CSIBD Enrichment Program

The CSIBD Enrichment Program has a history of facilitating the exchange of information between affiliated institutions.

Models, Inference & Algorithms (MIA) Initiative Meeting
November 6, 2024
Deciphering the Chemical Language of the Microbiome
Marnix Medema, PhD
Assistant Professor, Wageningen University, The Netherlands
Victoria Pascal Andreu, PhD
Germans Trias i Pujol Research Institute (IGTP), Spain

Broad Immunology Program Grand Rounds
February 20, 2024 (hybrid)
Chronic itch – from neuroimmune mechanisms to therapies
Caroline Sokol, MD, PhD
Principal Investigator, Center for Immunology and Inflammatory Diseases; Assistant Physician, MGH; Assistant Professor of Medicine, HMS
Rachel Meltzer, MD, MPH
Director, Pruritus Clinic at BWH; Instructor in Dermatology, HMS

Broad Immunology Program Seminar
June 20, 2023 (hybrid)
Kenya Honda, MD, PhD
Professor, Keio University; Team Leader, RIKEN Center for Integrative Medical Science
Toward the development of defined microbial therapeutics

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
July 7, 2022 (virtual)
Beverly Fu (Balskus Group, Harvard University)
Discovery of a skatole-forming glycyl radical enzyme

Paula Pelayo (Balskus Group, Harvard University)
Characterizing Prevotella sialidases from the vaginal microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 9, 2022 (virtual)
Maisa Takenaka, PhD (Moon Group, MGH)
CD4 T cell memory in the gut

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
May 12, 2022 (virtual)
Yuezhou Chen, MD, PhD (Wesemann Group, BWH)
Microbiota regulate primary Ig repertoire polyreactivity

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
April 28, 2022 (virtual)
Featuring the Broad Metabolite Profiling Platform:
Clary Clish, PhD (Senior Director) and Julian Avila, PhD (Senior Research Scientist)
Nontargeted metabolomics and approaches for unknown identification

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
April 14, 2022 (virtual)
Megan McCurry (Devlin Group, HMS)
Gut bacteria convert glucocorticoids into progestins

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
March 31, 2022 (virtual)
Yancong Zhang, PhD (Huttenhower Group, Harvard School of Public Health)
Identifying novel bioactive microbial gene products in inflammatory bowel disease

Broad Immunology Program Seminar
March 29, 2022 (hybrid)
Michael Karin, PhD
Distinguished Professor of Pharmacology & Pathology, UCSD School of Medicine
From mitochondrial stress to inflammation: NLRP3 inflammasome activation and beyond

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
March 17, 2022 (virtual)
Daniel Graham, PhD and Thomas Pedersen (Xavier Group, Broad Institute)
Functional heterogeneity of SusC-specific T cells in health and disease

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
March 3, 2022 (virtual)
Katharina Ribbeck, PhD (Ribbeck Group, MIT)
Partners in slime: how mucus regulates microbial virulence

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
February 3, 2022 (virtual)
Caroline Taouk, PhD (Goodman Group, Yale)
Evolution of an infection-specific Bacteroides colonization factor during infection

Meetings in Previous Years

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
November 4, 2021 (virtual)
Lyle (Robert) McPherson, PhD (Kiessling Group, MIT)
Lectin-Seq: A novel tool for profiling lectin-microbe interactions

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
October 7, 2021 (virtual)
Eric Alm, PhD (Alm Group, MIT)
Mapper: a fast and accurate sequence alignment tool

An-Ni Zhang, PhD (Alm Group, MIT)
Widespread adaptive evolution of the human gut microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
September 23, 2021 (virtual)
Eric Brown, PhD (Xavier Group, Broad Institute)
Gut microbiome ADP-ribosyltransferases are phage-encoded fitness factors

Eva Karolina Sjoberg Jabbar, MD, PhD (Xavier Group, Broad Institute)
Development and transmission of the gut microbiome and metabolome in mother-infant pairs

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
July 8, 2021 (virtual)
Kate Jeffrey, PhD (Massachusetts General Hospital)
Exploration of the human colonic virome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 24, 2021 (virtual)
Jacob Baker and A. Delphine Tripp (Lieberman Group, MIT)
Transmission of a bacteria and its phage in the skin microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
May 6, 2021 (virtual)
Matt Volpe and Martin Daniel-Ivad, PhD (Balskus Group, Harvard University)
Discovering and Manipulating DNA-damaging Natural Products in Microbial Communities

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
February 11, 2021 (virtual)
Xiao Tan, MD, PhD (Collins Group, MIT)
Machine Learning Approaches to the Analysis of Microbial Glycans and Proteins

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
January 28, 2021 (virtual)
Caroline Taouk, PhD (Goodman Group, Yale University)
Infection Triggers a Rapid Selective Sweep in Gut Commensal

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
November 19, 2020 (virtual)
Bharat Ramakrishna, MD (OpenBiome)

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
November 12, 2020 (virtual)
Jim Moon, PhD (BWH)
Antigen-specific T cell responses to intestinal microbiota

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
October 22, 2020 (virtual)
Yuezhou Chen, MD, PhD (Wesemann Group, BWH and HMS)
Microbial symbionts influence the primary Ig repertoire

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
September 24, 2020 (virtual)
Jay Zhao and Anni Zhang, PhD (Alm Group, MIT)
Population genomics of the human gut microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
July 23, 2020 (virtual)
Mathieu Groussin, PhD (Alm Group, MIT and Global Microbiome Conservancy)
Impact of industrialization on the gut microbiome, cholesterol metabolism and homeostasis

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
July 9, 2020 (virtual)
Doug Kenny and Damian Plichta, PhD (Xavier Group, Broad Institute)
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
February 27, 2020
Suhyun Kim, PhD (Silver Group, Harvard Medical School)
Beyond Antibiotics: Learning from Nature in Designing Therapeutic Bacteria to Specifically Target Pathogens

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
January 23, 2020
Daniel Graham, PhD, Damian Plichta, PhD, and Eric Brown, PhD (Graham Group, Broad Institute)
Antigen Discovery: A View of the Microbiome Through the Lens of a T cell

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
January 9, 2020
Christine Isabella (Kiessling Group, MIT)
Lectins as Microbial Detectors

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 13, 2019
Shijie Zhao (Alm Group, MIT)
Evolutionary dynamics of commensal microbiome in health and disease across human populations

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 6, 2019
Lauren Rajakovich, PhD, and Yindi Jiang, PhD (Balskus Group, Harvard University)
Understanding and Harnessing Gut Microbiome-Small Molecule Interactions

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
May 9, 2019
Mathieu Groussin, PhD (Alm Group, MIT and Global Microbiome Conservancy)
Impact of industrialization on the human gut microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
April 11, 2019
Craig McLean (Kujawinski Group, Woods Hole Oceanographic Institution)
Improved informatics contribute to the characterization of metabolism in non-model organism through untargeted metabolomics

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
February 14, 2019
Siyuan Ma (Huttenhower Group, Harvard School of Public Health)
Meta-Analysis of Population Structure in the IBD Gut Microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
January 24, 2019
Amanda Dugan, PhD (Kiessling Group, MIT)
Microbial recognition properties of human lectins

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
December 20, 2018
Alexander Naydich (Silver Group, Harvard Medical School)
Engineering commensal gut bacteria for biomarker discovery

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
November 29, 2018
Daniel Graham, PhD (Xavier Group, Broad Institute)
Antigen Discovery: A View of the Microbiome Through the Lens of a T cell

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
October 4, 2018
Kelsey Wheeler (Ribbeck Group, MIT)
Probing microbial interactions with the mucus barrier

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
September 13, 2018
Ari Adhikari, PhD (Devlin Group, Harvard Medical School)
Targeting gut bacterial bile salt hydrolases for therapeutic applications

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 11, 2018
Siyuan Ma, PhD (Huttenhower Group, Harvard School of Public Health)
Meta-Analysis of Population Structure in the IBD Gut Microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
May 10, 2018
Kate Jeffrey, PhD (Massachusetts General Hospital)
Defining the immunomodulatory capacity of the intestinal virome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
May 4, 2018
Sumaiya Nazeen, PhD (Berger Group, MIT)
Towards improved discovery of functional dysbiosis in patient microbiomes: Alignment-free functional binning of metagenomic reads

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
April 12, 2018
Larson Hogstrom and Moran Yassour, PhD (Xavier and Lander Groups, Broad Institute)
Early life mother-to-child microbial transmission

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
March 2, 2018
Michael J. Fink, PhD (Whitesides Group, Harvard University)
How to separate mixtures of bacteria?

Christoffer Karl Abrahamsson, PhD (Whitesides Group, Harvard University)
MagLev for Density Measurements and Separation in Biology (C.K.A.)

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
January 11, 2018
Sean Kearney, PhD (Alm Group, MIT)
Principles for engineering niche space in the human gut microbiota

Le Thanh Tu Nguyen (Alm Group, MIT)
Functional heterogeneity of prebiotic fermentation capabilities in healthy humans (LTTN)

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
December 14, 2017
Yindi Jiang, PhD and Carina Chittim, PhD (Balskus Group, Harvard University)
Understanding and Harnessing Gut Microbiome-Small Molecule Interactions

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
December 1 2017
Sloan Devlin, PhD (Harvard Medical School)
In vivo control of gut bacterial bile acid metabolism

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
November 17, 2017
Melissa Takahashi, PhD, Nicolaas Manuel Angenent-Mari, PhD, & Shimyn Slomovic, PhD (Collins Group, MIT)
Synthetic Biology Diagnostics for the Gut Microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
November 9, 2017
Arlene Sharpe, MD, PhD (Harvard Medical School)
Defining the Crosstalk between the PD-1 Pathway and the Microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
September 14, 2017
Katharina Ribbeck, PhD (MIT)
Probing microbial interactions with the mucus barrier

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
August 10, 2017
Mohit Verma, PhD (Whitesides Group, Harvard)
Butyrate: a link Between Us and Our Microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
August 4, 2017
Doug Kenny (Xavier Group, Broad Institute)
Activity-guided discovery of small molecules from the gut microbiota

Brantley Hall, PhD (Xavier Group, Broad Institute)
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 30, 2017
Siyuan Ma, PhD (Huttenhower Group, Harvard T.H. Chan School of Public Health)
Meta-Analysis of Population Heterogeneity in IBD Patients' Gut Microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 8, 2017
Mark Mimee, PhD, Isaak Mueller, PhD, and Cheng Chang, PhD (Lu Group, MIT)
Engineering Probiotics as Diagnostics and Therapeutics

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 2, 2017
William Yu, PhD (Berger Group, MIT)
Compressive Metagenomics: Scaling Faster than Light

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
March 9, 2017
Kathryn Kauffman, PhD (Polz Group, MIT)
Ecology of Bacterial Viruses in the Human Microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
February 23, 2017
Jason Lloyd-Price, PhD (Huttenhower Group, Harvard T. H. Chan School of Public Health)
Expanding the NIH Human Microbiome Project: Metagenomics, functions, strains, and dynamics of the healthy microbiome

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
January 12, 2017
Nitzan Koppel, PhD, Vayu Maini Rekdal, PhD, and Yindi Jiang, PhD (Balskus Group, Harvard)
Understanding and harnessing microbiome-drug interactions

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
December 8, 2016
Moshe Biton, PhD, Rebecca Herbst, MSc, & Jose Ordovas-Montanes, PhD (Shalek Group, MIT & Regev Group, Broad Institute)
Single-Cell Genomic Approaches for Understanding the Human Gut

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
September 8, 2016
Angelina Bilate, PhD (Ploegh Group, Whitehead Institute)
Microbiota-dependent differentiation of intestinal regulatory T cells and intraepithelial lymphocytes from a clonal T-cell precursor

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
August 11, 2016
Dana Braff, PhD, Melissa Takahashi, PhD, and Xiao Tan, MD, PhD (Collins Group, MIT)
Paper-based Diagnostics for IBD

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
June 9, 2016
Phil Arevalo, PhD (Polz Group, MIT)
A biological definition of microbial populations and its application to a reverse ecology approach

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
May 12, 2016
Nathaniel Roquet, PhD (Lu Group, MIT)
Engineering synthetic state machines in living cells

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
April 14, 2016
Melanie Schirmer, PhD (Xavier Group, Broad Institute)
Interactions of the gut microbiome and the inflammatory cytokine response in healthy individuals

Aleksander Kostic, PhD (Xavier Group, Broad Institute)
Exploring Biosynthetic Gene Clusters Associated with Inflammatory Bowel Disease

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
March 10, 2016
William Yu, PhD (Berger Group, MIT)
Compressive algorithms: trade-offs in runtime, memory, and storage

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
February 11, 2016
Moshe Biton, PhD, & Adam Haber, PhD (Regev Group, Broad Institute)
Dissecting gut epithelial tissue to uncover novel cell state and function

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
January 14, 2016
Eric Alm, PhD (MIT)
Microbiome based medicine: from genomics to diagnostics and therapeutics

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
October 15, 2015
Jim Collins, PhD (MIT)
Paper-based Diagnostics for IBD

Center for Microbiome Informatics and Therapeutics (CMIT) Work-In-Progress
October 1, 2015
Timothy Lu, MD, PhD (MIT)
Synthetic Microbes as Next Generation Ulcerative Colitis Diagnostics and Treatments