Strong Laboratory for Computational and Molecular Genomics

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



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... Stephanie Dawrs et al. (submitted 2022).

Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection.
Jerry A. Nick, Rebekah M. Dedrick, Alice L. Gray, Eszter K. Vladar, Bailey E. Smith, Krista G. Freeman, Kenneth C. Malcolm, L. Elaine Epperson, Nabeeh A. Hasan, Jo Hendrix, Kimberly Callahan, Kendra Walton, Brian Vestal, Emily Wheeler, Noel M. Rysavy, Katie Poch, Silvia Caceres, Valerie K. Lovell, Katherine B. Hisert, Vinicius Calado de Moura, Delphi Chatterjee, Prithwiraj De, Natalia Weakly, Stacey L. Martiniano, David A. Lynch, Charles L. Daley, Michael Strong, Fan Jia, Graham F. Hatfull, Rebecca M. Davidson. Cell 185, 1 - 15 (2022).

Soil Properties and Moisture Synergistically Influence Nontuberculous Mycobacterial Prevalence in Natural Environments of Hawai'i.
Arielle W Parsons, Stephanie N Dawrs, Stephen T Nelson, Grant J Norton, Ravleen Virdi, Nabeeh A Hasan, L Elaine Epperson, Brady Holst, Edward D Chan, Vianey Leos-Barajas, Brian J Reich, James L Crooks, Michael Strong, Krishna Pacifici, Jennifer R Honda. Appl Environ Microbiol; e0001822 (2022).

Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations.
William M. Showers, Sonia M.Leach, Katerina Kechris, Michael Strong. Infection, Genetics and Evolution 105153 (2022).

Investigating Nontuberculous Mycobacteria Transmission at the Colorado Adult Cystic Fibrosis Program
Jane E. Gross, Silvia Caceres, Katie Poch, Nabeeh A Hasan, Fan Jia, L Elaine Epperson, Ettie Lipner, Charmie Vang, Jennifer R. Honda, Matthew Strand, Vinicius Calado Nogueira de Moura, Charles L. Daley, Michael Strong, Rebecca M Davidson, Jerry A Nick. American Journal of Respiratory and Critical Care Medicine. (2022).

Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome.
Marin M, Vargas R, Harris M, Jeffrey B, Epperson LE, Durbin D, Strong M, Salfinger M, Iqbal Z, Akhundova I, Vashakidze S, Crudu V, Rosenthal A, Farhat MR. Bioinformatics, btac023 (2022).

Population Genomics and Inference of Mycobacterium avium Complex Clusters in Cystic Fibrosis Care Centers, United States.
Nabeeh A. Hasan, Rebecca M. Davidson, L. Elaine Epperson, Sara M. Kammlade, Sean Beagle, Adrah R. Levin, Vinicius Calado de Moura, Joshua J. Hunkins, Natalia Weakly, Scott D. Sagel, Stacey L. Martiniano, Max Salfinger, Charles L. Daley, Jerry A. Nick, and Michael Strong. Emerging Infectious Diseases 27:11 (2021).

Healthcare-associated links in transmission of nontuberculous mycobacteria among people with cystic fibrosis (HALT NTM) study: Rationale and study design.
Jane E. Gross, Silvia Caceres, Katie Poch, Nabeeh A. Hasan, Rebecca M. Davidson, L. Elaine Epperson, Ettie Lipner, Charmie Vang, Jennifer R. Honda, Matthew Strand, Michael Strong, Lisa Saiman, D. Rebecca Prevots, Kenneth N. Olivier, Jerry A. Nick. PLOS One 16(12): e0261628. (2021).

Dissemination of Mycobacterium abscessus via global transmission networks.
Christopher Ruis, Josephine M. Bryant, Scott C. Bell, Rachel Thomson, Rebecca M. Davidson, Nabeeh A. Hasan, Jakko van Ingen, Michael Strong, R. Andres Floto, Julian Parkhill. Nature Microbiology Sept 20 (2021).

Genomic Analysis of a Hospital-Associated Outbreak of Mycobacterium abscessus: Implications on Transmission.
Rebecca M. Davidson, Sophie E. Nick, Sara M. Kammlade, Sruthi Vasireddy, Natalia Weakly, Nabeeh A. Hasan, L. Elaine Epperson, Michael Strong, Jerry A. Nick, Barbara A. Brown-Elliott, Jason E. Stout, Sarah S. Lewis, Richard J. Wallace Jr., Arthur W. Baker. Journal of Clinical Microbiology (2021).

Genomic characterization of sporadic isolates of the dominant clone of Mycobacterium abscessus subspecies massiliense.
Rebecca M. Davidson, Jeanne B. Benoit, Sara M. Kammlade, Nabeeh A. Hasan, L. Elaine Epperson, Terry Smith, Sruthi Vasireddy, Barbara A. Brown-Elliott, Jerry A. Nick, Kenneth N. Olivier, Adrian M. Zelazny, Charles L. Daley, Michael Strong, Richard J. Wallace Jr. Scientific Reports 11: 15336 (2021).

Culturing Mycobacteria
Elizabeth Wallace, Debra Hendrickson, Nicholas Tolli, Carolina Mehaffy, María Peña, Jerry A. Nick, Phillip Knabenbaur, Jackson Watkins, Anne Simpson, Anita G. Amin, Delphi Chatterjee, Karen M. Dobos, Ramanuj Lahiri, Linda Adams, Michael Strong, Max Salfinger, Rebecca Bradford, Timothy T. Stedman, Marco A. Riojas, Manzour Hernando Hazbon. Mycobacteria Protocols. Methods in Molecular Biology, vol 2314: 1-58 (2021).

Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences
Marco A. Riojas, Andrew M. Frank, Samuel R. Greenfield, Stephen P. King, Conor J. Meehan, Michael Strong, Alice R. Wattam, Manzour Hernando Hazbon. Mycobacteria Protocols. Methods in Molecular Biology, vol 2314: 399-457 (2021).

Nontuberculous mycobacterial infection and environmental molybdenum in persons with cystic fibrosis: a case-control study in Colorado.
Ettie M Lipner, James L Crooks, Joshua French, Michael Strong, Jerry A Nick, D Rebecca Prevots. Journal of Exposure Science & Environmental Epidemiology (2021).

Simulation study and comparative evaluation of viral contiguous sequence identification tools.
Cody Glickman, Jo Hendrix, Michael Strong. BMC Bioinformatics 22:329 (2021).

Population Genomics of Mycobacterium abscessus from United States Cystic Fibrosis Care Centers.
Rebecca M Davidson , Nabeeh A Hasan , L Elaine Epperson , Jeanne B Benoit , Sara M Kammlade , Adrah R Levin , Vinicius Calado de Moura , Joshua Hunkins , Natalia Weakly , Sean Beagle , Scott D Sagel ; Stacey L. Martiniano ; Max Salfinger ; Charles L. Daley ; Jerry A Nick ; Michael Strong. Annals of the American Thoracic Society. (2021).

A molecular beacon based multiplex real-time PCR assay to subspeciate Mycobacterium abscessus and determine macrolide susceptibility.
Salvatore A.E. Marras, Liang Chen, Elena Shashkina, Rebecca M. Davidson, Michael Strong, Charles L. Daley, Barry N. Kreiswirth. Journal of Clinical Microbiology. (2021).

Analysis of SARS-CoV-2 Mutations Over Time Reveals Increasing Prevalence of Variants in the Spike Protein and RNA-Dependent RNA Polymerase
William M. Showers, Sonia M. Leach, Katerina Kechris, Michael Strong. BioRxiv, preprint, 2021.03.05.433666 (2021).

Genomic sequence characteristics and the empiric accuracy of short-read sequencing.
Maximillian Marin, Roger Vargas Jr, Michael Harris, Brendan Jeffrey, L. Elaine Epperson, David Durbin, Michael Strong, Max Salfinger, Zamin Iqbal, Irada Akhundova, Sergo Vashakidze, Valeriu Crudu, Alex Rosenthal and Maha Reda Farhat. BioRxiv, preprint, 2021.04.08.438862 (2021).

Exposure Pathways of Nontuberculous Mycobacteria Through Soil, Streams, and Groundwater, Hawai'i, USA.
Stephen T. Nelson, Schuyler Robinson, Kevin Rey, Leeza Brown, Norm Jones, Stephanie N. Dawrs, Ravleen Virdi, Grant J. Norton, L. Elaine Epperson, Nabeeh A. Hasan, Edward D. Chan, Michael Strong, Jennifer R. Honda. GeoHealth, e2020GH000350. (2021).

Simulation Study and Comparative Evaluation of Viral Contiguous Sequence Identification Tools
Cody Glickman, Jo Hendrix, Michael Strong. ResearchSquare, preprint, 10.21203/ (2021).

In-host population dynamics of Mycobacterium tuberculosis complex during active disease
Roger Vargas Jr, Luca Freschi, Maximillian Marin, L Elaine Epperson, Melissa Smith, Irina Oussenko, David Durbin, Michael Strong, Max Salfinger, Maha Reda Farhat. eLife 10:e61805 (2021).

Defining events: 2020 in hindsight
John Protzko, Isaac Z. Tanner, Morgan Daly Dedyo, JiaJia Fu, Bhavya Perma, Daniel Ari Friedman, Ada Gabriela Blidner, Juliet Tegan Johnston, Anant Kumar Srivastava, Roland Ruscher, Andreas Kupz, Michael A. Tarselli, Felicia Beardsley, Mark Martin Jensen, Nikos Konstantinides, Divyansh Agarwal, Julia Yuen, Suchitra D. Gopinath, Michael Tran Duong, Michael Strong, Matus Sotak, Katie Burnette, Samuel Nathan Kirshner, Athanasia Nikolaou, Basant A. Ali, Benedito Alves de Oliveira Junior, Elvira Sojli. Science 371:22-24 (2021).

Measurable genomic changes in Mycobacterium avium subsp. hominissuis after long-term adaptation in Acanthamoeba lenticulata and reduced persistence in macrophages.
Nabeeh A. Hasan, Grant J. Norton, Ravleen Virdi, L. Elaine Epperson, Charmie K. Vang, Brandon Hellbusch, Xiyuan Bai, Edward D. Chan, Michael Strong, Jennifer R. Honda. Journal of Bacteriology doi: 10.1128/JB.00257-20. (2021).

Lower Recovery of Nontuberculous Mycobacteria from Outdoor Hawai'i Environmental Water Biofilms Compared to Indoor Samples
Ravleen Virdi, Melissa E. Lowe, Grant J. Norton, Stephanie N. Dawrs, Nabeeh A. Hasan, L. Elaine Epperson, Cody M. Glickman, Edward D. Chan, Michael Strong, James L. Crooks, Jennifer R. Honda. Microorganisms 9(2), 224. (2021).

Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates.
Jo Hendrix, L. Elaine Epperson, David Durbin, Jennifer R. Honda, Michael Strong. Microbial Genomics (2020).

NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data
Eliah G. Overbey, Amanda M. Saravia-Butler, Zhe Zhang, Komal S. Rathi, Homer Fogle, Willian A. da Silveira, Richard J. Barker, Joseph J. Bass, Afshin Beheshti, Daniel C. Berrios, Elizabeth A. Blaber, Egle Cekanaviciute, Helio A. Costa, Laurence B. Davin, Kathleen M. Fisch, Samrawit G. Gebre, Matthew Geniza, Rachel Gilbert, Simon Gilroy, Gary Hardiman, Raúl Herranz, Yared H. Kidane, Colin P.S. Kruse, Michael D. Lee, Ted Liefeld, Norman G. Lewis, J. Tyson McDonald, Robert Meller, Tejaswini Mishra, Imara Y. Perera, Shayoni Ray, Sigrid S. Reinsch, Sara Brin Rosenthal, Michael Strong, Nathaniel J Szewczyk, Candice G.T. Tahimic, Deanne M. Taylor, Joshua P. Vandenbrink, Alicia Villacampa, Silvio Weging, Chris Wolverton, Sarah E. Wyatt, Luis Zea, Sylvain V. Costes, Jonathan M. Galazka. iScience 102361 (2021).

Mycobacterial Lung Disease Education and Research Conference, Honolulu, Hawaii, February 1-2, 2020
Jennifer R. Honda, Yvonne L. Chan, Eric I. Tong, Megan Kawatachi, Ravleen Virdi, Grant J. Norton, Stephanie N. Dawrs, Nabeeh A. Hasan, L. Elaine Epperson, James T. Crooks, Edward D. Chan, Michael Strong. Microbes and Infection (2020).

Assessment of soil features on the growth of environmental nontuberculous mycobacterial isolates from Hawai'i.
Cody M. Glickman, Ravleen Virdi, Nabeeh A. Hasan, L. Elaine Epperson, Leeza Brown, Stephanie N. Dawrs, James L. Crooks, Edward D. Chan, Michael Strong, Stephen T. Nelson, Jennifer R. Honda. Applied and Environmental Microbiology (2020).

Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria.
Cody Glickman, Sara M. Kammlade, Nabeeh A. Hasan, L. Elaine Epperson, Rebecca M. Davidson, Michael Strong. Virology Journal 17:124 (2020).

News from a postpandemic world.
Joel Henrique Ellwanger, Mpho Diphago Stanley Lekgoathi, Kartik Nemani, Michael A. Tarselli, Ahmed Al Harraq, Anna Uzonyi, Ken Dutton-Regester, Rachel Yoho, Sudhakar Srivastava, Michael Strong, Yifan Li, JiaJia Fu, Khor Waiho, Isabel Marín Beltrán, Akash Mukherjee, Tyler D. P. Brunet. Science 369:26-29 (2020).

Cell Surface Remodeling of Mycobacterium abscessus under Cystic Fibrosis Airway Growth Conditions.
Wiersma CJ, Belardinelli JM, Avanzi C, Angala SK, Everall I, Angala B, Kendall E, de Moura VCN, Verma D, Benoit J, Brown KP, Jones V, Malcolm KC, Strong M, Nick JA, Floto RA, Parkhill J, Ordway DJ, Davidson RM, McNeil MR, Jackson M. ACS Infectious Diseases 2020 Jul 2.

Nontuberculous Mycobacterial Disease and Molybdenum in Colorado Watersheds.
Ettie M. Lipner, Joshua French, Carleton R. Bern, Katherine Walton-Day, David Knox, Michael Strong, D. Rebecca Prevots, James L. Crooks. International Journal of Environmental Research and Public Health, 17(11), 3854; (2020).

A composite method to infer drug resistance with mixed genomic data.
Gargi Datta, Nabeeh A Hasan, Michael Strong, Sonia M Leach. bioRxiv (2020).

Seeking career clarity.
Chloe Antoniou, Katie Burnette, Aaron Christensen-Quick, Monika Lewinska, Yongsheng Ji, Muhammad M. Khalifa, Athanasia Nikolaou, Pragya Srivastava, Brynn Anne Hollingsworth, Norman van Rhijn, Saumya Saurabh, Nikos Konstantinides, Ashley Barbara Heim, Eric Britt Moore, Michael Strong, Aleksandra Kosanic, Samuel Nathan Kirshner, Antarip Halder, Khor Waih. Science 368:6486, 26-28 (2020).

A Scalable, Efficient, and Safe Method to Prepare High Quality DNA from Mycobacteria and Other Challenging Cells
L. Elaine Epperson and Michael Strong. in press, Journal of Clinical Tuberculosis and Other Mycobacterial Diseases, 19:100150 (2020).

Nontuberculous Mycobacteria Show Differential Infectivity and Use Phospholipids to Antagonize LL-37.
Jennifer R. Honda, Tamara Hess, Rachel Carlson, Pitchaimani Kandasamy, Luisa Maria Nieto Ramirez, Grant J. Norton, Ravleen Virdi, M. Nurul Islam , Carolina Mehaffy, Nabeeh A Hasan, L Elaine Epperson, Danny Hesser, Scott Alper, Michael Strong, Sonia C Flores, Dennis R Voelker , Karen M Dobos, and Edward D. Chan. American Journal of Respiratory Cell and Molecular Biology 62:354–363 (2020).

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients.
Nabeeh A. Hasan*, Rebecca M. Davidson*, L. Elaine Epperson, Sara M. Kammlade, Rachael R. Rodger, Adrah R. Levin, Alyssa Sherwood, Scott D. Sagel, Stacey L. Martiniano. Charles L. Daley, Max Salfinger, Jerry A. Nick, Michael Strong. BioRxiv (2019) *equal contribution.

In-host population dynamics of M. tuberculosis during treatment failure.
Roger Vargas Jr., Luca Freschi, Maximillian Marin, Elaine Epperson, Melissa Smith, Irina Oussenko, David Durbin, Michael Strong, Max Salfinger, Maha R Farhat. BioRxiv (2019).

Genomic Analysis of Cardiac Surgery-Associated Mycobacterium chimaera Infections, United States.
Nabeeh Hasan, L. Elaine Epperson, Adrian Lawsin, Rachael Rodger, Kiran Perkins, Alison Laufer, K. Perry, Heather Moulton-Meissener, Daniel Diekema, Matthew Crist, Joseph Perz, Max Salfinger, Charles Daley, Michael Strong. Emerging Infectious Diseases 25:559-563 (2019).

Evaluation Of A Novel MALDI Biotyper Algorithm To Distinguish Mycobacterium intracellulare From Mycobacterium chimaera.
L. Elaine Epperson, Markus Timke, Paul Godo, David Durbin, Nabeeh A. Hasan, Niels K. Helstrom, Gongyi Shi, Markus Kostrzewa, Michael Strong, Max Salfinger. Frontiers in Microbiology (2018).

Mycobacterial biomaterials and resources for researchers
Manzour Hernando Hazbon, Leen Rigouts, Marco Schito, Matthew Ezewudo, Takuji Kudo, Takashi Itoh, Moriya Ohkuma, Katalin Kiss, Linhuan Wu, Juncai Ma, Moriyuki Hamada, Michael Strong, Max Salfinger, Charles L Daley, Jerry A Nick, Jung-Sook Lee, Nalin Rastogi, David Couvin, Raquel Hurtado-Ortiz, Chantal Bizet, Anita Suresh, Timothy Rodwell, Audrey Albertini, Karen A Lacourciere, Ana Deheer-Graham, Sarah Alexander, Julie E Russell, Rebecca Bradford, Marco A Riojas. Pathogens and Disease 76:042 (2018).

MW 2.0. Michael Strong. Science, 359: 170-171 (2018).

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. International Journal of Systematic and Evolutionary Microbiology 67:2640-2645 (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. 83: e00562-17, 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 14:1523-1532 (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).

ATS SARS-CoV-2 Genomics Lecture (April 29, 2020).
Michael Strong

National Jewish Health NTM Lecture Series, Genomic Approaches to Mycobacteria (2021).
Michael Strong

Copyright © Michael Strong