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Items: 1 to 50 of 83

1.

SynerClust: a highly scalable, synteny-aware orthologue clustering tool.

Georgescu CH, Manson AL, Griggs AD, Desjardins CA, Pironti A, Wapinski I, Abeel T, Haas BJ, Earl AM.

Microb Genom. 2018 Nov 12. doi: 10.1099/mgen.0.000231. [Epub ahead of print]

2.

Erratum: The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation.

Wallrapp A, Riesenfeld SJ, Burkett PR, Abdulnour RE, Nyman J, Dionne D, Hofree M, Cuoco MS, Rodman C, Farouq D, Haas BJ, Tickle TL, Trombetta JJ, Baral P, Klose CSN, Mahlakõiv T, Artis D, Rozenblatt-Rosen O, Chiu IM, Levy BD, Kowalczyk MS, Regev A, Kuchroo VK.

Nature. 2017 Nov 30;551(7682):658. doi: 10.1038/nature24480. Epub 2017 Nov 15.

PMID:
29143821
3.

The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation.

Wallrapp A, Riesenfeld SJ, Burkett PR, Abdulnour RE, Nyman J, Dionne D, Hofree M, Cuoco MS, Rodman C, Farouq D, Haas BJ, Tickle TL, Trombetta JJ, Baral P, Klose CSN, Mahlakõiv T, Artis D, Rozenblatt-Rosen O, Chiu IM, Levy BD, Kowalczyk MS, Regev A, Kuchroo VK.

Nature. 2017 Sep 21;549(7672):351-356. doi: 10.1038/nature24029. Epub 2017 Sep 13. Erratum in: Nature. 2017 Nov 15;:.

4.

Advances in Decoding Axolotl Limb Regeneration.

Haas BJ, Whited JL.

Trends Genet. 2017 Aug;33(8):553-565. doi: 10.1016/j.tig.2017.05.006. Epub 2017 Jun 22. Review.

5.

Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress.

Bentley BP, Haas BJ, Tedeschi JN, Berry O.

Mol Ecol. 2017 Jun;26(11):2978-2992. doi: 10.1111/mec.14087. Epub 2017 Apr 4.

PMID:
28267875
6.

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors.

Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo TH, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM Jr, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL.

Cell Rep. 2017 Jan 17;18(3):762-776. doi: 10.1016/j.celrep.2016.12.063.

7.

The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families.

Parente TE, Moreira DA, Magalhães MGP, de Andrade PCC, Furtado C, Haas BJ, Stegeman JJ, Hahn ME.

Mar Pollut Bull. 2017 Feb 15;115(1-2):352-361. doi: 10.1016/j.marpolbul.2016.12.012. Epub 2017 Jan 4.

8.

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):816-827. doi: 10.1016/j.molcel.2015.11.013.

9.

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. Epub 2015 Oct 1.

10.

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. doi: 10.1534/g3.115.020057.

11.

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.

12.

A universal genomic coordinate translator for comparative genomics.

Zamani N, Sundström G, Meadows JR, Höppner MP, Dainat J, Lantz H, Haas BJ, Grabherr MG.

BMC Bioinformatics. 2014 Jun 30;15:227. doi: 10.1186/1471-2105-15-227.

13.

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I.

Nat Commun. 2013;4:2325. doi: 10.1038/ncomms3325.

14.

Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.

Goldberg JM, Griggs AD, Smith JL, Haas BJ, Wortman JR, Zeng Q.

Bioinformatics. 2013 Oct 1;29(19):2387-94. doi: 10.1093/bioinformatics/btt419. Epub 2013 Jul 31.

15.

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.

16.

Evolutionary dynamics of the accessory genome of Listeria monocytogenes.

den Bakker HC, Desjardins CA, Griggs AD, Peters JE, Zeng Q, Young SK, Kodira CD, Yandava C, Hepburn TA, Haas BJ, Birren BW, Wiedmann M.

PLoS One. 2013 Jun 25;8(6):e67511. doi: 10.1371/journal.pone.0067511. Print 2013.

17.

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, Löbach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJ, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JH, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P.

PLoS Genet. 2013 Jun;9(6):e1003272. doi: 10.1371/journal.pgen.1003272. Epub 2013 Jun 13.

18.

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.

19.

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany.

Grad YH, Lipsitch M, Griggs AD, Haas BJ, Shea TP, McCowan C, Montmayeur A, FitzGerald M, Wortman JR, Krogfelt KA, Bingen E, Weill FX, Tietze E, Flieger A, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):E3629-30. No abstract available.

20.

Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen.

Grad YH, Godfrey P, Cerquiera GC, Mariani-Kurkdjian P, Gouali M, Bingen E, Shea TP, Haas BJ, Griggs A, Young S, Zeng Q, Lipsitch M, Waldor MK, Weill FX, Wortman JR, Hanage WP.

MBio. 2013 Jan 22;4(1):e00452-12. doi: 10.1128/mBio.00452-12.

21.

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J.

BMC Genomics. 2012 Dec 27;13:734. doi: 10.1186/1471-2164-13-734.

22.

Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.

Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF.

Mol Plant Microbe Interact. 2012 Oct;25(10):1350-60. doi: 10.1094/MPMI-02-12-0028-R.

23.

Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States.

Kos VN, Desjardins CA, Griggs A, Cerqueira G, Van Tonder A, Holden MT, Godfrey P, Palmer KL, Bodi K, Mongodin EF, Wortman J, Feldgarden M, Lawley T, Gill SR, Haas BJ, Birren B, Gilmore MS.

MBio. 2012 May 22;3(3). pii: e00112-12. doi: 10.1128/mBio.00112-12. Print 2012.

24.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.

Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A.

Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23.

25.

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-Møller 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 21;109(8):3065-70. doi: 10.1073/pnas.1121491109. Epub 2012 Feb 6. Erratum in: Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5547.

26.

Approaches to Fungal Genome Annotation.

Haas BJ, Zeng Q, Pearson MD, Cuomo CA, Wortman JR.

Mycology. 2011 Oct 3;2(3):118-141.

27.

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.

Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailão AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, León-Narváez H, Longo LV, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodríguez-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. doi: 10.1371/journal.pgen.1002345. Epub 2011 Oct 27.

28.

Branch point identification and sequence requirements for intron splicing in Plasmodium falciparum.

Zhang X, Tolzmann CA, Melcher M, Haas BJ, Gardner MJ, Smith JD, Feagin JE.

Eukaryot Cell. 2011 Nov;10(11):1422-8. doi: 10.1128/EC.05193-11. Epub 2011 Sep 16.

29.

UCHIME improves sensitivity and speed of chimera detection.

Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R.

Bioinformatics. 2011 Aug 15;27(16):2194-200. doi: 10.1093/bioinformatics/btr381. Epub 2011 Jun 23.

30.

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, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

31.

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, Müller 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. doi: 10.1126/science.1203357. Epub 2011 Apr 21.

32.

'Next-generation' sequencing becomes 'now-generation'.

Neafsey DE, Haas BJ.

Genome Biol. 2011;12(3):303. doi: 10.1186/gb-2011-12-3-303. Epub 2011 Mar 18.

33.

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.

Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ; Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW.

Genome Res. 2011 Mar;21(3):494-504. doi: 10.1101/gr.112730.110. Epub 2011 Jan 6.

34.

Draft genome sequence of the oilseed species Ricinus communis.

Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G, Cahoon EB, Gedil M, Stanke M, Haas BJ, Wortman JR, Fraser-Liggett CM, Ravel J, Rabinowicz PD.

Nat Biotechnol. 2010 Sep;28(9):951-6. doi: 10.1038/nbt.1674. Epub 2010 Aug 22.

35.

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, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Kraus E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé 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. doi: 10.1073/pnas.1003379107. Epub 2010 Jun 21. Erratum in: Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6335. Krause, Emily [corrected to Kraus, Emily].

36.

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. doi: 10.1126/science.1183605.

37.

Advancing RNA-Seq analysis.

Haas BJ, Zody MC.

Nat Biotechnol. 2010 May;28(5):421-3. doi: 10.1038/nbt0510-421. No abstract available.

PMID:
20458303
38.

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. doi: 10.1111/j.1364-3703.2009.00593.x. Review.

PMID:
19849785
39.

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AM, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JI, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grünwald NJ, Horn K, Horner NR, Hu CH, Huitema E, Jeong DH, Jones AM, Jones JD, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJ, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzón A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJ, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS, Nusbaum C.

Nature. 2009 Sep 17;461(7262):393-8. doi: 10.1038/nature08358. Epub 2009 Sep 9.

PMID:
19741609
40.

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.

Nature. 2009 Jul 16;460(7253):352-8. doi: 10.1038/nature08160.

41.

Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps.

Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fadrosh DW, Fuester RW, Pedroni MJ, Haas BJ, Schatz MC, Jones KM, Crabtree J, Forberger H, Nene V.

Genome Biol. 2008;9(12):R183. doi: 10.1186/gb-2008-9-12-r183. Epub 2008 Dec 30.

42.

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.

Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methé BA.

BMC Genomics. 2008 Nov 26;9:562. doi: 10.1186/1471-2164-9-562.

43.

Single-measurement therapeutic drug monitoring of the HIV/AIDS drugs abacavir, zidovudine, lamivudine, efavirenz, nevirapine, lopinavir and nelfinavir.

Donnerer J, Haas BJ, Kessler HH.

Pharmacology. 2008;82(4):287-92. doi: 10.1159/000164222. Epub 2008 Oct 17.

PMID:
18931536
44.

Analysis of alternative splicing in plants with bioinformatics tools.

Haas BJ.

Curr Top Microbiol Immunol. 2008;326:17-37. Review.

PMID:
18630745
45.

Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation.

Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ.

Nucleic Acids Res. 2008 May;36(9):3150-61. doi: 10.1093/nar/gkn158. Epub 2008 Apr 13.

46.

DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.

Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Björas M, Cunningham RP, Tainer JA.

Nat Struct Mol Biol. 2008 May;15(5):515-22. doi: 10.1038/nsmb.1414. Epub 2008 Apr 13.

PMID:
18408731
47.

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.

Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC.

PLoS Genet. 2008 Apr 11;4(4):e1000046. doi: 10.1371/journal.pgen.1000046.

48.

Characterization of paralogous protein families in rice.

Lin H, Ouyang S, Egan A, Nobuta K, Haas BJ, Zhu W, Gu X, Silva JC, Meyers BC, Buell CR.

BMC Plant Biol. 2008 Feb 19;8:18. doi: 10.1186/1471-2229-8-18.

49.

Insights into the Musa genome: syntenic relationships to rice and between Musa species.

Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CM, D'Hont A, Garsmeur O, Vilarinhos AD, Kanamori H, Matsumoto T, Ronning CM, Cheung F, Haas BJ, Althoff R, Arbogast T, Hine E, Pappas GJ Jr, Sasaki T, Souza MT Jr, Miller RN, Glaszmann JC, Town CD.

BMC Genomics. 2008 Jan 30;9:58. doi: 10.1186/1471-2164-9-58.

50.

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 O, Buell CR, Wortman JR.

Genome Biol. 2008 Jan 11;9(1):R7. doi: 10.1186/gb-2008-9-1-r7.

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