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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January 2025

Mohammed AlQuraishi is Taking His Deep Learning OpenFold Model to the Next Level        

Raul Rabadan’s New AI Model Predicts How Genes Inside a Cell Would Govern its Behavior        

From Lab to Clinic: New Genomic Tools Transform Disease Research        

Faculty Spotlight: Q&A with Raul Rabadan       
 


   

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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