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Joshua Cook
Graduent Student Researcher
As an undergrad, I studied the parasite Toxoplasma gondii, and I currently study cancer genetics using bioinformatics with a specific focus on Bayesian methods. I am looking to once again switch disciplines but continue utilizing and improving my Bayesian statistical analysis skills.
Education
Harvard Medical School
Biomedical and Biological Sciences PhD. program
Boston, MA
present - 2017
Studying cancer genetics with bioinformatics and statistical modeling.
University of California, Irvine
B.S. in Biochemistry and Molecular Biology & B.S. in Chemistry
Irvine, CA
2017 - 2013
Magna Cum Laude with a cumulative GPA of 3.94 and Honors in Biology.
Research Experience
Graduate Research
Harvard Medical School
Boston, MA
present - 2017
My first project was to study the tissue- and allele-specific genetic interactions of KRAS in cancer using thousands of human tumor samples. Currently, I am analyzing CRISPR-Cas9 loss-of-function screens using Bayesian hierarchical models.
Undergraduate Research
Dept. of Molecular Biology and Biochemistry, UCI
Irvine, CA
2017 - 2014
I investigated the patterns and mechanisms of dissemination by which Toxoplasma gondii, an obligate, intracellular parasite, infects a human host.
Research Interneship
Saban Research Institute, Los Angeles
Los Angeles, CA
2014
I studied the underlying causes of developmental disruptions within the hypothalamus that are characteristic of Prader-Willi syndrome.
Research Interneship
Saban Research Institute, Los Angeles
Los Angeles, CA
2012
I researched the role of liver progenitor cells in Alagille syndrome and biliary atresia, two rare, yet deadly, early-onset liver diseases.
Publications
The origins and genetic interactions of KRAS mutations are allele- and tissue-specific
Nat. Commun.
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2021
Joshua H Cook, Giorgio E M Melloni, Doga C Gulhan, Peter J Park, Kevin M Haigis
Tissue-Specific Oncogenic Activity of KRASA146T
Cancer Discov.
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2019
Emily J Poulin, Asim K Bera, Jia Lu, Yi-Jang Lin, Samantha Dale Strasser, Joao A Paulo, Tannie Q Huang, Carolina Morales, Wei Yan, Joshua Cook, Jonathan A Nowak, Douglas K Brubaker, Brian A Joughin, Christian W Johnson, Rebecca A DeStefanis, Phaedra C Ghazi, Sudershan Gondi, Thomas E Wales, Roxana E Iacob, Lana Bogdanova, Jessica J Gierut, Yina Li, John R Engen, Pedro A Perez-Mancera, Benjamin S Braun, Steven P Gygi, Douglas A Lauffenburger, Kenneth D Westover, Kevin M Haigis
Toxoplasma gondii disrupts β1 integrin signaling and focal adhesion formation during monocyte hypermotility
J. Biol. Chem.
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2018
Joshua H Cook, Norikiyo Ueno, Melissa B Lodoen
Loss of Magel2 impairs the development of hypothalamic Anorexigenic circuits
Hum. Mol. Genet.
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2016
Julien Maillard, Soyoung Park, Sophie Croizier, Charlotte Vanacker, Joshua H Cook, Vincent Prevot, Maithe Tauber, Sebastien G Bouret
Bayesian data analysis portfolio
Here is a collection of Bayesian data analyses I have done for my graduate research and personal projects.
Data visualization examples
You can peruse some of my data visualizations and analyses in my TidyTuesday repository.
Software
WaterMe
An iOS app for recording and scheduling when to water plants.
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For BMI 707 Deep Learning for Biomedical Data, my group trained a Generative Adversarial Network to produce high-resolution, realistic hand X-rays and then analyzed the latent space to control the age of the generated hand.
Examine the result in our report and watch this video of us controlling the GAN to make aging hand radiographs.
Workout Spinner
An Apple Watch app for randomly selecting an exercise.
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Telemetry Recorder
An Apple Watch app that records the watches acceleromter and gyroscope values and saves them a CSV in iCloud.
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Brief
A macOS app for summarizing text.
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Presentations
Cancer Research UK Trainee Meeting (oral): Modeling CRISPR-Cas9 screens to identify tissue-specific patterns.
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Sept 2021
Harvard Medical School Cancer Signaling Meeting (oral): Tissue- and allele-specific genetic interactions of KRAS.
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May 2021
Brigham and Women’s Hospital, Genetics Research in Progress (oral): The genetic interaction network of mutationally activated KRAS.
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Mar 2020
Cancer Research UK Progress Meeting (oral): Genetic description of oncogenic KRAS mutations.
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Oct 2019
UCI Undergraduate Research Opportunities Program Symposium (poster): Toxoplasma gondii-induced hypermotility in human primary monocytes through the dysregulation of β1 integrins.
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May 2016
UCI Excellence in Research (poster): Toxoplasma gondii-induced hypermotility in human primary monocytes through the dysregulation of β1 integrins.
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Apr 2016
UCI Excellence in Research (oral): Toxoplasma gondii-induced hypermotility in human primary monocytes through the dysregulation of β1 integrins.
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Apr 2016
West Coast Biological Sciences Undergraduate Research Conference (oral): Hypermotility of human primary monocytes through the dysregulation of β1 integrins by Toxoplasma gondii.
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Apr 2016
UCI Undergraduate Research Opportunities Program Symposium (oral): Destabilization of cell adhesion in human monocytes infected with Toxoplasma gondii.
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May 2015
Teaching Experience
Private Tutoring
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Cambridge, MA
Sept 2018 - June 2021
- Tutored a high school student every evening in a variety of topics
- Ensured that assignments were completed and submitted in time
Teaching Assistant for BMI 713 Computing Skills for Biomedical Sciences
Department of Biomedical Informatics, Harvard Medical School
Boston, MA
Aug 2019 - Nov 2019
- Assisted with instruction during lectures and helped students during periods of interactive group work
- Held weekly office hours and occasionally 1-on-1 tutoring sessions
- Created and graded problem sets
Tutor
UCI Learning and Academic Resource Center
Irvine, CA
Aug 2015 - Sept 2016
- Organized and led group tutoring sessions for undergraduate students
- Tutored for courses in introductory biology, biochemistry, molecular biology, and calculus
Leadership and Mentoring
Irvine Little League Manager
Little League Baseball
Irvine, CA
Feb 2016 - June 2016, Jan 2017 - July 2017
- Co-managed a Majors division (11-12 year-olds) baseball team
- Co-managed the 11 year-old’s All Star Team over the summer
- Managed my own team in the AA division (8-10 year-olds); season champions and won the Irvine City Championship Tournament
- Attended league meetings, organized parent volunteers, and scheduled practices and games
Tutor Advisor
UCI Learning and Academic Resource Center (LARC)
Irvine, CA
Mar 2016 - June 2017
- Trained other LARC tutors
- Met with tutors to make sure they were managing their course load and job in an efficient and healthy manner
- Scheduled LARC tutorials and handled day-to-day problems
Peer Mentor
UCI Campuswide Honors Program
Irvine, CA
Aug 2016 - June 2017
- Assisted and supported four incoming UC Irvine freshman
- Notified them of useful resources, answered questions they had about classes, and helped them work through the stress of beginning their undergraduate studies
Peer Scholars Mentor
Scholarship and Opportunities Program
Irvine, CA
Sept 2016 - Jan 2017
- Helped three UCI students apply for the Barry Goldwater Scholarship
Honors and Awards
NSF Graduate Research Fellowship Program Honorable Mention
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Apr 2019
Honors in Biological Sciences
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June 2017
Phi Lambda Upsilon
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May 2017
A national chemistry honorary society into which a few select graduating chemistry students are invited.
American Chemical Society Polymer Education Award
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May 2017
Jayne Unzelman Scholarship ($3,000)
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May 2017
Undergraduate student, academic excellence and service to the School of Biological Sciences and/or the University, and service to the community.
UC Irvine Chancellor’s Award of Distinction
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May 2017
Phi Beta Kappa
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May 2017
Fulbright Fellowship Alternate
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Mar 2017
Undergraduate Research Opportunities Program (UROP) Fellow and Grant Recipient ($400)
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Jan 2017
Malcolm R. Stacey Memorial Scholarship ($500)
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Oct 2016
Awarded to meritorious students of Jewish descent with financial need.
UCI Alumni Association 2016-17 Distinguished Anteaters Award ($1,500)
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June 2016
The anteater is the UCI mascot.
Summer Undergraduate Research Program ($1,300)
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June 2016
UCI School of Bio Sci Brian Atwood Scholarship ($3,000)
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May 2016
Awarded to a Junior-level Biological Sciences major who has demonstrated outstanding achievement in both scholarship and service to the UCI community.
Robert Ernst Prize for Excellence in Research in the Biological Sciences ($250)
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May 2016
Excellence in Research
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Apr 2016
A UCI School of Biological Sciences undergraduate competition whereby each student submits a manuscript of their research project, gives an oral presentation, and holds a poster session.
Barry Goldwater Scholar ($7,500)
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Mar 2016
UROP Fellow and Grant Recipient ($500)
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Jan 2016
UROP Honorary Fellowship
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June 2015
2015 UROP Fellow and Grant Recipient ($500)
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Jan
UCI Dean’s Honor List (all 12 academic quarters)
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2017 - 2014
UCI Campuswide Honors Program
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2017 - 2014