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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.

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

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.

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.” 

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.

We are pleased to announce that Columbia University Medical Center professors Oliver Hobert, Richard Mann, and Rodney Rothstein have been named to interdisciplinary appointments in the Department of Systems Biology. The addition of this new expertise will expand the breadth of science currently being explored in the Department, enhance educational opportunities for students, facilitate new collaborations, and promote the integration of systems biology perspectives and methods into research being conducted elsewhere in the university.

geWorkbench screenshot

A new version of geWorkbench lets researchers access a range of powerful, integrated bioinformatics tools using a standard web browser. Here, an ARACNe-generated gene regulatory network is displayed using the Cytoscape Web plugin.

Since its creation in 2005, investigators in Columbia University’s Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) have developed a large number of computational tools for studying biological systems from the perspectives of structural biology and systems biology. To consolidate and disseminate these tools to the wider research community, MAGNet developed geWorkbench (genomics Workbench), a free, open-source bioinformatics application that gathers all of the Center’s software and databases into one integrated software platform. These include applications for the analysis of cellular regulatory networks, protein structure, DNA and protein sequences, gene expression, and other kinds of biological data.

Initially, geWorkbench was made available as a software package that users could install and run on their local computers. Now, in a major upgrade, MAGNet has released a web-based version that makes these tools accessible through a browser interface.

Illumina NextSeq 500 at Columbia University

As genome sequencing technologies evolve, the JP Sulzberger Columbia Genome Center continues to provide the Columbia University biological and biomedical research community access to state-of-the-art tools. In its most recent acquisition, the Genome Center has just installed two Illumina NextSeq 500 sequencers. The NextSeq 500 is a flexible and efficient desktop sequencer that offers powerful high-throughput sequencing capabilities.

Columbia investigators who are experienced with the Illumina next-generation sequencing platform can now schedule time to use the NextSeq 500 for their own research. 

Molly PrzeworskiMolly Przeworski has joined Columbia University as Professor in the Department of Systems Biology and Department of Biological Sciences. The Przeworski lab investigates how natural selection, genetic drift, mutation, and recombination shape the heritable differences seen among individuals and species. To this end, they develop models of the evolutionary process, create statistical tools, and analyze large-scale variation data sets. Among the goals of their research are 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.

Peter SimsPeter Sims, an assistant professor in the Columbia University Department of Systems Biology, has been named Associate Director for Novel Technologies at the JP Sulzberger Columbia Genome Center. In this role he will devise, direct, and implement strategies for incorporating new high-throughput experimental methods into the research done at the Genome Center.

Trained as a physical chemist, Dr. Sims has been developing a number of innovative technologies for studying single cells in a high-throughput setting. Using a type of microfluidics called soft lithography, his laboratory has designed a method for creating arrays composed of wells just tens of microns in diameter, small enough to isolate and perform high-throughput experiments on individual cells.  

Appointing Dr. Sims to his new role will enable the Columbia Genome Center to develop a variety of new applications that will benefit researchers across the Columbia University community. 

Tuuli LappalainenTuuli Lappalainen has joined Columbia University as an assistant professor in the Department of Systems Biology. Dr. Lappalainen is a specialist in the analysis of RNA sequencing data, with research interests including functional variation in the human genome, population genetic background of variation in the human genome, and interpretation of genome function.

Dr. Lappalainen joins the Department of Systems Biology in co-appointment with the New York Genome Center (NYGC), where she will also serve as a Junior Investigator and Core Member. Based in lower Manhattan, NYGC is a consortium made up primarily of New York-area institutions that is designed to translate promising genomics-based research into new strategies for treating, preventing, and managing disease. This co-appointment with Columbia University — an institutional founding member of the NYGC — will enhance collaboration between the two institutions. (Read an interview with Dr. Lappalainen at the New York Genome Center website.)

Dr. Lappalainen earned her PhD in genetics at the University of Helsinki, Finland, and held appointments as a postdoctoral researcher in at the University of Geneva Medical School, Switzerland and at the Stanford University School of Medicine. She is the chair of the analysis group for the Genetic European Variation in Health and Disease (Geuvadis) Consortium’s RNA sequencing project, a member of the analysis group for the National Institute of Health’s Genotype Tissue Expression (GTEx) project, and a member of the analysis and functional interpretation groups for the 1000 Genomes Project.

Columbia University Department of Systems Biology

Attendees at the June 2013 Columbia University Department of Systems Biology retreat.

Effective July 1, 2013, the Columbia Initiative in Systems Biology is now the Columbia University Department of Systems Biology. Approved by a vote of the University Trustees, this step recognizes the growth in systems biology research and education that has taken place at Columbia, and formally establishes this emerging discipline as a major area for research at the university.

As Andrea Califano, chair of the new department, explained, "This achievement testifies to the dedicated community that has been gathering at Columbia over the past decade around the field of systems biology. We have witnessed the emergence of a compelling scientific agenda that combines innovative experimental and quantitative methods to address important biological and biomedical questions in ways that were unimaginable just a few years ago. It is very exciting to see Columbia take this step because systems biology is paving the way toward new, more rational approaches in basic and translational research."

Harris WangHarris Wang has joined Columbia University Medical Center as an Assistant Professor in the Columbia Initiative in Systems Biology and the Department of Pathology and Cell Biology. His research focuses on understanding the evolution of the ecosystems that develop within heterogeneous microbial communities. Using approaches from genome engineering, DNA synthesis, and next-generation sequencing, he studies how genomes in microbial populations form, maintain themselves, and change over time, both within and across microbial communities. His goal is to use synthetic biology approaches to engineer ecologies of microbial populations, such as those found in the gut and elsewhere in the human body, in ways that could improve human health.

The Center for Computational Biology and Bioinformatics (C2B2) has begun a major upgrade of its Advanced Research Computing core.

In the coming months, C2B2 will launch a new computing cluster that boasts 212 teraflops of performance. This figure is nearly nine times the total computing capacity of its current computing platform, called Titan. The new system will have 6,336 CPU-cores, over 70,000 CUDA-cores (GPU), and 22 TB of total system memory. The primary source of funding for this new system is a High-End Instrumentation grant from the National Institutes of Health.

The 6th Annual DREAM competition, the 7th Annual RECOMB Satellite Conference on Systems Biology, the 8th Annual RECOMB Satellite Conference on Regulatory Genomics, and the IDIBELL Conference on Cancer Informatics will be held jointly at the IDIBELL institute, in Barcelona, Spain, on October 14-19, 2011. The four conferences aim to bring together computational and experimental scientists in the area of regulatory genomics and systems biology, to discuss current research directions, latest findings, and establish new collaborations towards a systems-level understanding of gene regulation, with particular emphasis on cancer. Click here for more information. 

Saeed Tavazoie, Professor at the Department of Biochemistry and Molecular Biophysics at Columbia University, has joined C2B2. Dr. Tavazoie's research focuses on understanding the organizing principles that underlie the evolution and function of molecular networks. At one scale, his work uses large-scale genome-wide observations to reveal the nuts and bolts of these networks and to understand how they come together to orchestrate biological behavior. At the other extreme, it aims to achieve a holistic understanding of function by considering the native ecological context in which these networks have evolved. At the highest level, his goal is to understand how molecular networks embody an internal representation of the outside world and facilitate adaptive behaviors.

Dr. Tavazoie's research focuses on these problems in the context of transcriptional regulatory and genetic networks of organisms ranging from bacteria to human. In addition to using traditional experimental methods, his lab develops and employs novel technologies for making genome-wide observations, together with computational and analytic tools required to turn these observations into predictive models of the underlying biology.

Professor Tavazoie received his PhD from Harvard Medical School in 2000. He joins C2B2 and Columbia University from Princeton where he was Professor in the Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics.

Yufeng Shen, Assistant Professor at the Department of Biomedical Informatics, has joined C2B2 and the Columbia Initiative in Systems Biology. Dr. Shen's research focuses on the development and application of computational methods for the study of human genetics and disease. Specifically, his group is working in four areas, including high-throughput sequencing and de novo assembly, genetic mapping of human diseases, autoimmunity and major histocompatibility complex, pharmacogenomics and personalized treatment.

Dr. Shen received his PhD in computational biology from the Human Genome Sequencing Center at Baylor College of Medicine in 2007. In 2008 he joined Columbia University as a postdoctoral fellow.

Sagi Shapira, Assistant Professor of Systems Biology in the Department of Microbiology and Immunology, has joined the Columbia Initiative in Systems Biology (CISB). Dr. Shapira's research focuses on deciphering the genetic and molecular circuitry that is at the interface of host-pathogen interactions. The goal is to understand how this circuitry controls cellular responses to infection, imparts selective pressure on viruses and affects disease progression. A mechanistic understanding of these relationships will provide important insights into cellular machinery that control basic cell biology and will have broad implications in human translational immunology and infectious disease research.

Shapira received his PhD in immuno-parasitology under the guidance of Christopher A. Hunter at the University of Pennsylvania in 2005 and a Masters in Public Health at Yale University in 1999. He joins Columbia from the Broad Institute where he has a postdoctoral fellow.