569(7757):503-508. doi: 10.1038/s41586-019-1186-3. Epub 2019 May 8. PMID: 31068700; PMCID: PMC6697103.

Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution. Leigh ND, Dunlap GS, Johnson K, Mariano R, Oshiro R, Wong AY, Bryant DM, Miller BM, Ratner A, Chen A, Ye WW, Haas BJ, Whited JL. Nat Commun. 2018 Dec 4;9(1):5153. doi: 10.1038/s41467-018-07604-0. PMID: 30514844; PMCID: PMC6279788.

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors Donald M. Bryant, Kimberly Johnson, Tia DiTommaso, Timothy Tickle, Matthew Brian Couger, Duygu Payzin-Dogru, Tae J. Lee, Nicholas D. Leigh, Tzu-Hsing Kuo, Francis G. Davis, Joel Bateman, Sevara Bryant, Anna R. Guzikowski, Stephanie L. Tsai, Steven Coyne, William W. Ye, Robert M. Freeman Jr., Leonid Peshkin, Clifford J. Tabin, Aviv Regev, Brian J. Haas, Jessica L. Whited Cell Rep. 2017 Jan 17;18(3):762-776. doi: 10.1016/j.celrep.2016.12.063.

The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families. Parente TE, Moreira DA, Magalhes MG, de Andrade PC, Furtado C, Haas BJ,Stegeman JJ, Hahn ME. Mar Pollut Bull. 2017 Jan 3. pii: S0025-326X(16)30998-5. doi: 10.1016/j.marpolbul.2016.12.012

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS Mol Cell. 2015 Dec 3;60(5):816-27. doi:10.1016/j.molcel.2015.11.013. PubMed PMID: 26638175; PubMed Central PMCID:PMC4720255

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Kowalczyk MS, Tirosh I, Heckl D, Rao TN, Dixit A, Haas BJ, Schneider RK, Wagers AJ, Ebert BL, Regev A. Genome Res. 2015 Dec;25(12):1860-72. doi: 10.1101/gr.192237.115. PubMed PMID: 26430063; PubMed Central PMCID: PMC4665007.

Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi Okagaki LH, Nunes CC, Sailsbery J, Clay B, Brown D, John T, Oh Y, Young N, Fitzgerald M, Haas BJ, Zeng Q, Young S, Adiconis X, Fan L, Levin JZ, Mitchell TK, Okubara PA, Farman ML, Kohn LM, Birren B, Ma LJ, Dean RA. G3 (Bethesda). 2015 Sep 28;5(12):2539-45.

Evolution of invasion in a diverse set of Fusobacterium species Manson McGuire A, Cochrane K, Griggs AD, Haas BJ, Abeel T, Zeng Q, Nice JB, MacDonald H, Birren BW, Berger BW, Allen-Vercoe E, Earl AM. MBio. 2014 Nov 4;5(6):e01864. doi: 10.1128/mBio.01864-14. PubMed PMID: 25370491; PubMed Central PMCID: PMC4222103

The Capsaspora genome reveals a complex unicellular prehistory of animals. Suga H, Chen Z, de Mendoza A, Sebe-PedrosA, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sanchez-Ponz N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I. Nat Commun. 2013 Aug14;4:2325. doi: 10.1038/ncomms3325. PubMed PMID: 23942320.

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. Jiang RH*, de Bruijn I*, Haas BJ*, Belmonte R, Lobach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, D PLoS Genet. 2013 Jun;9(6):e1003272. doi: 10.1371/journal.pgen.1003272. Epub 2013 Jun 13. PubMed PMID: 23785293; PubMed Central PMCID: PMC3681718.

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans. Desjardins CA, Cerqueira GC, Goldberg JM, Dunning Hotopp JC, Haas BJ, Zucker J, Ribeiro JM, Saif S, Levin JZ, Fan L, Zeng Q, Russ C, Wortman JR, Fink DL, Birren BW, Nutman TB. Nat Genet. 2013 May;45(5):495-500. doi: 10.1038/ng.2585. Epub 2013 Mar 24. PubMed PMID: 23525074.

Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. Palmer KL, Godfrey P, Griggs A, Kos VN, Zucker J, Desjardins C, Cerqueira G, Gevers D, Walker S, Wortman J, Feldgarden M, Haas B, Birren B, Gilmore MS. MBio. 2012 Mar 1;3(1):e00318-11. doi: 10.1128/mBio.00318-11.

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Moller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP Proc Natl Acad Sci U S A. 2012 Feb 6.

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailao AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, Leon-Narvaez H, Longo LV, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodriquez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter ME, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CM, Birren BW, Cuomo CA. PLoS Genet. 2011 Oct;7(10):e1002345. Epub 2011 Oct 27. PubMed PMID: 22046142

Comparative functional genomics of the fission yeasts Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Muller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C. Science. 2011 May 20;332(6032):930-6. Epub 2011 Apr 21.

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JM, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JM, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MA, Raikhel AS, Atkinson PW. Science. 2010 Oct 1;330(6000):86-8.

Draft genome sequence of the oilseed species Ricinus communis Agnes P Chan, Jonathan Crabtree, Qi Zhao, Hernan Lorenzi, Joshua Orvis, Daniela Puiu, Admasu Melake-Berhan, Kristine M Jones, Julia Redman, Grace Chen, Edgar B Cahoon, Melaku Gedil, Mario Stanke, Brian J Haas, Jennifer R Wortman, Claire M Fraser-Liggett, Jacques Ravel & Pablo D Rabinowicz Nature Biotechnology (2010) doi:10.1038/nbt.1674

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubio JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Krause E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguad M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12168-73. Epub 2010 Jun 21.

A catalog of reference genomes from the human microbiome. Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D. Science. 2010 May 21;328(5981):994-9.

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans Brian J. Haas, Sophien Kamoun, Michael C. Zody, Rays H. Y. Jiang, Robert E. Handsaker, Liliana M. Cano, Manfred Grabherr, Chinnappa D. Kodira, Sylvain Raffaele, Trudy Torto-Alalibo, Tolga O. Bozkurt, Audrey M. V. Ah-Fong, Lucia Alvarado, Vicky L. Anderson, Miles R. Armstrong, Anna Avrova, Laura Baxter, Jim Beynon, Petra C. Boevink, Stephanie R. Bollmann, Jorunn I. B. Bos, Vincent Bulone, Guohong Cai, Cahid Cakir, James C. Carrington, Megan Chawner, Lucio Conti, Stefano Costanzo, Richard Ewan, Noah Fahlgren, Michael A. Fischbach, Johanna Fugelstad, Eleanor M. Gilroy, Sante Gnerre, Pamela J. Green, Laura J. Grenville-Briggs, John Griffith, Niklaus J. Grünwald, Karolyn Horn, Neil R. Horner, Chia-Hui Hu, Edgar Huitema, Dong-Hoon Jeong, Alexandra M. E. Jones, Jonathan D. G. Jones, Richard W. Jones, Elinor K. Karlsson, Sridhara G. Kunjeti, Kurt Lamour, Zhenyu Liu, LiJun Ma, Daniel MacLean, Marcus C. Chibucos, Hayes McDonald, Jessica McWalters, Harold J. G. Meijer, William Morgan, Paul F. Morris, Carol A. Munro, Keith O'Neill, Manuel Ospina-Giraldo, Andrés Pinzón, Leighton Pritchard, Bernard Ramsahoye, Qinghu Ren, Silvia Restrepo, Sourav Roy, Ari Sadanandom, Alon Savidor, Sebastian Schornack, David C. Schwartz, Ulrike D. Schumann, Ben Schwessinger, Lauren Seyer, Ted Sharpe, Cristina Silvar, Jing Song, David J. Studholme, Sean Sykes, Marco Thines, Peter J. I. van de Vondervoort, Vipaporn Phuntumart, Stephan Wawra, Rob Weide, Joe Win, Carolyn Young, Shiguo Zhou, William Fry, Blake C. Meyers, Pieter van West, Jean Ristaino, Francine Govers, Paul R. J. Birch, Stephen C. Whisson, Howard S. Judelson, Chad Nusbaum Nature 461, 393-398 (17 September 2009)

The genome of the blood fluke Schistosoma mansoni. Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, El-Sayed NM. (2009) Nature 460, 352-358 (16 July 2009)

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Ray Ming, Shaobin Hou, Yun Feng, Qingyi Yu, Alexandre Dionne-Laporte, Jimmy H. Saw, Pavel Senin, Wei Wang, Benjamin V. Ly, Kanako L. T. Lewis, Steven L. Salzberg, Lu Feng, Meghan R. Jones, Rachel L. Skelton, Jan E. Murray, Cuixia Chen, Wubin Qian, Junguo Shen, Peng Du, Moriah Eustice, Eric Tong, Haibao Tang, Eric Lyons, Robert E. Paull, Todd P. Michael, Kerr Wall, Danny W. Rice, Henrik Albert, Ming-Li Wang, Yun J. Zhu, Michael Schatz, Niranjan Nagarajan, Ricelle A. Acob, Peizhu Guan, Andrea Blas, Ching Man Wai, Christine M. Ackerman, Yan Ren, Chao Liu, Jianmei Wang, Jianping Wang, Jong-Kuk Na, Eugene V. Shakirov, Brian Haas, Jyothi Thimmapuram, David Nelson, Xiyin Wang, John E. Bowers, Andrea R. Gschwend, Arthur L. Delcher, Ratnesh Singh, Jon Y. Suzuki, Savarni Tripathi, Kabi Neupane, Hairong Wei, Beth Irikura, Maya Paidi, Ning Jiang, Wenli Zhang, Gernot Presting, Aaron Windsor, Rafael Navajas-Perez, Manuel J. Torres, F. Alex Feltus, Brad Porter8, Yingjun Li, A. Max Burroughs, Ming-Cheng Luo, Lei Liu, David A. Christopher, Stephen M. Mount, Paul H. Moore, Tak Sugimura, Jiming Jiang, Mary A. Schuler, Vikki Friedman, Thomas Mitchell-Olds, Dorothy E. Shippen, Claude W. dePamphilis, Jeffrey D. Palmer, Michael Freeling, Andrew H. Paterson, Dennis Gonsalves, Lei Wang and Maqsudul Alam (2008) Nature 452, 991-996 (24 April 2008)

Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. Brayton KA, Lau AO, Herndon DR, Hannick L, Kappmeyer LS, Berens SJ, Bidwell SL, Brown WC, Crabtree J, Fadrosh D, Feldblum T, Forberger HA, Haas BJ, Howell JM, Khouri H, Koo H, Mann DJ, Norimine J, Paulsen IT, Radune D, Ren Q, Smith RK Jr, Suarez CE, White O, Wortman JR, Knowles DP Jr, McElwain TF, Nene VM. (2007) PLoS Pathog. 2007 Oct 19;3(10):1401-13.

Draft genome of the filarial nematode parasite Brugia malayi. Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrin-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL. Science. 2007 Sep 21;317(5845):1756-60.

Schistosoma mansoni genome: Closing in on a final gene set. Haas BJ, Berriman M, Hirai H, Cerqueira GG, Loverde PT, El-Sayed NM. Exp Parasitol. 2007 Jun 21

Genome sequence of Aedes aegypti, a major arbovirus vector. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW. Science. 2007 Jun 22;316(5832):1703-4.

Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fuester RW, Schatz MC, Pedroni MJ, Fadrosh DW, Haas BJ, Toms BS, Chen D, Nene V. BMC Microbiol. 2007 Jun 26;7:61

Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis Jane M. Carlton, Robert P. Hirt, Joana C. Silva, Arthur L. Delcher, Michael Schatz, Qi Zhao, Jennifer R. Wortman, Shelby L. Bidwell, U. Cecilia M. Alsmark, Sebastien Besteiro, Thomas Sicheritz-Ponten, Christophe J. Noel, Joel B. Dacks, Peter G. Foster, Cedric Simillion, Yves Van de Peer, Diego Miranda-Saavedra, Geoffrey J. Barton, Gareth D. Westrop, Sylke Muller, Daniele Dessi, Pier Luigi Fiori, Qinghu Ren, Ian Paulsen, Hanbang Zhang, Felix D. Bastida-Corcuera, Augusto Simoes-Barbosa, Mark T. Brown, Richard D. Hayes, Mandira Mukherjee, Cheryl Y. Okumura, Rachel Schneider, Alias J. Smith, Stepanka Vanacova, Maria Villalvazo, Brian J. Haas, Mihaela Pertea, Tamara V. Feldblyum, Terry R. Utterback, Chung-Li Shu, Kazutoyo Osoegawa, Pieter J. de Jong, Ivan Hrdy, Lenka Horvathova, Zuzana Zubacova, Pavel Dolezal, Shehre-Banoo Malik, John M. Logsdon, Jr., Katrin Henze, Arti Gupta, Ching C. Wang, Rebecca L. Dunne, Jacqueline A. Upcroft, Peter Upcroft, Owen White, Steven L. Salzberg, Petrus Tang, Cheng-Hsun Chiu, Ying-Shiung Lee, T. Martin Embley, Graham H. Coombs, Jeremy C. Mottram, Jan Tachezy, Claire M. Fraser-Liggett, Patricia J. Johnson (2007) Science 12 January 2007: Vol. 315. no. 5809, pp. 207-212

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote Jonathan A Eisen, Robert S Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R Wortman, Jonathan H Badger, Qinghu Ren, Paolo Amedeo, Kristie M Jones, Luke J Tallon, Arthur L Delcher, Steven L Salzberg, Joana C Silva, Brian J Haas, William H Majoros, Maryam Farzad, Jane M Carlton, Roger K Smith, Jr., Jyoti Garg, Ronald E Pearlman, Kathleen M Karrer, Lei Sun, Gerard Manning, Nels C Elde, Aaron P Turkewitz, David J Asai, David E Wilkes, Yufeng Wang, Hong Cai, Kathleen Collins, B. Andrew Stewart, Suzanne R Lee, Katarzyna Wilamowska, Zasha Weinberg, Walter L Ruzzo, Dorota Wloga, Jacek Gaertig, Joseph Frankel, Che-Chia Tsao, Martin A Gorovsky, Patrick J Keeling, Ross F Waller, Nicola J Patron, J. Michael Cherry, Nicholas A Stover, Cynthia J Krieger, Christina del Toro, Hilary F Ryder, Sondra C Williamson, Rebecca A Barbeau, Eileen P Hamilton, and Eduardo Orias (2006) PLoS Biol. 2006 September; 4(9): e286.

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. William C. Nierman, Arnab Pain, Michael J. Anderson, Jennifer R. Wortman, H. Stanley Kim, Javier Arroyo, Matthew Berriman, Keietsu Abe, David B. Archer, Clara Bermejo, Joan Bennett, Paul Bowyer, Dan Chen, Matthew Collins, Richard Coulsen, Robert Davies, Paul S. Dyer, Mark Farman, Nadia Fedorova, Natalie Fedorova, Tamara V. Feldblyum, Reinhard Fischer, Nigel Fosker, Audrey Fraser, Jose L. Garc=EDa, Maria J. Garc=EDa, Arlette Goble, Gustavo H. Goldman, Katsuya Gomi, Sam Griffith-Jones, Ryan Gwilliam, Brian Haas, Hubertus Haas, David Harris, H. Horiuchi, Jiaqi Huang, Sean Humphray, Javier Jim=E9nez, Nancy Keller, Hoda Khouri, Katsuhiko Kitamoto, Tetsuo Kobayashi, Sven Konzack, Resham Kulkarni, Toshitaka Kumagai, Anne Lafton, Jean-Paul Latg=E9, Weixi Li, Angela Lord, Charles Lu, William H. Majoros, Gregory S. May, Bruce L. Miller, Yasmin Mohamoud, Maria Molina, Michel Monod, Isabelle Mouyna, Stephanie Mulligan, Lee Murphy, Susan O'Neil, Ian Paulsen, Miguel A. Pe=F1alva, Mihaela Pertea, Claire Price, Bethan L. Pritchard, Michael A. Quail, Ester Rabbinowitsch, Neil Rawlins, Marie-Adele Rajandream, Utz Reichard, Hubert Renauld, Geoffrey D. Robson, Santiago Rodriguez de C=F3rdoba, Jose M. Rodr=EDguez-Pe=F1a, Catherine M. Ronning, Simon Rutter, Steven L. Salzberg, Miguel Sanchez, Juan C. S=E1nchez-Ferrero, David Saunders, Kathy Seeger, Rob Squares, Steven Squares, Michio Takeuchi, Fredj Tekaia, Geoffrey Turner, Carlos R. Vazquez de Aldana, Janice Weidman, Owen White, John Woodward, Jae-Hyuk Yu, Claire Fraser, James E. Galagan, Kiyoshi Asai, Masayuki Machida, Neil Hall, Bart Barrell and David W. Denning (2005) Nature 438, 1151-1156 (22 December 2005) | doi:10.1038/nature04332

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium (2005) Genome Res. 2005 Sep;15(9):1284-91. Epub 2005 Aug 18.

Comparative genomics of trypanosomatid parasitic protozoa. Najib M. El-Sayed, Peter J. Myler, Ga=EBlle Blandin, Matthew Berriman, Jonathan Crabtree, Gautam Aggarwal, Elisabet Caler, Hubert Renauld, Elizabeth A. Worthey, Christiane Hertz-Fowler, Elodie Ghedin, Christopher Peacock, Daniella C. Bartholomeu, Brian J. Haas, Anh-Nhi Tran, Jennifer R. Wortman, U. Cecilia M. Alsmark, Samuel Angiuoli, Atashi Anupama, Jonathan Badger, Frederic Bringaud, Eithon Cadag, Jane M. Carlton, Gustavo C. Cerqueira, Todd Creasy, Arthur L. Delcher, Appolinaire Djikeng, T. Martin Embley, Christopher Hauser, Alasdair C. Ivens, Sarah K. Kummerfeld, Jose B. Pereira-Leal, Daniel Nilsson, Jeremy Peterson, Steven L. Salzberg, Joshua Shallom, Joana C. Silva, Jaideep Sundaram, Scott Westenberger, Owen White, Sara E. Melville, John E. Donelson, Bj=F6rn Andersson, Kenneth D. Stuart, Neil Hall (2005) Science. 2005 Jul 15;309(5733):404-9

The genome of the African trypanosome Trypanosoma brucei. Matthew Berriman, Elodie Ghedin, Christiane Hertz-Fowler, Ga=EBlle Blandin, Hubert Renauld, Daniella C. Bartholomeu, Nicola J. Lennard, Elisabet Caler, Nancy E. Hamlin, Brian Haas, Ulrike B=F6hme, Linda Hannick, Martin A. Aslett, Joshua Shallom, Lucio Marcello, Lihua Hou, Bill Wickstead, U. Cecilia M. Alsmark, Claire Arrowsmith, Rebecca J. Atkin, Andrew J. Barron, Frederic Bringaud, Karen Brooks, Mark Carrington, Inna Cherevach, Tracey-Jane Chillingworth, Carol Churcher, Louise N. Clark, Craig H. Corton, Ann Cronin, Rob M. Davies, Jonathon Doggett, Appolinaire Djikeng, Tamara Feldblyum, Mark C. Field, Audrey Fraser, Ian Goodhead, Zahra Hance, David Harper, Barbara R. Harris, Heidi Hauser, Jessica Hostetler, Al Ivens, Kay Jagels, David Johnson, Justin Johnson, Kristine Jones, Arnaud X. Kerhornou, Hean Koo, Natasha Larke, Scott Landfear, Christopher Larkin, Vanessa Leech, Alexandra Line, Angela Lord, Annette MacLeod, Paul J. Mooney, Sharon Moule, David M. A. Martin, Gareth W. Morgan, Karen Mungall, Halina Norbertczak, Doug Ormond, Grace Pai, Chris S. Peacock, Jeremy Peterson, Michael A. Quail, Ester Rabbinowitsch, Marie-Adele Rajandream, Chris Reitter, Steven L. Salzberg, Mandy Sanders, Seth Schobel, Sarah Sharp, Mark Simmonds, Anjana J. Simpson, Luke Tallon, C. Michael R. Turner, Andrew Tait, Adrian R. Tivey, Susan Van Aken, Danielle Walker, David Wanless, Shiliang Wang, Brian White, Owen White, Sally Whitehead, John Woodward, Jennifer Wortman, Mark D. Adams, T. Martin Embley, Keith Gull, Elisabetta Ullu, J. David Barry, Alan H. Fairlamb, Fred Opperdoes, Barclay G. Barrell, John E. Donelson, Neil Hall, Claire M. Fraser, Sara E. Melville, Najib M. El-Sayed Science. 2005 Jul 15;309(5733):416-22.

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Najib M. El-Sayed, Peter J. Myler, Daniella C. Bartholomeu, Daniel Nilsson, Gautam Aggarwal, Anh-Nhi Tran, Elodie Ghedin, Elizabeth A. Worthey, Arthur L. Delcher, Gaelle Blandin, Scott J. Westenberger, Elisabet Caler, Gustavo C. Cerqueira, Carole Branche, Brian Haas, Atashi Anupama, Erik Arner, Lena Aslund, Philip Attipoe, Esteban Bontempi, Frederic Bringaud, Peter Burton, Eithon Cadag, David A. Campbell, Mark Carrington, Jonathan Crabtree, Hamid Darban, Jose Franco da Silveira, Pieter de Jong, Kimberly Edwards, Paul T. Englund, Gholam Fazelina, Tamara Feldblyum, Marcela Ferella, Alberto Carlos Frasch, Keith Gull, David Horn, Lihua Hou, Yiting Huang, Ellen Kindlund, Michele Klingbeil, Sindy Kluge, Hean Koo, Daniela Lacerda, Mariano J. Levin, Hernan Lorenzi, Tin Louie, Carlos Renato Machado, Richard McCulloch, Alan McKenna, Yumi Mizuno, Jeremy C. Mottram, Siri Nelson, Stephen Ochaya, Kazutoyo Osoegawa, Grace Pai, Marilyn Parsons, Martin Pentony, Ulf Pettersson, Mihai Pop, Jose Luis Ramirez, Joel Rinta, Laura Robertson, Steven L. Salzberg, Daniel O. Sanchez, Amber Seyler, Reuben Sharma, Jyoti Shetty, Anjana J. Simpson, Ellen Sisk, Martti T. Tammi, Rick Tarleton, Santuza Teixeira, Susan Van Aken, Christy Vogt, Pauline N. Ward, Bill Wickstead, Jennifer Wortman, Owen White, Claire M. Fraser, Kenneth D. Stuart, Bjorn Andersson (2005) Science. 2005 Jul 15;309(5733):409-15.

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Malcolm J. Gardner, Richard Bishop, Trushar Shah, Etienne P. de Villiers, Jane M. Carlton, Neil Hall, Qinghu Ren, Ian T. Paulsen, Arnab Pain, Matthew Berriman, Robert J. M. Wilson, Shigeharu Sato, Stuart A. Ralph, David J. Mann, Zikai Xiong, Shamira J. Shallom, Janice Weidman, Lingxia Jiang, Jeffery Lynn, Bruce Weaver, Azadeh Shoaibi, Alexander R. Domingo, Delia Wasawo, Jonathan Crabtree, Jennifer R. Wortman, Brian Haas, Samuel V. Angiuoli, Todd H. Creasy, Charles Lu, Bernard Suh, Joana C. Silva, Teresa R. Utterback, Tamara V. Feldblyum, Mihaela Pertea, Jonathan Allen, William C. Nierman, Evans L. N. Taracha, Steven L. Salzberg, Owen R. White, Henry A. Fitzhugh, Subhash Morzaria, J. Craig Venter, Claire M. Fraser, Vishvanath Nene Science. 2005 Jul 1;309(5731):72-3.

The Institute for Genomic Research Osa1 Rice Genome Annotation Database. Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR. (2005) Plant Physiol. 2005 May; 138(1):18-26

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. Haas BJ, Wortman JR, Ronning CM, Hannick LI, Smith RK Jr, Maiti R, Chan AP, Yu C, Farzad M, Wu D, White OR, Town CD. (2005) BMC Biology 2005 Mar 22;3(1):7

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Brendan J. Loftus, Eula Fung, Paola Roncaglia, Don Rowley, Paolo Amedeo, Dan Bruno, Jessica Vamathevan, Molly Miranda, Iain J. Anderson, James A. Fraser, Jonathan E. Allen, Ian E. Bosdet, Michael R. Brent, Readman Chiu, Tamara L. Doering, Maureen J. Donlin, Cletus A. D'Souza, Deborah S. Fox, Viktoriya Grinberg, Jianmin Fu, Marilyn Fukushima, Brian J. Haas, James C. Huang, Guilhem Janbon, Steven J. M. Jones, Hean L. Koo, Martin I. Krzywinski, June K. Kwon-Chung, Klaus B. Lengeler, Rama Maiti, Marco A. Marra, Robert E. Marra, Carrie A. Mathewson, Thomas G. Mitchell, Mihaela Pertea, Florenta R. Riggs, Steven L. Salzberg, Jacqueline E. Schein, Alla Shvartsbeyn, Heesun Shin, Martin Shumway, Charles A. Specht, Bernard B. Suh, Aaron Tenney, Terry R. Utterback, Brian L. Wickes, Jennifer R. Wortman, Natasja H. Wye, James W. Kronstad, Jennifer K. Lodge, Joseph Heitman, Ronald W. Davis, Claire M. Fraser, Richard W. Hyman (2005) Science 2005 Feb 25;307(5713):1321-4.

The sequence and analysis of Trypanosoma brucei chromosome II. El-Sayed NM, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C, Wanless D, Peterson J, Hou L, Taylor S, Tweedie A, Biteau N, Khalak HG, Lin X, Mason T, Hannick L, Caler E, Blandin G, Bartholomeu D, Simpson AJ, Kaul S, Zhao H, Pai G, Van Aken S, Utterback T, Haas B, Koo HL, Umayam L, Suh B, Gerrard C, Leech V, Qi R, Zhou S, Schwartz D, Feldblyum T, Salzberg S, Tait A, Turner CM, Ullu E, White O, Melville S, Adams MD, Fraser CM, Donelson JE. (2003) Nucleic Acids Res, 31, 4856-4863.

In-depth view of structure, activity, and evolution of rice chromosome 10. Rice Chromosome 10 Sequencing Consortium. (2003) Science,300, 1566-1569.

Annotation of the Arabidopsis genome. Wortman JR, Haas BJ, Hannick LI, Smith RK Jr, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, White OR, Town CD. Plant Physiol, 132, 461-468.(2003)

Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis A, Ecker JR, Palm CJ, Federspiel NA, Kaul S, White O, Alonso J, Altafi H, Araujo R, Bowman CL, Brooks SY, Buehler E, Chan A, Chao Q, Chen H, Cheuk RF, Chin CW, Chung MK, Conn L, Conway AB, Conway AR, Creasy TH, Dewar K, Dunn P, Etgu P, Feldblyum TV, Feng J, Fong B, Fujii CY, Gill JE, Goldsmith AD, Haas B, Hansen NF, Hughes B, Huizar L, Hunter JL, Jenkins J, Johnson-Hopson C, Khan S, Khaykin E, Kim CJ, Koo HL, Kremenetskaia I, Kurtz DB, Kwan A, Lam B, Langin-Hooper S, Lee A, Lee JM, Lenz CA, Li JH, Li Y, Lin X, Liu SX, Liu ZA, Luros JS, Maiti R, Marziali A, Militscher J, Miranda M, Nguyen M, Nierman WC, Osborne BI, Pai G, Peterson J, Pham PK, Rizzo M, Rooney T, Rowley D, Sakano H, Salzberg SL, Schwartz JR, Shinn P, Southwick AM, Sun H, Tallon LJ, Tambunga G, Toriumi MJ, Town CD, Utterback T, Van Aken S, Vaysberg M, Vysotskaia VS, Walker M, Wu D, Yu G, Fraser CM, Venter JC, Davis RW Nature, 408, 816-820. (2000)

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blocker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomenech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quetier F, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Lohnert TH, Nordsiek G, Reichelt J, Scharfe M, Schon O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwalder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S; European Union Chromosome 3 Arabidopsis Sequencing Consortium; Institute for Genomic Research; Kazusa DNA Research Institute. Nature, 408, 820-822. (2000)

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Arabidopsis Genome Initiative. Nature, 408, 796-815. (2000)

Research Interests

[+] Genome, Transcriptome, and Research Publications

[+]Bioinformatics Method Development and Reviews