Department of Systems Biology ×

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Faculty

Mikko Turunen

Assistant Professor of Systems Biology at Columbia University Irving Medical Center

Faculty

Jeremy Worley

Assistant Professor of Systems Biology at Columbia University Irving Medical Center

Director, Genome Engineering CoLab

Director, Genome Engineering CoLab

Faculty

Dian Yang

Assistant Professor of Molecular Pharmacology and Therapeutics

Faculty

Charles Karan Jr.

Assistant Professor of Systems Biology

Scientific Director, High-Throughput Screening, Columbia Genome Center

Scientific Director, High-Throughput Screening

Faculty

Benjamin Izar

Assistant Professor of Medicine and Systems Biology

Welcome, Dr. Sara Zaccara

The Department of Systems Biology at Columbia University Irving Medical Center welcomes new faculty member Sara Zaccara, PhD. Dr. Zaccara joins Columbia as an assistant professor, effective Sept. 1. Prior to coming to Columbia, she was a postdoctoral researcher at Weill Cornell Medicine.

Dr. Zaccara grew up in a small town in Italy. She received her PhD from the University of Trento, in Trento, Italy, where her thesis work was on p53-dependent translational regulation. She received her bachelor’s and master’s degrees in biotechnology from the University of Florence. “I studied biotechnology,” she says, “because I was fascinated by the idea of developing new methods that could improve our future in medicine.”

Dr. Zaccara’s research focuses on the intricate cellular mechanisms that control the chemical tag called m6A, which cells insert into almost 30 percent of their mRNA molecules. She has proposed a unified model of how m6A mRNAs are controlled in cells. She also helped show why the number of m6A sites in mRNAs has functional consequences for mRNA fate.

Currently, Dr. Zaccara’s group is working on characterizing the mechanisms that trigger m6A mRNA degradation in normal and disease states, in particular, acute myeloid leukemia. The group is also investigating the impact of the functional specialization of RNA binding proteins on mRNA fate. Their multidisciplinary approach includes the use of CRISPR-Cas9 base editor screens, massively parallel tethering screens, molecular tagging, imaging, and in vitro experiments. The integrated combination of these methodologies will enable investigation of critical components of the mRNA degradation pathway and their contribution to mRNA fate with unprecedented throughput and resolution.

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Faculty

Sara Zaccara

Assistant Professor, Department of Systems Biology

Nikhil Sharma

Faculty

Nikhil Sharma

Assistant Professor, Department of Molecular Pharmacology and Therapeutics

Assistant Professor, Department of Systems Biology

Xuebing Wu, PhD, Wins Pershing Square Sohn Prize

The 2021 Pershing Square Sohn Prize for Young Investigators in Cancer Research has been awarded to Xuebing Wu, PhD, for his innovative approaches to cancer research. The Pershing Square Sohn Prize is an annual award that provides early career scientists the freedom to take risks and pursue bold research at a stage when traditional funding is lacking. At Columbia University Irving Medical Center, Dr. Wu shares the designation with Christine Iok In Chio, PhD, whose work focuses on the biological mechanisms that drive pancreatic ductal adenocarcinoma.

With the support from the Pershing Foundation, Dr. Wu and his lab aim to develop a technology for mutation-specific elimination of tumor cells, by integrating a highly programmable CRISPR “gene-editing” system with advanced machine learning algorithms. 

Read the full article in the HICCC Newsroom. 

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Raul Rabadan, PhD, Named Highly Cited Researcher

Raul Rabadan, PhD, professor of systems biology and of biomedical informatics, has been named a 2020 Highly Cited Researcher by Clarivate. Announced Nov. 18, Dr. Rabadan is one of 45 Columbia University faculty members who were selected for the annual list. 

The Highly Cited Researchers annual report recognizes researchers who have had major impacts in their fields. To be named to the list, researchers must produce multiple papers ranking in the top 1% globally by citations for their field and year of publication, demonstrating significant research influence among their peers.

Dr. Rabadan, founding director of Columbia's Program for Mathematical Genomics, also was named to the list in 2019, along with fellow Systems Biology faculty member, Xuebing Wu, PhD.

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Nature Showcases Precision Medicine Research led by the Califano Lab

Andrea Califano
Andrea Califano identifies 'master regulators' of cancer cells. (Credit: Tim Lee Photographers)

Genomics has revolutionized cancer research. Conventional classifications of disease, in terms of which organs and tissues it affects, are being divided into subtypes defined by the specific mutations that drive the disease. Some argue, however, that the impact on cancer care has not lived up to expectations. “Only about 5–10% of cancer patients derive any benefit from targeted therapy using genetics, and almost all of them eventually relapse,” says Andrea Califano , Dr, chair of the Department of Systems Biology at Columbia University Irving Medical Center. “The number that are actually cured is extremely small.”

Developing a genetically targeted therapy is no easy task. It can be tricky to identify which genetic mutations are driving the cancer and which are passengers — those that are statistically linked, but that do not cause cancer. And although developers of targeted therapies focus mainly on mutations to a subset of genes called oncogenes, there is more to malignancy. Read the full Nature Outlook article here . 

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Welcome, Dr. Mohammed AlQuraishi

Mohammed AlQuraishi, PhD

The Department of Systems Biology at Columbia University Irving Medical Center is pleased to welcome new faculty member, Mohammed AlQuraishi , PhD, effective Sept. 21. Dr. AlQuraishi joins Columbia as an assistant professor and as a member of Columbia’s Program for Mathematical Genomics. 

Prior to joining Columbia, Dr. AlQuraishi served as a fellow of systems pharmacology and systems biology at Harvard Medical School. He completed his PhD in genetics and master’s in statistics from Stanford University. At Santa Clara University, he earned two bachelor’s degrees in biology and in computer engineering. 

A Bay Area transplant via Baghdad and Kuala Lumpur, Dr. AlQuraishi spent most of his teenage years in the San Francisco Bay Area before moving to the east coast for postdoctoral work. Influenced by the dot-com boom of the early 2000s in the Bay Area, Dr. AlQuraishi founded two startups in the mobile computing space before focusing on a career in academia. His circuitous path to systems biology and academic research ultimately blended his genuine interest and expertise in computer programming, mathematics, molecular biology, and science more broadly.

“What drew me to biology is its similarity to software, the fact that cells are always executing a sort of program," he says. "And just like programs, cells are more than a parts list—they are complex and interconnected in myriad ways. To tame this complexity we need synthesis, and that is the promise and challenge of systems biology.”

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Ancient Part of Immune System May Underpin Severe COVID

One of the immune system’s oldest branches, called complement, may be influencing the severity of COVID disease, according to a new study from Drs. Sagi Shapira and Nicholas Tatonetti at the Department of Systems Biology.

Drs. Sagi Shapira (right) and Nick Tatonetti
Drs. Nicholas Tatonetti (left) and Sagi Shapira

Among other findings linking complement to COVID, the researchers found that people with age-related macular degeneration—a disorder caused by overactive complement—are at greater risk of developing severe complications and dying from COVID.

The connection with complement suggests that existing drugs that inhibit the complement system could help treat patients with severe COVID-19.

The study was published in Nature Medicine . For the full article , visit the Columbia University Irving Medical Center Newsroom. 

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New COVID-19 Pilot Grants Awarded to Systems Biology Faculty

Sagi Shapira,PhD, assistant professor of systems biology at Columbia’s Vagelos College of Physicians & Surgeons and Nicholas Tatonetti, PhD, associate professor of bioinformatics and of systems biology at VP&S, have recently been awarded a new pilot grant to support their collaboration in COVID-19 research.

Drs. Shapira and Tatonetti are one of three teams who have been awarded a COVID-19 research pilot grant from the Herbert Irving Comprehensive Cancer Center. The pair will work on accurately identifying pathophysiological factors that modulate SARS-CoV-2 infection and explain variability in disease outcomes.

Read the full article here. 

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New Book on Understanding the Novel Coronavirus

Raul Rabadan , PhD, is an expert in uncovering patterns of evolution in highly dynamic biological systems, including in complex diseases like cancer. As the author of Understanding Coronavirus , a new book published by Cambridge University Press in June,  Dr. Rabadan, who originally began his academic career in mathematical physics, has set out to provide readers an accessible overview that quells misinformation about the novel virus, its origin, causes, and spread.

New Book by Raul Rabadan, PhD

Dr. Rabadan co-directs the Cancer Genomics and Epigenomics research program at the Herbert Irving Comprehensive Cancer Center (HICCC) , is professor of systems biology and of biomedical informatics at Columbia University Vagelos College of Physicians & Surgeons , and directs Columbia’s Program for Mathematical Genomics . He joined Columbia in 2008 right before the novel influenza, H1N1 or “swine flu”, emerged and quickly spread across the U.S. and the world.

At the time, Dr. Rabadan’s work honed in on understanding the genomic changes in a virus infecting a host and investigating how these changes contribute to the virus’ transfer to a different species. He continues to be fascinated by what can be gleaned from examining disease evolution.

When COVID-19 cases surged through the U.S., particularly in New York City in March, Dr. Rabadan—like many fellow scientists—contributed his research toward developing a treatment or vaccine. Scheduled to be on sabbatical this year, Dr. Rabadan instead remained quarantined with his family in New York City, shifting his attention to the new book and his own ongoing work in the genomics of cancer and COVID-19 research.

Read a Q+A with Dr. Rabadan, here . 

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Dynamics of Gut Bacteria Follow Ecological Laws

The seemingly chaotic bacterial soup of the gut microbiome is more organized than it first appears and follows some of the same ecological laws that apply to birds, fish, tropical rainforests, and even complex economic and financial markets, according to a new paper in Nature Microbiology by researchers led by Dennis Vitkup , PhD, associate professor of systems biology , at Columbia Univesrity Irving Medical Center .

One of the main challenges facing researchers who study the gut microbiome is its sheer size and amazing organizational complexity. Many trillions of bacteria, representing thousands of different species, live in the human intestinal tract, interacting with each other and the environment in countless and constantly changing ways.

"Up to now, it has been an open question whether there are any natural laws describing dynamics of these complex bacterial communities.”-Dr. Vitkup

The study’s discovery of multiple principles of gut bacterial dynamics should help researchers to understand what makes a gut microbiome healthy, how it may become perturbed in disease and unhealthy diets, and also suggest ways we could alter microbiomes to improve health. Read the full article in the CUIMC Newsroom. 

The study is titled “Macroecological dynamics of gut microbiota.” The other contributors are Brian W. Ji (Columbia), Ravi U. Sheth (Columbia), Purushottam D. Dixit (Columbia and University of Florida, Gainesville, FL), and Konstantine Tchourine (Columbia).

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Decoding and Targeting RNA with CRISPR

At first, Xuebing Wu , PhD, was on track to pursue a research career in computer engineering. After taking a course by Dr. Yanda Li, a pioneer of bioinformatics, Dr. Wu’s interest quickly shifted and he soon got hooked on genomics research and computational biology.

Xuebing Wu, PhD
Xuebing Wu, PhD

“Around that time—2003 to 2004—the human genome project had just been completed, and there had been lots of enthusiasm about using computational approaches to decipher the human genome,” he said. “I was excited to dive into this field that seemed wide open for research possibilities.”

Dr. Wu joined Columbia University’s Department of Systems Biology in the fall of 2018, with a joint appointment in the Department of Medicine’s Cardiology Division . He also is a member of the Herbert Irving Comprehensive Cancer Center at NewYork-Presbyterian/Columbia and the Columbia Data Science Institute , and his lab straddles basic science and computational biology. Dr. Wu and collaborators often consider how their work can make an impact in novel therapeutics. 

At the center of his interests is understanding the fundamental principles of gene regulation in human cells through integrative genomics approaches. His previous work has uncovered important roles of RNA sequence and structure signals in controlling the expression and evolution of the mammalian genome. His lab currently studies RNA-centric gene regulation, focusing on mRNA structures and mRNA translation. Dr. Wu and his team are increasingly turning their attention to the development of genomic technologies such as the revolutionary CRISPR/Cas system and a high throughput analysis technology called massively parallel reporter assays (MPRA), as well as novel computational tools and deep learning models to study gene regulation at a global scale. 

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A Systems Biology Approach to Target Pancreatic Cancer

In recognition of Dr. Andrea Califano's recent Ruth Leff Siegel Award , an annual prize that honors and supports an investigator who has made outstanding contributions to our understanding of pancreatic cancer, Let's Win! Pancreatic Cancer has published the following feature article spotlighting his innovative approach to cancer research.

Dr. Andrea Califano
Dr. Andrea Califano, 2019 recipient of annual Ruth Leff Sigel Award for pancreatic cancer research. (Photo: Jörg Meyer/Columbia Magazine)

If you look at our basic biology, humans are big, cumbersome living organisms with a lot of moving parts.

For most of our lives, the cellular machinery that keeps us functioning goes off without a hitch. Starting at conception, cells have been growing and dividing, structuring themselves in a highly organized fashion. Liver cells know their job. And brain and spinal cord cells know their jobs, too.

Cancer is also a living organism. After all, it grows and evolves just like healthy cells. But cancer cells are cheats, ignoring the rules that other healthy cells play by. They mutate and divide uncontrollably, finding ways to evade our immune systems, which try to keep these invaders in check. To complicate matters, cancer cells are what scientists call heterogeneous. That means that even in the same malignant tumor there can be a variety of mutations, which is one reason why cancer treatment often fails. Drugs simply can’t target all of those mutations.

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