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Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.66050
By:
- Nair, Rohini R.;
- Zabezhinsky, Dmitry;
- Gelin-Licht, Rita;
- Haas, Brian J.;
- Dyhr, Michael C. A.;
- Sperber, Hannah S.;
- Nusbaum, Chad;
- Gerst, Jeffrey E.
Publication type:
Article
Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome.
Published in:
Plant Journal, 2005, v. 41, n. 2, p. 212, doi. 10.1111/j.1365-313X.2004.02295.x
By:
- Stanley Kim, H.;
- Yu, Yan;
- Snesrud, Erik C.;
- Moy, Linda P.;
- Linford, Lara D.;
- Haas, Brian J.;
- Nierman, William C.;
- Quackenbush, John
Publication type:
Article
Technical Advance Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.
Published in:
Plant Journal, 2004, v. 38, n. 3, p. 545, doi. 10.1111/j.1365-313X.2004.02061.x
By:
- Redman, Julia C.;
- Haas, Brian J.;
- Tanimoto, Gene;
- Town, Christopher D.
Publication type:
Article
Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation.
Published in:
Nucleic Acids Research, 2008, v. 36, n. 9, p. 3150, doi. 10.1093/nar/gkn158
By:
- Shen, Yingjia;
- Ji, Guoli;
- Haas, Brian J.;
- Wu, Xiaohui;
- Zheng, Jianti;
- Reese, Greg J.;
- Li, Qingshun Quinn
Publication type:
Article
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Published in:
Nature Biotechnology, 2011, v. 29, n. 7, p. 644, doi. 10.1038/nbt.1883
By:
- Grabherr, Manfred G;
- Haas, Brian J;
- Yassour, Moran;
- Levin, Joshua Z;
- Thompson, Dawn A;
- Amit, Ido;
- Adiconis, Xian;
- Fan, Lin;
- Raychowdhury, Raktima;
- Zeng, Qiandong;
- Chen, Zehua;
- Mauceli, Evan;
- Hacohen, Nir;
- Gnirke, Andreas;
- Rhind, Nicholas;
- di Palma, Federica;
- Birren, Bruce W;
- Nusbaum, Chad;
- Lindblad-Toh, Kerstin;
- Friedman, Nir
Publication type:
Article
Draft genome sequence of the oilseed species Ricinus communis.
Published in:
Nature Biotechnology, 2010, v. 28, n. 9, p. 951, doi. 10.1038/nbt.1674
By:
- Chan, Agnes P.;
- Crabtree, Jonathan;
- Zhao, Qi;
- Lorenzi, Hernan;
- Orvis, Joshua;
- Puiu, Daniela;
- Melake-Berhan, Admasu;
- Jones, Kristine M.;
- Redman, Julia;
- Chen, Grace;
- Cahoon, Edgar B.;
- Gedil, Melaku;
- Stanke, Mario;
- Haas, Brian J.;
- Wortman, Jennifer R.;
- Fraser-Liggett, Claire M.;
- Ravel, Jacques;
- Rabinowicz, Pablo D.
Publication type:
Article
Advancing RNA-Seq analysis.
Published in:
Nature Biotechnology, 2010, v. 28, n. 5, p. 421, doi. 10.1038/nbt0510-421
By:
- Haas, Brian J.;
- Zody, Michael C.
Publication type:
Article
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.
Published in:
Nature Genetics, 2013, v. 45, n. 5, p. 495, doi. 10.1038/ng.2585
By:
- Desjardins, Christopher A;
- Cerqueira, Gustavo C;
- Goldberg, Jonathan M;
- Hotopp, Julie C Dunning;
- Haas, Brian J;
- Zucker, Jeremy;
- Ribeiro, José M C;
- Saif, Sakina;
- Levin, Joshua Z;
- Fan, Lin;
- Zeng, Qiandong;
- Russ, Carsten;
- Wortman, Jennifer R;
- Fink, Doran L;
- Birren, Bruce W;
- Nutman, Thomas B
Publication type:
Article
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
Published in:
Nature Structural & Molecular Biology, 2008, v. 15, n. 5, p. 515, doi. 10.1038/nsmb.1414
By:
- Garcin, Elsa D.;
- Hosfield, David J.;
- Desai, Sunil A.;
- Haas, Brian J.;
- Björas, Magnar;
- Cunningham, Richard P.;
- Tainer, John A.
Publication type:
Article
Loggerhead sea turtle embryos ( Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress.
Published in:
Molecular Ecology, 2017, v. 26, n. 11, p. 2978, doi. 10.1111/mec.14087
By:
- Bentley, Blair P.;
- Haas, Brian J.;
- Tedeschi, Jamie N.;
- Berry, Oliver
Publication type:
Article
Evolutionary Dynamics of the Accessory Genome of <i>Listeria monocytogenes</i>.
Published in:
PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0067511
By:
- den Bakker, Henk C.;
- Desjardins, Christopher A.;
- Griggs, Allison D.;
- Peters, Joseph E.;
- Zeng, Qiandong;
- Young, Sarah K.;
- Kodira, Chinnappa D.;
- Yandava, Chandri;
- Hepburn, Theresa A.;
- Haas, Brian J.;
- Birren, Bruce W.;
- Wiedmann, Martin
Publication type:
Article
Characterization of paralogous protein families in rice.
Published in:
BMC Plant Biology, 2008, v. 8, p. 1, doi. 10.1186/1471-2229-8-18
By:
- Haining Lin;
- Shu Ouyang;
- Egan, Amy;
- Nobuta, Kan;
- Haas, Brian J.;
- Wei Zhu;
- Xun Gu;
- Silva, Joana C.;
- Meyers, Blake C.;
- Buell, C. Robin
Publication type:
Article
Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07604-0
By:
- Leigh, Nicholas D.;
- Dunlap, Garrett S.;
- Johnson, Kimberly;
- Mariano, Rachelle;
- Oshiro, Rachel;
- Wong, Alan Y.;
- Bryant, Donald M.;
- Miller, Bess M.;
- Ratner, Alex;
- Chen, Andy;
- Ye, William W.;
- Haas, Brian J.;
- Whited, Jessica L.
Publication type:
Article
Insights into the Musa genome: Syntenic relationships to rice and between Musa species.
Published in:
BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-58
By:
- Lescot, Magali;
- Piffanelli, Pietro;
- Ciampi, Ana Y.;
- Ruiz, Manuel;
- Blanc, Guillaume;
- Leebens-Mack, Jim;
- da Silva, Felipe R.;
- R. Santos, Candice M.;
- D'Hont, Angélique;
- Garsmeur, Olivier;
- Vilarinhos, Alberto D.;
- Kanamori, Hiroyuki;
- Matsumoto, Takashi;
- Ronning, Catherine M.;
- Foo Cheung;
- Haas, Brian J.;
- Althoff, Ryan;
- Arbogast, Tammy;
- Hine, Erin;
- Pappas Jr., Georgios J.
Publication type:
Article
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis.
Published in:
BMC Genomics, 2006, v. 7, p. 327, doi. 10.1186/1471-2164-7-327
By:
- Campbell, Matthew A;
- Haas, Brian J;
- Hamilton, John P;
- Mount, Stephen M;
- Buell, C Robin
Publication type:
Article
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology.
Published in:
BMC Genomics, 2006, v. 7, p. 1, doi. 10.1186/1471-2164-7-272
By:
- Cheung, Foo;
- Haas, Brian J;
- Goldberg, Susanne MD;
- May, Gregory D;
- Xiao, Yongli;
- Town, Christopher D
Publication type:
Article
A universal genomic coordinate translator for comparative genomics.
Published in:
BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-227
By:
- Zamani, Neda;
- Sundström, Görel;
- Meadows, Jennifer R. S.;
- Höppner, Marc P.;
- Dainat, Jacques;
- Lantz, Henrik;
- Haas, Brian J.;
- Grabherr, Manfred G.
Publication type:
Article
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.
Published in:
Nature, 2009, v. 461, n. 7262, p. 393, doi. 10.1038/nature08358
By:
- Haas, Brian J.;
- Kamoun, Sophien;
- Zody, Michael C.;
- Jiang, Rays H. Y.;
- Handsaker, Robert E.;
- Cano, Liliana M.;
- Grabherr, Manfred;
- Kodira, Chinnappa D.;
- Raffaele, Sylvain;
- Torto-Alalibo, Trudy;
- Bozkurt, Tolga O.;
- Ah-Fong, Audrey M. V.;
- Alvarado, Lucia;
- Anderson, Vicky L.;
- Armstrong, Miles R.;
- Avrova, Anna;
- Baxter, Laura;
- Beynon, Jim;
- Boevink, Petra C.;
- Bollmann, Stephanie R.
Publication type:
Article
The genome of the blood fluke Schistosoma mansoni.
Published in:
Nature, 2009, v. 460, n. 7253, p. 352, doi. 10.1038/nature08160
By:
- Berriman, Matthew;
- Haas, Brian J.;
- LoVerde, Philip T.;
- Wilson, R. Alan;
- Dillon, Gary P.;
- Cerqueira, Gustavo C.;
- Mashiyama, Susan T.;
- Al-Lazikani, Bissan;
- Andrade, Luiza F.;
- Ashton, Peter D.;
- Aslett, Martin A.;
- Bartholomeu, Daniella C.;
- Blandin, Gaelle;
- Caffrey, Conor R.;
- Coghlan, Avril;
- Coulson, Richard;
- Day, Tim A.;
- Delcher, Art;
- DeMarco, Ricardo;
- Djikeng, Appolinaire
Publication type:
Article
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
Published in:
Nucleic Acids Research, 2003, v. 31, n. 19, p. 5654, doi. 10.1093/nar/gkg770
By:
- Haas, Brian J.;
- Delcher, Arthur L.;
- Mount, Stephen M.;
- Wortman, Jennifer R.;
- Smith Jr, Roger K.;
- Hannick, Linda I.;
- Maiti, Rama;
- Ronning, Catherine M.;
- Rusch, Douglas B.;
- Town, Christopher D.;
- Salzberg, Steven L.;
- White, Owen
Publication type:
Article
Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi.
Published in:
G3: Genes | Genomes | Genetics, 2015, v. 5, n. 12, p. 2539, doi. 10.1534/g3.115.020057
By:
- Okagaki, Laura H.;
- Nunes, Cristiano C.;
- Sailsbery, Joshua;
- Clay, Brent;
- Brown, Doug;
- John, Titus;
- Yeonyee Oh;
- Young, Nelson;
- Fitzgerald, Michael;
- Haas, Brian J.;
- Qiandong Zeng;
- Young, Sarah;
- Adiconis, Xian;
- Lin Fan;
- Levin, Joshua Z.;
- Mitchell, Thomas K.;
- Okubara, Patricia A.;
- Farman, Mark L.;
- Kohn, Linda M.;
- Birren, Bruce
Publication type:
Article
Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa.
Published in:
PLoS Pathogens, 2007, v. 3, n. 10, p. e148, doi. 10.1371/journal.ppat.0030148
By:
- Brayton, Kelly A.;
- Lau, Audrey O. T.;
- Herndon, David R.;
- Hannick, Linda;
- Kappmeyer, Lowell S.;
- Berens, Shawn J.;
- Bidwell, Shelby L.;
- Brown, Wendy C.;
- Crabtree, Jonathan;
- Fadrosh, Doug;
- Feldblum, Tamara;
- Forberger, Heather A.;
- Haas, Brian J;
- Howell, Jeanne M.;
- Khouri, Hoda;
- Hean Koo;
- Mann, David J.;
- Norimine, Junzo;
- Paulsen, Ian T.;
- Radune, Diana
Publication type:
Article
The Capsaspora genome reveals a complex unicellular prehistory of animals.
Published in:
Nature Communications, 2013, v. 4, n. 8, p. 2325, doi. 10.1038/ncomms3325
By:
- Suga, Hiroshi;
- Chen, Zehua;
- de Mendoza, Alex;
- Sebé-Pedrós, Arnau;
- Brown, Matthew W.;
- Kramer, Eric;
- Carr, Martin;
- Kerner, Pierre;
- Vervoort, Michel;
- Sánchez-Pons, Núria;
- Torruella, Guifré;
- Derelle, Romain;
- Manning, Gerard;
- Lang, B. Franz;
- Russ, Carsten;
- Haas, Brian J.;
- Roger, Andrew J.;
- Nusbaum, Chad;
- Ruiz-Trillo, Iñaki
Publication type:
Article
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.
Published in:
Genome Biology, 2012, v. 13, n. 3, p. 1, doi. 10.1186/gb-2012-13-3-r23
By:
- Giannoukos, Georgia;
- Ciulla, Dawn M.;
- Huang, Katherine;
- Haas, Brian J.;
- Izard, Jacques;
- Levin, Joshua Z.;
- Livny, Jonathan;
- Earl, Ashlee M.;
- Gevers, Dirk;
- Ward, Doyle V.;
- Nusbaum, Chad;
- Birren1, Bruce W.;
- Gnirke1, Andreas
Publication type:
Article
'Next-generation' sequencing becomes 'now-generation'.
Published in:
Genome Biology, 2011, v. 12, n. 3, p. 1, doi. 10.1186/gb-2011-12-3-303
By:
- Neafsey, Daniel E.;
- Haas, Brian J.
Publication type:
Article
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
Published in:
BMC Biology, 2005, v. 3, p. 1, doi. 10.1186/1741-7007-3-7
By:
- Haas, Brian J.;
- Wortman, Jennifer R.;
- Ronning, Catherine M.;
- Hannick, Linda I.;
- Smith Jr., Roger K.;
- Maiti, Rama;
- Chan, Agnes P.;
- Chunhui Yu;
- Farzad, Maryam;
- Dongying Wu;
- White, Owen;
- Town, Christopher D.
Publication type:
Article
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote.
Published in:
PLoS Biology, 2006, v. 4, n. 9, p. 1620, doi. 10.1371/journal.pbio.0040286
By:
- Eisen, Jonathan A.;
- Coyne, Robert S.;
- Wu, Martin;
- Wu, Dongying;
- Thiagarajan, Mathangi;
- Wortman, Jennifer R.;
- Badger, Jonathan H.;
- Ren, Qinghu;
- Amedeo, Paolo;
- Jones, Kristie M.;
- Tallon, Luke J.;
- Delcher, Arthur L.;
- Salzberg, Steven L.;
- Silva, Joana C.;
- Haas, Brian J.;
- Majoros, William H.;
- Farzad, Maryam;
- Carlton, Jane M.;
- Smith, Jr., Roger K.;
- Garg, Jyoti
Publication type:
Article
DAGchainer: a tool for mining segmental genome duplications and synteny.
Published in:
Bioinformatics, 2004, v. 20, n. 18, p. 3643, doi. 10.1093/bioinformatics/bth397
By:
- Haas, Brian J.;
- Delcher, Arthur L.;
- Wortman, Jennifer R.;
- Salzberg, Steven L.
Publication type:
Article
Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen <i>Saprolegnia parasitica</i>.
Published in:
PLoS Genetics, 2013, v. 9, n. 6, p. 1, doi. 10.1371/journal.pgen.1003272
By:
- Jiang, Rays H. Y.;
- de Bruijn, Irene;
- Haas, Brian J.;
- Belmonte, Rodrigo;
- Löbach, Lars;
- Christie, James;
- van den Ackerveken, Guido;
- Bottin, Arnaud;
- Bulone, Vincent;
- Díaz-Moreno, Sara M.;
- Dumas, Bernard;
- Fan, Lin;
- Gaulin, Elodie;
- Govers, Francine;
- Grenville-Briggs, Laura J.;
- Horner, Neil R.;
- Levin, Joshua Z.;
- Mammella, Marco;
- Meijer, Harold J. G.;
- Morris, Paul
Publication type:
Article
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus.
Published in:
PLoS Genetics, 2008, v. 4, n. 4, p. 1, doi. 10.1371/journal.pgen.1000046
By:
- Fedorova, Natalie D.;
- Khaldi, Nora;
- Joardar, Vinita S.;
- Maiti, Rama;
- Amedeo, Paolo;
- Anderson, Michael J.;
- Crabtree, Jonathan;
- Silva, Joana C.;
- Badger, Jonathan H.;
- Albarraq, Ahmed;
- Angiuoli, Sam;
- Bussey, Howard;
- Bowyer, Paul;
- Cotty, Peter J.;
- Dyer, Paul S.;
- Egan, Amy;
- Galens, Kevin;
- Fraser-Liggett, Claire M.;
- Haas, Brian J.;
- Inman, Jason M.
Publication type:
Article
Structure and transcription of integrated HPV DNA in vulvar carcinomas.
Published in:
NPJ Genomic Medicine, 2024, v. 9, n. 1, p. 1, doi. 10.1038/s41525-024-00418-8
By:
- Van Arsdale, Anne;
- Turker, Lauren;
- Chang, Yoke-Chen;
- Gould, Joshua;
- Harmon, Bryan;
- Maggi, Elaine C.;
- Meshcheryakova, Olga;
- Brown, Maxwell P.;
- Luong, Dana;
- Van Doorslaer, Koenraad;
- Einstein, Mark H.;
- Kuo, Dennis Y. S.;
- Zheng, Deyou;
- Haas, Brian J.;
- Lenz, Jack;
- Montagna, Cristina
Publication type:
Article
Cover Image: Volume 22, Issue 4.
Published in:
Evolution & Development, 2020, v. 22, n. 4, p. i, doi. 10.1111/ede.12349
By:
- Leigh, Nicholas D.;
- Sessa, Sofia;
- Dragalzew, Aline C.;
- Payzin‐Dogru, Duygu;
- Sousa, Josane F.;
- Aggouras, Anthony N.;
- Johnson, Kimberly;
- Dunlap, Garrett S.;
- Haas, Brian J.;
- Levin, Michael;
- Schneider, Igor;
- Whited, Jessica L.
Publication type:
Article
von Willebrand factor D and EGF domains is an evolutionarily conserved and required feature of blastemas capable of multitissue appendage regeneration.
Published in:
Evolution & Development, 2020, v. 22, n. 4, p. 297, doi. 10.1111/ede.12332
By:
- Leigh, Nicholas D.;
- Sessa, Sofia;
- Dragalzew, Aline C.;
- Payzin‐Dogru, Duygu;
- Sousa, Josane F.;
- Aggouras, Anthony N.;
- Johnson, Kimberly;
- Dunlap, Garrett S.;
- Haas, Brian J.;
- Levin, Michael;
- Schneider, Igor;
- Whited, Jessica L.
Publication type:
Article
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.
Published in:
Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1842-9
By:
- Haas, Brian J.;
- Dobin, Alexander;
- Li, Bo;
- Stransky, Nicolas;
- Pochet, Nathalie;
- Regev, Aviv
Publication type:
Article
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Published in:
Nature Protocols, 2013, v. 8, n. 8, p. 1494, doi. 10.1038/nprot.2013.084
By:
- Haas, Brian J;
- Papanicolaou, Alexie;
- Yassour, Moran;
- Grabherr, Manfred;
- Blood, Philip D;
- Bowden, Joshua;
- Couger, Matthew Brian;
- Eccles, David;
- Li, Bo;
- Lieber, Matthias;
- MacManes, Matthew D;
- Ott, Michael;
- Orvis, Joshua;
- Pochet, Nathalie;
- Strozzi, Francesco;
- Weeks, Nathan;
- Westerman, Rick;
- William, Thomas;
- Dewey, Colin N;
- Henschel, Robert
Publication type:
Article
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
Published in:
BMC Genomics, 2012, v. 13, n. 1, p. 734, doi. 10.1186/1471-2164-13-734
By:
- Haas, Brian J.;
- Chin, Melissa;
- Nusbaum, Chad;
- Birren, Bruce W.;
- Livny, Jonathan
Publication type:
Article
Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.
Published in:
Bioinformatics, 2013, v. 29, n. 19, p. 2387, doi. 10.1093/bioinformatics/btt419
By:
- Goldberg, Jonathan M.;
- Griggs, Allison D.;
- Smith, Janet L.;
- Haas, Brian J.;
- Wortman, Jennifer R.;
- Zeng, Qiandong
Publication type:
Article
UCHIME improves sensitivity and speed of chimera detection.
Published in:
Bioinformatics, 2011, v. 27, n. 16, p. 2194, doi. 10.1093/bioinformatics/btr381
By:
- Edgar, Robert C.;
- Haas, Brian J.;
- Clemente, Jose C.;
- Quince, Christopher;
- Knight, Rob
Publication type:
Article
Ten things to know about oomycete effectors.
Published in:
Molecular Plant Pathology, 2009, v. 10, n. 6, p. 795, doi. 10.1111/j.1364-3703.2009.00593.x
By:
- Schornack, Sebastian;
- Huitema, Edgar;
- Cano, Liliana M.;
- Bozkurt, Tolga O.;
- Oliva, Ricardo;
- Van Damme, Mireille;
- Schwizer, Simon;
- Raffaele, Sylvain;
- Chaparro-Garcia, Angela;
- Farrer, Rhys;
- Segretin, Maria Eugenia;
- Bos, Jorunn;
- Haas, Brian J.;
- Zody, Michael C.;
- Nusbaum, Chad;
- Win, Joe;
- Thines, Marco;
- Kamoun, Sophien
Publication type:
Article

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