The Columbia University Department of Systems Biology periodically publishes a newsletter reporting on research highlights and other news from our community. Previously, the newsletter was published under the auspices of the Center for Multiscale Analysis of Genetic and Cellular Networks (MAGNet). Click on the thumbnails to download a copy of the newsletter as a PDF.

Department of Systems Biology Research Highlights



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December 2023

Andrea Califano to Lead New Biohub      

Preterm Birth Linked to Chemicals Found in the Vagina      

Illuminating Tumor Cells with Dark Proteins     

A Better Way to Decontaminate Samples for Early Cancer Detection    

AI-Guided Robotic Culturomics for Microbiome Studies     

  The Evolutionary History of SARS-CoV-2 

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December 2022

Deciphering Cancer Is Messy and Complex. We’re Here for It.      
Andrea Califano, PhD

Study Shows Why Many Cancer Cells Need to Import Fat      
Dennis Vitkup, PhD

Precision Medicine Sends Cancer for a Loop      
Cory Abate-Shen, PhD      
Andrea Califano, PhD

Insights from Chaolin Zhang’s Lab      

  The Evolutionary History of SARS-CoV-2 

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December 2021

The Evolutionary History of SARS-CoV-2       
Raul Rabadan, PhD

RNA-Based Oncology Platform       
Andrea Califano, Dr.

Diversity and Severity of Autism Symptoms Linked to Mutation Locations       
Dennis Vitkup, PhD

Research Highlights 2020   

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December 2020

Addressing the Global Pandemic 

New Tumor-Specific Molecular Interaction Maps Capture Complexity of Cancer Networks       
Andrea Califano, Dr       
Barry Honig, PhD

Dynamics of Gut Bacteria Follow Ecological Laws       
Dennis Vitkup, PhD

Ancient Part of Immune System May Underpin Severe COVID       
Sagi Shapira, PhD       
Nicholas Tatonetti, PhD


Research Highlights 2019   

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October 2019

A New Window into how Human-Infecting Viruses Work       
Sagi Shapira, PhD       

Designer Proteins Come with Built-In Safeguards       
Harris Wang, PhD       

Mapping the Human Cell Atlas       
Peter Sims, PhD       
Raul Rabadan, PhD       

Prostate Cancer Grant Spotlights Precision Cancer Medicine       
Andrea Califano, Dr       
Michael Shen, PhD

Research Highlights 2018   

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October 2018       

Bladder Cancer Organoids Mimic Patient Tumors       
Michael Shen, PhD

Introducing Columbia’s Program for Mathematical Genomics       
Raul Rabadan, PhD

Targeting the Engine Room of the Cancer Cell       
Andrea Califano, Dr

World’s Smallest Tape Recorder is Built from Microbes       
Harris Wang, PhD


Research Highlights 2016   

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September 2016

Columbia Awarded NCI Center for Cancer Systems Biology 

Glioblastoma Tumor Evolution and Strategies against Advanced Disease       
Raul Rabadan       

How Genomic Data Are Changing Population Genetics       
Molly Przeworski

Method for Determining Proten Function Opens Doors for Precision Medicine       
Andrea Califano


Research Highlights 2015 

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June 2015

Columbia Investigators Awarded New NCI Physical Sciences in Oncology Center        
Raul Rabadan

The Exposome: Relating Environmental Factors to Human Disease       
Nicholas Tatonetti

Tracing Bacterial Evolution across Billions of Years       
Dennis Vitkup

Mechanism of Kidney Transplant Tolerance Discovered       
Yufeng Shen


Research Highlights 2014   

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December 2014

A Comprehensive Map of Human B-Cell Development       
Dana Pe'er       

New Directions in Genome Engineering       
Harris Wang       

Algorithm Identifies Genetic Driver of Mesenchymal Glioblastoma       
Andrea Califano

Systems Biology Throws You Out of the Box       
Saeed Tavazoie

MAGNet Newsletters


MAGNet Newsletter 2014   

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Spring 2014 - Featured Articles

Cross-Species Computational Analysis Identifies a Synergistic Interaction that Drives Prostate Cancer Malignancy        
Cory Abate-Shen, Andrea Califano, Michael Shen

A Topological Approach for Characterizing Evolution        
Kevin Emmett, Raul Rabadan

A Global View of Tumor-Induced Gene Expression Changes in Human Metabolism        
Dennis Vitkup


MAGNet Newsletter 2013   

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Spring 2013 - Featured Articles

PrePPI: A Novel Structure-Based Method for Predicting Protein-Protein Interactions        
Barry Honig

An Integrative Genomics Approach to Define RNA Regulatory Networks        
Chaolin Zhang

From Genome-Scale Sequencing to Angstrom-Scale Insights: The Enzyme DNase I Reveals Its True Colors        
Harmen J. Bussemaker



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Spring 2012 - Featured Articles

A Mesenchymal Transition Signature Present in Invasive Solid Cancers        
Dimitris Anastassiou

Discovering the Regulatory Programs Underlying Mammalian Transcript Stability        
Hani Goodarzi & Saeed Tavazoie

Mapping the miRNA Regulatory Network in Glioblastoma        
Pavel Sumazin & Andrea Califano



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Spring 2011 - Featured Articles

Interrogating Molecular Pathways of Prostate Tumorigenesis in Mice and Men        
Cory Abate-Shen & Michael M. Shen

The Origin and Evolution of a Pandemic Virus        
Zachary Carpenter, Carlos Hernandez, Joseph Chan, Raul Rabadan

The Transcriptional Network for Mesenchymal Transformation of Brain Tumours        
Andrea Califano



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Spring 2010 - Featured Articles

Structural Organization, Evolution, and Heterogeneous Activation of a Bacterial Sporulation Network        
Dennis Vitkup

Breaking the Code of Non-coding DNA in the Human Genome        
Tom Tullius

The Family of Man: Methods and Applications for Discovering Shared Ancestry among Purported Unrelateds        
Itsik Pe'er



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Winter 2009 - Featured Articles

Three R's of Computer Assisted Biomedical Discovery: Reading, Reasoning and Reporting        
Hannah Tipney & Lawrence Hunter

Dissecting Transcription Factor Function on Multiple Scales Biophysics, and Computers        
Harmen J. Bussemaker

Making Sense of Transcription Factor Specificities, or How to Grow Legs in Strange Places: a Collaboration between Flies, Biophysics, and Computers        
Richard S. Mann & Barry Honig



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Winter 2008 - Featured Articles

Understanding Cadherin Specificity in the Development of Multicellular Structures: a Combined Experimental and Computational Theory        
Lawrence Shapiro & Barry Honig

Mapping the Transcription Factor Modulator Repertoire in Human B Lymphocytes        
Andrea Califano & Riccardo Dalla-Favera

National Centers for Biomedical Computing and Related Activities at NIH        
Dan Gallahan