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CV

CURRICULUM VITAE

 

J. Harry Caufield

Los Angeles, CA, USA 90036

Email: j.harry.caufield@gmail.com Site: harrycaufield.net Twitter: @harry_caufield

 

EDUCATION AND TRAINING

Postdoctoral Fellow

2017 – Present

HeartBD2K Center of Excellence at UCLA

University of California Los Angeles, Los Angeles, CA, USA

Supervisor: Peipei Ping, Departments of Physiology, Medicine/Cardiology, and Bioinformatics at the David Geffen School of Medicine at UCLA

Research focuses on two main areas: computational analysis of proteomics and protein-protein interaction data, and developing machine learning and natural language processing approaches to retrieving information and novel conclusions from medical case reports. Both research foci concern cardiovascular disease, proteins of the heart, and integrated data science approaches.

 

PhD in Integrative Life Sciences

2012 – 2016

Virginia Commonwealth University, Richmond, VA, USA

Advisor: Peter Uetz, Center for the Study of Biological Complexity

Research focused on detection, comparison, and interpretation of protein-protein interactions among microbial and viral proteomes using bioinformatics and high-throughput molecular biology methods. Funding for dissertation completion provided through a VCU Graduate School Dissertation Assistantship.

 

Master of Science in Bioinformatics

2009 – 2012

Virginia Commonwealth University, Richmond, VA, USA

Advisor: Gail Christie, Department of Microbiology & Immunology

Thesis: N-terminal Processing of Ribosomal Protein L27 in Staphylococcus aureus

Research focused on molecular biology of Staphylococcus aureus, post-translational protein modifications, and relationship with bacteriophage.

 

Bachelor of Science in Biological Sciences

2004 – 2008

University of Delaware, Newark, DE, USA

 

RESEARCH

A platform for automated interpretation of unstructured text in medical language

July 2017 – Present

Developing novel computational methods and ontological strategies to interpret text written in medical language, including clinical case reports. This project will produce a platform for answering natural-language clinical queries and matching them to relevant documents. In addition to research efforts, I am coordinating volunteer efforts into manual text annotation. More than ten HeartBD2K researchers across multiple university departments are involved in this project.

 

Cardiac meta-interactomics and protein turnover

Jan. 2017 – Present

Developing computational methods to combine curated protein-protein interaction data with sets of protein turnover data among heart proteins.

 

Resources for working with medical concepts in clinical case reports

Jan. 2017 – Present

Developing software packages to improve annotation of medical case reports and to identify novel phenomena among them using text mining and machine learning. Eight other HeartBD2K researchers and four student interns are involved in this project; I am coordinating development of the project into a unified resource.

 

Mycobacterium protein complex comparisons

April 2016 – Dec. 2016

Research supervised by Dr. Peter Uetz.

Assisted with project to compare composition of protein complexes with coding genes within Mycobacterium tuberculosis and M. leprae. Coordinated project direction, performing data analysis, and writing of the manuscript. One other Uetz Lab researcher was involved in this project.

 

Streptococcus sanguinis mutant phenotype comparisons

Dec. 2015 – Dec. 2016

Research supervised by Dr. Peter Uetz.

Assisted with project to compare conditional phenotypes of knockout mutants of the human oral pathogen Streptococcus sanguinis. Coordinated materials, strains, and methods development. Required robotic automation of high-throughput methods. Two other Uetz Lab researchers and two VCU School of Dentistry researchers was involved in this project.

 

Bacteriophage interactomics: Host vs. Phage protein interactions

April 2015 – Dec. 2016

Research supervised by Dr. Peter Uetz.

Developed and applied high-throughput methods for determining interactions between proteins from bacteriophage and their respective bacterial hosts, including E. coli and several species of Bacillus. Employed biological network and database analysis to interpret functional relevance of interactions. Required coding in Python and R. One other Uetz Lab researcher, one additional VCU faculty member, and one additional VCU student were involved in this project.

 

Bacterial protein interactome comparisons

May 2014 – Dec. 2016

Research supervised by Dr. Peter Uetz.

Developed methods for merging and analyzing combined sets of protein interactions from literature-curated sources. Required data mining, biological network analysis, and coding in Python and R in Unix environments. This research leveraged existing interactome data to draw broad conclusions about molecular phenomena within bacteria. Two other Uetz Lab researchers, one additional VCU faculty member, and one external researcher were involved in this project.

 

Protein complex interactions

May 2012 – Feb. 2015

Research supervised by Dr. Peter Uetz.

Led a project to compare potential for conservation of protein-coding genes and their protein-protein interactions among components of protein complexes in bacteria. I developed computational methods to combine existing data sets of complexes, gene orthology, and protein properties. Future research will attempt to confirm predicted protein-protein interactions in the lab. Three other Uetz Lab researchers were involved in this project.

 

Bacteriophage interactomics: Mycobacteriophage Giles

Dec. 2011 – May 2015

Research supervised by Dr. Peter Uetz.

Coordinated the analysis and experimental design for an interactomics analysis of the ORFeome of Mycobacteria phage Giles. Three other Uetz Lab researchers, two researchers from the lab of Graham Hatfull (U. Pitt.), and several undergraduate researchers were involved in this project.

 

High-throughput yeast two hybrid optimization

Dec. 2011 – Dec. 2015

Research supervised by Dr. Peter Uetz.

Improved implementation of the yeast two hybrid (Y2H) system, a method for detecting interactions between binary sets of proteins. We used the system in a high-throughput manner to screen thousands of protein pairs at a time. I compared modifications to existing protocols to determine their effect on yeast transformation (a critical first step in Y2H, though sensitive to method changes). I also compared sets of Y2H data to determine the extent of methodological differences on final results. Three other Uetz Lab researchers were involved in this project.

 

Processing of Staphylococcus aureus ribosomal protein L27

Mar. 2010 – May 2012

Research supervised by Dr. Gail Christie.

Investigated the potential for post-translational modification of a ribosomal protein sequence broadly conserved within many bacterial species, especially within the Firmicutes. Used numerous microbiology and molecular biology techniques, including those for bacterial culture, cloning, protein purification, PAGE, and Western blots. Employed bioinformatics through genome and protein sequence analysis and phylogenetics.

 

Staphylococcus aureus bacteriophage 80α genetics

Oct. 2009 – Mar. 2010

Research supervised by Dr. Gail Christie.

Studied two bacteriophage genes suspected to be involved in superinfection immunity. Improved methods for PCR amplification of the viral genes and their expression in an E. coli background prior to transfer to S. aureus.

 

PUBLICATIONS

Wuchty, S., Mueller, S. A., Caufield, J. H., Haeuser, R., Aloy, P., Kalkhof, S., & Uetz, P. (2017). The proteome and interactome of Helicobacter pylori (under review).

 

Mehla, J., Dedrick, R. M., Caufield, J. H., Wagemans, J., Sakhawalkar, N., Johnson, A., Hatfull, G. F., & Uetz, P. (2017). Virus-host protein-protein interactions of mycobacteriophage Giles. Scientific Reports (in press).

 

Babu, M., Bundalovic-Torma, C., Calmettes, C., … Caufield, J. H., et al. (2017). Global Landscape of Cell Envelope Protein Complexes in Escherichia coli. Nature Biotechnology. doi:10.1038/nbt.4024

 

Sakhawalkar, N., Caufield, J. H., & Uetz, P. (2017). Two-hybrid and Related Systems. In: eLS. 1–9. John Wiley & Sons, Ltd. doi:10.1002/9780470015902.a0000981.pub2

 

Caufield, J. H., Wimble, C., Shary, S., Wuchty, S., & Uetz, P. (2017). Bacterial Protein Meta-Interactomes Predict Cross-Species Interactions and Protein Function. BMC Bioinformatics, 18(1), 171. doi:10.1186/s12859-017-1585-0

 

Mehla, J., Caufield, J.H., Sakhawalkar, N., & Uetz, P. (2017). A Comparison of Two-Hybrid Approaches for Detecting Protein–Protein Interactions. In: Shukla, A. K. (editor), Methods in Enzymology 586: Proteomics in Biology, Part B. Elsevier. doi:10.1016/bs.mie.2016.10.020

 

Mehla, J., Dedrick, R., Caufield, J.H., Siefring, R., Mair, M., Johnson, A., Hatfull, G., & Uetz, P. (2015). The protein interactome of mycobacteriophage Giles predicts functions for unknown proteins. Journal of Bacteriology, 197(15), 2508-16. doi: 10.1128/JB.00164-15

 

Caufield, J.H., Abreu, M., Wimble, C., & Uetz, P. (2015). Protein complexes in Bacteria. PLoS Computational Biology, 11(2), e1004107. doi:10.1371/journal.pcbi.1004107

 

Mehla, J., Caufield, J.H., & Uetz, P. (2015). The Yeast Two Hybrid system: A tool for mapping protein-protein interactions. In: Boone, C. (editor), Budding Yeast: A Laboratory Manual. CSHL Press.

 

Mehla, J., Caufield, J.H., & Uetz, P. (2015). Mapping Protein–Protein Interactions Using Yeast Two-Hybrid Assays. In: Boone, C. (editor), Budding Yeast: A Laboratory Manual. CSHL Press.

 

Wall, E., Caufield, J., Manning, K., Dokland, T., Christie, G. (2015). Specific N-terminal cleavage of ribosomal protein L27 in Staphylococcus aureus and related bacteria. Molecular Microbiology, 95(2), 258-69. doi:10.1111/mmi.12862

 

Rajagopala, S. V., Sikorski, P., Caufield, J. H., Tovchigrechko, A., & Uetz, P. (2012). Studying protein complexes by the yeast two-hybrid system. Methods, 58(4), 392-9. doi:10.1016/j.ymeth.2012.07.015

 

Caufield, J. H., Sakhawalkar, N., & Uetz, P. (2012). A comparison and optimization of yeast two-hybrid systems. Methods, 58(4), 317-24. doi:10.1016/j.ymeth.2012.12.001

 

See Google Scholar profile at: goo.gl/9E2ZTB

 

CONFERENCE PRESENTATIONS: ORAL

Proteomic Forum 2017, Potsdam, Germany

Apr. 2017

“Connecting the dots – digital objects in cardiovascular diseases: Meta-Interactomics”

Presented as part of HUPO Workshop.

 

US HUPO Annual Conference, San Diego, CA, USA

Mar. 2017

“Meta-Interactomics and the Evolution of Bacterial Protein Complexes”

 

VCU CSBC Research Review, Richmond, VA, USA

Dec. 2014

“Predicted protein complexomes and their use in studying Bacteriophage-mediated protein interactions”

 

VA Branch American Society for Microbiology meeting, Harrisonburg, VA, USA

Nov. 2014

“Predicted protein complexomes and their use in studying bacteriophage-mediated protein interactions”

Won 2nd prize for Best Student Presentation out of 19 presenters.

 

VCU Forbes Day Research Symposium, Richmond, VA, USA

May 2014

“Protein Complex Conservation across Bacterial Species and Genome Characteristics”

 

UVA German Graduate Conference, Charlottesville, VA, USA

Feb. 2014

“Let’s Do Some Networking: Interactomics across domains of life”

 

VA Branch American Society for Microbiology meeting, Charlottesville, VA, USA

Nov. 2013

“The Impact of Genome Reduction on Conservation of Microbial Protein Complexes and Their Components” (oral presentation)

Won 3rd prize for Best Student Presentation out of 17 presenters.

 

Virginia Branch American Society for Microbiology meeting, Virginia Beach, VA, USA

Nov. 2012

“Protein-protein interaction networks of bacteriophage using the yeast two-hybrid system”

 

Virginia Branch American Society for Microbiology meeting, Lynchburg, VA, USA

Nov. 2010

“Potential N-terminal processing of ribosomal protein L27 in Staphylococcus aureus

 

CONFERENCE PRESENTATIONS: POSTER

NHLBI Systems Biology Symposium 2017, Bethesda, MD, USA

Oct. 2017

“Implications for cardiac remodeling among the interactions of 14-3-3 proteins” and “Clinical case report analysis provides the foundation for new approaches to biomedical data integration”

 

ISMB/ECCB 2017, Prague, Czech Republic

July 2017

“HeartCases - a medical case report analysis system for understanding cardiovascular disease”

 

American Society for Microbiology Microbe 2016, Boston, MA, USA

June 2016

“Bacterial Proteins and Complexes: Evolution, Function, and Perturbations”

 

VCU Institute for Structural Biology, Drug Discovery and Development Summit, Richmond, VA, USA

Feb. 2016

“Meta-interactomics provides functional context for

microbial proteins and their interactions”

Won 2nd prize for Best Student Presentation out of 8 student presenters.

 

VCU Integrative Life Sciences Student Research Showcase, Richmond, VA, USA

Nov. 2015

“Meta-interactomics provides functional context for

microbial proteins and their interactions”

 

VCU Integrative Life Sciences Student Research Showcase, Richmond, VA, USA

Nov. 2014

“Predicted protein complexomes and their use in studying bacteriophage-mediated protein interactions”

 

VCU Graduate Student Association Research Symposium, Richmond, VA, USA

Apr. 2014

“From protein interaction domains to complexes to networks: computational approaches”

 

VA Branch American Society for Microbiology meeting, Charlottesville, VA, USA

Nov. 2013

“The Impact of Genome Reduction on Conservation of Microbial Protein Complexes and Their Components” (poster)

 

VCU Integrative Life Sciences Student Research Showcase, Richmond, VA, USA

Nov. 2013

“From protein interaction domains to complexes to networks: computational approaches”

 

VCU Watts Day Symposium, Richmond, VA, USA

Oct. 2013

“From protein interaction domains to complexes to networks: computational approaches”

 

VCU Watts Day Symposium, Richmond, VA, USA

Oct. 2012

“Phage Interactomics: Identification of Phage-Phage and Phage-Host Protein Interactions by Systematic Yeast Two-Hybrid Screens”

 

SEA-PHAGES meeting, graduate student section

Aug. 2012

HHMI Janelia Farm campus, Ashburn, VA, USA

“Phage Interactomics: Identification of Phage-Phage and Phage-Host Protein Interactions by Systematic Yeast Two-Hybrid Screens”

 

TEACHING

Teaching Assistant

Aug. 2015 – Dec. 2015

Virginia Commonwealth University, Richmond, VA

Assisted with Integrative Life Sciences Research course (LFSC 301) for undergraduate students in the life sciences. Led weekly discussion session involving topics relevant to research conduct, including ethics, effective communication, and experimental design.

 

Teaching Assistant

Jan. 2015 – May 2015

Virginia Commonwealth University, Richmond, VA

Assisted with Molecular Genetics Lab course (BIOL/BNFO 541) for undergraduate and graduate students. Facilitated wet lab exercises and prepared lab materials. Aided class protocol design. Graded tests and quizzes. Lectured on 16S rRNA gene-specific primer design. Advised students on scientific writing.

 

Teaching Assistant

Aug. 2013 – Dec. 2013

Virginia Commonwealth University, Richmond, VA

Assisted with Phage Discovery Lab course (BNFO 251) for undergraduates. Facilitated wet lab exercises and prepared lab materials. Prior to assisting with course, attended Phage Phest student symposia in Spring 2012 and Spring 2013.

 

Teaching Assistant

Jan. 2010 – May 2010

Virginia Commonwealth University, Richmond, VA

Assisted with introductory bioinformatics course (BNFO 301) for undergraduates. Advised students on introductory bioinformatics and programming concepts using BioBike, a visual programming language.

 

ADDITIONAL EXPERIENCE

Lab Manager

May 2012 – Dec. 2016

Virginia Commonwealth University, Richmond, VA

Maintained Uetz Lab operation, inventory, and safety standards. Purchased new consumables and equipment. Performed price comparisons and do product research. Developed protocols for new equipment, including Beckman Coulter Biomek FX lab automation robot. Trained new lab members and mentor them in research projects; mentored fourteen students in total since Spring 2012.

 

R&D Technician

Nov. 2008 – Aug. 2009

DuPont Stine-Haskell Research Center, Newark, DE

Maintained several complete insect cultures on a daily basis. Aided insect control compound discovery and plant/soil sample analysis.

 

SERVICE AND OUTREACH

BD2K Activities at ISCB/ECCB 2017

July 2017

Coordinated and managed outreach efforts for the NIH Big Data to Knowledge initiative (though the BD2K Centers – Coordination Center, BD2KCCC) during the 5 days of the 2017 Intelligent Systems for Molecular Biology and European Conference on Computational Biology joint conference in Prague. Activities included an outreach booth, a Special Track with 18 speakers providing talks on machine learning and data science, and a discussion session.

 

VCU Integrative Life Science Student Organization (ILSSO)

Sep. 2013 – Dec. 2016

Founding member of this student organization. Served on executive board. Primary organizer for the 2014 ILS Research Showcase, a research meeting with 21 presenters and more than 70 attendees. Assisted with organization of the 2015 Research Showcase. Vice President for the 2015 - 2016 academic year.

 

PROFESSIONAL MEMBERSHIPS AND EXPERIENCE

International Society for Computational Biology (ISCB) – Member

Spring 2017 – Present

 

American Society for Microbiology (ASM), Virginia Branch – Member

Fall 2010 – Fall 2016

 

American Society for Microbiology (ASM) – Member, Division M

Fall 2010 – Fall 2016

Completed the ASM Scientific Writing and Publishing Institute (SWPI) webinar series in Jan. to Mar. 2015.