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Principal Investigator

JL Weissman (they/she)

Assistant Professor, Department of Ecology & Evolution and the Institute for Advanced Computational Science (IACS)

Email: jackie.weissman@stonybrook.edu

Bluesky: @jlw-ecoevo.bsky.social

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CV

Bio: Jackie Lee “JL” Weissman (they/she) is an Assistant Professor at Stony Brook University in the Department of Ecology and Evolution and at the Institute for Advanced Computational Science. Her research examines how microbes survive and thrive across diverse environments.

Click for more info JL develops new tools to infer what microbes are doing and can do from DNA sequences captured directly from the environment (“metagenomes”), aiming to improve the representation of microbially-mediated biogeochemical cycles in global climate models. She also has a special interest in using a combination of comparative genomics, population genetics, and mathematical models to understand the ancient and ongoing battle between microbes and their viruses. She believes all students, with supportive training and mentorship, can become highly-capable computational biologists, and loves to show students how a little coding can go a long way. Previously, JL served as the inaugural Director for Proposal Development at the City College of New York, where they managed large, interdisciplinary efforts to bring center-level funding to the college and trained early-career researchers in grantmaking. They maintain research affiliations in biology at CCNY and the University of Southern California and have taught at The Cooper Union School of Art. Before returning to New York, they were faculty at Chapman University, where they ran a computational biology research lab, taught, and developed initiatives to improve mentorship at the college level.

       

Postdoctoral Researchers

Alexandra Walling (they/them)

Email: alexandra.walling@stonybrook.edu

CV

Bio: Alexandra (they/them) is a postdoctoral researcher in the mGAMUT lab. Their research currently focuses on analyzing the distribution of different forms of anoxygenic photosynthesis across diverse habitats.

 

Click for more info They earned their B.S. in Biology at California State University, Monterey Bay before joining the American Museum of Natural History first as a Helen Fellow and then as a PhD student through the Richard Gilder Graduate School. Their research at AMNH has included comparative questions in prokaryotic and viral evolution. Their PhD work used comparative genomic and phylogenetic techniques to untangle how horizontal gene transfer and secondary loss shaped the evolution of photosynthesis in Erythrobacteraceae, a family of Alphaproteobacteria which show a scattered distribution of a gene cluster encoding photosynthesis. Alexandra's first postdoc at the University of Rhode Island was spent focusing on the problem of how we can filter large genomic datasets to increase signal and reduce noise by developing tools to predict which genomic loci have the most utility for downstream phylogenetic analysis. They used extensive simulations and compared machine learning models for phylogenetic utility determination. Alexandra is broadly interested in using a wide range of computational tools to answer questions related to microbial evolution and ecology, particularly how horizontal gene transfer among populations of bacteria may drive bacterial evolution in response to biogeochemical cycling. Alexandra also enjoys teaching and mentoring undergraduate and graduate students just starting out in evolutionary and computational biology. When not working, Alexandra enjoys exploring the great outdoors with their former laboratory beagle, Darwin.

       

Graduate Students

M. Salim Dason

Email: mohammedsalim.dason@stonybrook.edu

Bio: Salim is a PhD Student in Ecology & Evolution. His research interests include metagenomics, microbial community assembly, computational modeling, and microbial metabolism.

 

Click for more info Salim earned his bachelor’s degree in Life Sciences with a focus on microbial biotechnology in Morocco, then completed a master’s in Medical Biotechnologies in Italy. His thesis focused on identifying clade-specific microbial markers in shotgun metagenomic data from transgenic Alzheimer’s disease mouse models to profile and better understand shifts in gut microbiome composition linked to neurodegeneration. After graduating, Salim worked as a bioinformatics research fellow on a project to develop a computational pipeline for the de novo reconstruction and functional annotation of metagenome-assembled genomes from gut microbiome data, with a particular focus on previously uncharacterized bacteria.

       

Lyra Lu

Email: lyra.lu@stonybrook.edu

Bio: Lyra is a PhD Student in Ecology & Evolution. She is interested in using comparative genomics and mathematical models on microbial systems.

 

Click for more info Lyra received their B.S. in Biology at Binghamton University before joining the mGamut Lab.

             

Undergraduates

See the join us page for details.

Past Mentees

Stony Brook University

Jesse Natarajan (she/her)

Bio: Jesse graduated with a Computer Science major and Biology/Chemistry minor from Stony Brook University. She completed her undergraduate honors thesis in the mGAMUT lab on predicting microbial growth rates using short genomic sequences.


Chapman University

University of Southern California

University of Maryland College Park