bhaas picture
Brian J. Haas
Manager, Bioinformatics Outreach, Genome Annotation and Analysis
The Broad Institute
7 Cambridge Center
Cambridge, MA 02142
EMAIL: b h a a s @ b r o a d . m i t . e d u

Research Interests

Gene discovery and genome annotation Alternative splicing Sequence alignment Comparative genomics Evolutionary biology Structural biology Repeat identification Transposable elements Bioinformatics tools, resources, and databases

Genome Publications

P. infestans Nature Cover 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 Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans Nature 461, 393-398 (17 September 2009)
Schistosome Nature Cover 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) The genome of the blood fluke Schistosoma mansoni. Nature 460, 352-358 (16 July 2009)
Papaya Nature Cover 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) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Nature 452, 991-996 (24 April 2008)
Babesia bovis image 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) Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog. 2007 Oct 19;3(10):1401-13.
Brugia malayi image 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. Draft genome of the filarial nematode parasite Brugia malayi. Science. 2007 Sep 21;317(5845):1756-60.
Schistosoma mansoni Haas BJ, Berriman M, Hirai H, Cerqueira GG, Loverde PT, El-Sayed NM. Schistosoma mansoni genome: Closing in on a final gene set. Exp Parasitol. 2007 Jun 21
Aedes image 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. Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007 Jun 22;316(5832):1703-4.
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. Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. BMC Microbiol. 2007 Jun 26;7:61
Tvaginalis img 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) Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis Science 12 January 2007: Vol. 315. no. 5809, pp. 207-212
Tetrahymena image 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) Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote PLoS Biol. 2006 September; 4(9): e286.
Afumigatus Image 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) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438, 1151-1156 (22 December 2005) | doi:10.1038/nature04332
The Rice Chromosome 3 Sequencing Consortium (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res. 2005 Sep;15(9):1284-91. Epub 2005 Aug 18.
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) Comparative genomics of trypanosomatid parasitic protozoa. Science. 2005 Jul 15;309(5733):404-9
T.brucei Image 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 (2005) The genome of the African trypanosome Trypanosoma brucei. Science. 2005 Jul 15;309(5733):416-22.
Trypanosomes Image 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) The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science. 2005 Jul 15;309(5733):409-15.
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 (2005) Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science. 2005 Jul 1;309(5731):72-3.
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) The Institute for Genomic Research Osa1 Rice Genome Annotation Database. Plant Physiol. 2005 May; 138(1):18-26
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) Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biology 2005 Mar 22;3(1):7
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) The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 2005 Feb 25;307(5713):1321-4.
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) The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Res, 31, 4856-4863.
Rice Image Rice Chromosome 10 Sequencing Consortium. (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science,300, 1566-1569.
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. (2003) Annotation of the Arabidopsis genome. Plant Physiol, 132, 461-468.
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 (2000) Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature, 408, 816-820.
Nature Arabidopis Cover 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. (2000) Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature, 408, 820-822.
Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.

Select Bioinformatics and Research Publications

evm logo Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White OR, Buell CR, Wortman JR (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008 Jan 11;9(1):R7
Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 2006, 7:327
Foo Cheung, Brian J Haas, Susanne M D Goldberg, Gregory D May, Yongli Xiao and Christopher D Town (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology BMC Genomics 2006, 7:272
Xiao YL, Smith SR, Ishmael N, Redman JC, Kumar N, Monaghan EL, Ayele M, Haas BJ, Wu HC, Town CD. (2005) Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants. Plant Physiol. 2005 Nov;139(3):1323-37. Epub 2005 Oct 21.
Loke JC, Stahlberg EA, Strenski DG, Haas BJ, Wood PC, Li QQ. (2005) Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol. 2005 Jul;138(3):1457-68. Epub 2005 Jun 17
Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Van Aken S, Utterback TR, Wortman JR, White OR, Town CD. (2005) Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. GenomeRes. 2005 Apr;15(4):487-95.
Redman, J.C., Haas, B.J., Tanimoto, G. and Town, C.D. (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J, 38, 545-561.
dagchainer logo Haas, B.J., Delcher, A.L., Wortman, J.R. and Salzberg, S.L. (2004) DAGchainer: A tool for mining segmental genome duplications and synteny. Bioinformatics. 2004, vol 20, issue 18
Volfovsky, N., Haas, B.J. and Salzberg, S.L. (2003) Computational discovery of internal micro-exons. Genome Res, 13, 1216-1221.
PASA logo Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr, R.K., Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D. Salzberg, S., White, O. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res, 31, 5654-5666.
Schubert, M., Petersson, U.A., Haas, B.J., Funk, C., Schroder, W.P. and Kieselbach, T. (2002) Proteome map of the chloroplast lumen of Arabidopsis thaliana. J Biol Chem, 277, 8354-8365
Haas, B.J., Volfovsky, N., Town, C.D., Troukhan, M., Alexandrov, N., Feldmann, K.A., Flavell, R.B., White, O. and Salzberg, S.L. (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol, 3, RESEARCH0029.
Volfovsky, N., Haas, B.J. and Salzberg, S.L. (2001) A clustering method for repeat analysis in DNA sequences. Genome Biol, 2, RESEARCH0027.