Brian J. Haas
Senior Computational Biologist
Klarman Cell Observatory
Broad Institute
415 Main Street
Cambridge, MA 02142
EMAIL: b h a a s @ b r o a d i n s t i t u t e . o r g
Research Interests
Bioinformatics tools, resources, and databasesCancer InformaticsTranscriptomicsGene discovery and genome annotation
[+] Genome, Transcriptome, and Research Publications
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration FactorsDonald 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. WhitedCell Rep. 2017 Jan 17;18(3):762-776. doi: 10.1016/j.celrep.2016.12.063.
Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of FungiOkagaki 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.
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.
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 WPProc 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 yeastsRhind 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 RabinowiczNature 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 infestansBrian 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 EukaryoteJonathan 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
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.
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Genome sequence of Theileria parva, a bovine pathogen that
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The Institute for Genomic Research Osa1 Rice Genome
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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
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BMC Biology 2005 Mar 22;3(1):7
The genome of the basidiomycetous
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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
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The sequence and analysis of Trypanosoma brucei
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In-depth view of structure, activity, and
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Sequence and analysis of chromosome 1 of the plant Arabidopsis
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Sequence and analysis of chromosome 3 of the plant
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Analysis of the genome sequence of
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Arabidopsis Genome Initiative.
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STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-SeqBrian Haas, Alexander Dobin, Nicolas Stransky, Bo Li, Xiao Yang, Timothy Tickle, Asma Bankapur, Carrie Ganote, Thomas Doak, Natalie Pochet, Jing Sun, Catherine Wu, Thomas Gingeras, Aviv RegevbioRxiv 2017 - doi: https://doi.org/10.1101/120295
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.Haas BJ*, Papanicolaou A*, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A.Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. PubMed PMID: 23845962.
Full-length transcriptome assembly from RNA-Seq data without a reference genome.Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X,
Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N,
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Ten things to know about oomycete effectors.Schornack S, Huitema E, Cano LM, Bozkurt TO, Oliva R, Van Damme M, Schwizer S, Raffaele S, Chaparro-Garcia A, Farrer R, Segretin ME, Bos J, Haas BJ, Zody MC, Nusbaum C, Win J, Thines M, Kamoun S.Mol Plant Pathol. 2009 Nov;10(6):795-803.
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White OR, Buell CR, Wortman JR (2008)
Genome Biol. 2008 Jan 11;9(1):R7
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis.Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006)
BMC Genomics 2006, 7:327
Sequencing Medicago truncatula expressed sequenced
tags using 454 Life Sciences technologyFoo Cheung, Brian J Haas, Susanne M D Goldberg,
Gregory D May, Yongli Xiao and Christopher D Town
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BMC Genomics 2006, 7:272
Analysis of the cDNAs of hypothetical genes on
Arabidopsis chromosome 2 reveals numerous transcript variants.Xiao YL, Smith SR, Ishmael N, Redman JC, Kumar N,
Monaghan EL, Ayele M, Haas BJ, Wu HC, Town CD.
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Plant
Physiol. 2005 Nov;139(3):1323-37. Epub 2005 Oct 21.
Compilation of mRNA polyadenylation signals in Arabidopsis revealed
a new signal element and potential secondary structures.Loke JC, Stahlberg EA, Strenski DG, Haas BJ, Wood
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Plant Physiol. 2005 Jul;138(3):1457-68. Epub 2005 Jun 17
Whole genome shotgun sequencing of Brassica oleracea and its
application to gene discovery and annotation in Arabidopsis.Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Van
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GenomeRes. 2005 Apr;15(4):487-95.
Development and evaluation of an Arabidopsis whole genome Affymetrix
probe array. Redman, J.C., Haas, B.J., Tanimoto, G. and Town,
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DAGchainer: A tool for mining segmental genome duplications and
synteny. Haas, B.J., Delcher, A.L., Wortman, J.R. and
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Bioinformatics. 2004, vol 20, issue 18
Computational discovery of internal micro-exons.Volfovsky, N., Haas, B.J. and Salzberg,
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Genome Res, 13, 1216-1221.
Improving the Arabidopsis genome annotation using maximal
transcript alignment assemblies.Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr, R.K.,
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Salzberg, S., White, O.
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Nucleic Acids Res, 31, 5654-5666.
Proteome map of the chloroplast lumen of Arabidopsis thaliana.Schubert, M., Petersson, U.A., Haas, B.J., Funk, C., Schroder, W.P. and
Kieselbach, T.
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