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1

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

Comas, Iñaki, Borrell, Sonia, Roetzer, Andreas, Rose, Graham, Malla, Bijaya, Kato-Maeda, Midori, Galagan, James, Niemann, Stefan, Gagneux, Sebastien

Journal:

Nature Genetics

Year:

2011

Language:

english

File:

PDF, 647 KB

english, 2011

2

Cryptococcal antigenemia is associated with meningitis or death in HIV-infected adults with CD4 100â200 cells/mm3

Wykowski, James, Galagan, Sean R., Govere, Sabina, Wallis, Carole L., Moosa, Mahomed-Yunus, Celum, Connie, Drain, Paul K.

Journal:

BMC Infectious Diseases

Year:

2020

Language:

english

File:

PDF, 455 KB

english, 2020

3

Redefining fundamental concepts of transcription initiation in bacteria

MejÃa-Almonte, Citlalli, Busby, Stephen J. W., Wade, Joseph T., van Helden, Jacques, Arkin, Adam P., Stormo, Gary D., Eilbeck, Karen, Palsson, Bernhard O., Galagan, James E., Collado-Vides, Julio

Journal:

Nature Reviews Genetics

Year:

2020

File:

PDF, 1.94 MB

2020

4

The genome sequence of the filamentous fungus Neurospora crassa

Read, Nick D., Jaffe, David, FitzHugh, William, Ma, Li-Jun, Smirnov, Serge, Purcell, Seth, Galagan, James E., Calvo, Sarah E., Borkovich, Katherine A., Selker, Eric U.

Journal:

Year:

2003

Language:

english

File:

PDF, 641 KB

english, 2003

5

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

Galagan, James E., Calvo, Sarah E., Cuomo, Christina, Ma, Li-Jun, Wortman, Jennifer R., Batzoglou, Serafim, Lee, Su-In, Baştürkmen, Meray, Spevak, Christina C., Clutterbuck, John

Journal:

Year:

2005

Language:

english

File:

PDF, 1.29 MB

english, 2005

6

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

Comas, Iñaki, Chakravartti, Jaidip, Small, Peter M, Galagan, James, Niemann, Stefan, Kremer, Kristin, Ernst, Joel D, Gagneux, Sebastien

Journal:

Nature Genetics

Year:

2010

Language:

english

File:

PDF, 600 KB

english, 2010

7

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

Ford, Christopher B, Lin, Philana Ling, Chase, Michael R, Shah, Rupal R, Iartchouk, Oleg, Galagan, James, Mohaideen, Nilofar, Ioerger, Thomas R, Sacchettini, James C, Lipsitch, Marc

Journal:

Nature Genetics

Year:

2011

Language:

english

File:

PDF, 784 KB

english, 2011

8

Prognostic significance of the labeling of Adnab-9 in pancreatic intraductal papillary mucinous neoplasms

Martin Tobi, James Hatfield, Volkan Adsay, Katherine Galagan, Richard Kozarek, Mitsuhiro Inagaki, Shinichi Kasai, Yoshihiko Tokusashi, Takeshi Obara, Ralph H. Hruban, John Lough, Alan N. Barkun, Manso

Journal:

Journal of Gastrointestinal Cancer

Year:

2001

Language:

english

File:

PDF, 179 KB

english, 2001

9

RIP: the evolutionary cost of genome defense

James E. Galagan, Eric U. Selker

Journal:

Trends in Genetics

Year:

2004

Language:

english

File:

PDF, 405 KB

english, 2004

10

TB database 2010: Overview and update

James E. Galagan, Peter Sisk, Christian Stolte, Brian Weiner, Michael Koehrsen, Farrell Wymore, T.B.K. Reddy, Jeremy D. Zucker, Reinhard Engels, Marcel Gellesch, Jeremy Hubble, Heng Jin, Lisa Larson,

Journal:

Year:

2010

Language:

english

File:

PDF, 3.59 MB

english, 2010

11

Positive selection for unpreferred codon usage in eukaryotic genomes

Daniel E Neafsey, James E Galagan

Journal:

BMC Evolutionary Biology

Year:

2007

Language:

english

File:

PDF, 321 KB

english, 2007

12

Short-term genome evolution ofListeria monocytogenesin a non-controlled environment

Renato H Orsi, Mark L Borowsky, Peter Lauer, Sarah K Young, Chad Nusbaum, James E Galagan, Bruce W Birren, Reid A Ivy, Qi Sun, Lewis M Graves, Bala Swaminathan, Martin Wiedmann

Journal:

Year:

2008

Language:

english

File:

PDF, 574 KB

english, 2008

13

How accurate can genetic predictions be?

Dreyfuss, Jonathan M, Levner, Daniel, Galagan, James E, Church, George M, Ramoni, Marco F

Journal:

Year:

2012

Language:

english

File:

PDF, 289 KB

english, 2012

14

Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi

Hood, Heather M., Neafsey, Daniel E., Galagan, James, Sachs, Matthew S.

Journal:

Annual Review of Microbiology

Year:

2009

Language:

english

File:

PDF, 3.18 MB

english, 2009

15

The Mycobacterium tuberculosis regulatory network and hypoxia

Galagan, James E., Minch, Kyle, Peterson, Matthew, Lyubetskaya, Anna, Azizi, Elham, Sweet, Linsday, Gomes, Antonio, Rustad, Tige, Dolganov, Gregory, Glotova, Irina, Abeel, Thomas, Mahwinney, Chris, Ke

Journal:

Year:

2013

Language:

english

File:

PDF, 569 KB

english, 2013

16

Cross-kingdom patterns of alternative splicing and splice recognition

Abigail M McGuire, Matthew D Pearson, Daniel E Neafsey, James E Galagan

Journal:

Year:

2008

Language:

english

File:

PDF, 515 KB

english, 2008

17

Mechanisms of intron gain and loss inCryptococcus

Thomas J Sharpton, Daniel E Neafsey, James E Galagan, John W Taylor

Journal:

Year:

2008

Language:

english

File:

PDF, 639 KB

english, 2008

18

Genomic insights into tuberculosis

Galagan, James E.

Journal:

Nature Reviews Genetics

Year:

2014

Language:

english

File:

PDF, 2.60 MB

english, 2014

19

Adnab-9, a prognostic marker in pancreatic neoplasia

Tobi, Martin, James, Hatfield, Suzanne, Fligiel E., Adsay, Volkan, Galagan, Kate, Kozarek, Richard A., Inagaki, Mitsuhiro, Kasai, Shinichi, Tokusashi, Yoshihiko, Obara, Takeshi, Hruban, Ralph H., Loug

Journal:

Gastroenterology

Year:

2000

Language:

english

File:

PDF, 180 KB

english, 2000

20

Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction

Gomes, Antonio L.C., Abeel, Thomas, Peterson, Matthew, Azizi, Elham, Lyubetskaya, Anna, Carvalho, Luís, Galagan, James

Journal:

Genome Research

Year:

2014

Language:

english

File:

PDF, 1.12 MB

english, 2014

21

The DNA-binding network of Mycobacterium tuberculosis

Minch, Kyle J., Rustad, Tige R., Peterson, Eliza J. R., Winkler, Jessica, Reiss, David J., Ma, Shuyi, Hickey, Mark, Brabant, William, Morrison, Bob, Turkarslan, Serdar, Mawhinney, Chris, Galagan, Jame

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 1.07 MB

english, 2015

22

The American Dental Association Film Library/Content and financing of state dental health programs: introduction to symposium/Determining the Content of a State Dental Health Program/Financial Support for the State Dental Program/Why State Funds were Obtained/How State Funds were ObtainedRole of The Dentist on State and Local Boards of Health/Proper Administrative Status for the Dental Health Unit in a State Health Department/The Amended Hospital Construction Act: How It Affects Dentistry/Summary of Discussion on Cooperative Projects of State Health Departments and State Dental Societies/Changes in the distribution of dentists during 1952–1954/Operation cue/Revision of list of certified dental materials/Resin cements/Revision of list of cer

Brock, David W., Galagan, Donald J., Sebelius, Carl L., Smith, Doyle J., Vaughn, James J., Oliver, Oren A., Dodd, Lloyd H., Garvey, Francis J., Sebelius, Carl L.

Journal:

Journal of the American Dental Association

Year:

1955

Language:

english

File:

PDF, 1.77 MB

english, 1955

23

[American Thoracic Society American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California - ()] C60. ADVANCES IN DIAGNOSIS OF ACTIVE TUBERCULOSIS DISEASE - Mutations In Genes For Efflux Pumps And Pentapeptide Repeat Proteins Are Associated With Fluoroquinolone Resistance In Mycobacterium Tuberculosis

Eilertson, Brandon O., Maruri, Fernanda, Blackman, Amondrea, Shaffer, Christian, Mawhinney, Chris, Peterson, Matthew, Galagan, James, Sterling, Timothy R.

Year:

2012

Language:

english

File:

PDF, 21 KB

english, 2012

24

SPIE Proceedings [SPIE Symposium on High-Power Lasers and Applications - San Jose, CA (Saturday 22 January 2000)] Solid State Lasers IX - Co2+:MgAl2O4 crystal passive Q-switch performance at 1.34, 1.44, and 1.54 μm

Wu, Ruikun, Myers, John D., Myers, Michael J., Denker, Boris I., Galagan, Boris I., Sverchkov, Sergey E., Hutchinson, James A., Trussel, Ward, Scheps, Richard

Year:

2000

Language:

english

File:

PDF, 533 KB

english, 2000

25

Large-scale identification of genetic design strategies using local search

Lun, Desmond S, Rockwell, Graham, Guido, Nicholas J, Baym, Michael, Kelner, Jonathan A, Berger, Bonnie, Galagan, James E, Church, George M

Journal:

Molecular Systems Biology

Year:

2009

Language:

english

File:

PDF, 723 KB

english, 2009

26

Patterns of Intron Gain and Loss in Fungi

Nielsen, Cydney B., Friedman, Brad, Birren, Bruce, Burge, Christopher B., Galagan, James E.

Journal:

Year:

2004

Language:

english

File:

PDF, 527 KB

english, 2004

27

The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations

Pepperell, Caitlin S., Casto, Amanda M., Kitchen, Andrew, Granka, Julie M., Cornejo, Omar E., Holmes, Eddie C., Birren, Bruce, Galagan, James, Feldman, Marcus W., Sassetti, Christopher M.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.22 MB

english, 2013

28

Pneumococcal Capsular Polysaccharide Structure Predicts Serotype Prevalence

Weinberger, Daniel M., Trzciński, Krzysztof, Lu, Ying-Jie, Bogaert, Debby, Brandes, Aaron, Galagan, James, Anderson, Porter W., Malley, Richard, Lipsitch, Marc, Bishai, William

Journal:

Year:

2009

Language:

english

File:

PDF, 389 KB

english, 2009

29

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

Colijn, Caroline, Brandes, Aaron, Zucker, Jeremy, Lun, Desmond S., Weiner, Brian, Farhat, Maha R., Cheng, Tan-Yun, Moody, D. Branch, Murray, Megan, Galagan, James E., Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.16 MB

english, 2009

30

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

Dreyfuss, Jonathan M., Zucker, Jeremy D., Hood, Heather M., Ocasio, Linda R., Sachs, Matthew S., Galagan, James E., Maranas, Costas D.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.74 MB

english, 2013

31

Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon

Ranganathan, Sridevi, Bai, Guangchun, Lyubetskaya, Anna, Knapp, Gwendowlyn S., Peterson, Matthew W., Gazdik, Michaela, Gomes, Antonio L. C., Galagan, James E., McDonough, Kathleen A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 5.95 MB

english, 2015

32

Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value

Farhat, Maha R, Sultana, Razvan, Iartchouk, Oleg, Bozeman, Sam, Galagan, James, Sisk, Peter, Stolte, Christian, Nebenzahl-Guimaraes, Hanna, Jacobson, Karen, Sloutsky, Alexander, Kaur, Devinder, Posey,

Journal:

American Journal of Respiratory and Critical Care Medicine

Year:

2016

Language:

english

File:

PDF, 2.13 MB

english, 2016

33

Dothideomycete-Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum

James K. Hane, Rohan G. T. Lowe, Peter S. Solomon, Kar-Chun Tan, Conrad L. Schoch, Joseph W. Spatafora, Pedro W. Crous, Chinappa Kodira, Bruce W. Birren, James E. Galagan, Stefano F. F. Torriani, Bruc

Journal:

Year:

2007

Language:

english

File:

PDF, 4.64 MB

english, 2007

34

Metabolic modeling predicts metabolite changes inMycobacterium tuberculosis

Garay, Christopher D., Dreyfuss, Jonathan M., Galagan, James E.

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

35

Committee on Professional Education

Parran, Thomas, Mattison, Berwyn F., Bierman, Jessie M., Boatman, Ralph H., Coker, Robert E., Felix, Robert H., Galagan, Donald J., James, George, Mason, Karl M., Murphy, Marion I., Reader, George G.,

Journal:

American Journal of Public Health and the Nations Health

Year:

1962

Language:

english

File:

PDF, 213 KB

english, 1962

36

Rhinovirus Inhibits Antigen-Specific T Cell Proliferation through an Intercellular Adhesion Molecule-1-Dependent Mechanism

James E. Gern, Bina Joseph, Dawn M. Galagan, Wayne R. Borcherding and Elliot C. Dick

Journal:

The Journal of Infectious Diseases

Year:

1996

Language:

english

File:

PDF, 1.55 MB

english, 1996

37

Transcription Factor Binding Site Mapping Using ChIP-Seq

Galagan, James, Lyubetskaya, Anna, Schoolnik, Gary, Jaini, Suma, Peterson, Matthew, Gomes, Antonio, Raman, Sahadevan, Tae Park, Sang

Journal:

Microbiology Spectrum

Year:

2014

Language:

english

File:

PDF, 2.87 MB

english, 2014

38

Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics

Manson, Abigail L., Abeel, Thomas, Galagan, James E., Sundaramurthi, Jagadish Chandrabose, Salazar, Alex, Gehrmann, Thies, Shanmugam, Siva Kumar, Palaniyandi, Kannan, Narayanan, Sujatha, Swaminathan,

Journal:

Clinical Infectious Diseases

Year:

2017

Language:

english

File:

PDF, 930 KB

english, 2017

39

Reply to Lee and Howden

Manson, Abigail L, Abeel, Thomas, Galagan, James, Chandrabose Sundaramurthi, Jagadish, Shanmugam, Siva Kumar, Palaniyandi, Kannan, Narayanan, Sujatha, Swaminathan, Soumya, Earl, Ashlee M

Journal:

Clinical Infectious Diseases

Year:

2017

Language:

english

File:

PDF, 79 KB

english, 2017

40

The Luke S. Class Action Suit: A Lesson in System Change

Taylor, John M., Tucker, James A., Galagan, James E.

Journal:

Exceptional Children

Year:

1986

Language:

english

File:

PDF, 872 KB

english, 1986

41

Psychoeducational Testing: Turn Out the Lights, the Party's over

Galagan, James E.

Journal:

Exceptional Children

Year:

1985

Language:

english

File:

PDF, 1.57 MB

english, 1985

42

Conserved Secondary Structures in Aspergillus

McGuire, Abigail Manson, Galagan, James E., Christoffels, Alan

Journal:

Year:

2008

Language:

english

File:

PDF, 432 KB

english, 2008

43

Resource Competition May Lead to Effective Treatment of Antibiotic Resistant Infections

Gomes, Antonio L. C., Galagan, James E., Segrè, Daniel, McCaw, James M.

Journal:

Year:

2013

Language:

english

File:

PDF, 915 KB

english, 2013

44

Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

Krueger, Andrew S., Munck, Christian, Dantas, Gautam, Church, George M., Galagan, James, Lehár, Joseph, Sommer, Morten O. A., Fong, Stephen S.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.56 MB

english, 2016

45

A FÃ¶rster Resonance Energy TransferâBased Ratiometric Sensor with the Allosteric Transcription Factor TetR

Nguyen, Thuy T., Chern, Margaret, Baer, R C., Galagan, James, Dennis, Allison M.

Journal:

Year:

2020

File:

PDF, 708 KB

2020

46

Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria

Wu, Xiaolin, Cao, Bo, Aquino, Patricia, Chiu, Tsu-Pei, Chen, Chao, Jiang, Susu, Deng, Zixin, Chen, Shi, Rohs, Remo, Wang, Lianrong, Galagan, James E., Dedon, Peter C.

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 1.38 MB

2020

47

Surface Immobilized Nucleic AcidâTranscription Factor Quantum Dots for Biosensing

Chen, Mingfu, Nguyen, Thuy T., Varongchayakul, Nitinun, Grazon, ChloÃ©, Chern, Margaret, Baer, R. C., Lecommandoux, SÃ©bastien, Klapperich, Catherine M., Galagan, James E., Dennis, Allison M., Grinsta

Journal:

Advanced Healthcare Materials

Year:

2020

File:

PDF, 1.86 MB

2020

48

Transcription Factor Based SmallâMolecule Sensing with a Rapid Cell Phone Enabled Fluorescent Bead Assay

Chern, Margaret, Garden, Padric M., Baer, R C., Galagan, James E., Dennis, Allison M.

Journal:

Angewandte Chemie International Edition

Year:

2020

File:

PDF, 1.54 MB

2020