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Afternoon of Science Series: Department of Systems Biology

The Afternoon of Science series at the Vagelos College of Physicians and Surgeons continued Sept. 25 with presentations from the Department of Systems Biology.

The event was hosted by the department's interim chair, Harris Wang, associate professor of systems biology, pathology & cell biology, and biomedical engineering, who shared his vision for the department. The Department of Systems Biology was founded in 2013 and now has more than a dozen primary faculty and 19 additional cross-appointed faculty members, who work to advance the integration of computational and experimental research methods in the biological and biomedical sciences. Research in the department is highly collaborative and integrates specialists in molecular biology, genetics, computational biology and bioinformatics, mathematics, chemistry and chemical biology, physics, and other fields.

Read full article on the CUIMC page.

Photo credit CUIMC.

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DSB Retreat

Group picture

 

The Department of Systems Biology’s 2024 annual retreat was held in September at Woodloch Pines Resort, PA. The retreat gave DSB faculty, post-docs, and students a chance to get away from the bustle of New York City, learn about their peers’ research, and network.

 

Opening

       Poster


 

DSB researchers and graduate students participated in a poster competition held the first evening, and reviewed by Systems Biology faculty judges. The three poster winners were  Daniel Caron for “Maintenance of human macrophage tissue identity and plasticity during acute polarization”;  Yiwei Sun for “Fecal exfoliated RNA (eRNA) profiling captures immune dynamics of healthy and inflamed gut”;  and Ruchika Mishra for “Deciphering RNA recognition code for Pentatricopeptide repeat (PPR) editing factors.”

 

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Andrea Califano 2024 Fellow of the AACR Academy

Andrea Califano, Dr, President, Chan Zuckerberg Biohub; Clyde and Helen Wu Professor of Chemical and Systems Biology, Columbia University, New York, New York

Elected for pioneering research efforts in systems biology dedicated to developing methods that combine computational biology and cancer pharmacology approaches to model cancer cell regulatory networks, and for developing the first genome-wide regulatory model of human cells and novel network-based approach for identifying master regulators of cancer maintenance and tumor progression.

Read full article on the AACR Page. 

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Andrea Califano Selected to Lead Chan Zuckerberg Biohub New York

Andrea Califano, Dr, the Clyde and Helen Wu Professor of Chemical and Systems Biology at Columbia University Vagelos College of Physicians and Surgeons, will lead the new Chan Zuckerberg Biohub New York in its mission to harness and engineer immune cells for the early detection and eradication of human disease.

The Chan Zuckerberg Biohub New York (CZ Biohub NY) brings together Columbia University, The Rockefeller University, and Yale University to create new technologies to characterize and bioengineer immune cells—with the ultimate goal of creating disease-specific “cellular endoscopes” that can detect early stages of disease in cells, monitor cell changes, and resolve diseases before they become untreatable.

The CZ Biohub NY is the fourth research institute in the Chan Zuckerberg Biohub Network, a groundbreaking collaborative model for scientific research. The network includes the first CZ Biohub, in San Francisco, a second in Chicago, and the Chan Zuckerberg Institute for Advanced Biological Imaging in Redwood City, California. Together, the CZ Biohub Network institutions pursue science and technologies that quantify human biology in action to help researchers measure how cells and tissues function to increase our understanding of health and disease.

Read full article on the Irving Medical Center news page.

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Harris Wang, PhD becomes Department of Systems Biology Interim Chair, September 1st

Andrea Califano, Dr, the founding chair of the Department of Systems Biology, will be leaving the chair role this fall to launch an exciting new program in collaboration with multiple universities in the tri-state area. We look forward to sharing further details on this new endeavor soon. In the meantime, we are pleased to share that Harris Wang, PhD, another founding member of the department, has agreed to serve as the interim chair.

While Dr. Califano is leaving his post as chair, his lab will remain at Columbia and he will continue to be a full-time faculty member in systems biology, biochemistry & molecular biophysics, medicine, and biomedical informatics, as well as a member of the Herbert Irving Comprehensive Cancer Center. As Dr. Wang steps into his role as interim chair, Dr. Califano will work closely with him to ensure continuity during the leadership transition.

Dr. Wang is well respected within the department and widely acknowledged as a pioneer in the field of synthetic biology. He holds dual bachelor’s degrees in physics and applied mathematics from the Massachusetts Institute of Technology and a PhD in biophysics & medical engineering from Harvard University, where he served as an instructor in systems biology before joining the Columbia faculty in 2013. Dr. Wang's research focuses on advancing next-generation microbiome and cellular therapeutics using systems and synthetic biology approaches. His development of Multiplex Automated Genome Engineering (MAGE), a technique allowing rapid genome editing of microbial cells, was celebrated as a breakthrough in the field of synthetic biology in 2009. More recently, Dr. Wang has been recognized for his pioneering work in spatial mapping and precision editing of the gut microbiome and using CRISPR technologies to track and record transient cellular processes. He was named a Schaefer Research Scholar at VP&S in 2018, one of many honors he has received. He received the 2022 Vilcek Prize for Creative Promise in Biomedical Science, the Presidential Early Career Award for Scientists and Engineers (PECASE) from the White House, and the NIH Director’s Early Independence award.  

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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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Study Shows Why Many Cancer Cells Need to Import Fat

Columbia and MIT researchers are revealing the surprising reasons why cancer cells are often forced to rely on fat imports, a finding that could lead to new ways to understand and slow down tumor growth.

The research, led by Dennis Vitkup, PhD, associate professor of systems biology at Columbia University Vagelos College of Physicians, and Matthew G. Vander Heiden(link is external and opens in a new window), MD, PhD, director of the Koch Center at MIT, was published June 23 in Nature Metabolism(link is external and opens in a new window).

Read full article on CUIMC Newsroom.

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Disruptors: Deciphering Cancer Is Messy and Complex. We’re Here for It.

Precision medicine has been a buzzword across the medical field for over a decade. But what does it really mean for cancer care and how is it influencing new therapies for patients? Initially, precision cancer medicine focused on targeting specific mutated genes. We thought that understanding the genetic mutations of a tumor would help us develop targeted drugs that would solve the problem, one broken gene at a time.

What we found instead is that when you build an inventory of all the broken parts in cancer, the number of mutational patterns that could give rise to cancer is larger than the number of atoms in the universe.

Read full article on the Columbia News page.

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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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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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Dr. Xuebing Wu Named Pew-Stewart Scholar

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. 

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Molly Przeworski, PhD, Elected to the National Academy of Sciences

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 )

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Columbia's Coronavirus Resource Center

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.

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Book Offers Intro to Rapidly Growing Field of Topological Data Analysis

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.

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Highly Cited Researchers

Raul Rabadan Highly Cited
Raul Rabadan, PhD, (standing) with Francesco Brundu, postdoctoral research scientist in the Rabadan lab (Credit: Jeffrey Schifman)

Congratulations to Drs. Raul Rabadan and Xuebing Wu who were recently named a Highly Cited Researcher, according to the 2019 list from the Web of Science Group . Overall, Columbia University ranked 15th on the list of global institutions, with a total of 47 Highly Cited Researchers.

The Highly Cited Researchers list, which was released Nov. 19,  identifies scientists and social scientists who have produced multiple papers ranking in the top 1% by citations for their field and year of publication, demonstrating significant research influence among their peers.

Xuebing Wu, PhD
Xuebing Wu, PhD

Dr. Rabadan is professor of systems biology , with a joint appointment in biomedical informatics, at Columbia’s Vagelos College of Physicians and Surgeons . At Columbia, the Rabadan lab consists of an interdisciplinary team developing mathematical and computational tools to extract useful biological information from large data sets. In 2017, Dr. Rabadan established the Program for Mathematical Genomics , a multidisciplinary research hub that brings together researchers from the fields of mathematics, physics, computer science, engineering, and medicine, with the common goal of solving pressing biomedical problems through quantitative methods and analyses. He also serves as program lead for the Cancer Genomics and Epigenomics Program at the Herbert Irving Comprehensive Cancer Center at NYP/Columbia. 

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Newly Tenured Systems Biology Faculty

Newly Tenured Faculty
Awarded tenure this year in the Department of Systems Biology, left to right: Dr. Nicholas Tatonetti, Dr. Yufeng Shen, and Dr. Chaolin Zhang.

Congratulations to Drs. Yufeng Shen, Nicholas Tatonetti, and Chaolin Zhang of the Department of Systems Biology, who have been awarded tenure and promoted to associate professor. Their new appointments are effective July 1, 2019. 

Yufeng Shen, PhD

Dr. Shen joined Columbia University Irving Medical Center in 2011 as an Assistant Professor in Systems Biology and Biomedical Informatics. He directs a research group focused on studies of human biology and diseases using genomic and computational approaches. They are developing new methods to interpret genomic variations by machine learning based on biological mechanisms, and using these methods in large-scale genome sequencing studies to identify new genetic causes of human diseases, such as autism, birth defects, and cancer. His group also works on modeling of clonal and transcriptional dynamics of immune cells to improve our understanding of human adaptive immune system under normal and clinical conditions. Dr. Shen serves as an Associate Director of the JP Sulzberger Columbia Genome Center, a member of the Program in Mathematical Genomics, and an adjunct member of Columbia Center for Translational Immunology. 

Nicholas Tatonetti, PhD

Dr. Tatonetti, whose primary appointment is in the Department of Bioinformatics, has an interdisciplinary appointment with both the Departments of Systems Biology and Medicine. Dr. Tatonetti’s lab specializes in advancing the application of data science in biology and health science. His group integrates their medical observations with systems and chemical biology models to not only explain drug effects, but also to gain further understanding of basic biology and human disease.

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Dr. Cory Abate-Shen Named Chair of Pharmacology at Columbia

Cory Abate-Shen, PhD, a distinguished scientist whose multidisciplinary research has advanced our understanding of the molecular basis of cancer initiation and progression, has been named chair of the Department of Pharmacology at Columbia University Vagelos College of Physicians and Surgeons. Her appointment will be effective April 1, 2019.

Recruited to Columbia in 2007, Dr. Abate-Shen is currently the Michael and Stella Chernow Professor of Urologic Sciences and professor of pathology & cell biology, medicine, and systems biology. She has served as the leader of the prostate program, associate director, and twice as interim director of the Herbert Irving Comprehensive Cancer Center (HICCC) at Columbia University Irving Medical Center and NewYork-Presbyterian.

An internationally recognized leader in genitourinary malignancies, Dr. Abate-Shen is particularly interested in advancing our understanding of the mechanisms and modeling of prostate and bladder tumors. An innovator in the generation of novel mouse models for these cancers, her work has led to the discovery of new biomarkers for early detection, as well as key advances in cancer prevention and treatment.

In the fall of 2018, Dr. Abate-Shen was elected a fellow of the American Association for the Advancement of Science (AAAS). She is an American Cancer Society Professor, the first faculty member at Columbia University Vagelos College of Physicians and Surgeons to have received this honor. Previously, she served as a member of the National Cancer Institute’s Board of Scientific Counselors, and she currently is a member of the board of directors of the American Association of Cancer Research. 

Dr. Abate-Shen will succeed Robert S. Kass, PhD, the Hosack Professor of Pharmacology, Alumni Professor of Pharmacology, and chair of pharmacology since 1995.

Visit the CUIMC Newsroom for the full announcement. 

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Faculty Members Join Department of Systems Biology and C2B2

The Department of Systems Biology and Center for Computational Biology and Bioinformatics are pleased to announce that three Columbia University faculty members have recently joined our community. Kam Leong, the Samuel Y. Sheng Professor of Biomedical Engineering at Columbia University, is now an interdisciplinary faculty member in the Department of Systems Biology. In addition, Yaniv Erlich and Guy Sella are now members of the Center for Computational Biology and Bioinformatics (C2B2). Their addition to the Department and to C2B2 will bring new expertise that will benefit our research and education activities, incorporating perspectives from fields such as nanotechnology, bioinformatics, and evolutionary genomics.

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Department of Systems Biology Opens New Biotechnology Development Hub

Peter Sims, Sagi Shapira, and Harris Wang

Assistant Professors Peter Sims, Sagi Shapira, and Harris Wang recently moved into a new Department of Systems Biology laboratory space designed to facilitate the development of new technologies for biological and biomedical research. Photo: Lynn Saville.

The Columbia University Department of Systems Biology has opened a new experimental research hub focused on biotechnology development. Occupying one and a half floors in the Mary Woodard Lasker Biomedical Research Building at Columbia University Medical Center, the facility will promote the design and implementation of new experimental methods for the study and engineering of biological systems. It will also enable a substantial expansion of Columbia’s next-generation genome sequencing capabilities.

The first occupants of the new facility are the laboratories of Department of Systems Biology Assistant Professors Sagi Shapira, Peter Sims, and Harris Wang, along with the Genome Sequencing and Analysis Center of the JP Sulzberger Columbia Genome Center. The community is slated to grow, as currently unoccupied space will soon accommodate additional Columbia University faculty labs that are also developing new biotechnologies.

“Technology drives science,” says Department of Systems Biology Chair Andrea Califano, “and the ability to design new technologies can make it possible to answer questions that no one else can. By bringing technology-focused investigators and the Genome Center’s sequencing infrastructure together in the same physical location, our goal is that the new Lasker facility will give the Department of Systems Biology — and the entire Columbia University research community — access to unique applications for biological and biomedical research.” 

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Hynek Wichterle Appointed to Columbia Genome Center

Hynek WichterleThe JP Sulzberger Columbia Genome Center is pleased to announce that Hynek Wichterle has been appointed as associate director. In this role he will advise on stem cell related projects and coordinate interactions between Columbia Stem Cell Facility and the Columbia Genome Center's High-Throughput Screening Facility.

In addition to his position at the Columbia Genome Center, Dr. Wichterle is also an associate professor holding a joint appointment in the Departments of Pathology & Cell Biology and Neuroscience (in Neurology) at Columbia University Medical Center. He received his MS degree from Charles University in Prague and his PhD degree from The Rockefeller University. He trained at Columbia University, where he became assistant professor in 2004 and associate professor in 2012. He serves as a co-director of the Columbia Stem Cell Initiative and as a Vice-Chief of the Division of Regenerative Medicine in the Department of Rehabilitation & Regenerative Medicine.

Dr. Wichterle developed groundbreaking methods for producing spinal cord neurons from pluripotent embryonic stem cells in a culture dish. The process faithfully recapitulates normal embryonic development, providing a unique opportunity to study and experimentally probe nerve cells in a controlled environment outside of the embryo. He is using the system to decode transcriptional programs that control genes important for neuronal differentiation and function. His lab also capitalizes on the unlimited source of spinal neurons to study motor neuron degenerative diseases, such as amyotrophic lateral sclerosis (ALS or Lou Gehrig’s disease), with the goal of discovering new drugs for these currently untreatable, devastating conditions.

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