JL Weissman, PhD

Positions

• Postdoctoral Fellow, University of Southern California, 2020 - Present
  • Adviser: Jed Fuhrman
  • Funding: Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology (Simons Foundation, 2019)

Education

PhD in Behavior, Ecology, Evolution, and Systematics (BEES)

Fall 2019, University of Maryland College Park, College Park, MD

• Dissertation: Investigating the Distribution of CRISPR Adaptive Immune Systems Among Prokaryotes
• Advisers: Philip L.F. Johnson & William F. Fagan

Graduate Certificate in Computation and Mathematics for Biological Networks

Fall 2019, University of Maryland College Park, College Park, MD

B.A. in Mathematics and Biology

Spring 2015, Bard College, Annandale-on-Hudson, NY

• Thesis: Modeling Stochastic Traps The Evolution of Preference in a Temporally Heterogeneous Ecological Trap
• Advisers: Bruce Robertson & Csilla Szabo

Summer Schools

• Microbial Diversity Course, Marine Biological Laboratory, Woods Hole, MA, 2018
• The Search for Selection, NIMBioS, Knoxville, TN, 2018
• Complex Systems Summer School, Santa Fe Institute, Santa Fe, NM, 2017

Publications

Preprints

Weissman J.L., M. Peras, T.P. Barnum, J.A. Fuhrman. Benchmarking community-wide estimates of growth potential from metagenomes using codon usage statistics. bioRxiv

Weissman J.L., E.R.O. Dimbo, A.I. Krinos, C. Neely, Y. Yag"ues, D. Nolin, S. Hou, S. Laperriere, D.A. Caron, B. Tully, H. Alexander, J.A. Fuhrman. Estimating the maximal growth rates of eukaryotic microbes from cultures and metagenomes via codon usage patterns. bioRxiv

Ignacio-Espinoza C., S. Laperriere, Y.C. Yeh, J.L. Weissman, S. Hou, A. Long, J.A. Fuhrman. Ribosome-linked mRNA-rRNA chimeras reveal active novel virus-host associations. bioRxiv

Peer-Reviewed

Gleich S.J, J.A. Cram, J.L. Weissman, D.A. Caron. NetGAM: Using generalized additive models to improve the predictive power of ecological network analyses constructed using time-series data. ISME Communications

Weissman J.L., S. Hou, J.A. Fuhrman. 2021. Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns. Proceedings of the National Academy of Sciences

Weissman J.L., E.O. Alseth, S. Meaden, E.R. Westra, J.A. Fuhrman. 2021. Immune Lag Is a Major Cost of Prokaryotic Adaptive Immunity During Viral Outbreaks. Proceedings of the Royal Society B

Weissman J.L., S. Dogra, K. Javadi, S. Bolten, R. Flint, C. Davati, J. Beattie, K. Dixit, T. Peesay, S. Awan, P. Thielen, F. Breitwieser, P.L.F. Johnson, D. Karig, W.F. Fagan, S. Bewick. 2021. Exploring the functional composition of the human microbiome using a hand-curated microbial trait database. BMC Bioinformatics

Tully B.J, J. Buongiorno, …, L.E. Valentin-Alvarado, J.L. Weissman, BVCN Instructor Consortium. 2021. The Bioinformatics Virtual Coordination Network: an open-source and interactive learning environment. Frontiers in Education

Marti-Carreras J., A.R. Gener, …, J.L. Weissman, V. Zalunin, A. Efremov, B. Busby. 2020. NCBI’s Virus Discovery Codeathon: Building “FIVE” – The Federated Index of Viral Experiments API Index. Viruses

Weissman J.L., A. Stoltzfus, E.R. Westra, P.L.F. Johnson. 2020. Avoidance of Self During CRISPR Immunization. Trends in Microbiology 28(7), 543-553

Weissman J.L. & P.L.F. Johnson. 2020. Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes. mSystems J 5(1), e00752-19..

Weissman J.L., W.F. Fagan, P.L.F. Johnson. 2019. Linking high GC content to the repair of double strand breaks in prokaryotic genomes. PLOS Genetics 15(11), e1008493..

Weissman J.L., R. Laljani, W.F. Fagan, P.L.F. Johnson. 2019. Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy. The ISME Journal 13(10), 2589-2602.

Bewick S., E. Gurarie, J.L. Weissman, J. Beattie, C. Davati, R. Flint, P. Thielen, F. Breitwieser, D. Karig, W.F. Fagan. 2019. Trait-Based Analysis of the Human Skin Microbiome. Microbiome 7(1), 101.

Weissman J.L., W.F. Fagan, P.L.F. Johnson. 2018. Selective maintenance of multiple CRISPR arrays across prokaryotes. The CRISPR Journal 1(6), 405-413.

Weissman J.L., R. Holmes, R. Barrangou, S. Moineau, W.F. Fagan, B. Levin, P.L.F. Johnson. 2018. Immune Loss as a Driver of Coexistence During Host-Phage Coevolution. The ISME Journal 12(2), 585-597.

Outreach Publications

Weissman J. L., H.H. Yiu, P.L.F. Johnson. 2019. What Bacteria Do When They Get Sick. Frontiers Young Minds.

Fellowships and Awards

• Biology Travel Award (UMD-CP, 2019 and 2016)
• COMBINE Network Science Fellowship (UMD/NSF DGE-1632976, 2018)
• Devra Kleiman Memorial Scholarship (UMD, 2018)
• GAANN Mathematical Biology Fellowship (UMD/U.S. Department of Education, 2015)
• The Flagship Fellowship (UMD, 2015)
• The Dean’s Fellowship (UMD, 2015)
• The Harry J. Carman Scholarship (Bard College, 2014)
• The John Bard Scholarship (Division of Science, Math and Computing, Bard College, 2013)
• George I. Alden Scholar (George I. Alden Trust, 2012)
• The Excellence and Equal Cost Scholarship (Bard College, 2011)
• The Bishop Scholarship (The Bishop Scholarship Foundation, 2011)

Invited Talks

1. Center for Advanced Biotechnology and Medicine, Rutgers University, NJ, May 2021
2. Department of Biology, San Diego State University, CA, May 2021
3. Computation and Mathematics for Biological Networks, UMD, MD, December 2020
4. Department of Marine and Environmental Biology, USC, CA, September 2020
5. Environment and Sustainability Institute, University of Exeter, Penryn, UK, February 2019
6. Clemson University, Clemson, SC, December 2018

Workshops

• Virus Hunting in the Cloud Codeathon, NCBI/UMIACS, College Park, MD, 2019
• Quantitative Laws II Workshop, Lake Como School of Advanced Studies, Italy, 2016

Teaching

Instructor

Bioinformatics Virtual Coordination Network, Spring 2020 - Present

• Co-developed and taught Network Science and Population Genetics online coursework during the COVID-19 lockdown

Guest Lecturer

University of Maryland College Park

• BIOL709F: Statistics and Modeling for Biologists, The Bootstrap, Spring 2018
• BSCI464: Microbial Ecology, Microbial Diversity, Spring 2018
• BSCI405: Population and Evolutionary Genetics, Horizontal Gene Transfer, Spring 2017

Teaching Assistant

• Calculus for the Life Sciences, Department of Biology, University of Maryland College Park, Fall 2015
• Bridge to Enter Advanced Mathematics (BEAM), The Art of Problem Solving Foundation, Cambridge, MA, Summer 2012 and 2015

Mentoring

Workshop Organizer

• Mentoring Undergraduate Researchers: A Practical Guide for Graduate Student Mentors, University of Maryland College Park, Spring 2019

Undergraduates Mentored

University of Southern California

• James Rosas (Summer 2021, National Summer Undergraduate Research Project)
• Edward-Robert Dimbo (Spring 2021 - Present; Genomics and Geobiology Undergraduate Research Experience, C-DEBI)
• Yuniba Yagües (Summer 2020, National Summer Undergraduate Research Project)
• Oscar Escobedo (Summer 2020, National Summer Undergraduate Research Project)

University of Maryland College Park

• Rohan Laljani (Fall 2017 - Summer 2019; co-author on Weissman et al. 2019, ISME J)
• Vinay Veluvolu (Summer 2018 - Summer 2019; poster at UMD Biosciences Research Day)
• Julia Gall (Fall 2018 - Spring 2019; College Park Scholars project & poster presentation)
• Cori Butkiewicz (Summer 2017 - Spring 2018; now in grad. program at UW-Madison)
• Nicholas Penn (Spring 2017 - Summer 2017)

Service

DEI Committee & Subcommittee on Reporting

Department of Marine and Environmental Biology (MEB), USC. May 2021 - Present

Conference Organizing Committee

Holistic Bioinformatics Approaches Used in Microbiome Research, Bioinformatics Virtual Coordination Network, Summer 2020 - Summer 2021

Co-Organizer

Pride Month Programming for MEB, USC, June 2021

Organizer

MEB Statistics Reading Group, USC, Spring 2020 - Present

Participant

Unlearning Racism in Geoscience (URGE), USC, Spring 2021

BEES Student Taskforce (BEESst)

University of Maryland College Park

• Co-President, Fall 2017-Spring 2018
• Secretary-Treasurer, Fall 2018-Spring 2019

Graduate Mentor

Biological Sciences Graduate Program, University of Maryland College Park, Fall 2016, 2017

Reviewer

• The ISME Journal
• PNAS
• Nature Communications
• mSystems
• Microbiome
• PLoS Computational Biology

Outreach

Co-Organizer

MEB Postdoc Outreach Project, USC, Winter 2020 - Present

Tutor & Mentor

Joint Educational Project, USC, Spring 2020

Organizer

Frontiers Young Minds Writing Group, USC, Winter-Spring 2020

Mentor & Panel Reviewer

Student Spaceflight Experiments Program (SSEP) 2016-2019

Maryland Day Organizer

Biological Sciences, UMD-CP, 2016-2018

Project Leader,

Bard Math Circle, Annandale-on-Hudson, NY, 2013-2015

Public Talk

GradTerps Exchange, University of Maryland, Spring 2019

Public Talk

Skype a Scientist, Summer 2020