Publications

2014

Bakowski MA, Priest M, Young S, Cuomo CA, Troemel ER. Genome Sequence of the Microsporidian Species Nematocida sp1 Strain ERTm6 (ATCC PRA-372). 2014. Genome Announcements 2 (5), e00905-14.

Billmyre RB, Croll D, Li W, Mieczkowski P, Carter DA, Cuomo CA, Kronstad J, Heitman J. Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution. 2014. mBio 5 (4), e01494-14.

Rollins, Cuomo CA, Dickman MB, Kohn LM. Genomics of Sclerotinia sclerotiorum. 2014. Genomics of Plant-Associated Fungi and Oomycetes: Dicot Pathogens, 1-17.

Szabo LJ, Cuomo CA, Park RF. Puccinia graminis. 2014. Genomics of Plant-Associated Fungi: Monocot Pathogens, 177-196.

White TC, Findley K, Dawson TL, Scheynius A, Boekhout T, Cuomo CA, Xu J, Saunders CW. Fungi on the Skin: Dermatophytes and Malassezia. 2014. Cold Spring Harbor perspectives in medicine 4 (8), a019802.

Lee SC, Billmyre RB, Li A, Carson S, Sykes SM, Huh EY, Mieczkowski P, Ko DC, Cuomo CA, Heitman J. 2014. Analysis of a foodborne fungal pathogen outbreak: virulence and genome of a
Mucor circinelloides isolate from yogurt. MBio 8;5(4):e01390-14.

Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TA, Lopez-Moyado IF, Rifkin SA, Cuomo CA, Troemel ER. Ubiquitin-Mediated Response to Microsporidia and Virus Infection in C. elegans. 2014. PLoS Pathogens 10 (6), e1004200.

Cuomo CA, Rodriguez-Del Valle N, Lizaida Perez-Sanchez L, Abouelleil A, Goldberg J, Young S, Zeng Q, Birren BW. Genome sequence of the pathogenic fungus Sporothrix schenckii (ATCC 58251). 2014. Genome Announcements 2 (3), e00446-14.

Janbon G, Ormerod KL, Paulet D, Byrnes EJ rd, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS. Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation. 2014. PLoS Genetics.

Chen Z, Martinez DA, Gujja S, Sykes SM, Zeng Q, Szaniszlo PJ, Wang Z, Cuomo CA. Comparative Genomic and Transcriptomic Analysis of Wangiella dermatitidis, a Major Cause of Phaeohyphomycosis and a Model Black Yeast Human Pathogen. G3. 2014 Feb 4. pii: g3.113.009241v1. doi: 10.1534/g3.113.009241.

Bruce M, Neugebauer KA, Joly DL, Migeon P, Cuomo CA, Wang S, Akhunov E, Bakkeren G, Kolmer JA, Fellers JP. Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat. Frontiers in Plant Sci. 2014 Jan 13;4:520. doi: 10.3389/fpls.2013.00520. eCollection 2014 Jan 13.

2013

Marty AJ, Wuthrich M, Carmen JC, Sullivan TD, Klein BS, Cuomo CA, Gauthier GM. Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling. 2013. Fungal Genetics and Biology. Jul;56:1-8. doi: 10.1016/j.fgb.2013.03.001. Epub 2013 Mar 14. 

Ma L, Huang DW, Cuomo CA, Sykes S, Fantoni G, Das B, Sherman BT, Yang J, Huber C, Xia Y, Davey E, Kutty G, Bishop L, Sassi M, Lempicki RA, Kovacs JA. Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis. 2013. FASEB J. May;27(5):1962-72. doi: 10.1096/fj.12-224444. Epub 2013 Feb 7.

Geiser DM, Aoki T, Bacon CW, Baker SE, Bhattacharyya MK, Brandt ME, Brown DW, Burgess LW, Chulze SN, Coleman JJ, Correll JC, Covert S, Crous PW, Cuomo CA, de Hoog GS, Di Pietro A, Elmer WH, Epstein L, Frandsen RJ, Freeman S, Gagkaeva T, Glenn AE, Gordon T, Gregory NF, Hammond-Kosack K, Hanson L, Jimenez-Gasco MD, Kang S, Kistler HC, Kuldau GA, Leslie JF, Logrieco A, Lü G, Lysøe E, Ma LJ, McCormick S, Migheli Q, Moretti A, Munaut F, O'Donnell K, Pfenning LH, Ploetz R, Proctor R, Rehner SA, Robert VA, Rooney AP, Salleh B, Scandiani MM, Scauflaire J, Short DP, Steenkamp E, Suga H, Summerell BA, Sutton DA, Thrane U, Trail F, van Diepeningen A, Vanetten H, Viljoen A, Waalwijk C, Ward T, Wingfield MJ, Xu JR, Yang XB, Yli-Matilla T, Zhang N. One Fungus, One Name: Defining the genus Fusarium in a scientifically robust way that preserves longstanding use. 2013. Phytopathology May;103(5):400-8. doi: 10.1094/PHYTO-07-12-0150-LE.

Fellers JP, Soltani BM, Bruce M, Linning R, Cuomo CA, Szabo L, Bakkeren G. Conserved loci of leaf and stem rust share synteny interrupted by lineage-specific influx of repeat elements. 2013. BMC Genomics, Jan 29;14:60. doi: 10.1186/1471-2164-14-60.

Pombert JF, Xu J, Smith DR, Heiman D, Young S, Cuomo CA, Weiss LM, Keeling PJ. Complete genome sequences from three genetically distinct strains reveal a high intra-species genetic diversity in the microsporidian Encephalitozoon cuniculi. Eukaryotic Cell. Apr;12(4):503-11. doi: 10.1128/EC.00312-12. Epub 2013 Jan 4.

Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3. 2013 Jan;3(1):41-63. doi: 10.1534/g3.112.004044.

Li W, Sullivan T, Walton E, Averette A, Sakthikumar S, Cuomo CA, Klein B, and Heitman J. Identification of the mating-type (MAT) locus that controls sexual reproduction of Blastomyces dermatitidis. 2013. Eukaryotic Cell 12:109-117.

2012

Robertson KL, Mostaghim A, Cuomo CA, Soto CM Lebedev N, Bailey RF, Wang Z. Adaptation of the Black Yeast Wangiella dermatitidis to Ionizing Radiation: Molecular and Cellular Mechanisms. 2012. PLoS One. 7(11): e48674.

Martinez D, Oliver BG, Graser Y, Goldberg JM, Li W, Martinez-Rossi NM, Monod M, Shelest E, Barton RC, Birch E, Brakhage AA, Chen Z, Gurr SJ, Heiman D, Heitman J, Kosti I, Rossi A, Saif S, Samalova M, Saunders CW, Shea T, Summerbell RC, Xu J, Young S, Zeng Q, Birren BW, Cuomo CA*, White TC*. Comparative analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. 2012. mBio. Sep 4;3(5):e00259-12. doi: 10.1128/mBio.00259-12.

Schloegel LM, Toledo LF, Longcore JE, Greenspan SE, Vieira CA, Lee M, Zhao S, Wangen C, Ferreira CM, Hipolito M, Davies AJ, Cuomo CA, Daszak P, James TY. Novel, panzootic and hybrid genotypes of amphibian chytridiomycosis associated with the bullfrog trade. Molecular Ecology Nov. 12(12): 5162-5177.

Cuomo CA*, Desjardins CA*, Bakowski MA*, Goldberg J, Ma AT, Becnel JJ, Didier ES, Fan L, Heiman DI, Levin JZ, Young S, Zeng Q, Troemel ER. Microsporidia genome analysis reveals evolutionary strategies for obligate intracellular growth. 2012. Genome Research. Dec;22(12):2478-88. doi: 10.1101/gr.142802.112. Epub 2012 Jul 18.

Petit E, Giraud T, De Vienne D, Coelho M, Aguileta G, Amselem J, Kreplak J,Poulian J, Gavory F, Wincker P, Young S, Cuomo C, Perlin M, Hood M. Linkage to the Mating-Type Locus across the Genus Microbotryum: Insights into Non-Recombining Chromosomes. 2012. Evolution DOI: 10.1111/j.1558-5646.2012.01703.x

2011

Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailão AM, Brigido MM, Ferreira MES, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, León-Narváez H, Longo LVG, 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 MEMT, 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 CMA, Birren BW, Cuomo CA. 2011. Comparative Genomic Analysis of Human Fungal pathogens causing Paracoccidioidomycosis. PLoS Genetics. Oct;7(10):e1002345.

Haas BJ, Zeng Q, Pearson MD, Cuomo CA, Wortman JR. 2011. Approaches to Fungal Genome Annotation. Mycology Oct 3;2(3):118-141.

Amselem J*, Cuomo CA*, van Kan JAL*, Viaud M*, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier J-M, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett B, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A,Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA**, Lebrun M-H**, Dickman M**. 2011. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics, Aug;7(8):e1002230.

Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BP, Chen Z, Henrissat B, Lee YH, Park J, Garcia-Pedrajas MD, Barbara DJ, Anchieta A, de Jonge R, Santhanam P, Maruthachalam K, Atallah Z, Amyotte SG, Paz Z, Inderbitzin P, Hayes RJ, Heiman DI, Young S, Zeng Q, Engels R, Galagan J, Cuomo CA, Dobinson KF, Ma LJ. 2011. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathogens Jul;7(7):e1002137.

Duplessis S*, Cuomo CA*, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel BL, Chiu R, Couthinho P, Feau N, Field M, Frey P, Gelhaye E, Goldberg J, Grabherr M, Kodira CD, Kohler A, Kues U, Lindquist EA, Lucas S, Mago R, Mauceli E, Morin E, Murat C, Pangilinan JL, Park R, Pearson M, Quesneville H, Rouhier N, Sakthikumar S, Salamov AA, Schmutz J, Selles B, Shapiro H, Tangay P, Tuskan GA, Henrissat B, Peer YV, Rouze P, Ellis JG, Dodds PN, Schein JE, Zhong S, Hamelin RC, Grigoriev IV, Szabo LJ, Martin F. 2011 Obligate biotrophy features unraveled by the genomic analysis of rust fungi. PNAS 108 (22): 9166-71.

D’Souza CA*, Kronstad JW*, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BFF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA. 2011. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio 2(1): e00342-10.

2010

Cuomo CA and Birren BW. 2010. The Fungal Genome Initiative and lessons learned from genome sequencing. Methods in Enzymology, Guide to Yeast Genetics and Molecular Cell Biology, Volume 470 (34): 833-855.

Gauthier GM, Sullivan TD, Gallardo SS, Brandhorst TT, Vanden Wymelenberg AJ, Cuomo CA, Suen G, Currie CR, Klein BS. 2010. SREB, a GATA transcription factor that directs disparate fates in Blastomyces dermatitidis including morphogenesis and siderophore biosynthesis. PLoS Pathogens, 6 (4): e1000846.

Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Coutinho PM, Danchin EGJ, Diener A, Gale L, Gardier DM, Goff S, Kammond-Kosak KE, Hilburn K, Hua-Van A, JonkersW, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra DM, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum. Nature 464 (7287): 367-373.

Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD. 2010. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research 20 (7): 938-36.

2009

Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M*,Cuomo CA*. 2009. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459:657-62.

Hood HM, Neafsey DE, Galagan J, Sachs MS. 2009. Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annual Review of Microbiology 63: 385-409.

Lambreghts R, Shi M, Belden WJ, DeCaprio D, Park D, Henn MR, Galagan JE, Bastürkmen M, Birren BW, Sachs MS, Dunlap JC, Loros JJ. 2009. A high-density single nucleotide polymorphism map for Neurospora crassa. Genetics 181:767-781.

Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF, Sone T, Abe A, Calvo SE, Corrochano LM, Engels R, Fu J, Hansberg W, Kim JM, Kodira CD, Koehrsen MJ, Liu B, Miranda-Saavedra D, O'Leary S, Ortiz-Castellanos L, Poulter R, Rodriguez-Romero J, Ruiz-Herrera J, Shen YQ, Zeng Q, Galagan J, Birren BW, Cuomo CA, Wickes BL. 2009. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genetics 5(7): e1000549.

Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research 19: 1722-1731.

2008

McGuire AM, Galagan JE. 2008. Conserved secondary structures in Aspergillus. PLoS One 3:e2812.

Rossignol T, Lechat P, Cuomo C, Zeng Q, Moszer I, d’Enfert C. 2008. CandidaDB: a multi-genome database for Candida species and related Saccharomycotina. Nucleic Acids Research 36: D557-61.

Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. 2008. Mechanisms of intron gain and loss in Cryptococcus. Genome Biology 9: R24.

2007

Cuomo CA, Güldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, Walton JD, Ma LJ, Baker SE, Rep M, Adam G, Antoniw J, Baldwin T, Calvo S, Chang YL, Decaprio D, Gale LR, Gnerre S, Goswami RS, Hammond-Kosack K, Harris LJ, Hilburn K, Kennell JC, Kroken S, Magnuson JK, Mannhaupt G, Mauceli E, Mewes HW, Mitterbauer R, Muehlbauer G, Münsterkötter M, Nelson D, O'donnell K, Ouellet T, Qi W, Quesneville H, Roncero MI, Seong KY, Tetko IV, Urban M, Waalwijk C, Ward TJ, Yao J, Birren BW, Kistler HC. 2007. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317: 1400-2.

Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Baştürkmen M, Altamirano L, Xu J. 2007. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Advances in Genetics 57: 49-96.

Hane JK, Lowe RG, Solomon PS, Tan KC, Schoch CL, Spatafora JW, Crous PW, Kodira C, Birren BW, Galagan JE, Torriani SF, McDonald BA, Oliver RP. Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. Plant Cell 19:3347-3368.

Neafsey DE and Galagan JE. Dual modes of natural selection on upstream open reading frames. Molecular Biology and Evolution 24: 1744-1751.

Paper JM, Scott-Craig JS, Adhikari N.D, Cuomo CA, Walton, J.D. 2007. Comparative proteomics of extracellular proteins in vitro and in planta from the pathogenic fungus Fusariumgraminearum. Proteomics 7:3717-83.

Van het Hoog M, Rast TJ, Martchenko M, Grindel S, Dignard D, Hogues H, Cuomo C, Berriman M, Scherer S, Magee BB, Whiteway M, Chibana H, Nantel A, Magee PT. 2007. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biology 8: R52.

2006

Kamper J, Kahmann R., Bolker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Muller O, Perlin MH, Wosten HA, de Vries R, Ruiz-Herrera J,Reynaga-Pena CG, Snetselaar K , McCann M, Perez-Martin J, Feldbrugge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P,Farman M, Stajich JE, Sentandreu R, Gonzalez-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Munch K, Rossel N, Scherer M, Vranes M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho EC, Cahill MJ, Boyce KJ, Klose J, KlostermanSJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Hauser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schluter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Guldener U, Munsterkotter M, Haase D, Oesterheld M, Mewes HW, Mauceli EW, DeCaprio D,Wade CM, Butler J,Young S, Jaffe DB, Calvo, S, Nusbaum C, Galagan, J, Birren BW. 2006. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444(7115): 97-101.

2005

Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu JR, Pan H, Read ND, Lee YH, Carbone I, Brown D, Oh YY, Donofrio N, Jeong JS, Soanes DM, Djonovic S, Kolomiets E, Rehmeyer C, Li W, Harding M, Kim S, Lebrun MH, Bohnert H, Coughlan S, Butler J, Calvo S, Ma LJ, Nicol R, Purcell S, Nusbaum C, Galagan JE, Birren BW. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434: 980-986.

Galagan JE, Calvo SE, Cuomo C, Ma L, Wortman J, Batzoglou S, Lee S, Brudno M, Basturkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW. 2005. Sequencing and Comparative Analysis of Aspergillus nidulans. Nature 438: 1105-1115.

Galagan JE, Henn MR, Ma LJ, Cuomo CA, and Birren, B. 2005. Genomics of the fungal kingdom: Insights into eukaryotic biology. Genome Research 15: 1620-1631.

2004

Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D,Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R. 2004. Lessons from the genome sequence of Neurospora crassa: tracing thepath from genomic blueprint to multicellular organism. Microbiology and Molecular Biology Reviews 68: 1-108.

Galagan JE and Selker EU. 2004. RIP: the evolutionary cost of genome defense. Trends in Genetics 20: 417-423.

Nielsen CB, Friedman B, Birren B, Burge CB, Galagan JE. 2004. Patterns of intron gain and loss in fungi. PLoS Biology 2:e422.

2003

Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA,Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M,Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.

Kellis M, Birren BW, Lander ES. 2003. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.

Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.