Publications
Wu, X., Cao B., Aquino P., Chiu T. P., Chen C., Jiang S., Deng Z., Chen S., Rohs R., Wang L., Galagan J. E., Dedon P. C. (2020) Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. Proceedings of the National Academy of Sciences of the United States of America.117(25):14322-30 PMCID:PMC7322087 https://www.ncbi.nlm.nih.gov/pubmed/32518115
Nguyen, T. T., Chern M., Baer R. C., Galagan J., Dennis A. M. (2020) A Forster Resonance Energy Transfer-Based Ratiometric Sensor with the Allosteric Transcription Factor TetR. Small.16(17):e1907522 PMCID:PMC7359203 https://www.ncbi.nlm.nih.gov/pubmed/32249506
Mejia-Almonte, C., Busby S. J. W., Wade J. T., van Helden J., Arkin A. P., Stormo G. D., Eilbeck K., Palsson B. O., Galagan J. E., Collado-Vides J. (2020) Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet https://www.ncbi.nlm.nih.gov/pubmed/32665585
Grazon, C.*, Baer R. C.*, Kuzmanovic U., Nguyen T., Chen M., Zamani M., Chern M., Aquino P., Zhang X., Lecommandoux S., Fan A., Cabodi M., Klapperich C., Grinstaff M. W., Dennis A. M., Galagan J. E. (2020) A progesterone biosensor derived from microbial screening. Nature communications.11(1):1276 PMCID:PMC7062782 https://www.ncbi.nlm.nih.gov/pubmed/32152281 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7062782/pdf/41467_2020_Article_14942.pdf
Chen, M., Nguyen T. T., Varongchayakul N., Grazon C., Chern M., Baer R. C., Lecommandoux S., Klapperich C. M.*, Galagan J. E.*, Dennis A. M.*, Grinstaff M. W.* (2020) Surface Immobilized Nucleic Acid-Transcription Factor Quantum Dots for Biosensing. Adv Healthc Mater:e2000403 https://www.ncbi.nlm.nih.gov/pubmed/32691962
Chen, Mingfu, Grazon Chloé, Sensharma Prerana, Nguyen Thuy, Feng Yunpeng, Chern Margaret, Baer R, Varongchayakul Nitinun, Cook Katherine, Lecommandoux Sebastian, Klapperich Catherine*, Galagan James*, Dennis Allison*, Grinstaff Mark*. (2020) Hydrogel embedded quantum dot-transcription factor sensor for quantitative progesterone detection. ACS Applied Materials & Interfaces
Santos-Zavaleta, A., Salgado H., Gama-Castro S., Sanchez-Perez M., Gomez-Romero L., Ledezma-Tejeida D., Garcia-Sotelo J. S., Alquicira-Hernandez K., Muniz-Rascado L. J., Pena-Loredo P., Ishida-Gutierrez C., Velazquez-Ramirez D. A., Del Moral-Chavez V., Bonavides-Martinez C., Mendez-Cruz C. F., Galagan J., Collado-Vides J. (2019) RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. Nucleic Acids Res.47(D1):D212-D20 PMCID:PMC6324031 https://www.ncbi.nlm.nih.gov/pubmed/30395280
Manson, A. L., Abeel T., Galagan J., Sundaramurthi J. C., Shanmugam S. K., Palaniyandi K., Narayanan S., Swaminathan S., Earl A. M. (2018) Reply to Lee and Howden. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.66(1):160-1 https://www.ncbi.nlm.nih.gov/pubmed/29040415
Grazon, C., Nguyen T., Baer R.C., Kuzmanovic U., Chern M., Chen M., Zamani M., Fan A., Zhang X., Lecommandoux S., Klapperich C., Dennis A. M., Grinstaff M., Galagan J. Fluorescent nanoparticle sensor for hormones based on a native microbial transcription factor. Gordon Research Conference - Bioanalytical Sensors (2018).
Manson, A. L., Cohen K. A., Abeel T., Desjardins C. A., Armstrong D. T., Barry C. E., 3rd, Brand J., Consortium T. BResist Global Genome, Chapman S. B., Cho S. N., Gabrielian A., Gomez J., Jodals A. M., Joloba M., Jureen P., Lee J. S., Malinga L., Maiga M., Nordenberg D., Noroc E., Romancenco E., Salazar A., Ssengooba W., Velayati A. A., Winglee K., Zalutskaya A., Via L. E., Cassell G. H., Dorman S. E., Ellner J., Farnia P., Galagan J. E., Rosenthal A., Crudu V., Homorodean D., Hsueh P. R., Narayanan S., Pym A. S., Skrahina A., Swaminathan S., Van der Walt M., Alland D., Bishai W. R., Cohen T., Hoffner S., Birren B. W., Earl A. M. (2017) Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nature genetics.49(3):395-402 https://www.ncbi.nlm.nih.gov/pubmed/28092681
Manson, A. L., Abeel T., Galagan J. E., Sundaramurthi J. C., Salazar A., Gehrmann T., Shanmugam S. K., Palaniyandi K., Narayanan S., Swaminathan S., Earl A. M. (2017) Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.64(11):1494-501 PMCID:PMC5434337 http://www.ncbi.nlm.nih.gov/pubmed/28498943
Dekhang, R., Wu C., Smith K. M., Lamb T. M., Peterson M., Bredeweg E. L., Ibarra O., Emerson J. M., Karunarathna N., Lyubetskaya A., Azizi E., Hurley J. M., Dunlap J. C., Galagan J. E., Freitag M., Sachs M. S., Bell-Pedersen D. (2017) The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion. G3 (Bethesda).7(1):129-42 PMCID:PMC5217103 https://www.ncbi.nlm.nih.gov/pubmed/27856696
Aquino, P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu J. G., Ekladious I., Hu D., Jin L., Sayeg M. K., Stettner A. I., Wang J., Wong B. G., Wong W. S., Alexander S. L., Ba C., Bensussen S. I., Bernstein D. B., Braff D., Cha S., Cheng D. I., Cho J. H., Chou K., Chuang J., Gastler D. E., Grasso D. J., Greifenberger J. S., Guo C., Hawes A. K., Israni D. V., Jain S. R., Kim J., Lei J., Li H., Li D., Li Q., Mancuso C. P., Mao N., Masud S. F., Meisel C. L., Mi J., Nykyforchyn C. S., Park M., Peterson H. M., Ramirez A. K., Reynolds D. S., Rim N. G., Saffie J. C., Su H., Su W. R., Su Y., Sun M., Thommes M. M., Tu T., Varongchayakul N., Wagner T. E., Weinberg B. H., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger A. J., Stringer A. M., Foster J. W., Wade J., Raman S., Broude N., Wong W. W., Galagan J. E. (2017) Coordinated regulation of acid resistance in Escherichia coli. BMC Syst Biol.11(1):1 PMCID:PMC5217608 https://www.ncbi.nlm.nih.gov/pubmed/28061857 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217608/pdf/12918_2016_Article_376.pdf
Sharp, J. D., Singh A. K., Park S. T., Lyubetskaya A., Peterson M. W., Gomes A. L., Potluri L. P., Raman S., Galagan J. E., Husson R. N. (2016) Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses. PloS one.11(3):e0152145 PMCID:PMC4803200 https://www.ncbi.nlm.nih.gov/pubmed/27003599
Ranganathan, S., Bai G., Lyubetskaya A., Knapp G. S., Peterson M. W., Gazdik M., AL C. Gomes, Galagan J. E., McDonough K. A. (2016) Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon. Nucleic Acids Res.44(1):134-51 PMCID:PMC4705688 https://www.ncbi.nlm.nih.gov/pubmed/26358810
Farhat, M. R., Sultana R., Iartchouk O., Bozeman S., Galagan J., Sisk P., Stolte C., Nebenzahl-Guimaraes H., Jacobson K., Sloutsky A., Kaur D., Posey J., Kreiswirth B. N., Kurepina N., Rigouts L., Streicher E. M., Victor T. C., Warren R. M., van Soolingen D., Murray M. (2016) Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. American journal of respiratory and critical care medicine.194(5):621-30 PMCID:PMC5027209 https://www.ncbi.nlm.nih.gov/pubmed/26910495
Ranganathan, S., Bai G., Lyubetskaya A., Knapp G. S., Peterson M. W., Gazdik M., Gomes A. L., Galagan J. E., McDonough K. A. (2015) Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon. Nucleic Acids Res http://www.ncbi.nlm.nih.gov/pubmed/26358810
Minch, K. J., Rustad T. R., Peterson E. J., Winkler J., Reiss D. J., Ma S., Hickey M., Brabant W., Morrison B., Turkarslan S., Mawhinney C., Galagan J. E., Price N. D., Baliga N. S., Sherman D. R. (2015) The DNA-binding network of Mycobacterium tuberculosis. Nature communications.6:5829 PMCID:4301838 http://www.ncbi.nlm.nih.gov/pubmed/25581030
Knapp, G. S., Lyubetskaya A., Peterson M. W., Gomes A. L., Ma Z., Galagan J. E., McDonough K. A. (2015) 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.43(11):5377-93 PMCID:PMC4477654 http://www.ncbi.nlm.nih.gov/pubmed/25940627
Garay, C. D., Dreyfuss J. M., Galagan J. E. (2015) Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis. BMC Syst Biol.9:57 PMCID:PMC4574064 http://www.ncbi.nlm.nih.gov/pubmed/26377923
Wu, C., Yang F., Smith K. M., Peterson M., Dekhang R., Zhang Y., Zucker J., Bredeweg E. L., Mallappa C., Zhou X., Lyubetskaya A., Townsend J. P., Galagan J. E., Freitag M., Dunlap J. C., Bell-Pedersen D., Sachs M. S. (2014) Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa. G3 (Bethesda).4(9):1731-45 PMCID:4169166 http://www.ncbi.nlm.nih.gov/pubmed/25053707
Jaini, S, Lyubetskaya A., Gomes A, Peterson M, Park S. T., Raman S, Schoolnik G., Galagan J.E. Transcription Factor Binding Site Mapping Using ChIP-Seq. In: Hatfull G, Jacobs WR, Jr., editors. Molecular Genetics of Mycobacteria, 2nd Edition: ASM Press; (2014). https://www.wiley.com/en-us/Molecular+Genetics+of+Mycobacteria%2C+2nd+Edition-p-9781555818838
Hurley, J. M., Dasgupta A., Emerson J. M., Zhou X., Ringelberg C. S., Knabe N., Lipzen A. M., Lindquist E. A., Daum C. G., Barry K. W., Grigoriev I. V., Smith K. M., Galagan J. E., Bell-Pedersen D., Freitag M., Cheng C., Loros J. J., Dunlap J. C. (2014) Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proceedings of the National Academy of Sciences of the United States of America.111(48):16995-7002 PMCID:4260557 http://www.ncbi.nlm.nih.gov/pubmed/25362047 http://www.pnas.org/content/111/48/16995.full.pdf
Gomes, A. L., Abeel T., Peterson M., Azizi E., Lyubetskaya A., Carvalho L., Galagan J. (2014) Decoding ChIP-Seq peaks with a double-binding signal refines binding peaks to single-nucleotide and predicts cooperative interaction. Genome research http://www.ncbi.nlm.nih.gov/pubmed/25024162 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199365/pdf/1686.pdf
Galagan, JE. (2014) Genomic Insights into Tuberculosis. Nature Reviews Genetics https://www.nature.com/articles/nrg3664
Azizi, E., Airoldi E.M., Galagan J.E. (2014). Learning Modular Structure from Network Data and Node Variables (Winner: Best Student Paper Award). Proceedings of the New England Statistics Symposium.
Azizi, E., Airoldi E.M., Galagan J.E. (2014). Learning Modular Structures from Network Data and Node Variables. Proceedings of the 31st International Conference on Machine Learning (ICML).
Pepperell, C. S., Casto A. M., Kitchen A., Granka J. M., Cornejo O. E., Holmes E. C., Birren B., Galagan J., Feldman M. W. (2013) The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS pathogens.9(8):e1003543 PMCID:3744410 http://www.ncbi.nlm.nih.gov/pubmed/23966858
Gomes, A. L., Galagan J. E., Segre D. (2013) Resource competition may lead to effective treatment of antibiotic resistant infections. PloS one.8(12):e80775 PMCID:3862480 http://www.ncbi.nlm.nih.gov/pubmed/24349015
Galagan, J. E., Minch K., Peterson M., Lyubetskaya A., Azizi E., Sweet L., Gomes A., Rustad T., Dolganov G., Glotova I., Abeel T., Mahwinney C., Kennedy A. D., Allard R., Brabant W., Krueger A., Jaini S., Honda B., Yu W. H., Hickey M. J., Zucker J., Garay C., Weiner B., Sisk P., Stolte C., Winkler J. K., Van de Peer Y., Iazzetti P., Camacho D., Dreyfuss J., Liu Y., Dorhoi A., Mollenkopf H. J., Drogaris P., Lamontagne J., Zhou Y., Piquenot J., Park S. T., Raman S., Kaufmann S. H., Mohney R. P., Chelsky D., Moody D. B., Sherman D. R., Schoolnik G. K. (2013) The Mycobacterium tuberculosis regulatory network and hypoxia. Nature.499(7457):178-83 PMCID:Pending http://www.ncbi.nlm.nih.gov/pubmed/23823726 http://www.nature.com/nature/journal/v499/n7457/pdf/nature12337.pdf
Galagan, J., Lyubetskaya A., Gomes A. ChIP-Seq and the complexity of bacterial transcriptional regulation. Current topics in microbiology and immunology. 2012/09/18 ed2013. p. 43-68. https://pubmed.ncbi.nlm.nih.gov/22983621/
Farhat, M. R., Shapiro B. J., Kieser K. J., Sultana R., Jacobson K. R., Victor T. C., Warren R. M., Streicher E. M., Calver A., Sloutsky A., Kaur D., Posey J. E., Plikaytis B., Oggioni M. R., Gardy J. L., Johnston J. C., Rodrigues M., Tang P. K., Kato-Maeda M., Borowsky M. L., Muddukrishna B., Kreiswirth B. N., Kurepina N., Galagan J., Gagneux S., Birren B., Rubin E. J., Lander E. S., Sabeti P. C., Murray M. (2013) Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nature genetics.45(10):1183-9 PMCID:3887553 http://www.ncbi.nlm.nih.gov/pubmed/23995135
Dreyfuss, J. M., Zucker J. D., Hood H. M., Ocasio L. R., Sachs M. S., Galagan J. E. (2013) Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS computational biology.9(7):e1003126 PMCID:3730674 http://www.ncbi.nlm.nih.gov/pubmed/23935467
Weiner, B., Gomez J., Victor T. C., Warren R. M., Sloutsky A., Plikaytis B. B., Posey J. E., van Helden P. D., Gey van Pittius N. C., Koehrsen M., Sisk P., Stolte C., White J., Gagneux S., Birren B., Hung D., Murray M., Galagan J. (2012) Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region. PloS one.7(2):e26038 PMCID:3274525 http://www.ncbi.nlm.nih.gov/pubmed/22347359
McGuire, A. M., Weiner B., Park S. T., Wapinski I., Raman S., Dolganov G., Peterson M., Riley R., Zucker J., Abeel T., White J., Sisk P., Stolte C., Koehrsen M., Yamamoto R. T., Iacobelli-Martinez M., Kidd M. J., Maer A. M., Schoolnik G. K., Regev A., Galagan J. (2012) Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. BMC Genomics.13(1):120 PMCID:3388012 http://www.ncbi.nlm.nih.gov/pubmed/22452820 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3388012/pdf/1471-2164-13-120.pdf
Dreyfuss, J. M., Levner D., Galagan J. E., Church G. M., Ramoni M. F. (2012) How accurate can genetic predictions be?. BMC Genomics.13(1):340 PMCID:3534619 http://www.ncbi.nlm.nih.gov/pubmed/22827772
Comas, I., Borrell S., Roetzer A., Rose G., Malla B., Kato-Maeda M., Galagan J., Niemann S., Gagneux S. (2012) Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nature genetics.44(1):106-10 PMCID:3246538 http://www.ncbi.nlm.nih.gov/pubmed/22179134
Brandes, A., Lun D. S., Ip K., Zucker J., Colijn C., Weiner B., Galagan J. E. (2012) Inferring carbon sources from gene expression profiles using metabolic flux models. PloS one.7(5):e36947 PMCID:3351459 http://www.ncbi.nlm.nih.gov/pubmed/22606312
Abeel, T., Van Parys T., Saeys Y., Galagan J., Van de Peer Y. (2012) GenomeView: a next-generation genome browser. Nucleic Acids Res.40(2):e12 PMCID:3258165 http://www.ncbi.nlm.nih.gov/pubmed/22102585
Klosterman, S. J., Subbarao K. V., Kang S., Veronese P., Gold S. E., Thomma B. P., Chen Z., Henrissat B., Lee Y. H., Park J., Garcia-Pedrajas M. D., Barbara D. J., Anchieta A., de Jonge R., Santhanam P., Maruthachalam K., Atallah Z., Amyotte S. G., Paz Z., Inderbitzin P., Hayes R. J., Heiman D. I., Young S., Zeng Q., Engels R., Galagan J., Cuomo C. A., Dobinson K. F., Ma L. J. (2011) Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS pathogens.7(7):e1002137 PMCID:3145793 http://www.ncbi.nlm.nih.gov/pubmed/21829347
D'Souza, C. A., Kronstad J. W., Taylor G., Warren R., Yuen M., Hu G., Jung W. H., Sham A., Kidd S. E., 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 J. E., Fraser J. A., Meyer W., Carter D., Schein J., Krzywinski M., Kwon-Chung K. J., Varma A., Wang J., Brunham R., Fyfe M., Ouellette B. F., Siddiqui A., Marra M., Jones S., Holt R., Birren B. W., Galagan J. E., Cuomo C. A. (2011) Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. mBio.2(1):e00342-10 PMCID:3037005 http://www.ncbi.nlm.nih.gov/pubmed/21304167
Aderem, A., Adkins J. N., Ansong C., Galagan J., Kaiser S., Korth M. J., Law G. L., McDermott J. G., Proll S. C., Rosenberger C., Schoolnik G., Katze M. G. (2011) A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm. mBio.2(1):e00325-10 PMCID:3034460 http://www.ncbi.nlm.nih.gov/pubmed/21285433
Ma, L. J., van der Does H. C., Borkovich K. A., Coleman J. J., Daboussi M. J., Di Pietro A., Dufresne M., Freitag M., Grabherr M., Henrissat B., Houterman P. M., Kang S., Shim W. B., Woloshuk C., Xie X., Xu J. R., Antoniw J., Baker S. E., Bluhm B. H., Breakspear A., Brown D. W., Butchko R. A., Chapman S., Coulson R., Coutinho P. M., Danchin E. G., Diener A., Gale L. R., Gardiner D. M., Goff S., Hammond-Kosack K. E., Hilburn K., Hua-Van A., Jonkers W., Kazan K., Kodira C. D., Koehrsen M., Kumar L., Lee Y. H., Li L., Manners J. M., Miranda-Saavedra D., Mukherjee M., Park G., Park J., Park S. Y., Proctor R. H., Regev A., Ruiz-Roldan M. C., Sain D., Sakthikumar S., Sykes S., Schwartz D. C., Turgeon B. G., Wapinski I., Yoder O., Young S., Zeng Q., Zhou S., Galagan J., Cuomo C. A., Kistler H. C., Rep M. (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature.464(7287):367-73 PMCID:3048781 http://www.ncbi.nlm.nih.gov/pubmed/20237561
Galagan, J. E., Sisk P., Stolte C., Weiner B., Koehrsen M., Wymore F., Reddy T. B., Zucker J. D., Engels R., Gellesch M., Hubble J., Jin H., Larson L., Mao M., Nitzberg M., White J., Zachariah Z. K., Sherlock G., Ball C. A., Schoolnik G. K. (2010) TB database 2010: overview and update. Tuberculosis (Edinb).90(4):225-35 http://www.ncbi.nlm.nih.gov/pubmed/20488753 http://ac.els-cdn.com/S1472979210000417/1-s2.0-S1472979210000417-main.pdf?_tid=0f970198-9e86-11e4-aed5-00000aab0f26&acdnat=1421526115_334ab12d41a38b7d8a950fa5d56374ec
Comas, I., Chakravartti J., Small P. M., Galagan J., Niemann S., Kremer K., Ernst J. D., Gagneux S. (2010) Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nature genetics.42(6):498-503 PMCID:2883744 http://www.ncbi.nlm.nih.gov/pubmed/20495566
Weinberger, D. M., Trzcinski K., Lu Y. J., Bogaert D., Brandes A., Galagan J., Anderson P. W., Malley R., Lipsitch M. (2009) Pneumococcal capsular polysaccharide structure predicts serotype prevalence. PLoS pathogens.5(6):e1000476 PMCID:2689349 http://www.ncbi.nlm.nih.gov/pubmed/19521509
Reddy, T. B., 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 Z. K., Sherlock G., Galagan J. E., Ball C. A., Schoolnik G. K. (2009) TB database: an integrated platform for tuberculosis research. Nucleic Acids Res.37(Database issue):D499-508 PMCID:2686437 http://www.ncbi.nlm.nih.gov/pubmed/18835847
Ma, L. J., Ibrahim A. S., Skory C., Grabherr M. G., Burger G., Butler M., Elias M., Idnurm A., Lang B. F., Sone T., Abe A., Calvo S. E., Corrochano L. M., Engels R., Fu J., Hansberg W., Kim J. M., Kodira C. D., Koehrsen M. J., Liu B., Miranda-Saavedra D., O'Leary S., Ortiz-Castellanos L., Poulter R., Rodriguez-Romero J., Ruiz-Herrera J., Shen Y. Q., Zeng Q., Galagan J., Birren B. W., Cuomo C. A., Wickes B. L. (2009) Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS genetics.5(7):e1000549 PMCID:2699053 http://www.ncbi.nlm.nih.gov/pubmed/19578406
Lun, D. S., Sherrid A., Weiner B., Sherman D. R., Galagan J. E. (2009) A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data. Genome Biol.10(12):R142 PMCID:2812949 http://www.ncbi.nlm.nih.gov/pubmed/20028542 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812949/pdf/gb-2009-10-12-r142.pdf
Lun, D. S., Rockwell G., Guido N. J., Baym M., Kelner J. A., Berger B., Galagan J. E., Church G. M. (2009) Large-scale identification of genetic design strategies using local search. Molecular systems biology.5:296 PMCID:2736654 http://www.ncbi.nlm.nih.gov/pubmed/19690565
Lambreghts, R., Shi M., Belden W. J., Decaprio D., Park D., Henn M. R., Galagan J. E., Basturkmen M., Birren B. W., Sachs M. S., Dunlap J. C., Loros J. J. (2009) A high-density single nucleotide polymorphism map for Neurospora crassa. Genetics.181(2):767-81 PMCID:2644964 http://www.ncbi.nlm.nih.gov/pubmed/19015548
Hood, H. M., Neafsey D. E., Galagan J., Sachs M. S. (2009) Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annu Rev Microbiol.63:385-409 http://www.ncbi.nlm.nih.gov/pubmed/19514854 http://www.annualreviews.org/doi/pdf/10.1146/annurev.micro.62.081307.162835
Colijn, C., Brandes A., Zucker J., Lun D. S., Weiner B., Farhat M. R., Cheng T. Y., Moody D. B., Murray M., Galagan J. E. (2009) Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS computational biology.5(8):e1000489 PMCID:2726785 http://www.ncbi.nlm.nih.gov/pubmed/19714220
Champion, M. D., Zeng Q., Nix E. B., Nano F. E., Keim P., Kodira C. D., Borowsky M., Young S., Koehrsen M., Engels R., Pearson M., Howarth C., Larson L., White J., Alvarado L., Forsman M., Bearden S. W., Sjostedt A., Titball R., Michell S. L., Birren B., Galagan J. (2009) Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies. PLoS pathogens.5(5):e1000459 PMCID:2682660 http://www.ncbi.nlm.nih.gov/pubmed/19478886
Sharpton, T. J., Neafsey D. E., Galagan J. E., Taylor J. W. (2008) Mechanisms of intron gain and loss in Cryptococcus. Genome Biol.9(1):R24 PMCID:2395259 http://www.ncbi.nlm.nih.gov/pubmed/18234113
Orsi, R. H., Borowsky M. L., Lauer P., Young S. K., Nusbaum C., Galagan J. E., Birren B. W., Ivy R. A., Sun Q., Graves L. M., Swaminathan B., Wiedmann M. (2008) Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics.9(1):539 PMCID:2642827 http://www.ncbi.nlm.nih.gov/pubmed/19014550
McGuire, A. M., Pearson M. D., Neafsey D. E., Galagan J. E. (2008) Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol.9(3):R50 PMCID:2397502 http://www.ncbi.nlm.nih.gov/pubmed/18321378
McGuire, A. M., Galagan J. E. (2008) Conserved secondary structures in Aspergillus. PloS one.3(7):e2812 PMCID:2467506 http://www.ncbi.nlm.nih.gov/pubmed/18665251
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