Tim Putman

Tim Putman

Bioinformatics Software Developer



Major Responsibilities:

  • Develop the Monarch web application
  • Aggregate and structure microbial model organism data in The Monarch Initiative Infrastructure
  • Develop tools and aggregate data in support of the NCATS Translator Project


  • B.S. General Science, University of Oregon 2009
  • Ph.D. Molecular and Cellular Biology, Oregon State University 2015


  • Postdoctoral Research Associate, The Scripps Research Institute 2015-2017

Select  Publications and Presentations: 


Suchland, Robert J., Zoe E. Dimond, Timothy E. Putman, and Daniel D. Rockey. “Whole-Genome Sequencing of Repeat-Positive, Same-Serovar Chlamydia Trachomatis Collected from the Female Genital Tract Demonstrate Persistent Infections and Genome Stability.” The Journal of Infectious Diseases, March 2017. doi:10.1093/infdis/jix155. 

Timothy E. Putman, Sebastien Lelong, Sebastian Burgstaller-Muelhbacher, Andra Waagmeester, Colin Diesh, Nathan Dunn, Monica Munoz-Torres, Gregory Stupp, Andrew Su, and Benjamin M Good. “WikiGenomes: An Open Web Application for Community Consumption and Curation of Gene Annotation Data in Wikidata,” January 24, 2017. doi:10.1093/database/bax025.  

Timothy E. Putman, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Chunlei Wu, Andrew I. Su, and Benjamin M. Good. “Centralizing Content and Distributing Labor: A Community Model for Curating the Very Long Tail of Microbial Genomes.” Database 2016 (2016): baw028. doi:10.1093/database/baw028.  

Muramatsu, Matthew K., Julie A. Brothwell, Barry D. Stein, Timothy E. Putman, Daniel D. Rockey, and David E. Nelson. “Beyond Tryptophan Synthase: Identification of Genes That Contribute to Chlamydia Trachomatis Survival during Gamma Interferon-Induced Persistence and Reactivation.” Infection and Immunity 84, no. 10 (2016): 2791–2801. doi:10.1128/IAI.00356-16.  

Xin, Jiwen, Adam Mark, Cyrus Afrasiabi, Ginger Tsueng, Moritz Juchler, Nikhil Gopal, Gregory S. Stupp … Timothy E. Putman et al. “High-Performance Web Services for Querying Gene and Variant Annotation.” Genome Biology 17, no. 1 (2016): 91. doi:10.1186/s13059-016-0953-9.  

Brothwell, Julie A., Matthew K. Muramatsu, Evelyn Toh, Daniel D. Rockey, Timothy E. Putman, Michael L. Barta, P. Scott Hefty, Robert J. Suchland, and David E. Nelson. “Interrogating Genes That Mediate Chlamydia Trachomatis Survival in Cell Culture Using Conditional Mutants and Recombination.” Journal of Bacteriology 198, no. 15 (2016): 2131–39. doi:10.1128/JB.00161-16.  

Burgstaller-Muehlbacher, Sebastian, Andra Waagmeester, Elvira Mitraka, Julia Turner, Timothy E. Putman, Justin Leong, Chinmay Naik, et al. “Wikidata as a Semantic Framework for the Gene Wiki Initiative.” Database 2016 (2016): baw015. doi:10.1093/database/baw015.  

Reed, Aimee N, Timothy E. Putman, Christopher Sullivan, and Ling Jin. “Application of a Nanoflare Probe Specific to a Latency Associated Transcript for Isolation of KHV Latently Infected Cells.” Virus Res. 208 (October 2, 2015): 129–35.  

Timothy E. Putman, Robert J Suchland, John D Ivanovitch, and Daniel D Rockey. “Culture-Independent Sequence Analysis of Chlamydia Trachomatis in Urogenital Specimens Identifies Regions of Recombination and in-Patient Sequence Mutations.” Microbiology 159, no. Pt 10 (October 2013): 2109–17.  

Timothy E. Putman, and D D Rockey. Chlamydia Trachomatis Genome Structure. Vol. 7. Karger Publishers, 2013.  

Sandoz, Kelsi M, Steven G Eriksen, Brendan M Jeffrey, Robert J Suchland, Timothy E. Putman, Dennis E Hruby, Robert Jordan, and Daniel D Rockey. “Resistance to a Novel Antichlamydial Compound Is Mediated through Mutations in Chlamydia Trachomatis secY.” Antimicrob. Agents Chemother. 56, no. 8 (August 2012): 4296–4302.  

Watson, G, W Xu, A Reed, B Babra, Timothy E. Putman, E Wick, S L Wechsler, G F Rohrmann, and L Jin. “Sequence and Comparative Analysis of the Genome of HSV-1 Strain McKrae.” Virology 433, no. 2 (November 25, 2012): 528–37.  

Oral Presentations 

WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata. Mar. 2017. Podium presentation at Biocuration 2017 at Standford School of Medicine. 

Linked data in the hands of biological researchers: A model organism database powered by Wikidata. Oct. 2016. Podium presentation at Wikiconference North America 2016 at The San Diego Public Library.  

GeneWIki: Curating Biomedical Knowledge on Wikidata and Wikipedia.  Sep. 2016. Webinar presentation at Wikimedia Foundation Laboratories SPARQL Workshop.  

A centralized model organism database web application powered by Wikidata. June 2016.  Podium presentation at the BioHackathon 2016 Symposium Keio University, Tsuruoka, Yamagata, Japan.  

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes. Apr. 2016.  Podium presentation at Biocuration 2016 in Geneva, Switzerland.  

Development of an open, community driven, central database for microbial genetic knowledge in Wikidata. Jan. 2016. Podium presentation at PAG XXIV at Town and Country Conference Center San Diego, CA.

Culture-independent genome sequencing as a tool for understanding chlamydial biology. May. 2015.  MacVicar Scholar Award Lecture. College of Veterinary Medicine, Oregon State University.  

Culture-independent genome sequencing of human and animal Chlamydia Jan. 2015. Podium presentation at Rockey Mountain Laboratories, NIH.  

Whole genome sequence comparison of the livestock pathogen Chlamydia abortus in the absence of cell culture. Sep. 2014. Podium presentation at Oregon State University, College of Veterinary Medicine Research Retreat, Philomath, OR  

Genome sequencing, bioinformatics and Chlamydia: Decoding a pathogen of ill repute. Aug. 2014. Public lecture as part of the OSU-Cascades Science Pub Series held at McMennamins Old St. Francis School Pub, Bend, Or.   Culture-independent sequence analysis identifies recombination within related Chlamydia trachomatis urogenital specimens. Mar. 2013. Podium presentation at The Chlamydia Basic Research Society 6th Biennial Meeting, San Antonio, TX.