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Genomics and Systems Microbiology

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  • Gene-Wei Li

    Associate Professor of Biology
    Gene-Wei Li Lab
    gwli@mit.edu
    617-324-6703
    Short Bio

    Gene-Wei Li investigates how quantitative information regarding precise proteome composition is encoded in and extracted from bacterial genomes. We seek to understand the optimization of bacterial proteomes at both mechanistic and systems levels. Our work combines high-precision assays, genome-wide measurements, and quantitative/biophysical modeling. Ongoing projects focus on the design principles of transcription, translation, and RNA maturation machineries in the face of competing cellular processes.

  • Tami Lieberman

    Associate Professor, Civil and Environmental Engineering
    MIT IMES
    tami@mit.edu
    617-258-6670
    Short Bio

    Tami Lieberman joined the MIT faculty in January 2018. She leads a computational and experimental research group focused on uncovering the principles governing colonization, niche range, and personalization in the human microbiome.

    Tami trained in molecular biology and mathematics at Northwestern University, where she conducted research in the laboratory of Jon Widom and was funded by a Barry M. Goldwater Scholarship. She then earned a PhD in Systems Biology from Harvard University, where she conducted research in Roy Kishony’s laboratory. During her graduate research, Tami developed new genomic approaches for understanding how bacteria evolve during infections of individual people. As a postdoc in Eric Alm’s lab at MIT, she further developed and applied these genomic approaches to understand the microbes that colonize us during health. Tami has also made contributions to our understanding of antibiotic resistance, including the co-invention of a new platform for visualizing evolution in real time. Her work has been covered in the popular press, including online coverage from The Atlantic, The Wall Street Journal, National Geographic, The Boston Globe, and ArsTechnia.

  • Sebastian Lourido

    Associate Professor of Biology; Core Member, Whitehead Institute
    MIT Biology
    lourido@wi.mit.edu
    617-324-4920
    Short Bio

    Our lab is interested in the molecular events that enable apicomplexan parasites to remain widespread and deadly infectious agents. We study many important human pathogens, including Toxoplasma gondii, to model features conserved throughout the phylum. We seek to expand our understanding of eukaryotic diversity and identify specific features that can be targeted to treat parasite infections.

  • J. Christopher Love

    Associate Professor of Chemical Engineering
    Koch Institute
    clove@mit.edu
    617-324-2300
    Short Bio

    The Love Laboratory seeks to advance the discovery and development of new therapeutics using patient-centric, data-driven approaches. Using a suite of technologies for single-cell analysis pioneered by the lab over the last decade, we aim to resolve essential cells involved in the evolution of diseases like cancer and food allergy, as well as those that may offer beneficial protection through interventions like therapies or vaccines. We also aim to accelerate the development and accessibility of biopharmaceuticals and vaccines for patients globally. Our lab is creating integrated holistic approaches to the development and manufacturing of these biologics with the aim of testing new medicines rapidly and ensuring accessibility to new and existing medicines through innovations in manufacturing. Using a combination of principles from chemical engineering and biological engineering including state-of-the-art tools for genome editing and RNA sequencing, we are advancing the breadth of products through molecular and host engineering as well as concepts in integrated process design.

  • Scott Manalis

    Professor of Biological and Mechanical Engineering
    Manalis Lab
    srm@mit.edu
    617-253-5039
    Short Bio

    Scott Manalis is the David H. Koch Professor in Engineering and member of the Koch Institute for Integrative Cancer Research at MIT. He received a B.S. in physics from the University of California, Santa Barbara and a Ph.D. in applied physics from Stanford University. His lab develops and applies high precision approaches for measuring biophysical properties of single cells.

  • Darcy McRose

    Assistant Professor
    McRose Lab
    dmcrose@mit.edu
    617-715-4244
    Short Bio

    Our research group is interested in understanding how small scale microbially-mediated chemical transformations in soils and sediments affect biogeochemistry and plant growth. We focus specifically on the chemical tools or “secondary metabolites” that microbes (and plants) use to navigate and alter their environment. While we have learned a great deal about the antibiotic properties of secondary metabolites and their utility in human health, we know significantly less about secondary metabolite function in natural contexts. This knowledge gap creates a unique opportunity: secondary metabolites are highly tractable study targets and while they do not encompass the whole of soil complexity, they epitomize many crucial aspects.

    We are particularly interested in secondary metabolites that are redox active and/or bind metals as these chemical properties can contribute to weathering and nutrient turnover in natural contexts. Our work incorporates bacterial genetics, genomics, and physiology as well as mass spectrometry and other geochemical measurements. Carbon storage and agricultural sustainability are two of the ultimate motivations for our work. Specific projects investigating macronutrient cycling via secondary metabolites are described below.

  • Leonid Mirny

    Associate Professor of Health Sciences and Technology and Physics
    Mirny Lab
    leonid@mit.edu
    617-452-4862
    Short Bio

    The challenge of understanding biological systems from first physical principles is what motivates our research. Biological systems are characterized by remarkable structural complexity at all levels of organization. However, we believe that simple physical models are valuable for describing these systems.

    Our laboratory develops multidisciplinary approaches involving:

    • Polymer physics theory and simulation
    • Statistical interpretation of genome-wide data
    • Population genetics and evolutionary theory

    A key feature of our approach are the direct collaborations we have with other scientists in the area.

    A number of graduate students in the lab are co-advised by an experimentalist.

    Nearly every student in the lab works directly with our experimental collaborators, contributing both to experimental design, data analysis, and modeling.

  • Jacquin Niles

    Professor of Biological Engineering; Co-Director MIT Microbiology PhD Program
    Niles Lab
    jcniles@mit.edu
    617-324-3701
    Short Bio

    Our research emphasizes developing and using novel molecular tools to address outstanding questions in infectious diseases. Our specific focus is on malaria and the causative pathogen, Plasmodium falciparum. We take advantage of model systems to efficiently validate and optimize the design of new tools intended to address unmet needs in our target pathogen. In this process, we simultaneously produce solutions that are applicable across a range of model and pathogenic organisms, and broadly useful in both basic and applied biology efforts.

    We are highly multi-disciplinary in our approach, and integrate expertise in diverse areas including: biomolecular engineering; chemical biology; synthetic biology; analytical chemistry; biochemistry; and molecular and cell biology.

  • Elizabeth Nolan

    Associate Professor of Chemistry
    Nolan Lab
    lnolan@mit.edu
    617-452-2495
    Short Bio

    Liz Nolan was raised in Niskayuna, New York and graduated magna cum laude from Smith College with highest honors in chemistry and a minor in music. Liz conducted her graduate studies in inorganic chemistry at MIT where she joined the laboratory of Professor Stephen J. Lippard and she pursued post-doctoral research in the laboratory of Christopher T. Walsh at Harvard Medical School. Liz joined the Department of Chemistry at MIT as an Assistant Professor in 2009 and was promoted to Associate Professor Without Tenure in 2014, Associate Professor with Tenure in 2016, and Professor with Tenure in 2019. She was selected as the Ivan R. Cottrell Professor of Immunology in 2020. Liz received a 2010 NIH New Innovator Award, a 2014 NSF CAREER Award, and was named a Searle Scholar in 2011, an Alfred P. Sloan Foundation Fellow in 2013, and a Camille Dreyfus Teacher-Scholar in 2014. She is the recipient of the 2016 Eli Lilly Award in Biological Chemistry and a 2017 Presidential Early Career Award for Scientists and Engineers (PECASE). For her contributions as an educator, Liz was awarded the 2016 MIT School of Science Teaching Prize for Graduate Education. In 2020, Liz began serving as the Associate Department Head overseeing the Department of Chemistry’s educational mission.

  • Sergey Ovchinnikov

    Assistant Professor of Biology
    Ovchinnikov Lab
    so3@mit.edu
    617-258-7851
    Short Bio

    Sergey Ovchinnikov uses phylogenetic inference, protein structure prediction/determination, protein design, deep learning, energy-based models, and differentiable programming to tackle evolutionary questions at environmental, organismal, genomic, structural, and molecular scales, with the aim of developing a unified model of protein evolution.