[PDF] Galagan CV 4 2021

31082_3Galagan_CV_4_2021.pdf

JAMES E. GALAGAN, PH.D.

Boston University

44 Cummington Mall

Boston, MA 02215

(617) 875-9874 jgalag@bu.edu

EDUCATION

Massachusetts Institute of Technology, Department of Neuroscience, Cambridge, MA

Ph.D., Computational Neuroscience, 1999

Marine Biological Laboratories, Woods Hole, MA

Neurobiology Course, 1993

University of Miami, Miami, FL

Molecular and Cellular Neuroscience Graduate Program, 1992-1994

University of California at Davis, Davis, CA

B.S., Computer Science and Engineering, 1992

PROFESSIONAL APPOINTMENTS

Boston University

Full Professor, Department of Biomedical Engineering and Microbiology; Graduate Program in Molecular Biology, Cell Biology, & Biochemistry; Bioinformatics Program 2021 - present Associate Professor, Department of Biomedical Engineering and Microbiology; Graduate Program in Molecular Biology, Cell Biology, & Biochemistry; Bioinformatics Program 2008 - 2021
Associate Director, Systems Biology, National Emerging Infectious Diseases Laboratory (NEIDL), 2008 - present Associate Director, Precision Diagnostic Center, Boston University, 2017 - present Director, BU Illumina Sequencing Core Facility, 2010 - 2013

Broad Institute of MIT and Harvard

Visiting Scientist, 2011 - 2017

Associate Director: Microbial Genome Analysis and Annotation, 2005 - 2011 Harvard School of Public Health, Department of Immunology and Infectious Disease

Visiting Scientist, 2006 - present

MIT, Department of Electrical Engineering and Computer Science

Visiting Faculty, 2008, 2009

MIT/Whitehead Institute Center for Genome Research

Computational Biologist, 2002-2005

Team Leader: Annotation and Analysis Informatics, 1999-2002 Software Engineer/Senior Software Engineer, 1998-1999

TEACHING

Molecular Bioengineering, BU, 2012 - present, Co-Instructor with Prof Wilson Wong Computational Biology: Genomes, Networks, Evolution, BU, 2010 - present, Instructor Computational Biology: Genomes, Networks, Evolution, BU, MIT, Harvard, & HSPH, 2009, Co-

Instructor with Prof Manolis Kellis

Introduction to Computational Genomics for Infectious Disease, Harvard School of Public Health, Department of Immunology and Infectious Disease, 2008, Instructor Computational Biology: Genomes, Networks, Evolution, BU, MIT, Harvard, & HSPH, 2008, Co-

Instructor with Prof Manolis Kellis

Computational Biology: Genomes, Networks, Evolution, BU, MIT, Harvard, & HSPH, 2007, Co-

Instructor with Prof Manolis Kellis

Introduction to Computational Genomics for Infectious Disease, Harvard School of Public Health, Department of Immunology and Infectious Disease, 2006, Instructor Computational Biology: Genomes, Networks, Evolution, BU, MIT, Harvard, & HSPH, 2005, Guest

Lecturer

HONORS AND AWARDS

Faculty Startup Award, Massachusetts Life Sciences Center, 2009

Deans Catalyst Award, Boston University, 2014

Distinguished Faculty Fellow, College of Engineering, Boston University, 2016 Institute Fellow, Institute for Health System Innovation & Policy, Boston University, 2020

FACULTY SERVICE

Chair, Graduate Committee, Biomedical Engineering, 2016 Chair, Biomedical Engineering Faculty Search Committee, 2016 - 2017 College of Engineering Appointments Promotion and Tenure Committee, 2015 - 2018 Biomedical Engineering Faculty Search Committee, 2015 - 2016 Hariri Institute Data Science Initiative Leadership Board, 2015 - 2018 Graduate Committee, Biomedical Engineering, Boston University, 2008 - present Bioinformatics Curriculum Committee, 2008 - present Bioinformatics Oral Qualifying Exam Committees, 2008 - 2018 Biomedical Engineering Oral Qualifying Exam Committees, 2008 - present BU Program in Nanomedicine Panel, 2010, November 23 MD/PhD Executive Committee, BME Representative, 2010

BME Faculty Search Committee, 2010

Biology Faculty Search Committee, 2010

Systems Biology Faculty Search Coordinating Committee, 2009 Responsible Conduct of Research Facilitator, 2010

OTHER PROFESSIONAL ACTIVITIES

Co-Founder, BioSens8 Inc., Jan 2021

Chair, PRiME 2020 Conference, Microorganisms and Electrochemistry Session, October 6, 2020 Reviewer, NIH Special Emphasis Panel, ZRG1 IDM-Y, Nov 2019

Appointed Reviewer, NIH, PCMB, 2017 - present

Reviewer, Department of Ene rgy, Office of Biological and Envir onmental Research, SFA,

September 23, 2016

Philips Genomics for Infectious Disease Advisory Board Member, 2016 - present

Reviewer NIH, MABS, 2016

Reviewer NIH, PCMB, 2015, 2016

Joint Genome Institute, Community Sequencing Program, Review Panel, 2015 Editorial Board Member, BMC Infectious Diseases, 2014 - present NIGMS, National Centers for Systems biology (P50) Review Panel, 2014, March 20 Department of Defense, Military Infectious Diseases Research Program; Computational Science

Panel, 2014

NIH Director's Early Independence Awards Review Panel, 2013, June 24 NIH Genomics, Computational Biology and Technology Study Section, 2013, June 6

ISMT R15 Special Review Panel, 2013, March 5

ISMB/ECCB 2013 Program Committee, 2013, July 21

Special Review Panel for Argonne National Genomic Sciences Program Foundational Scientific Focus Area: Envi ronment Sensing and Response, Office of Biological an d Environmental

Research, Department of Energy 2012, May 2

System Immunology Workshop - Bill & Melinda Gates Foundation, 2012, March 16

NIAID TB Community Annotation Project, 2011-2012

Associate Editor, Fungal Genetics and Biology, 2004 - present Scientific Working Group, PATRIC Bacterial Bioinformatics Resource Center, 2010 - present

NIAID Special PO1 Review Panel, 2012, January 12

NIAID TB Community Annotation Project, 2011-2012

Workshop on Attaining Operational Marine Biodiversity Observations, 1201 New York Ave, NW,

4th Floor, Washington, DC 20005, 2010, May 24-26

NIAID/DMID Blue Ribbon Panel on Genomics for Infectious Disease, Bethesda, 2010, February 3-4 Welcome Trust Pan Fungal Data Resources Policy Committee, 2010 Organizer. 2nd Annual Systems Biology Programmatic and SBWG Meeting. 2010 Co-Chair. U.S. - Japan Cooperative Medical Sciences Program: 45th TB and Leprosy Research

Conference. 2010

Program Committee Member, RECOMB 2009, Tucson, Arizona, , 2009, May 17 American Academy of Microbiology, Colloquium on Large-Scale Sequencing, Washington DC,

2008, September 19-21

American Academy of Microbiology Colloquium, Large Scale Genome Sequencing, Washington

DC, 2008, September 19

Co-Chair, Pathogens and Medical Genomics Session, Genome Informatics Meeting, Hinxton, UK,

2008, September 10

American Academy of Microb iology Colloquium, Bio informat ics, Baltimore Maryland, , 2008,

November 13

Department of Energy Review of the Joint Genome Institute, Joint Genome Institute, Walnut

Creek, CA, 2008, December 3

American Academy of Microbiology Colloquium: The Fungal Kingdom, Tucson, Arizona, 2007,

November

Panel on Case-Based Teaching, Conference on Emerging Infectious Disease, Harvard School of

Public Health, 2007, May

US-Japan Cooperative Medical Science Program, 12TH International Conference on Emerging Infectious Diseases in the Pacific Rim, Haikou, China, 2007, December 4 NIH Special Emphasis Panel: Genome Database Resource and Knockout Mouse Project Data

Coordination Center, 2006, April

Broad Distinguished Lecture in Computational Biology Selection Committee, 2006 Fourth Infectious Diseases Initiative Steering Committee Meeting, Broad Institute, 2006 Symposium Co-Chair: International Union of Microbiological Societies, 2005 Symposium Chair: Gordon Research Conference on Cellular and Molecular Fungal Biology, 2004 Program Committee Member, IEEE Computer Society, Bioinformatics Conference. Stanford, CA, 2002
Reviewer for Nature, Science, Nature Genetics, Nature Communications, eLife, PLoS, Genome Research, Genome Biology, Fungal Genetics and Biology, and other Journals. Scientific and engineering consultant for Lysosomal Therapeutics, Inc., Gene Network Sciences, Agencourt Bioscience Corp., Transnetyx, Inc.; Kinematix Inc., Combimatrix, and others.

INVENTIONS AND SOFTWARE

2018 Microbial Based Biosensors

J. Galagan; A. Dennis; C. Klapperich; M. Grinstaff; T. Nguyen; R. Baer; U. Kuzmanovic; M. Zamani; M. Chen; Grazon, C; M. Chern; (Patent Filed)

2018 Novel Oxidase Enzyme Compositions and Methods

J. Galagan, D. Densmore, L. Ortiz, U. Kuzmanovic, N. Shu; (Patent Filed)

2018 Enzyme-based Electrochemical Nicotine Biosensor

J. Galagan, M. Grinstaff, U. Kuzmanovic, M. Chen, K. Allen, M. Tararina (Patent Filed)

2014 A process for discovering biological sensing circuitry

J. Galagan (Invention Disclosed)

2007 Prediction of environment from expression data using metabolic modeling

2007 A computational method for the metabolic interpretation of gene expression data

2007 Conrad software for computational gene prediction using conditional random fields

2007 FLEXTOP software for predicting operon structure using conditional random fields

2001 Argo production tool for visualizing and manually annotating whole genomes

2000 Calhoun software system for whole genome annotation and analysis

PUBLICATIONS

Chen, Mingfu, Grazo n Chloé, Sensharma Prera na, Nguyen Thuy, Fe ng Yunpeng, Chern Ma rgaret, 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

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 competi tion reveals density-dependent regulation and targ et 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

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

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:e1907522

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

Grazon, C., Baer R. C. , Kuzmanovic U ., Nguyen T., Ch en M., Z amani M., Ch ern M., Aquino P., Zhan g X.,

Lecommandoux S., Fan A., Cabodi M., Klapperich C., Grinstaff M. W., Dennis A. M., Galagan J. E. (2020) A

progesterone biosensor derived from micr obial screening. Nature communicati ons.11(1):1276

PMCID:PMC7062782

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

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

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 an d Howden. Clinical infectious dise ases : an official

publication of the Infectious Diseases Society of America.66(1):160-1

Grazon, C., Nguyen T., Baer R.C., Kuzmanovic U., Chern M ., Chen M., Zam ani 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 em ergence and sp read of multidrug

resistance. Nature genetics.49(3):395-402

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 In dia Suggest Nove l Resistance Mechanisms and the Need for Region-Specific

Diagnostics. Clinical infectious dise ases : an official publication o f the Infectious Diseases S ociety of

America.64(11):1494-501 PMCID:PMC5434337

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

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

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

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 t he DosR (DevR) dor mancy regulon. Nucleic Acids Res.44(1):134-51

PMCID:PMC4705688

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

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

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

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

Garay, C. D., Dreyf uss J. M., Galagan J. E . (2015) Metabolic modeling predicts m etabolite changes in

Mycobacterium tuberculosis. BMC Syst Biol.9:57 PMCID:PMC4574064

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

Jaini, S, Lyubetskaya A., Gomes A, Peterson M, Park S. T., Raman S, Schoolnik G., Galagan J.E. Transcription

Factor Binding Sit e Mapping Using ChIP-Seq. In: Hatfull G, Jacobs WR, Jr ., editor s. Molecular Gen etics of

Mycobacteria, 2nd Edition: ASM Press; 2014.

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

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

Galagan, JE. (2014) Genomic Insights into Tuberculosis. Nature Reviews Genetics

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. (2 013) The role of selection in shap ing diversi ty of natural M. tubercul osis popula tions. PLoS

pathogens.9(8):e1003543 PMCID:3744410

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

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

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.

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 tub erculosis. Nature genetics.45(10):1183-9

PMCID:3887553

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

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

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 in to the evolution of My cobacterium tube rculosis pathog enesis. BMC Geno mics.13(1):120

PMCID:3388012

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

Comas, I., Borrell S., Roetzer A., Rose G., Malla B., Kato-Maeda M., Galagan J., Niemann S., Gagneux S. (2012)

Whole-genome sequencing of ri fampicin-resistant Mycobacterium tube rculosis strains ident ifies compensatory

mutations in RNA polymerase genes. Nature genetics.44(1):106-10 PMCID:3246538

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

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

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

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

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

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

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

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

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 st ructure predicts serotyp e prevalence. PLoS pathogens.5(6):e1000476 PMCID:2689349

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

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

Lun, D. S., Sherrid A., Weiner B., Sherman D. R., Galagan J. E. (2009) A blind deconvolution approach to high-

resolution mapping of transcript ion factor binding sites from ChIP -seq data. Genome Biol.10(12):R142

PMCID:2812949

Lun, D. S., Rockwell G., Guido N. J., Baym M., Kelner J. A., Berger B., Galagan J. E., Church G. M. (2009) Large-

scale identifi cation of genetic design strategies using local search. Molecular systems biology.5:296

PMCID:2736654

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

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

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

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

Sharpton, T. J., Neafsey D. E., Galaga n J. E., Taylor J. W. (2 008) Mechanisms of intron gain an d loss in

Cryptococcus. Genome Biol.9(1):R24 PMCID:2395259

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

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

McGuire, A. M., Galagan J. E. (20 08) Conserved secondary structure s in Aspergillus. PloS one.3(7):e2812

PMCID:2467506

Mathee, K., Narasimhan G., Valdes C., Qiu X., Matewish J. M., Koehrsen M., Rokas A., Yandava C. N., Engels R.,

Zeng E., Olavarietta R., Doud M., Smith R. S., Montgomery P., White J. R., Godfrey P. A., Kodira C., Birren B.,

Galagan J. E., Lory S. (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proceedings of the

National Academy of Sciences of the United States of America.105(8):3100-5 PMCID:2268591

Volkman, S. K., Sabeti P. C., DeCaprio D., Neafsey D. E., Schaffner S. F., Milner D. A., Jr., Daily J. P., Sarr O.,

Ndiaye D., Ndir O., Mboup S., Duraisingh M. T., Lukens A., Derr A., Stange-Thomann N., Waggoner S., Onofrio R.,

Ziaugra L., Mauceli E., Gnerre S., Jaffe D. B., Zainoun J., Wiegand R. C., Birren B. W., Hartl D. L., Galagan J. E.,

Lander E. S ., Wirth D. F. (2007) A ge nome-wide map of di versity in Pla smodium falciparum. Nature

genetics.39(1):113-9

Rokas, A, Galagan J.E. The Aspergillus nidulans genome and comparative analysis with other Aspergilli. In: Osmani

SA, Goldman GH, editors. The Aspergilli: Genomics, Medical Applications, Biotechnology, and Research Methods:

CRC Press; 2007.

Nene, V., Wortman J. R., Lawson D., Haas B., Kodira C., Tu Z. J., Loftus B., Xi Z., Megy K., Grabherr M., Ren Q.,

Zdobnov E. M., Lobo N. F., Campbell K. S., Brown S. E., Bonaldo M. F., Zhu J., Sinkins S. P., Hogenkamp D. G.,

Amedeo P., Arensburger P., Atkinson P. W., Bidwell S., Biedler J., Birney E., Bruggner R. V., Costas J., Coy M. R.,

Crabtree J., Crawford M., Debruyn B., Decaprio D., Eiglmeier K., Eisenstadt E., El-Dorry H., Gelbart W. M., Gomes

S. L., Hammond M., Hannick L. I., Hogan J. R., Holmes M. H., Jaffe D., Johnston J. S., Kennedy R. C., Koo H.,

Kravitz S., Kriventseva E. V., Kulp D., Labutti K., Lee E., Li S., Lovin D. D., Mao C., Mauceli E., Menck C. F., Miller

J. R., Montgomery P., Mori A., Nascimento A. L., Naveira H. F., Nusbaum C., O'Leary S., Orvis J., Pertea M.,

Quesneville H., Reidenbach K. R., Rogers Y. H., Roth C. W., Schneider J. R., Schatz M., Shumway M., Stanke M.,

Stinson E. O., Tubio J. M., Vanzee J. P., Verjovski-Almeida S., Werner D., White O., Wyder S., Zeng Q., Zhao Q.,

Zhao Y., Hill C. A., Raikhel A. S., Soares M. B., Knudson D. L., Lee N. H., Galagan J., Salzberg S. L., Paulsen I.

T., Dimopoulos G., Collins F. H., Birren B., Fraser-Liggett C. M., Severson D. W. (2007) Genome sequence of

Aedes aegypti, a major arbovirus vector. Science.316(5832):1718-23 PMCID:2868357

Neafsey, D. E., Galagan J. E. (2007) Dual modes of natural selection on upstream open reading frames. Mol Biol

Evol.24(8):1744-51

Neafsey, D. E., Galagan J. E. (2007) Positive selection for unpreferred codon usage in eukaryotic genomes. BMC

evolutionary biology.7:119 PMCID:1936986

Hane, J. K., Lowe R. G., Solomon P. S., Tan K. C., Schoch C. L., Spatafora J. W., Crous P. W., Kodira C., Birren

B. W., Galagan J. E., Torriani S. F., McDonald B. A., Oliver R. P. (2007) Dothideomycete plant interactions

illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. The Plant

cell.19(11):3347-68 PMCID:2174895

Dunlap, J. C., Borkovich K. A., Henn M. R., Turner G. E., Sachs M. S., Glass N. L., McCluskey K., Plamann M.,

Galagan J. E., Birren B. W., Weiss R. L., Townsend J. P., Loros J. J., Nelson M. A., Lambreghts R., Colot H. V.,

Park G., Collopy P., Ringelberg C., Crew C., Litvinkova L., DeCaprio D., Hood H. M., Curilla S., Shi M., Crawford

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pathogen Ustilago maydis. Nature.444(7115):97-101

Engels, R., Yu T., Burge C., Mesirov J. P., DeCaprio D., Galagan J. E. (2006) Combo: a whole genome comparative

browser. Bioinformatics.22(14):1782-3

Vinson, J. P., Jaffe D. B., O'Neill K., Karlsson E. K., Stange-Thomann N., Anderson S., Mesirov J. P., Satoh N.,

Satou Y., Nusbaum C., Birren B., Galagan J. E., Lander E. S. (2005) Assembly of polymorphic genomes: algorithms

and application to Ciona savignyi. Genome research.15(8):1127-35 PMCID:1182225

Nierman, W. C., Pain A., Anderson M. J., Wortman J. R., Kim H. S., Arroyo J., Berriman M., Abe K., Archer D. B.,

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White O., Woodward J., Yu J. H., Fraser C., Galagan J. E., Asai K., Machida M., Hall N., Barrell B., Denning D. W.

(2005) Genomic sequence of the p athogenic and allerge nic filame ntous fungus Aspergillus fumigatus.

Nature.438(7071):1151-6

Mikkelsen, T. S., Galagan J. E., Mesirov J. P. (2005) Improving genome annotations using phylogenetic profile

anomaly detection. Bioinformatics.21(4):464-70

Machida, M., Asai K., Sano M., Tanaka T., Kumagai T., Terai G., Kusumoto K., Arima T., Akita O., Kashiwagi Y.,

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C., Yu J., Archer D. B., Bennett J. W., Bhatnagar D., Cleveland T. E., Fedorova N. D., Gotoh O., Horikawa H.,

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(2005) Genome sequencing and analysis of Aspergillus oryzae. Nature.438(7071):1157-61

Galagan, J. E., Henn M. R., Ma L. J., Cuomo C. A., Birren B. (2005) Genomics of the fungal kingdom: insights into

eukaryotic biology. Genome research.15(12):1620-31

Galagan, J. E., Calvo S. E., Cuomo C., Ma L. J., Wortman J. R., Batzoglou S., Lee S. I., Basturkmen M., Spevak

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H., Draht O., Busch S., D'Enfert C., Bouchier C., Goldman G. H., Bell-Pedersen D., Griffiths-Jones S., Doonan J.

H., Yu J., Vienken K., Pain A., Freitag M., Selker E. U., Archer D. B., Penalva M. A., Oakley B. R., Momany M.,

Tanaka T., Kumagai T., Asai K., Machida M., Nierman W. C., Denning D. W., Caddick M., Hynes M., Paoletti M.,

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S., Ma L. J., Nicol R., Purcell S., Nusbaum C., Galagan J. E., Birren B. W. (2005) The genome sequence of the rice

blast fungus Magnaporthe grisea. Nature.434(7036):980-6

Nielsen, C. B., Friedman B., Birren B., Burge C. B., Galagan J. E. (2004) Patterns of intron gain and loss in fungi.

PLoS biology.2(12):e422 PMCID:532390

Galagan, J. E., Selker E. U. (2004 ) RIP: the evoluti onary cost of genome defense. Trends in genetics :

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Borkovich, K. A., Alex L. A., Yarden O., Freitag M., Turner G. E., Read N. D., Seiler S., Bell-Pedersen D., Paietta

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Selitrennikoff C., Galagan J. E., Dunlap J. C., Loros J. J., Catcheside D., Inoue H., Aramayo R., Polymenis M.,

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SELECTED PRESENTATIONS

Selected Invited Talks

PRiME2020, Symp osium K02: "Towards Interdisciplin ary Fusion of Bioengineering and Electrochemistry", Invited Speaker, Honolulu, HI, USA, October 4, 2020 "Health Information Technology Guest Speaker." Boston University; 2018. "1st CSSB International Symposium - Plenary Lecture." Center for Structural Systems Biology,

Hamburg, Germany; April 9, 2015.

"Mapping and Modeling of Microbial Molecular Networks." Invited Talk - Lablinks Symposium,

Broad Institute; March 14, 2014.

"Mapping and Modeling of Microbial Regulatory Networks." Invited Lecture, New England Biolabs;

January 30, 2014.

"Systems and Synthetic Biology for Tuberculosis." Systems Biology in Vaccines Meeting - Invited

Speaker, Brussells, Belgium; October 21, 2013.

"Mapping and Modeling of the Mycobacterium tuberculosis regulatory network." Invited Talk,

Wadsworth Institute; December 5, 2013.

"Reconstructing the Regulatory Network of TB: Deconstruction of the Hypoxic Response". Invited Lecture - Forsyth Institute.Cambridge, MA, April 12, 2012 "TB Systems Biology". Broad Infectious Disease Initiative.Broad Institute, Boston, MA, February

10, 2012

BU, BMC, NEIDL World TB Day Symposium.Boston University, March 23, 2012 "The Tuberculo sis Systems Biology Consortium ". Keystone Symposium: Tube rculosis: Immunology, Cell Biology and Novel Vaccination Strategies.Vancouver, CA, Jan 15, 2011 "TB Systems Biology ". The Public Health Research Institute - Department of Microbiology and Molecular Genetics of New Jersey Medical School Joint Seminar Program.New Jersey Medical

School, Newark, NJ, March 7, 2011

"Using Chip-Seq to Map Microbial Regulatory Binding Networks". The 26th Fungal Genetics Conference at Asilomar.Asilomar, CA, March 15, 2011 "Reconstructing the TB Regulatory Interac tion Network" . World Tuberculosis Day

Symposium.Albany, NY, March 24, 2011

"Reconstructing the TB Regulatory Interacti on Network". Indo-NIAID Forum on TB Drug

Discovery Research.Delhi, India, April 20, 2011

"TB Systems Biology". BU Bioinformatics Student-Faculty Retreat Keynote Address.Wachusett,

MA, June 3, 2011

"TB Systems B iology". National Emerging Infectio us Diseases Laboratory Special

Seminar.Boston, MA, June 20, 2011

"TB Systems Biology". Dunlap Laboratory Retreat Keynote Speaker.New Hampshire, June 21, 2011
"TB Systems Biology - Reconstructing the Global Regulatory Network". University of Washington

STRIDE Seminar Series.Seattle, WA, July 13, 2011

"Reconstructing the MTB Regulatory Network using ChIP-Seq: Deconstruct ing the Hypoxic Response". Invited Speaker: Genetic Department Seminar Special Seminar Series.Texas A&M

University, October 27, 2011

"TB Systems Biology". Multidisciplinary Research Conferences Infectious Diseases: Tuberculosis - Basic and Translational Research and Public Health Perspectives.Boston University, December

14, 2011

"Reconstruction and comparative analysis of the TB regulatory network ". TB Vaccines, A Second

Global Forum.Tallin, Estonia, Sept 22,, 2010

"TB Systems B iology". Bioinformatics Systems Biology Reception Lectur e Series.Boston

University, Boston MA, Dec 2, 2010

"TB Systems Biology". University Systems Biology Seminar Series.Boston University, December

2, 2010

"Systems Biology of TB". US - Japan Cooperative Medical Sciences Program: 45th TB and Leprosy Research Conference.Broad Institute, July 15, 2010 "Genomics and the Origins of Tuberculosis". Medical Exchange Club.Boston, MA, February 10, 2010
"Systems Biology of Tuberculosis". Biomolecular Seminar Series.BU, October 5, 2009 Invited Lecture, Joint Genome Institute User Group Meeting.Walnut Creek, CA, March 25, 2009

58th Meeting Society for Biotechnology.Osaka, Japan, 2007

New England Tuberculosis Retreat.Broad Institute, 2007 Institute Lecture, Gates Foundation Grand Challenges in Global Health Joint Meeting on TB Projects.Max Plank Institute, Berlin, Germany, June 5, 2007 Plenary Talk, "Genome Code s and Systems Geno mics", 6th Geo rgia Tech Inte rnational Conference on Bioinformatics.Atlanta, Georgia, Nov 15, 2007

Systems Biology of Yeast.Helsinki, 2006

Plenary Lecture, Eighth International Mycological Congress.Cairns Australia, August 20-25, 2006

TB Day.Broad Institute, 2006

Departmental Seminar, Program in Genet ics and Genomics and the Insti tute for Genome Sciences and Policy.Duke University, March 13, 2006 ESF-EMBO Symposium, Comparative Genomics of Euka ryotic Microorganisms.San Feliu d e

Guixols, 2005

105th General Meeting of the American Society for Microbiology.Atlanta GA, June 5-9, 2005

British Mycological Society Annual Meeting.Manchester UK, September 5-8, 2005 "Fungal Comparative Genomics". Royal Netherlands Academy of Arts and Sciences, Academy Colloquium: "Fungal Phylogenomics".Amsterdam, May 11-12, 2004 "Fungal Comparative G enomics". Institute Pasteur, Departme nt of Genome Structure and

Dynamics Seminar.Paris, May 13, 2004

"Fungal Comparative Genomics". Fourth Annual RECOMB Satellite meeting on DNA Sequencing

Technologies and ComputationMay 22-23, 2004

"Fungal Comparative Genomics". IMB Seminar.University of Oregon, Oct 19, 2004 The First International Fungal Proteomics Symposium.Portland, OR, October 20-24, 2004 "Fungal Genomics at the WICGR: N eurospora and beyond" . Biology of Filamentou s Fungi (PboFF) 12th Annual Symposium: "Fungal Genomics and Bioinformatics".Texas A&M University,

April 25-26, 2003

Biology of Filamentous Fungi (PboFF) 11th Annual Symposium.Texas A&M University, April 25, 2003
"Sequencing, annotation, and preliminary analysis of the Neurospora crassa genome". Biology of Filamentous Fungi (PboFF) 12th Annu al Symposium: "Fung al Genomics and Bioinformatics".Texas A&M University, April 25-26, 2002 Biology of Filamentous Fungi (PboFF) 11th Annual Symposium.Texas A&M University, April 25, 2002
"TB Systems Biology Consortium" . Systems Biology W orking Group Meeting.Seattle, WA,

November 6, 2001

Selected Conference Presentations

Discovering the Regulatory Network of TB: Dissecting the Regulation of the Hypoxic Response. Advances in Genome Biology and Technology (2012); Marco Island, FL. Neural Information Processing Systems (2006); Vancouver.

Fungal Genetics Conference (2005); Asilomar, CA.

Advances in Genome Biology and Technology (2004); Marco Island. Neurospora Genetics Conference (2004); Asilomar, CA.

Fungal Genetics Conference (2003); Asilomar, CA.

Human Annotation Workshop (2002); Hinxton, UK.

The Biology of Genomes (2002); Cold Spring Harbor Laboratories.

Genome Informatics (2002); Hinxton, UK.

Neurospora Genetics Conference (2002); Asilomar, CA. The Biology of Genomes (2001); Cold Spring Harbor Laboratories.

Genome Informatics (2001); Hinxton, UK.

Gordon Research Confer ence, Archaea:Ecolog y, Metabolism & Molecular Biology (2001);

Proctor Academy, NH.