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James E Galagan, Ph.D.

TitleVisiting Scientist
InstitutionHarvard School of Public Health
DepartmentImmunology and Infectious Diseases
AddressHarvard School of Public Health
Bldg 1-704
665 Huntington Ave
Boston MA 02115

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Gomes AL, Galagan JE, Segrè D. Resource competition may lead to effective treatment of antibiotic resistant infections. PLoS One. 2013; 8(12):e80775.
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  2. Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013 Oct; 45(10):1183-9.
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  3. Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, Birren B, Galagan J, Feldman MW. The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations. PLoS Pathog. 2013 Aug; 9(8):e1003543.
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  4. Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM. PLoS Comput Biol. 2013 Jul; 9(7):e1003126.
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  5. Galagan JE, Minch K, Peterson M, Lyubetskaya A, Azizi E, Sweet L, Gomes A, Rustad T, Dolganov G, Glotova I, Abeel T, Mahwinney C, Kennedy AD, Allard R, Brabant W, Krueger A, Jaini S, Honda B, Yu WH, Hickey MJ, Zucker J, Garay C, Weiner B, Sisk P, Stolte C, Winkler JK, Van de Peer Y, Iazzetti P, Camacho D, Dreyfuss J, Liu Y, Dorhoi A, Mollenkopf HJ, Drogaris P, Lamontagne J, Zhou Y, Piquenot J, Park ST, Raman S, Kaufmann SH, Mohney RP, Chelsky D, Moody DB, Sherman DR, Schoolnik GK. The Mycobacterium tuberculosis regulatory network and hypoxia. Nature. 2013 Jul 11; 499(7457):178-83.
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  6. Galagan J, Lyubetskaya A, Gomes A. ChIP-Seq and the Complexity of Bacterial Transcriptional Regulation. Curr Top Microbiol Immunol. 2013; 363:43-68.
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  7. Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF. How accurate can genetic predictions be? BMC Genomics. 2012; 13:340.
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  8. Brandes A, Lun DS, Ip K, Zucker J, Colijn C, Weiner B, Galagan JE. Inferring carbon sources from gene expression profiles using metabolic flux models. PLoS One. 2012; 7(5):e36947.
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  9. McGuire AM, Weiner B, Park ST, Wapinski I, Raman S, Dolganov G, Peterson M, Riley R, Zucker J, Abeel T, White J, Sisk P, Stolte C, Koehrsen M, Yamamoto RT, Iacobelli-Martinez M, Kidd MJ, Maer AM, Schoolnik GK, Regev A, Galagan J. Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. BMC Genomics. 2012; 13:120.
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  10. Weiner B, Gomez J, Victor TC, Warren RM, Sloutsky A, Plikaytis BB, Posey JE, van Helden PD, Gey van Pittius NC, Koehrsen M, Sisk P, Stolte C, White J, Gagneux S, Birren B, Hung D, Murray M, Galagan J. Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region. PLoS One. 2012; 7(2):e26038.
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  11. Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet. 2012 Jan; 44(1):106-10.
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  12. Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y. GenomeView: a next-generation genome browser. Nucleic Acids Res. 2012 Jan; 40(2):e12.
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  13. 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. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog. 2011 Jul; 7(7):e1002137.
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  14. Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, Flynn JL, Fortune SM. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet. 2011 May; 43(5):482-6.
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  15. Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C, Schoolnik G, Katze MG. A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm. MBio. 2011; 2(1):e00325-10.
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  16. 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 BF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio. 2011; 2(1):e00342-10.
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  17. Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, Kremer K, Ernst JD, Gagneux S. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet. 2010 Jun; 42(6):498-503.
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  18. Galagan JE, Sisk P, Stolte C, Weiner B, Koehrsen M, Wymore F, Reddy TB, Zucker JD, Engels R, Gellesch M, Hubble J, Jin H, Larson L, Mao M, Nitzberg M, White J, Zachariah ZK, Sherlock G, Ball CA, Schoolnik GK. TB database 2010: overview and update. Tuberculosis (Edinb). 2010 Jul; 90(4):225-35.
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  19. 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, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, 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. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010 Mar 18; 464(7287):367-73.
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  20. Lun DS, Sherrid A, Weiner B, Sherman DR, Galagan JE. A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data. Genome Biol. 2009; 10(12):R142.
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  21. Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol. 2009 Aug; 5(8):e1000489.
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  22. Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM. Large-scale identification of genetic design strategies using local search. Mol Syst Biol. 2009; 5:296.
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  23. 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. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet. 2009 Jul; 5(7):e1000549.
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  24. Weinberger DM, Trzcinski K, Lu YJ, Bogaert D, Brandes A, Galagan J, Anderson PW, Malley R, Lipsitch M. Pneumococcal capsular polysaccharide structure predicts serotype prevalence. PLoS Pathog. 2009 Jun; 5(6):e1000476.
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  25. Champion MD, Zeng Q, Nix EB, Nano FE, Keim P, Kodira CD, Borowsky M, Young S, Koehrsen M, Engels R, Pearson M, Howarth C, Larson L, White J, Alvarado L, Forsman M, Bearden SW, Sjöstedt A, Titball R, Michell SL, Birren B, Galagan J. Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies. PLoS Pathog. 2009 May; 5(5):e1000459.
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  26. Hood HM, Neafsey DE, Galagan J, Sachs MS. Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annu Rev Microbiol. 2009; 63:385-409.
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  27. Kuntzen T, Timm J, Berical A, Lennon N, Berlin AM, Young SK, Lee B, Heckerman D, Carlson J, Reyor LL, Kleyman M, McMahon CM, Birch C, Schulze Zur Wiesch J, Ledlie T, Koehrsen M, Kodira C, Roberts AD, Lauer GM, Rosen HR, Bihl F, Cerny A, Spengler U, Liu Z, Kim AY, Xing Y, Schneidewind A, Madey MA, Fleckenstein JF, Park VM, Galagan JE, Nusbaum C, Walker BD, Lake-Bakaar GV, Daar ES, Jacobson IM, Gomperts ED, Edlin BR, Donfield SM, Chung RT, Talal AH, Marion T, Birren BW, Henn MR, Allen TM. Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients. Hepatology. 2008 Dec; 48(6):1769-78.
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  28. Lambreghts R, Shi M, Belden WJ, Decaprio D, Park D, Henn MR, Galagan JE, Bastürkmen M, Birren BW, Sachs MS, Dunlap JC, Loros JJ. A high-density single nucleotide polymorphism map for Neurospora crassa. Genetics. 2009 Feb; 181(2):767-81.
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  29. Orsi RH, Borowsky ML, Lauer P, Young SK, Nusbaum C, Galagan JE, Birren BW, Ivy RA, Sun Q, Graves LM, Swaminathan B, Wiedmann M. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics. 2008; 9:539.
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  30. Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 2009 Jan; 37(Database issue):D499-508.
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  31. McGuire AM, Galagan JE. Conserved secondary structures in Aspergillus. PLoS One. 2008; 3(7):e2812.
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  32. McGuire AM, Pearson MD, Neafsey DE, Galagan JE. Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 2008; 9(3):R50.
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  33. Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, Koehrsen M, Rokas A, Yandava CN, Engels R, Zeng E, Olavarietta R, Doud M, Smith RS, Montgomery P, White JR, Godfrey PA, Kodira C, Birren B, Galagan JE, Lory S. Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci U S A. 2008 Feb 26; 105(8):3100-5.
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  34. Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 2008; 9(1):R24.
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  35. 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. 2007 Nov; 19(11):3347-68.
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  36. DeCaprio D, Vinson JP, Pearson MD, Montgomery P, Doherty M, Galagan JE. Conrad: gene prediction using conditional random fields. Genome Res. 2007 Sep; 17(9):1389-98.
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  37. Neafsey DE, Galagan JE. Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol. 2007; 7:119.
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  38. 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):1718-23.
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  39. Neafsey DE, Galagan JE. Dual modes of natural selection on upstream open reading frames. Mol Biol Evol. 2007 Aug; 24(8):1744-51.
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  40. 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, Bastürkmen M, Altamirano L, Xu J. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Adv Genet. 2007; 57:49-96.
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  41. Volkman SK, Sabeti PC, DeCaprio D, Neafsey DE, Schaffner SF, Milner DA, Daily JP, Sarr O, Ndiaye D, Ndir O, Mboup S, Duraisingh MT, Lukens A, Derr A, Stange-Thomann N, Waggoner S, Onofrio R, Ziaugra L, Mauceli E, Gnerre S, Jaffe DB, Zainoun J, Wiegand RC, Birren BW, Hartl DL, Galagan JE, Lander ES, Wirth DF. A genome-wide map of diversity in Plasmodium falciparum. Nat Genet. 2007 Jan; 39(1):113-9.
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  42. Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Müller O, Perlin MH, Wösten HA, de Vries R, Ruiz-Herrera J, Reynaga-Peña CG, Snetselaar K, McCann M, Pérez-Martín J, Feldbrügge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, González-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Münch K, Rössel N, Scherer M, Vranes M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho EC, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Häuser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schlüter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Güldener U, Münsterkötter 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. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature. 2006 Nov 2; 444(7115):97-101.
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  43. Engels R, Yu T, Burge C, Mesirov JP, DeCaprio D, Galagan JE. Combo: a whole genome comparative browser. Bioinformatics. 2006 Jul 15; 22(14):1782-3.
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  44. Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, García JL, García MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jiménez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafon A, Lafton A, Latgé JP, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O'Neil S, Paulsen I, Peñalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, Rodriguez de Córdoba S, Rodríguez-Peña JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sánchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez de Aldana CR, Weidman J, White O, Woodward J, Yu JH, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 2005 Dec 22; 438(7071):1151-6.
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  45. Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kobayashi T, Takeuchi M, Denning DW, Galagan JE, Nierman WC, Yu J, Archer DB, Bennett JW, Bhatnagar D, Cleveland TE, Fedorova ND, Gotoh O, Horikawa H, Hosoyama A, Ichinomiya M, Igarashi R, Iwashita K, Juvvadi PR, Kato M, Kato Y, Kin T, Kokubun A, Maeda H, Maeyama N, Maruyama J, Nagasaki H, Nakajima T, Oda K, Okada K, Paulsen I, Sakamoto K, Sawano T, Takahashi M, Takase K, Terabayashi Y, Wortman JR, Yamada O, Yamagata Y, Anazawa H, Hata Y, Koide Y, Komori T, Koyama Y, Minetoki T, Suharnan S, Tanaka A, Isono K, Kuhara S, Ogasawara N, Kikuchi H. Genome sequencing and analysis of Aspergillus oryzae. Nature. 2005 Dec 22; 438(7071):1157-61.
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  46. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Bastürkmen 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. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature. 2005 Dec 22; 438(7071):1105-15.
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  47. Galagan JE, Henn MR, Ma LJ, Cuomo CA, Birren B. Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Res. 2005 Dec; 15(12):1620-31.
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  48. Vinson JP, Jaffe DB, O'Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, Nusbaum C, Birren B, Galagan JE, Lander ES. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res. 2005 Aug; 15(8):1127-35.
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  49. 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. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature. 2005 Apr 21; 434(7036):980-6.
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  50. Nielsen CB, Friedman B, Birren B, Burge CB, Galagan JE. Patterns of intron gain and loss in fungi. PLoS Biol. 2004 Dec; 2(12):e422.
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  51. Mikkelsen TS, Galagan JE, Mesirov JP. Improving genome annotations using phylogenetic profile anomaly detection. Bioinformatics. 2005 Feb 15; 21(4):464-70.
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  52. Galagan JE, Selker EU. RIP: the evolutionary cost of genome defense. Trends Genet. 2004 Sep; 20(9):417-23.
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  53. 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. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev. 2004 Mar; 68(1):1-108.
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  54. 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. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 2003 Apr 24; 422(6934):859-68.
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  55. Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry JG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 2002 Apr; 12(4):532-42.
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