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James Galagan - Publications

Affiliations: 
Biomedical Engineering Boston University, Boston, MA, United States 
Area:
Biomedical Engineering, Systematic Biology
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Tierrafría VH, Rioualen C, Salgado H, Lara P, Gama-Castro S, Lally P, Gómez-Romero L, Peña-Loredo P, López-Almazo AG, Alarcón-Carranza G, Betancourt-Figueroa F, Alquicira-Hernández S, Polanco-Morelos JE, García-Sotelo J, Gaytan-Nuñez E, ... ... Galagan JE, et al. RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in K-12. Microbial Genomics. 8. PMID 35584008 DOI: 10.1099/mgen.0.000833  0.328
2020 Nguyen TT, Chern M, Baer RC, Galagan J, Dennis AM. A Förster Resonance Energy Transfer-Based Ratiometric Sensor with the Allosteric Transcription Factor TetR. Small (Weinheim An Der Bergstrasse, Germany). e1907522. PMID 32249506 DOI: 10.1002/Smll.201907522  0.304
2018 Santos-Zavaleta A, Salgado H, Gama-Castro S, Sánchez-Pérez M, Gómez-Romero L, Ledezma-Tejeida D, García-Sotelo JS, Alquicira-Hernández K, Muñiz-Rascado LJ, Peña-Loredo P, Ishida-Gutiérrez C, Velázquez-Ramírez DA, Del Moral-Chávez V, Bonavides-Martínez C, Méndez-Cruz CF, ... Galagan J, et al. RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. Nucleic Acids Research. PMID 30395280 DOI: 10.1093/Nar/Gky1077  0.426
2018 Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Velázquez-Ramírez DA, Gama-Castro S, Tierrafría VH, Busby SJW, Aquino P, Fang X, Palsson BO, Galagan JE, Collado-Vides J. A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. Bmc Biology. 16: 91. PMID 30115066 DOI: 10.1186/S12915-018-0555-Y  0.368
2017 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, ... ... Galagan JE, et al. Coordinated regulation of acid resistance in Escherichia coli. Bmc Systems Biology. 11: 1. PMID 28061857 DOI: 10.1186/S12918-016-0376-Y  0.669
2016 Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurely JM, Dunlap JC, Galagan JE, Freitag M, et al. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell-Fusion. G3 (Bethesda, Md.). PMID 27856696 DOI: 10.1534/G3.116.034298  0.754
2016 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. 11: e0152145. PMID 27003599 DOI: 10.1371/Journal.Pone.0152145  0.797
2016 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. 11: e0147651. PMID 26821252 DOI: 10.1371/Journal.Pone.0147651  0.323
2015 Garay CD, Dreyfuss JM, Galagan JE. Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis. Bmc Systems Biology. 9: 57. PMID 26377923 DOI: 10.1186/S12918-015-0206-7  0.651
2015 Ranganathan S, Bai G, Lyubetskaya A, Knapp GS, Peterson MW, Gazdik M, 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 Research. PMID 26358810 DOI: 10.1093/Nar/Gkv889  0.769
2015 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 Research. 43: 5377-93. PMID 25940627 DOI: 10.1093/Nar/Gkv420  0.797
2015 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. Nature Communications. 6: 5829. PMID 25581030 DOI: 10.1038/Ncomms6829  0.425
2014 Jaini S, Lyubetskaya A, Gomes A, Peterson M, Park ST, Raman S, Schoolnik G, Galagan J. Transcription Factor Binding Site Mapping Using ChIP-Seq. Microbiology Spectrum. 2. PMID 26105820 DOI: 10.1128/Microbiolspec.Mgm2-0035-2013  0.786
2014 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, et al. 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: 16995-7002. PMID 25362047 DOI: 10.1073/Pnas.1418963111  0.377
2014 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, et al. Genome-wide characterization of light-regulated genes in Neurospora crassa. G3 (Bethesda, Md.). 4: 1731-45. PMID 25053707 DOI: 10.1534/G3.114.012617  0.717
2014 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 Research. 24: 1686-97. PMID 25024162 DOI: 10.1101/Gr.161711.113  0.756
2014 Azizi E, Airoldi EM, Galagan JE. Learning modular structures from network data and node variables 31st International Conference On Machine Learning, Icml 2014. 4: 3300-3308.  0.423
2013 Gomes AL, Galagan JE, Segrè D. Resource competition may lead to effective treatment of antibiotic resistant infections. Plos One. 8: e80775. PMID 24349015 DOI: 10.1371/Journal.Pone.0080775  0.556
2013 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, ... ... Galagan J, et al. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nature Genetics. 45: 1183-9. PMID 23995135 DOI: 10.1038/Ng.2747  0.389
2013 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 Pathogens. 9: e1003543. PMID 23966858 DOI: 10.1371/Journal.Ppat.1003543  0.371
2013 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 Computational Biology. 9: e1003126. PMID 23935467 DOI: 10.1371/Journal.Pcbi.1003126  0.622
2013 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, et al. The Mycobacterium tuberculosis regulatory network and hypoxia. Nature. 499: 178-83. PMID 23823726 DOI: 10.1038/Nature12337  0.669
2013 Galagan J, Lyubetskaya A, Gomes A. ChIP-Seq and the complexity of bacterial transcriptional regulation. Current Topics in Microbiology and Immunology. 363: 43-68. PMID 22983621 DOI: 10.1007/82_2012_257  0.794
2012 Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF. How accurate can genetic predictions be? Bmc Genomics. 13: 340. PMID 22827772 DOI: 10.1186/1471-2164-13-340  0.528
2012 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, ... ... Galagan J, et al. Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. Bmc Genomics. 13: 120. PMID 22452820 DOI: 10.1186/1471-2164-13-120  0.367
2012 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, ... ... Galagan J, et al. Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region. Plos One. 7: e26038. PMID 22347359 DOI: 10.1371/Journal.Pone.0026038  0.383
2012 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. Nature Genetics. 44: 106-10. PMID 22179134 DOI: 10.1038/Ng.1038  0.346
2012 Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y. GenomeView: a next-generation genome browser. Nucleic Acids Research. 40: e12. PMID 22102585 DOI: 10.1093/Nar/Gkr995  0.301
2011 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, ... ... Galagan J, et al. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. Plos Pathogens. 7: e1002137. PMID 21829347 DOI: 10.1371/Journal.Ppat.1002137  0.353
2011 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. Nature Genetics. 43: 482-6. PMID 21516081 DOI: 10.1038/Ng.811  0.329
2010 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. Nature Genetics. 42: 498-503. PMID 20495566 DOI: 10.1038/Ng.590  0.39
2010 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, et al. TB database 2010: overview and update. Tuberculosis (Edinburgh, Scotland). 90: 225-35. PMID 20488753 DOI: 10.1016/J.Tube.2010.03.010  0.317
2009 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 Biology. 10: R142. PMID 20028542 DOI: 10.1186/gb-2009-10-12-r142  0.364
2009 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 Computational Biology. 5: e1000489. PMID 19714220 DOI: 10.1371/Journal.Pcbi.1000489  0.318
2009 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, ... ... Galagan J, et al. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. Plos Genetics. 5: e1000549. PMID 19578406 DOI: 10.1371/Journal.Pgen.1000549  0.375
2009 Hood HM, Neafsey DE, Galagan J, Sachs MS. Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annual Review of Microbiology. 63: 385-409. PMID 19514854 DOI: 10.1146/Annurev.Micro.62.081307.162835  0.386
2009 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, ... ... Galagan J, et al. Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies. Plos Pathogens. 5: e1000459. PMID 19478886 DOI: 10.1371/Journal.Ppat.1000459  0.313
2007 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, ... ... Galagan J, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science (New York, N.Y.). 316: 1718-23. PMID 17510324 DOI: 10.1126/Science.1138878  0.367
2006 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, ... ... Galagan J, et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature. 444: 97-101. PMID 17080091 DOI: 10.1038/Nature05248  0.381
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