Strong Laboratory for Computational and Molecular Genomics

Center for Genes, Environment, and Health
National Jewish Health, Denver, CO



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Mycobacterial Genomes



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Microbiology: Bacterial transmission tactics
Michael Strong and Rebecca M. Davidson. Nature, 543: 495-496 (2017).

Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease
Nabeeh Hasan, Rene L. Warren, L. Elaine Epperson, Allyson Malecha, David C. Alexander, Christine Y. Turenne, Daniel McMilan, Inanc Birol, Stephen Pleasance, Robin Coope, Steven J. M. Jones, Marc Romney, Monica Ng, Tracy Chan, Mabel Rodrigues, Patrick Tang, Jennifer Gardy, Michael Strong. Genome Announcements 5:37 e00963-17 (2017).

Complete Genome Sequence of Mycobacterium chimaera Strain CDC2015-22-71.
Nabeeh A Hasan, Adrian Lawsin, K. Allison Perry, Efe Alyanak, Nadege C. Toney, Allyson Malecha, Ms. Lori A Rowe, Dhwani Batra, Heather Moulton-Meissner, Jeffrey R. Miller, Michael Strong, Alison Laufer Halpin. Genome Announcements 5:31 e00693-17 (2017).

Mycobacterium talmoniae sp. nov., a slowly growing mycobacterium isolated from human respiratory samples.
Rebecca M. Davidson, Mary Ann De Groote, Jamie Marola, Sarah Buss, Victoria Jones, Michael R. McNeil, Alison G. Freifeld, L. Elaine Epperson, Nabeeh A. Hasan, Mary Jackson, Peter C. Iwen, Max Salfinger, Michael Strong. In Press, International Journal of Systematic and Evolutionary Microbiology (2017).

Mycobacterium abscessus displays fitness for fomite transmission.
Kenneth Malcolm, Silvia Caceres, Jennifer Honda, Rebecca Davidson, L. Epperson, Michael Strong, Edward Chan, and Jerry Nick. In press, Applied and Environmental Microbiology (2017).

Complete Genome Sequence of Mycobacterium avium subsp. hominissuis Strain H87 Isolated from an Indoor Water Sample
Xueyan Zhao, L. Elaine Epperson, Nabeeh A. Hasan, Jennifer R. Honda, Edward D. Chan, Michael Strong, Nicholas D. Walter, Rebecca M. Davidson. Genome Announcements, 5:e00189-17 (2017).

A Geospatial Epidemiologic Analysis of Nontuberculous Mycobacterial Infection: An Ecological Study in Colorado
Ettie M. Lipner, David Knox, Joshua French, Jordan Rudman, Michael Strong, James L. Crooks. Annals of the American Thoracic Society, In Press (2017).

... Gargi Datta, Nabeeh A Hasan, Michael Strong, Sonia M Leach. in prep. (2017).

... Jennifer R. Honda, Tamara Hess, Rachel Fickes, Pitchaimani Kandasamy, Thomas Danhorn, Nabeeh A. Hasan, L. Elaine Epperson, Rebecca M. Davidson, Kendra Walton, Danny Hesser, Scott Alper, Carolina Mehaffy, Sonia M. Leach, Brian O'Connor, Michael Strong, Sonia C. Flores, Dennis R. Voelker, Karen M. Dobos, Edward D. Chan. submitted (2017).

Complete Genome Sequence of Mycobacterium chimaera Strain AH16
Nabeeh Hasan, Jennifer Honda, Rebecca Davidson, L. Epperson, Matthew Bankowski, Edward Chan, and Michael Strong. Genome Announcements, 4:e01276-16 (2016).

Environmental Nontuberculous Mycobacteria in the Hawaiian Islands
Jennifer R. Honda, Nabeeh A. Hasan, Rebecca M. Davidson, Myra D. Williams, L. Elaine Epperson, Paul R. Reynolds, Terry R. Smith, Elena Iakhiaeva, Matthew J. Bankowski, Richard J. Wallace Jr., Edward D. Chan, Joseph O. Falkinham III, Michael Strong. PLOS Neglected Tropical Diseases, 10(10): e0005068. (2016).

Notes from the Field: Mycobacterium chimaera Contamination of Heater-Cooler Devices Used in Cardiac Surgery - United States.
Kiran M. Perkins, Adrian Lawsin, Nabeeh A. Hasan, Michael Strong, Alison L. Halpin, Rachael R. Rodger, Heather Moulton-Meissner, Matthew B. Crist, Suzanne Schwartz, Julia Marders, Charles L Daley, Max Salfinger, Joseph F. Perz. Morbidity and Mortality Weekly Report (MMWR) , 65(40);1117-1118 (2016).

Pathogen Surveillance and Characterization using Whole Genome Sequencing: The Colorado Cystic Fibrosis Research and Development Program - Molecular and Genomics Core.
Michael Strong, Nabeeh A. Hasan, L. Elaine Epperson. NTM-TB Insights. September Issue (2016).

Sequence analysis of fluoroquinolone resistance associated genes gyrA and gyrB in clinical Mycobacterium tuberculosis isolates from suspected multidrug-resistant tuberculosis patients in New Delhi, India.
Ritu Singhal, Paul R. Reynolds, Jamie Marola, L. Elaine Epperson, Jyoti Arora, Rohit Sarin, Vithal Prasad Myneedu, Michael Strong, Max Salfinger. Journal of Clinical Microbiology, 54:9 2298-2305 (2016).

Longitudinal Whole Genome Analysis of Pre and Post Drug Treatment Mycobacterium tuberculosis Isolates Reveals Progressive Steps to Drug Resistance.
Gargi Datta, Luisa M. Nieto, Rebecca M. Davidson, Carolina Mehaffy, Caroline Pederson, Karen M. Dobos, Michael Strong. Tuberculosis, 98: 50-55 (2016).

Network Analysis of Human Genes Influencing Susceptibility to Mycobacterial Infections
Ettie Lipner, Benjamin J. Garcia, Michael Strong. PLOS ONE. 11: e0146585, (2016).

Adaptation of M. tuberculosis to impaired host immunity in HIV-infected patients.
Nicholas D. Walter, Bouke C. de Jong, Benjamin J. Garcia, Gregory M. Dolganov, William Worodria, Patrick Byanyima, Emmanuel Musisi, Laurence Huang, Edward D. Chan, Tran T. Van, Martin Antonio, Abigail Ayorinde, Midori Kato-Maeda, Payam Nahid, Ann M. Leung, Andrew Yen, Tasha E. Fingerlin, Katerina Kechris, Michael Strong, Martin I. Voskuil, J. Lucian Davis, Gary K. Schoolnik. Journal of Infectious Diseases, 214: 1205 - 1211 (2016).

Sputum is a surrogate for bronchoalveolar lavage for monitoring Mycobacterium tuberculosis transcriptional profiles in TB patients
Benjamin J. Garcia, Andre G Loxton, Gregory M. Dolganov, Tran T Van, J. Lucian Davis, Bouke C de Jong, Martin I Voskuil, Sonia M. Leach, Gary K. Schoolnik, Gerhard Walzl, Michael Strong, Nicholas D. Walter. Tuberculosis 100: 89-94 (2016).

MycoBASE: expanding the functional annotation coverage of mycobacterial genomes.
Benjamin J. Garcia, Gargi Datta, Rebecca M. Davidson, Michael Strong. BMC Genomics 16:1102, (2015).

Draft Genome Sequence of Mycobacterium chelonae Type Strain ATCC 35752.
Nabeeh A. Hasan, Rebecca M. Davidson, Vinicius Calado Nogueira de Moura, Benjamin J. Garcia, Paul R. Reynolds, L. Elaine Epperson, Eveline Farias-Hesson, Mary Ann DeGroote, Mary Jackson, Michael Strong. Genome Announcements, e00536. (2015).

Blood transcriptional biomarkers for active TB among US patients: A case-control study with systematic cross-classifier evaluation.
Nicholas D Walter, Mikaela A. Miller, Joshua Vasquezd, Marc Weiner, Adam Chapman, Melissa Engle, Michael Higgins, Amy M. Quinones, Vanessa Roselli, Elizabeth Canon, Christina Yoon, Adithya Cattamanchi, J Lucian Davis, Tzu Phang, Robert S Stearman, Gargi Datta, Benjamin J Garcia, Charles L Daley, Michael Strong, Katerina Kechris, Tasha E. Fingerlin, Randall Reves, Mark W Geraci. Journal of Clinical Microbiology 18 November 2015, doi: 10.1128/JCM.01990-15 (2015).

Power and Limitations of Whole Genome Sequencing in Mycobacteria.
Michael Strong. NTM-TB Insights. May (2015).

Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis during treatment of human tuberculosis.
Nicholas D. Walter, Gregory M. Dolganov, Benjamin J. Garcia, William Worodria, Alfred Andama, Emmanuel Musisi, Irene Ayakaka, Tran T. Van, Martin I. Voskuil, Bouke C. de Jong, Rebecca M. Davidson, Tasha E. Fingerlin, Katerina Kechris, Claire Palmer, Payam Nahid, Charles L. Daley, Mark Geraci, Laurence Huang, Adithya Cattamanchi, Michael Strong, Gary K. Schoolnik, J. Lucian Davis. Journal of Infectious Diseases. 212: 990-998 (2015).

Genome sequencing of Mycobacterium abscessus isolates from patients in the United States and comparisons to globally diverse clinical strains.
Rebecca M. Davidson, Nabeeh A. Hasan, Paul R. Reynolds, Sarah Totten, Benjamin Garcia, Adrah Levin, Preveen Ramamoorthy, Leonid Heifets, Charles L. Daley, and Michael Strong. Journal of Clinical Microbiology, 52:3573-3582 (2014).

Network and Matrix Analysis of the Respiratory Disease Interactome.
Benjamin Garcia, Gargi Datta, Gregory P Cosgrove, Michael Strong. BMC Systems Biology, 8:34 (2014).

Extracellular HCV-Core Protein Induces an Immature Regulatory Phenotype in NK Cells: Implications for Outcome of Acute Infection
Lucy Golden-Mason, Young S. Hahn, Michael Strong, Linling Cheng, Hugo R. Rosen. PLOS ONE 9:e103219 (2014).

A Minimum Variance Method for Genome-wide Data-driven Normalization of qRT-PCR Expression Data.
Benjamin Garcia, Nicholas D Walter, Gregory Dolganov, Marc Coram, J. Lucian Davis, Gary K. Schoolnik, Michael Strong. Analytical Biochemistry, 458: 11-13 (2014).

Drug-Resistant Tuberculosis: A Genetic Analysis Using Online Bioinformatics Tools.
Jessica M. Taylor, Rebecca M. Davidson, Michael Strong. American Biology Teacher, 76:386-394 (2014).

High Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Geographically Distant Outbreaks.
Herv� Tettelin, Rebecca M. Davidson, Sonia Agrawal, Moira L. Aitken, Shamira Shallom, Nabeeh A. Hasan, Michael Strong, Vinicius Calado Nogueira de Moura, Mary Ann De Groote, Rafael S. Duarte, Erin Hine, Sushma Parankush, Qi Su, Sean C. Daugherty, Claire M. Fraser, Barbara A. Brown-Elliott, Richard J. Wallace Jr., Steven M. Holland, Elizabeth P. Sampaio, Kenneth N. Olivier, Mary Jackson, Adrian M. Zelazny. Emerging Infectious Diseases, 20:3 (2014).

HspX Vaccination and Role in Virulence in the Guinea Pig Model of Tuberculosis.
Agatha E. Wieczorek, Jolynn L. Troudt, Phillip Knabenbauer, Jennifer Taylor, Rebecca L. Pavlicek, Russell Karls, Anne Hess, Rebecca M. Davidson, Michael Strong, Helle Bielefeldt-Ohmann, Angelo A. Izzo, Karen M. Dobos. Pathogens and Disease, Feb 24 (2014).

Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains.
Rebecca M. Davidson, Nabeeh A Hasan, Vinicius Calado Nogueira de Moura, Rafael Silva Duarte, Mary Jackson, Michael Strong. Infection, Genetics, and Evolution 20C: 292-297. (2013).

Genome Sequence of an Epidemic Isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil.
Rebecca M. Davidson, Paul R. Reynolds, Eveline Farias-Hesson, Rafael Silva Duarte, Mary Jackson, Michael Strong. Genome Announcements 1:4 e00617-13. (2013).

Galectin-9 functionally impairs natural killer (NK) cells in humans and mice.
Lucy Golden-Mason, Rachel McMahan, Michael Strong, Richard Reisdorph, Spencer Mahaffey, Brent Palmer, Linling Cheng, Caroline Kulesza, Mitsuomi Hirashima, Toshiro Niki, and Hugo Rosen. Journal of Virology, 87:4835-4845. (2013).

Translating basic science insight into public health action for multidrug- and extensively drug-resistant tuberculosis.
Walter ND, Strong M, Belknap R, Ordway DJ, Daley CL, Chan ED. Respirology. 17(5):772-791. (2012).

Research, Collaboration, and Open Science using Web 2.0. Kevin Shee*, Michael Strong*, Nicholas J. Guido, Robert Lue, George M. Church, Alain Viel. *Equal contribution, Journal of Microbiology and Biology Education, 11:2 p130-134, (2010).

Reducing Global Health Disparities through Research, Education, and International Collaboration .
Michael Strong. Center for Strategic and International Studies, Smart Global Health Policy Report p47-48 (2010). Research Spotlight , Full Report

Tuberculosis Drug Resistance Mutation Database .
Andreas Sandgren, Michael Strong, Preetika Mutukrishnan, Brian K. Weiner, George M. Church, Megan B. Murray. PLoS Medicine 6:2 (2009). Link , Database

The Protein Network as a Tool for Finding Novel Drug Targets.
Michael Strong and David Eisenberg. Book Chapter in Systems Biological Approaches in Infectious Diseases. Edited by H.I.M Boshoff and C.E. Barry III, Birkhauser. Verlag Publishing. Progress in Drug Research, 64:191, 193-215 (2007). Link

Functional linkages can reveal protein complexes for structure determination.
Kim SM, Bowers PM, Pal D, Strong M, Terwilliger TC, Kaufmann M, Eisenberg D. Structure 15:1079-89 (2007). Link

Gem of an idea for a unique machine.
Michael Strong and George Church. Nature 447:112 (2007).

Toward the Structural Genomics of Complexes: Crystal Structure of a PE/PPE protein complex from Mycobacterium tuberculosis.
Michael Strong, Michael Sawaya, Shuishu Wang, Martin Philips, Duilio Cascio, and David Eisenberg. Proc. Natl. Acad. Sci. U. S. A. 103:8060-8065 (2006). Link PDB Proteopedia Link

Structural Proteomics and Computational Analysis of a Deadly Pathogen: Combating M. tuberculosis from Multiple Fronts.
Michael Strong and Celia Goulding. Book Chapter (Chapter 15) in Microbial Proteomics: Functional Biology of Whole Organisms. Edited by Ian Humphrey-Smith and Michael Hecker. Wiley Publishing, Inc. Methods Biochem Analysis 49:245-69 (2006). Link

Unique Transcriptome Signature of Mycobacterium tuberculosis in Pulmonary Tuberculosis.
Helmy Rachman, Michael Strong, Timo Ulrichs, Leander Grode, Johannes Schuchhardt, Hans Mollenkopf, George A. Kosmiadi, David Eisenberg, S.H.E. Kaufmann. Infection and Immunity 74:1233-1242. (2006). Link

Mycobacterium tuberculosis Gene Expression Profiling within the Context of Protein Networks.
Helmy Rachman*, Michael Strong*, Ulrich Schaible, Johannes Schuchhardt, Kristine Hagens, Hans Mollenkopf, David Eisenberg, Stefan H.E. Kaufmann. *Equal Contribution. Microbes and Infection. 8:747-757 (2006). Link

A specific secretion system mediates PPE41 transport in pathogenic mycobacteria.
Abdallah M. Abdallah, Theo Verboom, Fredericke Hannes, Mohamad Safi, Michael Strong, David Eisenberg, Rene Musters, Christina M.J.E. Vandenbroucke-Grauls, Ben J. Appelmelk, Joen Luirink4 and Wilbert Bitter. Molecular Microbiology 62:667-79 (2006). Link

Scientists and Societies: Community Outreach.
Michael Strong. Nature. 434, 418. (2005). Link

Protein Nanomachines.
Michael Strong. PLoS Biology Mar, 2:E73. (2004). Link

A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes.
Michael Strong, Duilio Cascio, and David Eisenberg. ASM Microbiology Education Journal 5: 30-35. (2004). Link

Genomes, Maps, and Modules: Navigating the M. tuberculosis Genome.
Michael Strong. UCLA Scientific Review 1: 28-32. (2004). Link

Visualization and Interpretation of Protein Networks in Mycobacterium tuberculosis Based on Hierarchical Clustering of Genome-Wide Functional Linkage Maps.
Michael Strong, Thomas G. Graeber, Morgan Beeby, Matteo Pellegrini, Michael J. Thompson, Todd O. Yeates, and David Eisenberg. Nucleic Acids Research, 31: 7099-7109. (2003). Link

Inference of Protein Function and Protein Linkages in M. tuberculosis Based on Prokaryotic Genome Organization: A Combined Computational Approach.
Michael Strong, Parag Mallick, Matteo Pellegrini, Michael J. Thompson, and David Eisenberg. Genome Biology 4:R59.1-R59.16. (2003). Link

2'-Ribose-ferrocene oligonucleotides for electronic detection of nucleic acids.
Yu CJ, Wang H, Wan Y, Yowanto H, Kim JC, Donilon LH, Tao C, Strong M, Chong Y. Journal of Organic Chemistry 66:2937-2942. (2001). Link

Uridine-Conjugated Ferrocene DNA Oligonucleotides: Unexpected Cyclization Reaction of the Uridine Base.
Yu, C. J.; Yowanto, H.; Wan, Y.; Meade, T. J.; Chong, Y.; Strong, M.; Donilon, L. H.; Kayyem, J. F.; Gozin, M.; Blackburn, G. F. Journal of the American Chemical Society. 122: 6767-6768. (2000). Link

Published Online

Michael Strong. NextGen VOICES, top online essay category, Response: Describe a specific experience and how it changed your science, training, or career goals. Science Online, July (2012).

Michael Strong. NextGen VOICES, top online essay category, Response: You've just been elected to your nation's highest office! In your inaugural address, announce the biggest challenge facing your country today and how you will use science to address it. Science Online, January (2013).

Michael Strong. NextGen VOICES, top online essay category, Response: What recent discovery in your field will still be remembered 200 years from now? Why? Science Online, January (2014).

Genomic and computational analysis of Mycobacterium tuberculosis drug resistance.
Gargi Datta, Rebecca Davidson, Jessica Taylor, Nabeeh Hasan, Benjamin Garcia, Michael Strong. Faculty of 1000, F1000 Posters 4: 164. (2013).

Copyright © 2011 Michael Strong