James Galagan | Profiles RNS

James E. Galagan, PhD

Professor

Boston University College of Engineering

Biomedical Engineering

PhD, Massachusetts Institute of Technology
BS, University of California, Davis

Websites

	College of Engineering Faculty
	LinkedIn
	National Emerging Infectious Diseases Laboratories Faculty

ORCID : 0000-0003-0542-3291

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

Associate Professor
Boston University Chobanian & Avedisian School of Medicine
Virology, Immunology & Microbiology

Faculty
Boston University
National Emerging Infectious Disease Lab

Member
Boston University
Evans Center for Interdisciplinary Biomedical Research

Associate Director of Systems Biology
Boston University Chobanian & Avedisian School of Medicine
National Emerging Infectious Disease Lab

Associate Director of Microbial Genome Analysis
Broad Institute

Member
Boston University
Genome Science Institute

BU Research
NIH RePORTER Research

Novel Biosensors based on Mining Bacterial Transcription Factors
07/01/2020 - 03/31/2025 (Multi-PI)
PI: James E. Galagan, PhD
NIH/National Institute of Biomedical Imaging & Bioengineering
5R01EB029795-04

Biosensors for Physiological Monitoring from Bacterial Mining
05/01/2021 - 09/30/2024 (PI)
Department of Defense/ONR

Continuous Multiplexed Sensing from Sweat and ISF with A Next Generation Wearable
05/10/2023 - 04/30/2024 (PI)
Defense and Security Accelerator

Novel progesterone biosensor for monitoring fertility health
08/01/2021 - 12/29/2023 (Subcontract PI)
BioSens8 National Science Fdn
IIP-2126992

Biological and Physiological Monitoring and Modeling
08/01/2022 - 07/30/2023 (PI)
Department of Defense/ONR

Development of a Wearable Physiological Status Monitor
09/25/2018 - 03/31/2023 (Multi-PI)
PI: James E. Galagan, PhD
Uniformed Services University of the Health Sciences Federal Medical School

Biosensor Engineering from Metagenomic Screening
09/14/2021 - 09/13/2022 (PI)
Department of Defense/ONR

Global Mapping and Analysis of Bacterial Transcriptional Regulatory Network
06/01/2015 - 05/31/2022 (PI)
NIH/National Institute of General Medical Sciences
5R01GM114812-04

Development of a Wearable Physiological Status Monitor
09/25/2018 - 09/24/2021 (Subcontract PI)
Uniformed Services University Health Sciences HJF AdvOfMilitaryMed

Chemical and biochemical determinants of phosphorothioate stability and location in bacterial genomes
08/01/2017 - 07/31/2020 (Subcontract PI)
Massachusetts Institute of Technology National Science Fdn
CHE-1709364

Showing 10 of 16 results. Show All Results

Title

Yr	Title	Project-Sub Proj	Pubs
2024	Novel Biosensors based on Mining Bacterial Transcription Factors	5R01EB029795-04
2023	Novel Biosensors based on Mining Bacterial Transcription Factors	5R01EB029795-03
2022	Novel Biosensors based on Mining Bacterial Transcription Factors	5R01EB029795-02
2020	Novel Biosensors based on Mining Bacterial Transcription Factors	1R01EB029795-01
2018	Global mapping and analysis of a bacterial transcriptional regulatory network	5R01GM114812-04	4
2018	Systems Biology of the Circadian Clock Output Network	5R01GM113673-04	3
2017	Global mapping and analysis of a bacterial transcriptional regulatory network	5R01GM114812-03	4
2017	Systems Biology of the Circadian Clock Output Network	5R01GM113673-03	3
2016	Predictive modeling of the Mycobacterium tuberculosis regulatory and metabolic networks	1R56AI119491-01A1
2016	Global mapping and analysis of a bacterial transcriptional regulatory network	5R01GM114812-02	4

Showing 10 of 19 results. Show All Results

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.

iCite Analysis Copy PMIDs To Clipboard

Lally P, Tierrafría VH, Gómez-Romero L, Stringer A, Collado-Vides J, Wade JT, Galagan JE. A Cryptic Prophage Transcription Factor Drives Phenotypic Changes via Host Gene Regulation. bioRxiv. 2024 Sep 21. PMID: 39345586; PMCID: PMC11430063; DOI: 10.1101/2024.09.21.614188;

Lally P, Gómez-Romero L, Tierrafría VH, Aquino P, Rioualen C, Zhang X, Kim S, Baniulyte G, Plitnick J, Smith C, Babu M, Collado-Vides J, Wade JT, Galagan JE. Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli. bioRxiv. 2024 May 24. PMID: 38826350; PMCID: PMC11142182; DOI: 10.1101/2024.05.23.594371;

Sankar K, Kuzmanovic U, Schaus SE, Galagan JE, Grinstaff MW. Strategy, Design, and Fabrication of Electrochemical Biosensors: A Tutorial. ACS Sens. 2024 May 24; 9(5):2254-2274.View Related Profiles.

Galagan, James
Grinstaff, Mark
Schaus, Scott

PMID: 38636962

Grazon C, Garanger E, Lalanne P, Ibarboure E, Galagan JE, Grinstaff MW, Lecommandoux S. Transcription-Factor-Induced Aggregation of Biomimetic Oligonucleotide-b-Protein Micelles. Biomacromolecules. 2023 Nov 13; 24(11):5027-5034.View Related Profiles.

Galagan, James
Grinstaff, Mark

PMID: 37877162

Muellers SN, Tararina MA, Kuzmanovic U, Galagan JE, Allen KN. Structural Insights into the Substrate Range of a Bacterial Monoamine Oxidase. Biochemistry. 2023 Feb 07; 62(3):851-862. PMID: 36662673

Grazon C, Chern M, Lally P, Baer RC, Fan A, Lecommandoux S, Klapperich C, Dennis AM, Galagan JE, Grinstaff MW. The quantum dot vs. organic dye conundrum for ratiometric FRET-based biosensors: which one would you chose? Chem Sci. 2022 Jun 07; 13(22):6715-6731.View Related Profiles.

Dennis, Allison
Klapperich, Catherine
Galagan, James
Grinstaff, Mark

PMID: 35756504; PMCID: PMC9172442; DOI: 10.1039/d1sc06921g;

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, Méndez-Cruz CF, Muñiz LJ, Bonavides-Martínez C, Moreno-Hagelsieb G, Galagan JE, Wade JT, Collado-Vides J. RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12. Microb Genom. 2022 May; 8(5). PMID: 35584008; PMCID: PMC9465075; DOI: 10.1099/mgen.0.000833;

Sankar K, Baer R, Grazon C, Sabatelle RC, Lecommandoux S, Klapperich CM, Galagan JE, Grinstaff MW. An Allosteric Transcription Factor DNA-Binding Electrochemical Biosensor for Progesterone. ACS Sens. 2022 Apr 22; 7(4):1132-1137.View Related Profiles.

Klapperich, Catherine
Galagan, James
Grinstaff, Mark

PMID: 35412319; PMCID: PMC9985479; DOI: 10.1021/acssensors.2c00133;

Zamani M, Dupaty J, Baer RC, Kuzmanovic U, Fan A, Grinstaff MW, Galagan JE, Klapperich CM. Paper-Based Progesterone Sensor Using an Allosteric Transcription Factor. ACS Omega. 2022 Feb 22; 7(7):5804-5808.View Related Profiles.

Klapperich, Catherine
Galagan, James
Grinstaff, Mark

PMID: 35224340; PMCID: PMC8867790; DOI: 10.1021/acsomega.1c05737;

Kolluri N, Kamath S, Lally P, Zanna M, Galagan J, Gitaka J, Kamita M, Cabodi M, Lolabattu SR, Klapperich CM. Development and Clinical Validation of Iso-IMRS: A Novel Diagnostic Assay for P. falciparum Malaria. Anal Chem. 2021 02 02; 93(4):2097-2105.View Related Profiles.

Klapperich, Catherine
Galagan, James
Cabodi, Mario

PMID: 33464825; PMCID: PMC7859932; DOI: 10.1021/acs.analchem.0c03847;

Showing 10 of 95 results. Show More

Chern M, Garden PM, Baer RC, Galagan JE, Dennis AM. Transcription Factor Based Small-Molecule Sensing with a Rapid Cell Phone Enabled Fluorescent Bead Assay. Angew Chem Int Ed Engl. 2020 11 23; 59(48):21597-21602.View Related Profiles.

Dennis, Allison
Galagan, James
Baer, R

PMID: 32945589; PMCID: PMC8243852; DOI: 10.1002/anie.202007575;

Chen M, Grazon C, Sensharma P, Nguyen TT, Feng Y, Chern M, Baer RC, Varongchayakul N, Cook K, Lecommandoux S, Klapperich CM, Galagan JE, Dennis AM, Grinstaff MW. Hydrogel-Embedded Quantum Dot-Transcription Factor Sensors for Quantitative Progesterone Detection. ACS Appl Mater Interfaces. 2020 Sep 30; 12(39):43513-43521.View Related Profiles.

Dennis, Allison
Klapperich, Catherine
Galagan, James
Grinstaff, Mark
Baer, R

PMID: 32893612

Chen M, Nguyen TT, Varongchayakul N, Grazon C, Chern M, Baer RC, Lecommandoux S, Klapperich CM, Galagan JE, Dennis AM, Grinstaff MW. Surface Immobilized Nucleic Acid-Transcription Factor Quantum Dots for Biosensing. Adv Healthc Mater. 2020 09; 9(17):e2000403.View Related Profiles.

Dennis, Allison
Klapperich, Catherine
Galagan, James
Grinstaff, Mark
Baer, R

PMID: 32691962

Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet. 2020 11; 21(11):699-714. PMID: 32665585; PMCID: PMC7990032; DOI: 10.1038/s41576-020-0254-8;

Wu X, Cao B, Aquino P, Chiu TP, Chen C, Jiang S, Deng Z, Chen S, Rohs R, Wang L, Galagan JE, Dedon PC. Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. Proc Natl Acad Sci U S A. 2020 06 23; 117(25):14322-14330. PMID: 32518115; PMCID: PMC7322087; DOI: 10.1073/pnas.2002933117;

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. 2020 04; 16(17):e1907522.View Related Profiles.

Dennis, Allison
Galagan, James
Baer, R

PMID: 32249506; PMCID: PMC7359203; DOI: 10.1002/smll.201907522;

Grazon C, Baer RC, Kuzmanovic U, Nguyen T, Chen M, Zamani M, Chern M, Aquino P, Zhang X, Lecommandoux S, Fan A, Cabodi M, Klapperich C, Grinstaff MW, Dennis AM, Galagan JE. A progesterone biosensor derived from microbial screening. Nat Commun. 2020 03 09; 11(1):1276.View Related Profiles.

Dennis, Allison
Klapperich, Catherine
Galagan, James
Cabodi, Mario
Grinstaff, Mark
Baer, R

PMID: 32152281; PMCID: PMC7062782; DOI: 10.1038/s41467-020-14942-5;

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, Collado-Vides J. RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. Nucleic Acids Res. 2019 01 08; 47(D1):D212-D220. PMID: 30395280; PMCID: PMC6324031; DOI: 10.1093/nar/gky1077;

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 Biol. 2018 08 16; 16(1):91. PMID: 30115066; PMCID: PMC6094552; DOI: 10.1186/s12915-018-0555-y;

Manson AL, Abeel T, Galagan J, Sundaramurthi JC, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM. Reply to Lee and Howden. Clin Infect Dis. 2018 01 06; 66(1):160-161. PMID: 29040415; PMCID: PMC6248590; DOI: 10.1093/cid/cix751;

Manson AL, Abeel T, Galagan JE, Sundaramurthi JC, Salazar A, Gehrmann T, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM. Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clin Infect Dis. 2017 Jun 01; 64(11):1494-1501. PMID: 28498943; PMCID: PMC5434337; DOI: 10.1093/cid/cix169;

Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, Brand J, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat Genet. 2017 Mar; 49(3):395-402.View Related Profiles.

Galagan, James
Ellner, Jerrold

PMID: 28092681; PMCID: PMC5402762; DOI: 10.1038/ng.3767;

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.View Related Profiles.

Galagan, James
Wong, Wilson

PMID: 28061857; PMCID: PMC5217608; DOI: 10.1186/s12918-016-0376-y;

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; PMCID: PMC5217103; DOI: 10.1534/g3.116.034298;

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.View Related Profiles.

Galagan, James
Jacobson, Karen

PMID: 26910495; PMCID: PMC5027209; DOI: 10.1164/rccm.201510-2091OC;

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; PMCID: PMC4803200; DOI: 10.1371/journal.pone.0152145;

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.View Related Profiles.

Krueger, Andrew
Galagan, James

PMID: 26821252; PMCID: PMC4731467; DOI: 10.1371/journal.pone.0147651;

Garay CD, Dreyfuss JM, Galagan JE. Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis. BMC Syst Biol. 2015; 9:57. PMID: 26377923; PMCID: PMC4574064; DOI: 10.1186/s12918-015-0206-7;

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; PMCID: PMC4705688; DOI: 10.1093/nar/gkv889;

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; PMCID: PMC4477654; DOI: 10.1093/nar/gkv420;

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; PMCID: PMC4301838; DOI: 10.1038/ncomms6829;

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; PMCID: PMC4260557; DOI: 10.1073/pnas.1418963111;

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; PMCID: PMC4169166; DOI: 10.1534/g3.114.012617;

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; PMCID: PMC4199365; DOI: 10.1101/gr.161711.113;

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; DOI: 10.1128/microbiolspec.MGM2-0035-2013;

Galagan JE. Genomic insights into tuberculosis. Nat Rev Genet. 2014 May; 15(5):307-20. PMID: 24662221; DOI: 10.1038/nrg3664;

Gomes AL, Galagan JE, Segrè D. Resource competition may lead to effective treatment of antibiotic resistant infections. PLoS One. 2013; 8(12):e80775.View Related Profiles.

Segre, Daniel
Galagan, James

PMID: 24349015; PMCID: PMC3862480; DOI: 10.1371/journal.pone.0080775;

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.View Related Profiles.

Galagan, James
Jacobson, Karen

PMID: 23995135; PMCID: PMC3887553; DOI: 10.1038/ng.2747;

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; PMCID: PMC3744410; DOI: 10.1371/journal.ppat.1003543;

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; PMCID: PMC3730674; DOI: 10.1371/journal.pcbi.1003126;

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; PMCID: PMC4087036; DOI: 10.1038/nature12337;

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; DOI: 10.1007/82_2012_257;

Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF. How accurate can genetic predictions be? BMC Genomics. 2012; 13:340. PMID: 22827772; PMCID: PMC3534619; DOI: 10.1186/1471-2164-13-340;

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; PMCID: PMC3351459; DOI: 10.1371/journal.pone.0036947;

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; PMCID: PMC3388012; DOI: 10.1186/1471-2164-13-120;

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; PMCID: PMC3274525; DOI: 10.1371/journal.pone.0026038;

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; PMCID: PMC3246538; DOI: 10.1038/ng.1038;

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; PMCID: PMC3258165; DOI: 10.1093/nar/gkr995;

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; PMCID: PMC3145793; DOI: 10.1371/journal.ppat.1002137;

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; PMCID: PMC3101871; DOI: 10.1038/ng.811;

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; PMCID: PMC3034460; DOI: 10.1128/mBio.00325-10;

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; PMCID: PMC3037005; DOI: 10.1128/mBio.00342-10;

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; PMCID: PMC2883744; DOI: 10.1038/ng.590;

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; DOI: 10.1016/j.tube.2010.03.010;

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; PMCID: PMC3048781; DOI: 10.1038/nature08850;

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; PMCID: PMC2812949; DOI: 10.1186/gb-2009-10-12-r142;

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; PMCID: PMC2726785; DOI: 10.1371/journal.pcbi.1000489;

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; PMCID: PMC2736654; DOI: 10.1038/msb.2009.57;

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; PMCID: PMC2699053; DOI: 10.1371/journal.pgen.1000549;

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; PMCID: PMC2689349; DOI: 10.1371/journal.ppat.1000476;

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; PMCID: PMC2682660; DOI: 10.1371/journal.ppat.1000459;

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; DOI: 10.1146/annurev.micro.62.081307.162835;

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.View Related Profiles.

Berical, Andrew
Galagan, James

PMID: 19026009; PMCID: PMC2645896; DOI: 10.1002/hep.22549;

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; PMCID: PMC2644964; DOI: 10.1534/genetics.108.089292;

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; PMCID: PMC2642827; DOI: 10.1186/1471-2164-9-539;

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; PMCID: PMC2686437; DOI: 10.1093/nar/gkn652;

McGuire AM, Galagan JE. Conserved secondary structures in Aspergillus. PLoS One. 2008; 3(7):e2812. PMID: 18665251; PMCID: PMC2467506; DOI: 10.1371/journal.pone.0002812;

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; PMCID: PMC2397502; DOI: 10.1186/gb-2008-9-3-r50;

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; PMCID: PMC2268591; DOI: 10.1073/pnas.0711982105;

Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 2008; 9(1):R24. PMID: 18234113; PMCID: PMC2395259; DOI: 10.1186/gb-2008-9-1-r24;

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; PMCID: PMC2174895; DOI: 10.1105/tpc.107.052829;

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; PMCID: PMC1950907; DOI: 10.1101/gr.6558107;

Neafsey DE, Galagan JE. Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol. 2007; 7:119. PMID: 17640368; PMCID: PMC1936986; DOI: 10.1186/1471-2148-7-119;

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; PMCID: PMC2868357; DOI: 10.1126/science.1138878;

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

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; PMCID: PMC3673015; DOI: 10.1016/S0065-2660(06)57002-6;

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

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

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

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. PMID: 16372000

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. PMID: 16372010

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. PMID: 16372009

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. PMID: 16339359

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. PMID: 16077012; PMCID: PMC1182225; DOI: 10.1101/gr.3722605;

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. PMID: 15846337

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. PMID: 15562318; PMCID: PMC532390

Mikkelsen TS, Galagan JE, Mesirov JP. Improving genome annotations using phylogenetic profile anomaly detection. Bioinformatics. 2005 Feb 15; 21(4):464-70. PMID: 15374867

Galagan JE, Selker EU. RIP: the evolutionary cost of genome defense. Trends Genet. 2004 Sep; 20(9):417-23. PMID: 15313550

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. PMID: 15007097; PMCID: PMC362109

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. PMID: 12712197

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. PMID: 11932238; PMCID: PMC187521

Lemay MA, Galagan JE, Hogan N, Bizzi E. Modulation and vectorial summation of the spinalized frog's hindlimb end-point force produced by intraspinal electrical stimulation of the cord. IEEE Trans Neural Syst Rehabil Eng. 2001 Mar; 9(1):12-23. PMID: 11482358

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15; 409(6822):860-921.View Related Profiles.

Galagan, James
Kasif, Simon

PMID: 11237011

Taylor JM, Tucker JA, Galagan JE. The Luke S. class action suit: a lesson in system change. Except Child. 1986 Jan; 52(4):376-82. PMID: 3943544

Galagan JE. Psychoeducational testing: turn out the lights, the party's over. Except Child. 1985 Nov; 52(3):288-99. PMID: 2934263

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 95 publications over 26 distinct years, with a maximum of 8 publications in 2008

Bar chart showing 95 publications over 26 distinct years, with a maximum of 8 publications in 2008

Year	Publications
1985	1
1986	1
2001	2
2002	1
2003	1
2004	4
2005	6
2006	3
2007	6
2008	8
2009	7
2010	3
2011	6
2012	4
2013	6
2014	5
2015	4
2016	3
2017	4
2018	2
2019	1
2020	7
2021	1
2022	4
2023	2
2024	3

In addition to these self-described keywords below, a list of MeSH based concepts is available here.

Computational Biology
Genomics
Infectious Diseases
Microbiology
Systems Biology
Tuberculosis

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