CV

Curriculum Vitae

=====================

Phillip T. Brooks


Updated [September, 13 2017]

PERSONAL DETAILS


Mailing Address: 253 Center for Companion Animal Health, One Shields Avenue, Davis, CA 95618

EDUCATION


Degree, University and location, Month/Year

B.S. Psychology Georgia State University December 2010

Ph.D. Comparative Medicine Michigan State University August 2016 and Integrative Biology and Environmental Integrative Toxicological Sciences

PROFESSIONAL EXPERIENCE


Year(s), Job title, Location

2011-2016 Graduate Student Michigan State University

2016-Present Post-doctoral Fellow University of California Davis

PUBLICATIONS


Phillip T. Brooks, Kelsey A. Brakel, Julia A. Bell, Christopher E. Bejcek, Trey Gilpin, Jean M. Brudvig, and Linda S. Mansfield (2017). Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice.

Chee Bing Ong, Kazuyoshi Kumagai, Phillip T. Brooks, Christina Brandenberger, Ryan P. Lewandowski, Daven N. Jackson-Humbles, Rance Nault, Timothy Zacharewski, James G. Wagner, and Jack R. Harkema (2015). Ozone-Induced Type 2 Immunity in Nasal Airways: Development and Lymphoid Cell Dependence in Mice. American Journal of Respiratory Cell and Molecular Biology. DOI:10.1165/rcmb.2015-0165OC

Yuan, H., Fu, G., Brooks, P.T., Weber, I., & Gadda G. (2010). Steady State Kinetic Mechanism and Reductive Half-Reaction of D-Arginine dehydrogenase from Pseudomonas aeruginosa. Journal of Biochemistry, 49, pp. 9542-9550 DOI: 10.1021/BI101420w

TEACHING EXPERIENCE


Title of course, organization, years

[2017 Data Intensive Biology Summer Research Institute Environmental Metagenomics Workshop] (http://2017-dibsi-metagenomics.readthedocs.io/en/latest/toc.html), UC Davis, 2017

[2017 Data Intensive Biology Summer Research Institute Two Week Introductory Bioinformatics Course (ANGUS)] (http://angus.readthedocs.io/en/2017/kmers-and-sourmash.html), UC Davis, 2017, Instructor

[2017 USCS Metagenomics Workshop] (https://2017-ucsc-metagenomics.readthedocs.io/en/latest/), UC Davis, 2017, Co-instructor

[2015 Beacon Next Generation Sequencing Course] (http://angus.readthedocs.org/en/2015/ ), Michigan State University, 2015, Teaching Assistant

PROFESSIONAL ORGANIZATIONS


Name of organization, year(s)

American Society for Microbiology, 2012-Present

Society for Neuroscience, 2015

HONORS AND AWARDS


Name of award, year(s)

Institute for Integrative Toxicology Fellowship, 2012-2015

Alliance for Graduate Education in the Professoriate Fellowship, Spring 2015

Best oral presentation by a Ph.D. candidate at Phi Zeta Day, Fall 2014

CIVIC AND COMMUNITY INVOLVEMENT


Function, name of association, year(s)

Graduate Assistant, Michigan State University Summer Research Opportunities Program (SROP), 2014-2015

Graduate Assistant, Michigan State University Bridge to the Ph.D. Neuroscience Program (BPNP), 2012-2014

RELEVANT TRAINING AND COURSEWORK


(Year, Course title, Location)

2015 Write Winning Grant Proposals Workshop, Michigan State University, East Lansing, Michigan 48824

[2014 Beacon Next Generation Sequencing Analysis Course] (http://angus.readthedocs.org/en/2014/), Kellogg Biological Station, Hickory Corners, Michigan 49012,

  • An intensive two-week workshop hosted by C. Titus Brown focusing on the analysis of next generation sequencing (NGS) data. I learned cutting edge techniques for the exploration of NGS genomic, metagenomic, and RNASeq data sets.

2014 Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) Kellogg Biological Station, Kalamazoo, Michigan 49012,

  • An intensive one-week workshop hosted by Ashley Shade, Tracy Teal, and Josh Herr on NGS sequencing applications for Microbial Ecologists. We explored different methods for the analysis of amplicon sequences using mothur and QIMME. Metagenomic analysis was also covered using several pipelines.

2014 Writing/Designing NIH Grant Proposals Workshop, Ann Arbor, Michigan 48109

[2013 Computational Biology for Evolutionary Biologists] (http://ged.msu.edu/courses/2013-fall-cse-801/), Michigan State University, East Lansing, Michigan 48824

  • A semester long course taught by C. Titus Brown focusing on programming in python and NGS sequencing analysis.

[2013 MSU Applied Bioinformatics Workshop] (http://buell-lab.plantbiology.msu.edu/workshop2013.shtml) , Michigan State University, East Lansing, Michigan 48824

Presentations


ORAL

2017 microBOOmes: UC Davis Genome Center Halloween Symposium on Microbiomes

  • Composition of Gut Microbiota Affects Campylobacter jejuni Mediated Inflammation and Autoimmunity in Murine Models
  • Link to talk

2015 Ph.D. Proposal Seminar

  • Host Microbiota as a Factor in the Adaptation of Campylobacter jejuni Guillain-Barré Associated Strains

2014 MSU College of Veterinary Medicine Annual Phi-Zeta day

  • Characterization of Campylobacter jejuni Infection in C57BL/6 Il1-10^-/- Mice with Conventional or Antibiotic Altered Microbiota

2014 MSU Alliance for Graduate Education and the Professoriate

  • Pathogens, antibiotics and evolution

2009 McNair/SRI Symposium, Michigan State University, East Lansing, MI

  • Biophysical Interaction of palmitate with the kinase domain of Protein Kinase R (PKR)

2008 Annual Biomedical Research Conference for Minority Students in Orlando, FL

  • Metal (Zn2+) Activated C-peptide Induced ATP Release via Red Blood Cells (RBCs) with the Addition of Albumin

2008 McNair/SROP Symposium, Michigan State University, East Lansing, MI

  • Metal (Zn2+) Activated C-peptide Induced ATP Release via Red Blood Cells (RBCs) with the Addition of Albumin
POSTER

2017 2nd ASM CONFERENCE ON RAPID NEXT-GENERATION SEQUENCING AND BIOINFORMATIC PIPELINES

  • Dahak: A Sustainable Approach to High Confidence Metagenomics Analysis of Complex Samples
  • Phillip Brooks, Bruce Budowle, Chris Grahlmann, Stephanie L. Guertin, F. Curtis Hewitt, Dana R. Kadavy, Alexander F. Koeppel, Oana I. Lungu, Krista L. Ternus, Stephen D. Turner, and C. Titus Brown

2017 Gordon Research Conference

  • A Human-derived Microbiome Enhanced Campylobacter jejuni Colonization Levels in C57BL/6 and NOD Mice in Association with Likely Changes in the Gut Microbial Food Web
  • Phil Brooks, Kelsey Brakel, Alexander Etheridge, Julia Bell, and Linda Mansfield

2017 6th Annual in-FLAME (Inflammation, Ecosystems, and the transformation of Global Health) Workshop

  • Developing transplanted human microbiota mouse models to study the effects of the early microbiome on development of inflammation, autoimmunity and allergy
  • L.S. Mansfield, P.T. Brooks, K.A. Brakel, J.A. Bell, S.L. Ewart, D. Claiborne, and S. H. Arshad

2017 ASM-Microbe

  • Taxonomic Classification Of Microbial Metagenomes Using MinHash Signatures
  • P.T. Brooks, L.C. Irber Jr., T.E. Reiter, and C. Titus Brown
  • Link to poster

2015 Society for Neuroscience Annual Meeting

  • Humanized microbiota alter host immune response to Campylobacter jejuni infection

2014 Annual Society for Microbiology

  • Characterization of Campylobacter jejuni Infection in C57BL/6 IL-10-/- Mice with Conventional or Antibiotic Altered Microbiota

2009 McNair/SRI Symposium, Michigan State University, East Lansing, MI

  • Biophysical Interaction of palmitate with the kinase domain of Protein Kinase R (PKR)

2008 Ronald E. McNair Symposium, Georgia State University, Atlanta GA

  • Metal (Zn2+) Activated C-peptide Induced ATP Release via Red Blood Cells (RBCs) with the Addition of Albumin

2008 CIC/SROP Conference, Michigan State University, East Lansing, MI

  • Metal (Zn2+) Activated C-peptide Induced ATP Release via Red Blood Cells (RBCs) with the Addition of Albumin 2008 McNair/SROP Symposium, Michigan State University, East Lansing, MI
  • Metal (Zn2+) Activated C-peptide Induced ATP Release via Red Blood Cells (RBCs) with the Addition of Albumin

TRAINING GRANTS AND FELLOWSHIPS


(Year(s), Grant or fellowship title, source of funding, total amount of funding

2012-2015 Institute for Integrative Toxicology Fellowship (Ruth L. Kirschstein National Research Service Award (NRSA))

2014 Alliance for Graduate Education in the Professoriate (AGEP) Fellowship, MSU Graduate School