CSIBD Enrichment Program

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

The CSIBD and the Center for Microbiome Informatics and Therapeutics (CMIT) hold joint Work-In-Progress meetings that focus heavily on the work of graduate students and postdoctoral fellows.

November 4, 2021 (virtual)
Lyle (Robert) McPherson, PhD (Kiessling Group, MIT)
Lectin-Seq: A novel tool for profiling lectin-microbe interactions

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

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

July 8, 2021 (virtual)
Kate Jeffrey, PhD (Massachusetts General Hospital)
Exploration of the human colonic virome

June 24, 2021 (virtual)
Jacob Baker and A. Delphine Tripp (Lieberman Group, MIT)
Transmission of a bacteria and its phage in the skin microbiome

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

February 11, 2021 (virtual)
Xiao Tan, MD, PhD (Collins Group, MIT)
Machine Learning Approaches to the Analysis of Microbial Glycans and Proteins

January 28, 2021 (virtual)
Caroline Taouk, PhD (Goodman Group, Yale University)
Infection Triggers a Rapid Selective Sweep in Gut Commensal

Work-In-Progress Meetings in Previous Years

November 19, 2020 (virtual)
Bharat Ramakrishna, MD (OpenBiome)

November 12, 2020 (virtual)
Jim Moon, PhD (BWH)
Antigen-specific T cell responses to intestinal microbiota

October 22, 2020 (virtual)
Yuezhou Chen, MD, PhD (Wesemann Group, BWH and HMS)
Microbial symbionts influence the primary Ig repertoire

September 24, 2020 (virtual)
Jay Zhao and Anni Zhang, PhD (Alm Group, MIT)
Population genomics of the human gut microbiome

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

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

February 27, 2020
Suhyun Kim, PhD (Silver Group, Harvard Medical School)
Beyond Antibiotics: Learning from Nature in Designing Therapeutic Bacteria to Specifically Target Pathogens

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

January 9, 2020
Christine Isabella (Kiessling Group, MIT)
Lectins as Microbial Detectors

June 13, 2019
Shijie Zhao (Alm Group, MIT)
Evolutionary dynamics of commensal microbiome in health and disease across human populations

June 6, 2019
Lauren Rajakovich, PhD, and Yindi Jiang, PhD (Balskus Group, Harvard University)
Understanding and Harnessing Gut Microbiome-Small Molecule Interactions

May 9, 2019
Mathieu Groussin, PhD (Alm Group, MIT and Global Microbiome Conservancy)
Impact of industrialization on the human gut microbiome

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

February 14, 2019
Siyuan Ma (Huttenhower Group, Harvard School of Public Health)
Meta-Analysis of Population Structure in the IBD Gut Microbiome

January 24, 2019
Amanda Dugan, PhD (Kiessling Group, MIT)
Microbial recognition properties of human lectins

December 20, 2018
Alexander Naydich (Silver Group, Harvard Medical School)
Engineering commensal gut bacteria for biomarker discovery

November 29, 2018
Daniel Graham, PhD (Xavier Group, Broad Institute)
Antigen Discovery: A View of the Microbiome Through the Lens of a T cell

October 4, 2018
Kelsey Wheeler (Ribbeck Group, MIT)
Probing microbial interactions with the mucus barrier

September 13, 2018
Ari Adhikari, PhD (Devlin Group, Harvard Medical School)
Targeting gut bacterial bile salt hydrolases for therapeutic applications

June 11, 2018
Siyuan Ma, PhD (Huttenhower Group, Harvard School of Public Health)
Meta-Analysis of Population Structure in the IBD Gut Microbiome

May 10, 2018
Kate Jeffrey, PhD (Massachusetts General Hospital)
Defining the immunomodulatory capacity of the intestinal virome

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

April 12, 2018
Larson Hogstrom and Moran Yassour, PhD (Xavier and Lander Groups, Broad Institute)
Early life mother-to-child microbial transmission

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.)

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)

December 14, 2017
Yindi Jiang, PhD and Carina Chittim, PhD (Balskus Group, Harvard University)
Understanding and Harnessing Gut Microbiome-Small Molecule Interactions

December 1 2017
Sloan Devlin, PhD (Harvard Medical School)
In vivo control of gut bacterial bile acid metabolism

November 17, 2017
Melissa Takahashi, PhD, Nicolaas Manuel Angenent-Mari, PhD, & Shimyn Slomovic, PhD (Collins Group, MIT)
Synthetic Biology Diagnostics for the Gut Microbiome

November 9, 2017
Arlene Sharpe, MD, PhD (Harvard Medical School)
Defining the Crosstalk between the PD-1 Pathway and the Microbiome

September 14, 2017
Katharina Ribbeck, PhD (MIT)
Probing microbial interactions with the mucus barrier

August 10, 2017
Mohit Verma, PhD (Whitesides Group, Harvard)
Butyrate: a link Between Us and Our Microbiome

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

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

June 8, 2017
Mark Mimee, PhD, Isaak Mueller, PhD, and Cheng Chang, PhD (Lu Group, MIT)
Engineering Probiotics as Diagnostics and Therapeutics

June 2, 2017
William Yu, PhD (Berger Group, MIT)
Compressive Metagenomics: Scaling Faster than Light

March 9, 2017
Kathryn Kauffman, PhD (Polz Group, MIT)
Ecology of Bacterial Viruses in the Human Microbiome

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

January 12, 2017
Nitzan Koppel, PhD, Vayu Maini Rekdal, PhD, and Yindi Jiang, PhD (Balskus Group, Harvard)
Understanding and harnessing microbiome-drug interactions

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

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

August 11, 2016
Dana Braff, PhD, Melissa Takahashi, PhD, and Xiao Tan, MD, PhD (Collins Group, MIT)
Paper-based Diagnostics for IBD

June 9, 2016
Phil Arevalo, PhD (Polz Group, MIT)
A biological definition of microbial populations and its application to a reverse ecology approach

May 12, 2016
Nathaniel Roquet, PhD (Lu Group, MIT)
Engineering synthetic state machines in living cells

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

March 10, 2016
William Yu, PhD (Berger Group, MIT)
Compressive algorithms: trade-offs in runtime, memory, and storage

February 11, 2016
Moshe Biton, PhD, & Adam Haber, PhD (Regev Group, Broad Institute)
Dissecting gut epithelial tissue to uncover novel cell state and function

January 14, 2016
Eric Alm, PhD (MIT)
Microbiome based medicine: from genomics to diagnostics and therapeutics

October 15, 2015
Jim Collins, PhD (MIT)
Paper-based Diagnostics for IBD

October 1, 2015
Timothy Lu, MD, PhD (MIT)
Synthetic Microbes as Next Generation Ulcerative Colitis Diagnostics and Treatments