Awards and Grants×

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The annual Precision Medicine Pilot Grants have been awarded to five teams of  researchers conducting innovative basic science, translational, and clinical research across multiple diseases. 

Jointly awarded by the Columbia Precision Medicine Initiative (CPMI), the Herbert Irving Comprehensive Cancer Center (HICCC), and the Irving Institute for Clinical and Translational Research (Irving Institute), the Precision Medicine Pilot Grants underscore Columbia’s commitment to supporting diverse, cross-disciplinary research targeting the promise of precision medicine.

The five winning teams are being led by faculty at Columbia’s Vagelos College of Physicians & Surgeons (VP&S), including: Srilaxmi Bearelly, MD, associate  professor of ophthalmology; Brian Henick, MD, assistant professor of medicine; Chi-Min Ho, PhD, assistant professor of microbiology and immunology; Yufeng Shen, PhD, associate professor of systems biology and of biomedical informatics; and Xuebing Wu, PhD, assistant professor of systems biology and of medicine. The projects being funded are focusing on a range of research, from novel cancer therapeutics to health disparities research. 

The Vagelos Precision Medicine Pilot Grant program is made possible by a generous donation from Roy and Diana Vagelos and is intended to support groundbreaking basic research in the field of precision medicine. Each research team receives $100,000 in funding for one year. The researchers will present their projects at an annual symposium for the precision medicine awards in fall 2022.

Read full article in the HICCC Newsroom

Systems Biology will receive $3,829,859 over five years from the National Institute of Mental Health for “Discovery and Analysis of Brain Circuits and Cell Types Affected in Autism and Schizophrenia.” The project will be led by Dennis Vitkup, PhD, and Joseph Gogos, MD, PhD.

Read full article in CUIMC Newsroom.

Melissa McKenzie, PhD

Melissa McKenzie, PhD, a second-year postdoctoral research scientist in the lab of Chaolin Zhang , PhD, has been awarded a K99/R00 “Pathway to Independence” award. This honor supports her goal to identify how alternative RNA splicing networks influence cortical interneuron specification.

Dr. McKenzie graduated summa cum laude from Cornell University where she was an Irving Tanner Dean’s scholar double majoring in biological sciences and philosophy. She joined the Zhang lab with a growing interest in leveraging emerging sequencing and other genomics technologies to investigate the role of RNA transcripts in the developing brain. 

This award program is designed to facilitate a timely transition of outstanding postdoctoral researchers or clinician-scientists from mentored research positions to independent, tenure-track or equivalent faculty positions, and to provide independent NIH research support during the transition that will help these individuals launch competitive, independent research careers.

Read more about Dr. McKenzie and research by the Zhang lab

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. 

Tal Korem, PhD, Systems Biology and Obstetrics & Gynecology, will receive $307,136 over five years from the National Institute of Nursing Research for a subaward of “The Role of Host-Microbial Interactions in Altering Preterm Birth Risk Among Black Women.”

Read the full article in the CUIMC Newsroom.

Two Systems Biology GRAs Receive Awards

Tomasz Blazejewski has received the 2021 Dean's Award for Excellence in Research. His PhD research centered on generative models for biological sequences, a relatively new area at the interface of machine learning and biology. “I'm deeply appreciative to my advisor, Harris Wang,” says Blazejewski, “for giving me the freedom to investigate this relatively uncharted area, and to my thesis committee for its guidance as I tried to figure out the best approaches to the problem.”

Hanna Mendes Levitin has received the Titus M Coan Award for Excellence in Research. Her PhD research focused on extracting biological signals from-high dimensional data, specifically in the context of high-grade glioma, and on human tissue T cell activation. “I was surprised to receive the award,” says Levitin, “and believe it speaks to the excellence of my collaborators and mentors—especially my advisor, Dr. Peter Sims, and the entire Sims lab, as well as our collaborators, Dr. Donna Farber, Dr. Peter Canoll, and Dr. David Blei, and their respective labs.

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

Tal Korem, PhD
Dr. Tal Korem

Tal Korem, PhD, has been named a CIFAR Azrieli Global Scholar, a fellowship that supports leading early-career researchers in science and technology. 

Dr. Korem is an assistant professor of systems biology with a joint appointment in obstetrics and gynecology at Columbia University Vagelos College of Physicians & Surgeons, and a faculty member of the Program for Mathematical Genomics . As a global scholar, he is joining CIFAR’s Humans and the Microbiome research program, where his work will focus on harnessing human microbial communities to identify and develop novel diagnostic and therapeutic tools.

CIFAR’s  Azrieli Global Scholars program supports its fellows through funding and mentorship, emphasizing essential network and professional skills development. The scholars join CIFAR research programs for a two-year period where they collaborate with fellows and brainstorm new approaches to pressing science and technology problems. Research topics are diverse, ranging from bio-solar energy and visual consciousness to engineered proteins and the immune system. 

Dr. Korem is one of 14 researchers out of an applicant pool of 217 selected by the Canadian-based nonprofit organization. This year’s cohort represents citizenship in eight countries and appointments in institutions from Canada, the U.S.,  Israel, Australia, the Netherlands, and Spain.

-Melanie A. Farmer

Dr. Harris Wang of Systems Biology
Dr. Harris Wang is lead PI on a new DARPA-funded project developing novel therapies to counter effects of high-dose ionizing radiation.

Harris Wang, PhD, assistant professor of systems biology at Columbia University Irving Medical Center , is leading a team of experts in radiation research, CRISPR-Cas technologies, and drug delivery on an innovative new project announced June 27 funded by the Defense Advanced Research Projects Agency (DARPA) . The up to $9.5M project focuses on pursuing a therapy to protect the body from the effects of high-dose ionizing radiation, and is part of DARPA's initiative to fund research into new strategies to combat public health and national security threats.

In humans, acute radiation syndrome primarily affects stem cells in the blood and gut, yet existing treatments only help to regenerate blood cells, and only with limited effect. There is no possibility for prophylactic administration of these drugs, and most must be delivered immediately following radiation exposure to provide any benefit. There are no existing medical countermeasures for radiation damage to the gut.

The Columbia team aims to develop an orally delivered programmable gene modulator therapeutic. The multimodal treatment the team envisions would take hold in both the gut and liver, triggering protection and regeneration of intestinal cells, while also inducing liver cells to produce protective cues that trigger the regeneration of blood cells in bone marrow.

Columbia investigators win Chan Zuckerberg Initiative grants to accelerate development of cellular roadmap of the human body.

In two groundbreaking research projects contributing to the Human Cell Atlas, Columbia University scientists are tasked with mapping complete cells in the immune system and the human spine. The global effort is aiming to identify and define every cell type of the human body and create a collection of maps for navigating the cellular basis of human health and disease.

Peter Sims, PhD
Peter Sims, PhD, assistant professor of systems biology

The Columbia teams, which include co-principal investigators from the Department of Systems Biology Drs. Peter Sims and Raul Rabadan , are among the 38 collaborative science teams launching the Chan Zuckerberg Initiative’s (CZI) Seed Networks for the Human Cell Atlas project announced today. The three-year projects, receiving a total of $68 million in award funding by Seed Networks, are collaborative groups that are bringing together expertise in science, computational biology, software engineering, and medicine to support the ongoing progress of the Human Cell Atlas .

Investigating the Immune System + Aging

Dr. Sims, part of an international team including close collaborator Dr. Donna Farber of the Department of Surgery , is combining single-cell sequencing technologies, data analysis, and immunology expertise to better understand how the immune system ages and gain new insights into how human diseases occur. 

Tuuli Lamport Research Award

Tuuli Lappalainen, PhD, was honored with the Lamport Research faculty award at the 2019 Commencement ceremony. Dr. Lappalainen is pictured here with Columbia University Trustee Andrew Barth (left) and Dean Lee Goldman of Columbia University Irving Medical Center. (Courtesy of CUIMC Communications)

Tuuli Lappalainen , PhD, assistant professor of systems biology at Columbia University and core faculty member at the New York Genome Center (NYGC) , has received the Harold and Golden Lamport Research award, presented on May 22 at the Vagelos College of Physicians and Surgeons Commencement Ceremony. 

The Lamport Research award is an annual prize given to junior faculty members that show promise in basic science or clinical science research. This year it recognizes Dr. Lappalainen’s ongoing research in functional genetic variation in human populations, and her work in elucidating the cellular mechanisms linked to genetic risk for various diseases and traits. Dr. Lappalainen and her lab combine computational analysis of high-throughput sequencing data, human population genetics approaches and experimental work. 

Her group at NYGC and Columbia is highly collaborative and has made important contributions to several international research consortia in human genomics, including the Genotype Tissue Expression (GTEx) Project and the TOPMed Consortium. 

Dr. Lappalainen joined the faculty at Columbia University in 2014 as part of the Department of Systems Biology and NYGC. In 2018, she received the annual Leena Peltonen Prize for Excellence in Human Genetics, which was presented to her in Milan, Italy, at the 52nd European Society of Human Genetics meeting. 

Dr. Raul Rabadan is leading a global research project as part of a new grant from the Pancreatic Cancer Collective to identify high-risk factors of pancreatic cancer. (Courtesy of Stand Up to Cancer)

A global team of researchers led by theoretical physicist Raul Rabadan, PhD, professor of systems biology at Columbia’s Vagelos School of Physicians and Surgeons, and Núria Malats, MD, PhD, head of the Genetic and Molecular Epidemiology Group of the Spanish National Cancer Research Centre (CNIO), are working to develop a comprehensive computational framework that will identify high-risk factors for pancreatic cancer.  

Armed with a new two-year, $1 million grant from the Pancreatic Cancer Collective, the team intends to attack pancreatic cancer research from multiple disciplines—genomics, mathematics and medicine—to provide an integrated, computational approach to studying genomic, environmental and immune factors that could identify populations at high risk of pancreatic cancer. The need for deeper understanding of the contributing factors to this lethal disease is pressing, as pancreatic cancer is projected to become the second leading cause of cancer-related mortality within the next decade. 

Rabadan-led Team for Pancreatic Cancer Collective
Drs. Raul Rabadan and Nuria Malats

Wang Lab
Ravi Sheth (left) and Harris Wang, PhD

Dr. Harris Wang , PhD, and systems biology graduate student, Ravi Sheth , have been awarded a new grant from the Bill and Melinda Gates Foundation to help advance a global health project aimed at reducing childhood mortality in sub-Saharan Africa. The project incorporates Dr. Wang’s innovative microbiome research techniques and applies them to study the antibiotic, Azithromycin, towards understanding its role as an intervention for improving childhood survival rates in rural low-income, low-resource settings.

The study supported by the Gates grant expands on breakthrough research conducted in the MORDOR study , a cluster-randomized trial in which communities in Malawi, Niger and Tanzania were assigned to four twice-yearly mass distributions of either oral Azithromycin or placebo. Children, as young as 12 months of age, participated, and results indicated that the all-cause mortality rate was significantly lower for communities receiving the antibiotic versus placebo. 

“This is an extremely exciting and, in many ways, very surprising result for such an underserved population,” says Sheth, who is a fourth-year PhD student in the systems biology track at Columbia University Irving Medical Center (CUIMC) . “Now it is crucial to understand how Azithromycin is acting to increase survival in such a profound way – to aid scale-up of the intervention and to help optimize the treatment regime and minimize any unintended consequences.” 

The researchers will focus on developing a mechanistic understanding of how Azithromycin reshapes the gut microbiome, and how this altered microbiome state affects the host. The effect of the antibiotic will be studied over space and time to understand the perturbation to the gut ecosystem and resulting community re-configuration and re-assembly, and this information will be utilized to predict and test optimal dosing strategies. 

Peter Sims, PhD
Peter Sims, PhD

The Mark Foundation for Cancer Research has awarded Peter Sims , PhD, an Emerging Leader Award and will support his work to advance a novel use of single-cell RNA sequencing to develop brain cancer treatments. Dr. Sims, assistant professor of systems biology at Columbia University Irving Medical Center, is one of just eight recipients of the inaugural grant, given to promising early career scientists for projects aimed at substantially unmet needs in cancer risk prediction, prevention, detection and treatment. 

Dr. Sims is an early contributor to the emerging field of large-scale single-cell RNA sequencing, which has made it possible to analyze tens of thousands of cells while simultaneously obtaining imaging and genomic data from each individual cell. He will be using this approach to improve patient-derived models of glioblastoma multiforme (GBM), an aggressive form of cancer that invades the brain, making complete resection difficult. In other words, making it extremely difficult in surgery to remove all cancerous cells from the brain. To date, drug therapies for this type of aggressive brain cancer have had limited success, partly because of the heterogeneity of these tumors. Furthermore,  current patient-derived models for researching glioblastoma do not fully recapitulate the cellular diversity of tumor cells that are present in the tumor, so it is extremely challenging to classify those cells in order to match them with the drug therapies that work. 

Indeed, there is a critical need to better characterize and understand GBM. Dr. Sims has collaborated with several brain tumor experts in the Herbert Irving Comprehensive Cancer Center , including Drs. Peter Canoll, Jeffrey Bruce, Antonio Iavarone and Anna Lasorella to advance single-cell genomic approaches to characterizing this disease. Approaching this problem at the single cell level could result in development of novel treatments that  prioritize and identify the specific drug therapies that may actually work on diminishing these tumor cells. The ultimate goal is to attain better predictions of therapeutic efficacy. 

A research team from Columbia University Irving Medical Center has received a 2018 PCF Challenge Award from the Prostate Cancer Foundation (PCF) to advance prostate cancer research. The interdisciplinary team at Columbia includes leading experts in systems biology, cancer research and medicine from Columbia’s Department of Systems Biology and the Herbert Irving Comprehensive Cancer Center (HICCC)

Announced today, PCF is awarding more than $5.5 million in funding to a total of six teams to conduct research with the highest potential for accelerating new and improved treatments for advanced prostate cancer. PCF is one of the largest non-governmental organizations dedicated solely to funding prostate cancer research, and its annual Challenge Awards are highly coveted in the scientific and medical fields. 

In the United States, prostate cancer is the most common non-skin cancer, and 1 out of every 9 men in the U.S. will be diagnosed with the disease in his lifetime. To date, treatment of the most aggressive forms of prostate cancer represents a clinical challenge. After treatment failure with anti-androgen drugs, which are part of the standard of care for advanced metastatic prostate cancer, only few current therapeutic options remain and the impact on patient survival is limited. Indeed, the field needs major innovative, out-of-the-box approaches to new therapies to combat advanced prostate cancer. 

Suying Bao, PhD
Suying Bao, PhD

Suying Bao, a postdoctoral research scientist in the Chaolin Zhang lab , has been named an inaugural Precision Medicine Research fellow by Columbia’s Irving Institute of Clinical and Translational Research . The two-year fellowship aims to train postdocs to use genomics and complex clinical data to improve personalized and tailored clinical care and clinical outcomes. 

This fellowship “will provide me with more opportunities to translate my findings from basic science research into clinical application,” says Bao, “and pave my way towards an independent researcher in this field.” 

Bao’s expertise lies in RNA regulation at the interface of systems biology, ranging from the specificity of protein-RNA interaction to function of specific splice variants. RNA regulation is critical in proper cellular function; gaining deeper insights into this complex molecular mechanism will promote the development of precision medicine therapies. 

In this project, Bao is aiming to develop new approaches to identify causal noncoding regulatory variants (RVs) modulating post-transcriptional gene expression regulation, such as RNA splicing and stability.  “A majority of genetic variants associated with human diseases reside in noncoding genomic regions with regulatory roles,” notes Bao. “Thus, elucidating how these noncoding regulatory variants contribute to gene expression variation is a crucial step towards unraveling genotype-phenotype relationships and advancing precision medicine for common and complex diseases.”

To identify these RVs, she will leverage massive datasets of high-throughput profiles of gene expression and protein-RNA interactions generated from large cohorts of normal and disease human tissues and cell lines by multiple consortia, such as ENCODE, GTEx and CommonMind, and develop innovative computational methods of data mining. 

Hyundai $2.5M Grant to Columbia
Julia Glade Bender, MD, (center) at the Hyundai Hope on Wheels announcement Mar. 29 during the New York International Auto Show at the Jacob Javitz Center. (Photo courtesy of HHOW)

A team of researchers at Columbia University Irving Medical Center (CUIMC) has recently been awarded a five-year $2.5 million grant from Hyundai Hope on Wheels (HHOW) to fund innovative pediatric cancer research. 

The team at Columbia is being led by principal investigator (PI), Julia Glade Bender , MD, associate professor of pediatrics at CUIMC, with co-PIs Andrea Califano , Dr, chair of Columbia’s Department of Systems Biology and Darrell Yamashiro , MD, PhD, director of pediatric hematology, oncology and stem cell transplantation, along with researchers from Memorial Sloan Kettering, University of San Francisco Children’s and Dana-Farber Cancer Center. 

The Quantum Collaboration award from HHOW is aimed at funding research focused on childhood cancers with poor prognosis. At Columbia, the team will target osteosarcoma, the most commonly diagnosed bone tumor in children and adolescents. No new treatment approaches have successfully been introduced for osteosarcoma in nearly 40 years, and patients with the disease have not benefited from recent breakthroughs like immunotherapy or DNA sequencing and require a shift in the understanding and approach to therapy. 

Michael Shen, PhD
Michael Shen, PhD (Image Courtesy of the Shen Lab)

The Bladder Cancer Advocacy Network (BCAN) has awarded Professor Michael Shen, PhD, the 2018 Bladder Cancer Research Innovation Award. The honor is given to scientists whose novel, creative research has great potential to produce breakthroughs in the management of bladder cancer.  

Dr. Shen, who is professor of medicine, genetics & development, urology and systems biology at Columbia University, has used new techniques of 3D cell culture to establish “organoids” from primary bladder tumors obtained from patients. These personalized laboratory models, which the Shen lab can create in a matter of weeks, provide a new, innovative way to study the molecular mechanisms associated with drug response and drug resistance in bladder cancer patients. 

The BCAN award supports the Shen lab’s efforts in furthering their work in patient-derived bladder tumor organoids

“We will employ these organoid lines to examine how specific oncogenic drivers may regulate the invasiveness and metastatic ability of muscle-invasive bladder cancer (MIBC), both in cell culture and in mouse models,” says Dr. Shen. “Our goal is to use these new experimental approaches to provide molecular insights into the lethal properties of human MIBC, which will hopefully lead to improved therapeutic approaches.”

Bladder cancer is the fifth most common cancer in the United States, and the primary treatment of the disease is surgery. Overall, this new project will examine central questions of bladder cancer biology using Dr. Shen’s innovative approach involving patient-derived tumor organoids, and may provide the basis for future therapies for metastatic bladder cancer.

Molly Przeworski Distinguished Columbia Faculty Award
Molly Przeworski

Molly Przeworski, PhD , professor of  biological sciences and of systems biology , has received the Distinguished Columbia Faculty Award for exceptional teaching. A leading population geneticist, Dr. Przeworski is one of eight recipients of the annual award, which recognizes faculty across a range of academic activities, including scholarship, University citizenship and professional involvement, with an emphasis on the instruction and mentoring of undergraduate and graduate students. 

The recipients this year were presented with the award at an April 11 event held at Columbia’s Italian Academy.

“It is wonderful to see the work we do teaching and mentoring graduate students recognized,” says Dr. Przeworski. “I have been really lucky to attract phenomenal students and postdocs, and find that interacting with them is one of the most rewarding aspects of what I do.”

According to one undergraduate referred to in the award citation, Dr. Przeworski “is definitely one of the best teachers I have ever been taught by.” The student also described her lectures as “well-designed” to build a keen understanding of and active engagement with the material. Columbia also lauded her for helping to launch the first annual New York area meeting in population genetics, successfully connecting researchers of varying career stages.

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. She is the recipient of 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. 

Andrea Califano
Andrea Califano, Dr, chair of Columbia's Department of Systems Biology

The Chan Zuckerberg Initiative (CZI) has awarded Andrea Califano, Dr, a new grant in support of his work to develop a comprehensive library of regulatory interactions within molecularly defined cellular populations and molecular determinants (master regulators) of individual cells’ state. This will arm scientists with a unique resource to study biology at the individual cell level and to gain further insight into the fundamental understanding of molecularly distinct cell types.

With the support of CZI, founded by Facebook CEO Mark Zuckerberg and his wife, Priscilla Chan, Dr. Califano, chair of Columbia’s Department of Systems Biology, and his group will apply their computational methods that accurately and systematically measure and analyze regulatory interaction at the single cell level to elucidate distinct cellular states and to establish both cell-state markers, as well as the proteins that are causally responsible for implementing that state. 

A critical advantage offered by the approaches that the Califano Lab brings to the CZI community is that of addressing one of the most critical issues in single cell biology characterization. Specifically, since the depth of transcriptional sequencing of single cells is generally a very small fraction of what can be achieved from bulk tissue, most of the genes are actually lost and only the 20% to 30% of the genes that are most highly expressed can be detected. This has been dubbed the gene dropout problem. By using the recently published metaVIPER algorithm, this problem is eliminated as regulatory networks are used to accurately infer the activity of 6,000 proteins that include all the critical players in cell state implementation and modulation, even if their RNA cannot be detected, thus fully addressing gene dropout and allowing much deeper investigation of single cell biology. 

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