Channing Network/Medicine/Microbiome Seminar

5th-floor Conference Room, Channing Division of Network Medicine, 181 Longwood Ave, Boston, MA 

(Due to the COVID-19 pandemics, currently we are also holding this seminar on Zoom.)

To join the mailing list or for more information, please contact yyl@channing.harvard.edu

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

01/10/2023 Mike McGeachie: A History of AI and Machine Learning

01/24/2023 Yi Zhao: Principal regression for covariance matrix outcomes with applications in neuroimaging data

02/07/2023 Marinka Zitnik: Graph AI to Enable Precision Medicine

02/28/2023 Can Chen : Deciphering Biological Networks through Hypergraph Learning

03/07/2023 Enrico Maiorino: Descriptive vs. inferential community detection

04/11/2023 Benjamin Gyori : Accelerating biomedical discovery with large-scale mechanistic knowledge assembly and model generation

05/02/2023 Margherita De Marzio: The role of vitamin D in autism: a network study

05/16/2023 Luca Becchetti: The Fair Densest Subgraph Problem and its Applications

05/30/2023 Yizhou Sun: Neural-Symbolic Reasoning on Knowledge Graphs

06/13/2023 Bonn Stephan: Integration of large biomedical data to robustly predict and understand human disease

09/12/2023 Tinashe Chikowore : Utility of recall-by-genotype approach for causal inference of drug target side-effects

09/26/2023 Jörg Menche : Network medicine beyond protein-protein interactions

10/10/2023 Qiang Zhang : Language and Knowledge driven Scientific Discovery

10/24/2023 Julian Hecker : Detecting parent-of-origin effects on omics data

11/7/2023  Carlo Maj : TBD 

11/21/2023 Santo Fortunato : Community detection in biological networks: problems, solutions and help from AI

12/5/2023   Weijie Su : TBD

12/19/2023 Anna Neufeld : TBD

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

11/10/2023  Zhang Wang : TBD

12/08/2023 Ali Zomorrodi : TBD

——————————————————————–        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

04/29/2022 Jean-Gabriel Young: Uncertain Network Science: Existing Methods and Next Steps

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

05/06/2022 Hillel Sanhedrai: Reviving a failed network through microscopic interventions

06/03/2022 Istvan Kovacs: Emergence of functional interactions in complex systems

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

06/17/2022 Pan Zhang: Computation with Tensor Networks

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

09/13/2022 Vince Carey: De-siloing Genomic Data Science

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

09/27/2022 Peter Castaldi: Learning from Biological Data with Interpretable Machine Learning Models

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

10/11/2022 Julian Hecker: Using machine learning in statistics: doubly robust inference

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

11/22/2022 Bernard Rosner: Two-stage model for time to breast cancer mortality among a cohort of initially disease-free women

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

07/30/2021 Orr Levey: Age-related loss of gene-to-gene transcriptional coordination among single cells

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

05/08/2020 Changjun Fan: FINDER: find key players in complex network using deep reinforcement learning

06/12/2020 Brett K. Beaulieu-Jones: Overcoming Obstacles for Practical Machine Learning in Healthcare

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

11/06/2020 Ye Yuan: Data driven discovery of cyber physical systems and an interpretable mortality prediction model for COVID-19 patients  

10/07/2020: Amir Bashan: Age-related loss of gene-to-gene transcriptional coordination among single cells  

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

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

07/19/2019 Eduardo Sontag : Dynamical aspects of antigen recognition, tumor/immune interactions, and spontaneous versus induced evolution of drug resistance during cancer treatment

07/12/2019 Shou-Wen Wang : Emergence of collective oscillations in adaptive cells

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

03/22/2019 Mauro Martino : Beautiful Bits – The beauty that excites in digital interfaces and artificial intelligence

03/19/2019 Yasser Omar : Introduction to Complex Quantum Networks

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

03/08/2019 Ginestra Bianconi : Multilayer networks: Structure and Function

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

02/11/2019 Hongfu Liu : Clustering, Multi-view Learning and Transfer Learning

02/08/2019 Nima Dehmami: Physical properties of minimally wired networks in 3D

01/29/2019 Louis Shekhtman: Resilience of networks with community structure

01/24/2019 Qi Song: Computational Analysis of Gene Regulations in Plants

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

11/07/2018: Guillermo Ramírez-Santiago : Model for Breast Cancer Diversity and Heterogeneity

09/28/2018: Honghuang Lin: Integrative omics study of atrial fibrillation: the Framingham Heart Study

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

07/23/2018: Pau Vilimelis Aceituno : Tailoring Dynamics in Recurrent Neural Network for Optimal Learning

07/13/2018: Gaogao Dong : Resilience of networks with community structure behaves as if under an external field

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

06/01/2018: Min Yu : Translating Artificial Intelligence into Health Care: Advances and Challenges

05/25/2018: Yannis Paschalidis : Distributionally Robust Learning and Applications to Predictive Health Analytics

04/05/2018: Sérgio Pequito : A Framework for Structural Input/Output and Control Configuration Selection of Complex Networks

03/23/2018: Chengxi Zang : Modeling the Dynamics of  WeChat Social System

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

03/09/2018: István Kovács : Network-based prediction of protein interactions

03/07/2018: Yutaka Shimada : From Networks to Time Series

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

10/6/2017 Vrushali Fangal : MIDAS – automatic translation of MechanIstic rules to DynAmic​ ​logic​ ​ruleS

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

8/11/2017 Tao Jia : Quantifying patterns of research interest evolution

7/28/2017 Mihir Pant : Quantum Computing and Percolation Theory

7/27/2017 Junming Huang : Exploring Gender Gap in Academia

7/19/2017 Jessie Lowell : Toward the Evolution of Modularity

6/16/2017 Lei Dai : Unraveling the Structure of Fitness Landscapes

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

6/2/2017 Arezou Ghazani : It Takes Two: The Complementary Roles of Constitutional And Tumor Genomes in Clinical Interpretation of Cancer

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

2/24/2017 Gang Yan : Network control principles unveil neuronal roles in C. elegans nervous system

2/7/2017 Michael Danziger : Beyond interdependent networks: bringing networks of networks to life

2/3/2017 Tina Eliassi-Rad : The Reasonable Effectiveness of Roles in Complex Networks

——————————————————————–        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

10/28/2016 Amar Dhand : Patients’ social networks and health outcomes

10/21/2016 Jorge Gómez Tejeda Zañudo : Network-based Dynamic Modeling and Control Strategies in Complex Diseases

10/19/2016 Jianhua Xing : Epithelial-to-Mesenchymal Transition, Cancer Metastasis and Fibrosis

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

5/20/2016 Dmitry Korkin : The Variation Game: Studying Impact of Genetic and Post-Transcriptional Variations at the Systems Level 

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

4/29/2016 Yanxin Jia : Electrochemical Micro-Oscillator Networks

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

4/8/2016 Lenore Cowen : Diffusion-Based Metrics for Biological Network Analysis

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

3/25/2016 Kirill Korolev : Mutations slow down cancer

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

2/26/2016 Pankaj Mehta : Combining statistical physics with genome-wide datasets to understand cellular reprogramming dynamics

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

2/5/2016  Jianxi Gao : Universal Resilience Patterns in Complex Networks

1/29/2016 Abhijeet Sonawane : The role of epigenetic information in PANDA’s message passing model

1/22/2016 Benjamin J Hescott : CANDL – Coarsely Aligning Networks with Diffusion and Landmarks

1/15/2016 Navid Dianati : Unwinding the hairball graph: pruning algorithms for weighted complex networks

——————————————————————–        2015        ————————————————————————–

12/18/2015 Marco Tulio Angulo : Rigorous analysis of complex networked systems combining Network Science and System Theory

12/11/2015 Marieke Kuijjer : Identification of key regulatory pathways in ovarian cancer subtypes

12/04/2015 Feixiong Cheng : Marriage of Network Biology and Panomics Yields New Promises for Precision Cancer Medicine

11/20/2015 Nidhi Sahni: Widespread Interactome Network Perturbations in Human Genetic Disorders

10/30/2015 Xin Jiang: Finding shortest paths on networks based on quantum bosonic mechanism

10/23/2015 Bingbo Wang : Diversified Control Paths: A Significant Way Disease Genes Perturb the Human Regulatory Network

09/25/2015 Ingo Scholtes : Analysis of Non-Markovian Temporal Networks: Spectral Methods and Centrality Measures

09/18/2015 Raymond Fu : When Data Meet Uncertainty

09/04/2015 Junming Huang : Identifying and quantifying social influence in information propagation

06/19/2015 Marc Santolini : Towards a personalized approach to Heart Failure

06/12/2015 Yongjin Park : Understanding tissue-specificity through static networks

05/29/2015 Ruisheng Wang : Illuminating Drug Action by Network Integration of Disease Genes: A Case Study of Myocardial Infarction

05/15/2015 Assieh Saadatpour : Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis

05/08/2015 JP Onnela : Incorporating contact network structure in cluster randomized trials

05/01/2015 Amitabh Sharmar : IDEAL: Impact of Differential Expression Across Layers in multiple omics networks associated with asthma 

04/17/2015 Damien Croteau-Chonka : (Journal Club) System Model Network for Adipose Tissue Signatures Related to Weight Changes in Response to Calorie Restriction and Subsequent Weight Maintenance

04/10/2015 Maksim Kitsak : Latent Geometry in Technological, Social and Biological Systems

04/03/2015 Navid Dianati : A family of network growth models with arbitrary degree distribution and high clustering from interacting random walkers in a metric space

03/20/2015 Wei Chen : Explosive percolation in random graphs

03/13/2015 Emre Guney :  Systematic drug efficacy screening using network-based drug-disease proximity

03/06/2015 Juan Fernandez Gracia : The power of a toy model: The Voter Model and presidential elections

02/20/2015 Yaonan Zhang : Estimating Network Degree Distributions Under Sampling: An Inverse Problem, with Applications to Monitoring Social Media Networks

02/06/2015 Avi Shapiro : Coevolutionary Dynamics of a Public Goods Game on a Network

01/23/2015  Shaoshuai Mou : Distributed Control of Multi-Agent Networks

01/16/2015  Istvan Kovacs : A unified data representation theory for network visualization, ordering and coarse-graining

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

12/12/2014   Megha Padi : Single-cell p53 dynamics in response to oncogenic activation

12/05/2014   Soumya Raychaudhuri : Disentangling effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex trait loci

11/21/2014    Lijun Peng : Bayesian Ridge-Regularized Covariance Selection with Community Behavior in Latent Gaussian Graphical Models

11/14/2014    Lei Dai : Spatio-temporal Dynamics Before Population Collapse

11/07/2014    Sriram Chandrasekaran : Predicting Cellular Metabolism using Genome-Scale Metabolic and Regulatory Network Models

10/31/2014    Daniel Larremore : A complex networks approach to understanding genetic recombination in malaria antigens

10/17/2014    Kimberly Glass : Integrating Epigenetic Information Into Message-Passing Network Models

10/10/2014    John Platig : Understanding Complex Traits with Complex Networks

09/12/2014     Endre Csóka :  What mathematicians can help you deal with large networks?

09/05/2014     Erzsébet Ravasz Regan  : Principles of dynamical modularity in biological regulatory networks

08/15/2014     (Samuel) Qing-Shan Jia :  Ordinal and Event-Based Optimization for Large Scale Networked Systems

07/02/2014     Eivind Almaas :   A story of biological networks

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