2020 News

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. 

Xuebing Wu, PhD, has been selected as a Pew-Stewart Scholar for his innovative approaches to cancer research.

The Pew Charitable Trusts and the Alexander and Margaret Stewart Trust named five early-career researchers to its prestigious Pew-Stewart Scholars Program for cancer research. This talented class of scholars will receive four years of funding to advance groundbreaking research into the development, diagnosis, and treatment of the disease. As a Pew-Stewart scholar, Dr. Wu will investigate the dysregulation of messenger RNA structure in the development of breast cancer.

Dr. Wu, who joined Columbia University in the fall of 2018, is an assistant professor of medical sciences in the Departments of Systems Biology and Medicine. Read the full article here

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

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

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).

Molly Przeworski , PhD, professor of biological sciences and of systems biology , has been elected to the prestigious National Academy of Sciences (NAS) . Announced on April 27, Dr. Przeworski joins two fellow Columbia University Irving Medical Center (CUIMC) faculty members named to the 2020 class, recognized for their distinguished and continuing achievements in original research.

Molly Przeworski, PhD
Molly Przeworski, PhD

Dr. Przeworski's work aims to understand how natural selection has shaped patterns of genetic variation and to identify the causes and consequences of variation in recombination and mutation rates in humans and other organisms. Earlier this month, she was also elected to the American Academy of Arts & Sciences , which recognizes and celebrates excellence of scientists, artists, scholars, and leaders in the public, non-profit, and private sectors.

A member of Columbia’s Program for Mathematical Genomics , Dr. Przeworski is the recipient of the Distinguished Columbia Faculty Award, the Howard Hughes Medical Institute Early Career Scientist award, the Rosalind Franklin Young Investigator award, the Friedrich Wilhelm Bessel Research award, and an Alfred P. Sloan fellowship. 

The NAS has elected 120 members and 26 international members to its new class.

Related: Three CUIMC Faculty Members Elected to National Academies ( CUIMC News )

Columbia University Irving Medical Center (CUIMC) has established this website for any and all coronavirus information. Columbia faculty, students, researchers, clinicians, and patients, should turn to this resource to learn up to date information about how the University is responding to the COVID-19 pandemic. Information on this website is updated on a daily basis and ranges from patient care, questions about research, changes for staff/employees, and more.

CUIMC students, faculty, or staff may direct questions to covid19questions@cumc.columbia.edu. The community is encouraged to check this resource center for frequent updates.

Video message for the CUIMC community from Lee Goldman, MD, dean of the Faculties of Health Sciences and Medicine and chief executive of CUIMC; Jack Cioffi, MD, president of ColumbiaDoctors; and Donna Lynne, DrPH, chief operating officer of CUIMC.

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. 

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.

New Book Coauthored by Raul Rabadan, PhD
Dr. Raul Rabadan coauthors new book that introduces techniques of topological data analysis, a rapidly growing subfield of mathematics. (Cambridge University Press)

The deluge of data in the diverse field of biology comes with it the challenge of extracting meaningful information from large biological data sets. A new book, Topological Data Analysis for Genomics and Evolution, introduces central ideas and techniques of topological data analysis and aims to explain in detail a number of specific applications to biology.

“High-throughput genomics has profoundly transformed the field of modern biology and has made it possible for scientists to make rapid scientific advances,” says the book’s co-author Dr. Raul Rabadan, professor of systems biology and founding director of Columbia University’s Program for Mathematical Genomics. “The explosion of data has hit biology, and as a result, we need new, more innovative analytical and computational tools to make sense of it all.”

Co-authored with Andrew J. Blumberg, PhD, professor of mathematics at University of Texas at Austin, the new book discusses techniques of topological data analysis, a rapidly developing subfield of mathematics that provides a methodology for analyzing the shape of data sets. The book offers several examples of these techniques and their use in multiple areas of biology, including the evolution of viruses, bacteria and humans, genomics of cancer, and single cell characterization of developmental processes.

Yufeng Shen , PhD, found his passion for science in childhood, but he developed a fascination for both math and physics as his education progressed. In an earlier generation, he would have needed to choose between divergent paths. Instead, he chased his calling within an important emerging discipline. 

Yufeng Shen, PhD
Dr. Yufeng Shen

Dr. Shen was awarded tenure and promoted to the rank of associate professor in Columbia University's Departments of Systems Biology and Biomedical Informatics (DBMI) last summer. Utilizing new methods, he answers long-standing questions that impact health. Specifically, his research has focused on discovering novel genetic variants that cause human diseases.

His current work focuses on developing new computational methods to interpret genome data, identifying genetic causes of human diseases by integrating multiple types of genomic data, and modeling of immune cell populations. That research has led to important findings, including his work on the Deep Genetic Connection between Cancer and Developmental Disorders , published in Human Mutation.

Using innovative sequencing techniques from published studies of cancer and developmental disorders, Dr. Shen and his students identified a significant number of genes implicated in both diseases.

“This project allows us to use the larger cancer data to inform analysis in genetic variations of developmental disorders, and to find new risk genes and new risk variance,” he said. “It also provides a new perspective on how to optimize care for kids with developmental disorders. There is probably two to three times more risk of developing cancer for kids with developmental disorders than otherwise healthy kids.”