Channing Microbiome Seminar

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——————————————————————–        2024        ————————————————————————– 

05/03/2024 Samuel Forster (Hudson Institute of Medical Research): TBD

03/22/2024 Pixu Shi (Duke University): Statistical Analysis of Longitudinal Microbiome Data

03/08/2024 11am Sean Gibbons (Institute for Systems Biology): You are what you eat!

03/08/2024 9am Yiyan Yang (NIH): Large-scale Genomic Survey with Deep Learning-based Method Reveals Strain-Level Phage Specificity Determinants

02/16/2024 Jie Deng (MIT): The development of ecological systems along paths of least resistance

01/26/2024 Seppe Kuehn (U Chicago): Predicting microbiome function from genomic and taxonomic composition

——————————————————————–        2023        ————————————————————————– 

12/08/2023 Ali Zomorrodi : Decoding the role of breast milk microbiome and probiotics in early life gut microbiome development

11/10/2023  Zhang Wang : The Respiratory Microbiome in COPD

10/27/2023  Lei Dai : Quantitative ecology of host-associated microbiomes

10/13/2023  Kyu Ha Lee: MMZIP: A scalable multivariate variable selection approach for zero-inflated count data

09/29/2023 Jason Norman: Developing a Defined Bacterial Consortium for Clostridioides Difficile Infection (CDI)

09/22/2023  Zheng Sun: Reduced-Representation Metagenome Expands the Boundary and Accuracy of Microbiome Research

09/16/2023 Jintao Liu: Spatial coordination of metabolism in bacterial communities

06/23/2023 Kangjin Kim : Phylogenetic Tree-based Microbiome Association Test for Composition Bias

06/09/2023 Ines Thiele : Large-scale reconstruction of the microbiome highlights widespread drug-metabolising capacities

05/26/2023 Francisco J. Planes : Network-based computational modeling of metabolism of the human gut microbiota with views to personalized nutrition

05/12/2023 Joseph Zackular : Pathogen-microbiota interactions during Clostridioides difficile infection

04/28/2023 Karoline Faust : Lessons from synthetic human gut bacterial communities

04/14/2023 Jun wang: Nanopore sequencing and Natural Language Processing in Microbiome analysis and translation

03/31/2023 Rita Almeida Oliveira : Gut microbiota modification of dietary metabolites to guide symbiotic bacterial consortium design against Klebsiella pneumoniae gut colonization

03/17/2023 Yu Deng : Use of sewage surveillance for SARS-CoV-2 in Hong Kong

03/03/2023  Zheng Sun: Eliminating false positives in metagenomic profiling based on type IIB restriction sites

01/27/2023 Sarah Berry: Personalised nutrition for metabolic health

01/13/2023 Kathy Lee-Sarwar: The Maternal Prenatal and Offspring Early-Life Gut Microbiome of Asthma

——————————————————————–        2022        ————————————————————————–

03/01/2022 Natasha Palacios: The gut microbiome and Parkinson’s disease

03/11/2022 Hannah Laue: The Role of the Microbiome in Environmental Epidemiology 

03/25/2022 Amy Willis: Model misspecification in microbiome studies 

04/08/2022 Jeff Xia: Using metabolomics and multi-omics for functional insights into microbiome

04/22/2022 Michael Wu: Statistical Analysis of Large-Scale Microbiome Profiling Studies: Batch Effects and Robust Testing

05/06/2022 Gang Fang: Illuminating bacterial DNA methylation to understand microbiome and human epigenome

06/17/2022 Susan Bullman: Assessing the contribution of the intratumoral microbiota to the tumor microenvironment

09/09/2022 Fangqing Zhao: Novel methods in microbiome data integration and their applications

09/23/2022 Sergei Maslov: Cross-feeding networks, diauxic shifts, and stable marriage in the human gut microbiome

10/07/2022 Qiyun Zhu: Upgrading microbiome data science with relationship graphs

10/21/2022 Jiliang Hu: Emergent phases of ecological diversity and dynamics mapped in microcosms  

11/04/2022 Ophelia Venturelli: Emergent phases of ecological diversity and dynamics mapped in microcosms

11/18/2022 Jingyuan Fu: The gut microbiome as a window into individual vulnerability and resilience

12/02/2022 Hannah Holscher: Effects of diet on the human microbiota and metabolome

12/06/2022 Ayan Chatterjee: Identifying interactions between novel protein targets and ligands – AI-Bind and AI-assisted molecular docking

12/16/2022 Yajuan Lin: Deep Learning for Predicting 16S rRNA Gene Copy Number

——————————————————————–        2021        ————————————————————————–

02/02/2021 Dong Wang: The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk

03/05/2021 Sebastián Michel Mata: Predicting microbiome compositions using deep learning

04/16/2021 Cameron Martino: Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

06/04/2021 Jun Chen: Linear Models for Differential Abundance Analysis of Microbiome Compositional Data

06/25/2021 Leyuan Li : Revealing Protein-Level Functional Redundancy in the Human Gut Microbiome using Ultra-deep Metaproteomics

10/22/2021 Amir Bashan: ​​Complexity-stability relationship in empirical microbial ecosystems

11/05/2021 Shanlin Ke: The relationship between emotions and gut microbiome in a women adult cohort

11/19/2021 Chen Liao: Oral bacteria in feces reflect loss of intestinal bacteria

12/17/2021 Yanjiao Zhou: The airway fungal and bacterial microbiome and loss of asthma control in asthmatic children

——————————————————————–        2020        ————————————————————————–

01/31/2020 Chulianng Song : An environment-dependent framework of ecological network structures

10/09/2020 Wenping Cui: Statistical Mechanics of Microbiomes 

12/04/2020 Andrea Aparicio: Identifying sensor species to predict critical transitions in complex ecosystems 

——————————————————————–        2019        ————————————————————————–

05/03/2019 Xuesong He : Human oral nanobacteria: walking the fine line between parasitism and mutualism

04/26/2019 Isabel Fernandez Escapa : Achieving species-level resolution from 16S rRNA gene short-read data using a high-resolution training set with the RDP naïve Bayesian Classifier

04/19/2019 Jaeyun Sung : Identifying Microbial Signatures of Gut Wellness through a Multi-study Integration of Human Stool Metagenomes

03/15/2019 Gabriel E Leventhal : Uncovering co-evolution in natural microbial consortia using genomics: from wastewater granules to pink berries

03/01/2019 Alvaro Sanchez: Predicting the assembly of complex communities in simple environments

01/11/2019 Emrah Altindis : Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host–microbe interactions

——————————————————————–        2018        ————————————————————————–

12/17/2018: Gang Fang : Illuminating Bacterial Epigenomes: Technologies, Pathogens and Microbiome

11/08/2018: Yanjiao Zhou : The Gut Microbiome in Cross-organ Interaction

08/10/2018: Naama Geva-Zatorsky : Mining the gut microbiota for immunomodulatory organisms

07/27/2018: Xiaofang Jiang : Comprehensive analysis of mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools

06/08/2018: Ali Ebrahimi : Microbial enzymatic strategies shape community assembly on particulate carbohydrates

03/16/2018: Xinhua Chen : Colonic vascular barrier function in C. difficile infection

02/16/2018: Ahmed Metwally : Longitudinal Computational Microbiome Methods: Identification, Modeling, and Classification in a Pediatric Lung Transplant Cohort 

——————————————————————–        2017        ————————————————————————–

12/01/2017: Katherine Lemon : Nose Picking for Progress: Mining the Nasal Microbiome for New Insights into Pathobionts

11/17/2017: Chuliang Song : Feasibility Analysis of Ecological Systems

10/20/2017: Yu Chen : Mechanistic studies of SRR adhesin biogenesis pathway of Streptococcus gordonii

10/10/2017: Marco Angulo : Controlling microbial communities: a theoretical framework

9/15/2017 Xin Wang : Optimal growth of microbes in the presence of mixed carbon sources

6/9/2017 Dingding An : Microbial sphingolipids modulate host epithelium homeostasis and disease

5/26/2017 Min Dong : Biology and Engineering of Bacterial Toxins

4/28/2017 Dong Kong : Genetic and Optic Dissection of Neuron-Metabolism

4/14/2017 Travis Gibson : Dynamics, Inference (Bayesian), and Experimental Design (for inference) in the Microbiome

3/31/2017 Sean Gibbons : How do we model gut microbial dynamics?

3/24/2017 Fangqiong Lin : Estimating human population from Sewage Samples

——————————————————————–        2016        ————————————————————————–
12/09/2016 Jonathan Friedman : Synthetic Ecology: Building Microbial Communities from the Bottom Up  

12/02/2016 Philip Strandwitz : The Gut-Brain-Axis: Discovering GABA-modulating bacteria

9/23/2016 Nissan Yissachar : Thinking outside the mouse: Dissecting host-microbiome communications ex-vivo

9/2/2016 Joseph N. Paulson : Accounting for artifacts in high-throughput sequencing data

7/22/2016 Aleksandar D. Kostic: Unraveling the links between the gut microbiome and type 1 diabetes 

5/6/2016 Ali R. Zomorrodi : Computational Systems and Ecosystems Biology of Microbial Metabolism

4/15/2016 Babak Momeni : Modeling microbial communities as a network of chemically mediated interactions

4/1/2016 Serguei Saavedra : How do ecological systems respond to environmental variations?

3/11/2016 Georg Gerber : Computational and synthetic biology approaches for developing bacteriotherapies

3/4/2016 Jaeyun Sung : Global metabolic interaction network of the human gut microbiota with community-level disease implications

2/12/2016 David Riglar : Gut Feelings: engineering bacterial circuits to probe the mammalian gut in sickness and in health

——————————————————————–        2014        ————————————————————————–

06/20/2014     Jaeyun Sung  :   Global Metabolic Interaction Network of the Human Gut Microbiota

03/28/2014     Jonathan Friedman :    Inferring Correlation Networks from Genomic Survey Data