Keywords
Last Name

James E. Galagan, PhD

TitleAssociate Professor
InstitutionBoston University College of Engineering
DepartmentBiomedical Engineering
Address24 Cummington St
Boston MA 02215
Phone(617) 358-0695
ORCID ORCID Icon0000-0003-0542-3291
Other Positions
TitleAssociate Professor
InstitutionBoston University School of Medicine
DepartmentMicrobiology

TitleAssociate Director, Systems Biology
InstitutionBoston University School of Medicine
DepartmentNational Emerging Infectious Disease Lab

TitleAssociate Director of Microbial Genome Analysis
InstitutionBroad Institute

 Research Expertise & Professional Interests
Dr. Galagan’s research is focused on Systems Biology of microbial organisms, specficially Mycobacterium tuberculosis – the causative agent of tuberculosis – and the fungus Neurospora crassa. The Galagan Lab is an interdisciplinary group that combines computational biology, genomics, and experimental lab work. Specific interests and projects include:

• Using a genomics, computational modeling, and experimental systems-identification techniques to reconstruct the gene regulatory network of M. tuberculosis.
• Developing and experimentally validating computational models of microbial metabolism for M. tuberculosis and N. crassa.
• Using high-throughput sequencing and comparative sequence analysis to study the functional evolution of M. tuberculosis.
• Developing computational methods for genomic data analysis (including gene prediction, gene expression analysis, and polymorphism discovery)
• Developing experimental methods for microbial systems identification and analysis, drawing on electrical and mechanical systems identification methods

 Self-Described Keywords
  • Computational Biology
  • Genomics
  • Infectious Diseases
  • Microbiology
  • Systems Biology
  • Tuberculosis
 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.
List All   |   Timeline
  1. Aquino P, Honda B, Jaini S, Lyubetskaya A, Hosur K, Chiu JG, Ekladious I, Hu D, Jin L, Sayeg MK, Stettner AI, Wang J, Wong BG, Wong WS, Alexander SL, Ba C, Bensussen SI, Bernstein DB, Braff D, Cha S, Cheng DI, Cho JH, Chou K, Chuang J, Gastler DE, Grasso DJ, Greifenberger JS, Guo C, Hawes AK, Israni DV, Jain SR, Kim J, Lei J, Li H, Li D, Li Q, Mancuso CP, Mao N, Masud SF, Meisel CL, Mi J, Nykyforchyn CS, Park M, Peterson HM, Ramirez AK, Reynolds DS, Rim NG, Saffie JC, Su H, Su WR, Su Y, Sun M, Thommes MM, Tu T, Varongchayakul N, Wagner TE, Weinberg BH, Yang R, Yaroslavsky A, Yoon C, Zhao Y, Zollinger AJ, Stringer AM, Foster JW, Wade J, Raman S, Broude N, Wong WW, Galagan JE. Coordinated regulation of acid resistance in Escherichia coli. BMC Syst Biol. 2017 Jan 06; 11(1):1. PMID: 28061857.
    View in: PubMed
  2. Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion. G3 (Bethesda). 2017 Jan 05; 7(1):129-142. PMID: 27856696.
    View in: PubMed
  3. Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med. 2016 Sep 01; 194(5):621-30. PMID: 26910495.
    View in: PubMed
  4. Sharp JD, Singh AK, Park ST, Lyubetskaya A, Peterson MW, Gomes AL, Potluri LP, Raman S, Galagan JE, Husson RN. Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses. PLoS One. 2016; 11(3):e0152145. PMID: 27003599.
    View in: PubMed
  5. Krueger AS, Munck C, Dantas G, Church GM, Galagan J, Lehár J, Sommer MO. Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis. PLoS One. 2016; 11(1):e0147651. PMID: 26821252.
    View in: PubMed
  6. Garay CD, Dreyfuss JM, Galagan JE. Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis. BMC Syst Biol. 2015; 9:57. PMID: 26377923.
    View in: PubMed
  7. Ranganathan S, Bai G, Lyubetskaya A, Knapp GS, Peterson MW, Gazdik M, C Gomes AL, Galagan JE, McDonough KA. Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon. Nucleic Acids Res. 2016 Jan 8; 44(1):134-51. PMID: 26358810.
    View in: PubMed
  8. Knapp GS, Lyubetskaya A, Peterson MW, Gomes AL, Ma Z, Galagan JE, McDonough KA. Role of intragenic binding of cAMP responsive protein (CRP) in regulation of the succinate dehydrogenase genes Rv0249c-Rv0247c in TB complex mycobacteria. Nucleic Acids Res. 2015 Jun 23; 43(11):5377-93. PMID: 25940627.
    View in: PubMed
  9. Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, Hickey M, Brabant W, Morrison B, Turkarslan S, Mawhinney C, Galagan JE, Price ND, Baliga NS, Sherman DR. The DNA-binding network of Mycobacterium tuberculosis. Nat Commun. 2015; 6:5829. PMID: 25581030.
    View in: PubMed
  10. Hurley JM, Dasgupta A, Emerson JM, Zhou X, Ringelberg CS, Knabe N, Lipzen AM, Lindquist EA, Daum CG, Barry KW, Grigoriev IV, Smith KM, Galagan JE, Bell-Pedersen D, Freitag M, Cheng C, Loros JJ, Dunlap JC. Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proc Natl Acad Sci U S A. 2014 Dec 2; 111(48):16995-7002. PMID: 25362047.
    View in: PubMed
  11. Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS. Genome-wide characterization of light-regulated genes in Neurospora crassa. G3 (Bethesda). 2014 Sep; 4(9):1731-45. PMID: 25053707.
    View in: PubMed
  12. Gomes AL, Abeel T, Peterson M, Azizi E, Lyubetskaya A, Carvalho L, Galagan J. Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction. Genome Res. 2014 Oct; 24(10):1686-97. PMID: 25024162.
    View in: PubMed
  13. Jaini S, Lyubetskaya A, Gomes A, Peterson M, Park ST, Raman S, Schoolnik G, Galagan J. Transcription Factor Binding Site Mapping Using ChIP-Seq. Microbiol Spectr. 2014 Apr; 2(2). PMID: 26105820.
    View in: PubMed
  14. Galagan JE. Genomic insights into tuberculosis. Nat Rev Genet. 2014 May; 15(5):307-20. PMID: 24662221.
    View in: PubMed
  15. Gomes AL, Galagan JE, Segrè D. Resource competition may lead to effective treatment of antibiotic resistant infections. PLoS One. 2013; 8(12):e80775. PMID: 24349015.
    View in: PubMed
  16. 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. PMID: 23995135.
    View in: PubMed
  17. Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, 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. PMID: 23966858.
    View in: PubMed
  18. 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; 9(7):e1003126. PMID: 23935467.
    View in: PubMed
  19. 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. PMID: 23823726.
    View in: PubMed
  20. Galagan J, Lyubetskaya A, Gomes A. ChIP-Seq and the complexity of bacterial transcriptional regulation. Curr Top Microbiol Immunol. 2013; 363:43-68. PMID: 22983621.
    View in: PubMed
  21. Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF. How accurate can genetic predictions be? BMC Genomics. 2012; 13:340. PMID: 22827772.
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  22. 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. PMID: 22606312.
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  23. 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. PMID: 22452820.
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  24. 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. PMID: 22347359.
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  25. 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. PMID: 22179134.
    View in: PubMed
  26. 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. PMID: 22102585.
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  27. 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. PMID: 21829347.
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  28. 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. PMID: 21516081.
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  29. 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. PMID: 21285433.
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  30. 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. PMID: 21304167.
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  31. 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. PMID: 20495566.
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  32. 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. PMID: 20488753.
    View in: PubMed
  33. 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. PMID: 20237561.
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  34. 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. PMID: 20028542.
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  35. 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. PMID: 19714220.
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  36. 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. PMID: 19690565.
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  37. 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. PMID: 19578406.
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  38. 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. PMID: 19521509.
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  39. 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. PMID: 19478886.
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  40. 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. PMID: 19514854.
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  41. 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. PMID: 19026009.
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  42. 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. PMID: 19015548.
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  43. 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. PMID: 19014550.
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  44. 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. PMID: 18835847.
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  45. McGuire AM, Galagan JE. Conserved secondary structures in Aspergillus. PLoS One. 2008; 3(7):e2812. PMID: 18665251.
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  46. McGuire AM, Pearson MD, Neafsey DE, Galagan JE. Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 2008; 9(3):R50. PMID: 18321378.
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  47. 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. PMID: 18287045.
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  48. Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 2008; 9(1):R24. PMID: 18234113.
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  49. 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. PMID: 18024570.
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  50. 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. PMID: 17690204.
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  51. Neafsey DE, Galagan JE. Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol. 2007; 7:119. PMID: 17640368.
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  52. 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. PMID: 17510324.
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  53. Neafsey DE, Galagan JE. Dual modes of natural selection on upstream open reading frames. Mol Biol Evol. 2007 Aug; 24(8):1744-51. PMID: 17494029.
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  54. 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. PMID: 17352902.
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  55. 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. PMID: 17159979.
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  56. 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. PMID: 17080091.
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  57. 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. PMID: 16709588.
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