Publications by authors named "James Galagan"

81Publications

Development and Clinical Validation of Iso-IMRS: A Novel Diagnostic Assay for Malaria.

Authors:
Nikunja Kolluri Shwetha Kamath Patrick Lally Mina Zanna James Galagan Jesse Gitaka Moses Kamita Mario Cabodi Srinivasa Raju Lolabattu Catherine M Klapperich

Anal Chem 2021 Jan 19. Epub 2021 Jan 19.

Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States.

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January 2021

Transcription Factor Based Small-Molecule Sensing with a Rapid Cell Phone Enabled Fluorescent Bead Assay.

Authors:
Margaret Chern Padric M Garden R C Baer James E Galagan Allison M Dennis

Angew Chem Int Ed Engl 2020 11 18;59(48):21597-21602. Epub 2020 Sep 18.

Division of Materials Science and Engineering, Boston University, Boston, MA, USA.

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November 2020

Hydrogel-Embedded Quantum Dot-Transcription Factor Sensors for Quantitative Progesterone Detection.

Authors:
Mingfu Chen Chloé Grazon Prerana Sensharma Thuy T Nguyen Yunpeng Feng Margaret Chern R C Baer Nitinun Varongchayakul Katherine Cook Sébastien Lecommandoux Catherine M Klapperich James E Galagan Allison M Dennis Mark W Grinstaff

ACS Appl Mater Interfaces 2020 Sep 18;12(39):43513-43521. Epub 2020 Sep 18.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States.

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September 2020

Surface Immobilized Nucleic Acid-Transcription Factor Quantum Dots for Biosensing.

Authors:
Mingfu Chen Thuy T Nguyen Nitinun Varongchayakul Chloé Grazon Margaret Chern R C Baer Sébastien Lecommandoux Catherine M Klapperich James E Galagan Allison M Dennis Mark W Grinstaff

Adv Healthc Mater 2020 09 21;9(17):e2000403. Epub 2020 Jul 21.

Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.

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September 2020

Redefining fundamental concepts of transcription initiation in bacteria.

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

Nat Rev Genet 2020 11 14;21(11):699-714. Epub 2020 Jul 14.

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.

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November 2020

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

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

Proc Natl Acad Sci U S A 2020 06 9;117(25):14322-14330. Epub 2020 Jun 9.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;

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June 2020

A Förster Resonance Energy Transfer-Based Ratiometric Sensor with the Allosteric Transcription Factor TetR.

Authors:
Thuy T Nguyen Margaret Chern R C Baer James Galagan Allison M Dennis

Small 2020 04 6;16(17):e1907522. Epub 2020 Apr 6.

Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.

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April 2020

A progesterone biosensor derived from microbial screening.

Authors:
Chloé Grazon R C Baer Uroš Kuzmanović Thuy Nguyen Mingfu Chen Marjon Zamani Margaret Chern Patricia Aquino Xiaoman Zhang Sébastien Lecommandoux Andy Fan Mario Cabodi Catherine Klapperich Mark W Grinstaff Allison M Dennis James E Galagan

Nat Commun 2020 03 9;11(1):1276. Epub 2020 Mar 9.

Department of Microbiology, Boston University, Boston, MA, 02118, USA.

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March 2020

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.

Authors:
Alberto Santos-Zavaleta Heladia Salgado Socorro Gama-Castro Mishael Sánchez-Pérez Laura Gómez-Romero Daniela Ledezma-Tejeida Jair Santiago García-Sotelo Kevin Alquicira-Hernández Luis José Muñiz-Rascado Pablo Peña-Loredo Cecilia Ishida-Gutiérrez David A Velázquez-Ramírez Víctor Del Moral-Chávez César Bonavides-Martínez Carlos-Francisco Méndez-Cruz James Galagan Julio Collado-Vides

Nucleic Acids Res 2019 01;47(D1):D212-D220

Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México.

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January 2019

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.

Authors:
Alberto Santos-Zavaleta Mishael Sánchez-Pérez Heladia Salgado David A Velázquez-Ramírez Socorro Gama-Castro Víctor H Tierrafría Stephen J W Busby Patricia Aquino Xin Fang Bernhard O Palsson James E Galagan Julio Collado-Vides

BMC Biol 2018 08 16;16(1):91. Epub 2018 Aug 16.

Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.

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August 2018

Reply to Lee and Howden.

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

Clin Infect Dis 2018 01;66(1):160-161

Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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January 2018

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

Authors:
Abigail L Manson Thomas Abeel James E Galagan Jagadish Chandrabose Sundaramurthi Alex Salazar Thies Gehrmann Siva Kumar Shanmugam Kannan Palaniyandi Sujatha Narayanan Soumya Swaminathan Ashlee M Earl

Clin Infect Dis 2017 Jun;64(11):1494-1501

Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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June 2017

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.

Authors:
Abigail L Manson Keira A Cohen Thomas Abeel Christopher A Desjardins Derek T Armstrong Clifton E Barry Jeannette Brand Sinéad B Chapman Sang-Nae Cho Andrei Gabrielian James Gomez Andreea M Jodals Moses Joloba Pontus Jureen Jong Seok Lee Lesibana Malinga Mamoudou Maiga Dale Nordenberg Ecaterina Noroc Elena Romancenco Alex Salazar Willy Ssengooba A A Velayati Kathryn Winglee Aksana Zalutskaya Laura E Via Gail H Cassell Susan E Dorman Jerrold Ellner Parissa Farnia James E Galagan Alex Rosenthal Valeriu Crudu Daniela Homorodean Po-Ren Hsueh Sujatha Narayanan Alexander S Pym Alena Skrahina Soumya Swaminathan Martie Van der Walt David Alland William R Bishai Ted Cohen Sven Hoffner Bruce W Birren Ashlee M Earl

Nat Genet 2017 Mar 16;49(3):395-402. Epub 2017 Jan 16.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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March 2017

Coordinated regulation of acid resistance in Escherichia coli.

Authors:
Patricia Aquino Brent Honda Suma Jaini Anna Lyubetskaya Krutika Hosur Joanna G Chiu Iriny Ekladious Dongjian Hu Lin Jin Marianna K Sayeg Arion I Stettner Julia Wang Brandon G Wong Winnie S Wong Stephen L Alexander Cong Ba Seth I Bensussen David B Bernstein Dana Braff Susie Cha Daniel I Cheng Jang Hwan Cho Kenny Chou James Chuang Daniel E Gastler Daniel J Grasso John S Greifenberger Chen Guo Anna K Hawes Divya V Israni Saloni R Jain Jessica Kim Junyu Lei Hao Li David Li Qian Li Christopher P Mancuso Ning Mao Salwa F Masud Cari L Meisel Jing Mi Christine S Nykyforchyn Minhee Park Hannah M Peterson Alfred K Ramirez Daniel S Reynolds Nae Gyune Rim Jared C Saffie Hang Su Wendell R Su Yaqing Su Meng Sun Meghan M Thommes Tao Tu Nitinun Varongchayakul Tyler E Wagner Benjamin H Weinberg Rouhui Yang Anastasia Yaroslavsky Christine Yoon Yanyu Zhao Alicia J Zollinger Anne M Stringer John W Foster Joseph Wade Sahadaven Raman Natasha Broude Wilson W Wong James E Galagan

BMC Syst Biol 2017 01 6;11(1). Epub 2017 Jan 6.

Department of Biomedical Engineering, Boston University, Boston, USA.

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January 2017

The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion.

Authors:
Rigzin Dekhang Cheng Wu Kristina M Smith Teresa M Lamb Matthew Peterson Erin L Bredeweg Oneida Ibarra Jillian M Emerson Nirmala Karunarathna Anna Lyubetskaya Elham Azizi Jennifer M Hurley Jay C Dunlap James E Galagan Michael Freitag Matthew S Sachs Deborah Bell-Pedersen

G3 (Bethesda) 2017 01 5;7(1):129-142. Epub 2017 Jan 5.

Department of Biology, Texas A&M University, College Station, Texas 77843

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January 2017

Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses.

Authors:
Jared D Sharp Atul K Singh Sang Tae Park Anna Lyubetskaya Matthew W Peterson Antonio L C Gomes Lakshmi-Prasad Potluri Sahadevan Raman James E Galagan Robert N Husson

PLoS One 2016 22;11(3):e0152145. Epub 2016 Mar 22.

Division of Infectious Diseases, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America.

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August 2016

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

Authors:
Maha R Farhat Razvan Sultana Oleg Iartchouk Sam Bozeman James Galagan Peter Sisk Christian Stolte Hanna Nebenzahl-Guimaraes Karen Jacobson Alexander Sloutsky Devinder Kaur James Posey Barry N Kreiswirth Natalia Kurepina Leen Rigouts Elizabeth M Streicher Tommie C Victor Robin M Warren Dick van Soolingen Megan Murray

Am J Respir Crit Care Med 2016 09;194(5):621-30

2 Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts.

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September 2016

Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis.

Authors:
Andrew S Krueger Christian Munck Gautam Dantas George M Church James Galagan Joseph Lehár Morten O A Sommer

PLoS One 2016 28;11(1):e0147651. Epub 2016 Jan 28.

Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Hørsholm, Denmark.

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July 2016

Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis.

Authors:
Christopher D Garay Jonathan M Dreyfuss James E Galagan

BMC Syst Biol 2015 Sep 16;9:57. Epub 2015 Sep 16.

Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.

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September 2015

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

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

Nucleic Acids Res 2016 Jan 10;44(1):134-51. Epub 2015 Sep 10.

Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA

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January 2016