Howard J. Jacob to Deliver Daniel T. O’Connor Memorial Lecture February 23

Dr. Howard J. Jacob will present the Daniel T. O’Connor 2nd Annual Memorial Lecture on Thursday, February 23, 2017, at UC San Diego School of Medicine. His topic is “From Hypertension to Genomic Medicine.”

Dr. Jacob’s lecture will take place in the Leichtag Auditorium (Room 107), with a reception immediately following on the patio.

Dr. Jacob is Executive Vice President for Medical Genomics, Chief Medical Genomics Officer, and Faculty Investigator at HudsonAlpha Institute for Biotechnology. His UC San Diego hosts are Bruce A. Hamilton, PhD, and Nicholas J. Schork, PhD.

Dr. Hamilton is Professor, Cellular and Molecular Medicine, Department of Medicine; Director, Genetics Training Program; and Associate Director, Institute for Genomic Medicine. Dr. Schork is UC San Diego Adjunct Professor, Psychiatry, Family and Preventive Medicine and Director of Human Biology, J. Craig Venter Institute.

The lecture is presented in conjunction with the UC San Diego CTRI Seminar Series and the Genetics, Bioinformatics and Systems Biology Colloquium Series.

New UC San Diego Program Expands Campus Innovation Pipeline

The innovation ecosystem at UC San Diego will open more opportunities for campus entrepreneurs with the launch of Accelerating Innovations to Market (AIM), an ambitious program that encourages graduate students, postdoctoral scholars, researchers and faculty to develop and commercialize their problem-solving ideas.

Coordinated by the Office of Innovation and Commercialization (OIC), the program invests in milestone-based projects that develop proofs-of-concept and reduce the risk of early-stage technologies. According to Paul Roben, Associate Vice Chancellor for Innovation, a central focus of AIM is value-driven engagement with industry. … Read the Full Story from the UC San Diego Newsroom

Creating Clinical Bioengineers

New class teaches undergrads to use engineering-based solutions to bridge gap between engineering and medicine —

A group of UC San Diego bioengineering students huddle around a computer screen as colored images of blood being pumped through a heart flash across the screen. The students are observing as a physician annotates an MRI of a patient’s heart and recommend treatment.

“It looks like there is fat here where there shouldn’t be,” says the physician as he pointed to a spot on the screen. “See how this part of the heart isn’t contracting?” … Read the Full Story from the UC San Diego Newsroom

The Division of Cardiology in the Department of Medicine is one of the rotation sites in the Clinical Bioengineering class.

Active Genetics Goes Global

Tata Trusts & University of California San Diego partner to establish Tata Institute for Active Genetics and Society (TIAGS) —

UC San Diego has received a $70 million commitment from the India-based philanthropic Tata Trusts, which includes the Sir Dorabji Tata Trust, the Sir Ratan Tata Trust and the Tata Education and Development Trust, to establish the Tata Institute for Active Genetics and Society (TIAGS), a collaborative partnership between the university and research operations in India. UC San Diego, which will be home to the lead unit of the institute (TIAGS-UC San Diego), will receive $35 million in funding, while the remainder of the committed funds is anticipated to support a complementary research enterprise in India (TIAGS-India). … Read the Full Story from the UC San Diego Newsroom

Anita Raj, PhD

Anita Raj, PhD

Anita Raj, PhD, Professor of Medicine in the Division of Global Public Health, is one of the UC San Diego researchers who will contribute to the TIAGS.

Researchers ID Cancer Gene-Drug Combinations Ripe for Precision Medicine

Yeast, human cells and bioinformatics help develop one-two punch approach to personalized cancer therapy —

In an effort to expand the number of cancer gene mutations that can be specifically targeted with personalized therapies, researchers at University of California San Diego School of Medicine and Moores Cancer Center looked for combinations of mutated genes and drugs that together kill cancer cells. Such combinations are expected to kill cancer cells, which have mutations, but not healthy cells, which do not. The study, published July 21 in Molecular Cell, uncovered 172 new combinations that could form the basis for future cancer therapies.

“Oncologists here at Moores Cancer Center at UC San Diego Health and elsewhere can often personalize cancer therapy based on an individual patient’s unique cancer mutations,” said senior author Trey Ideker, PhD, … Read the Full Story by Heather Buschman from the UC San Diego Newsroom

Trey Ideker, PhD

Trey Ideker, PhD

Senior author of the study report in Molecular Cell is Trey Ideker, PhD, Professor of Medicine in the Division of Medical Genetics and Professor of Bioengineering at UC San Diego.

No. 1 From the Start

UC San Diego Bioengineering ranked first by National Research Council since founding 50 years ago —

Bioengineers at UC San Diego have helped us understand why atherosclerosis develops and how it is impacted by blood flow. They have pioneered the development of very thin, small and flexible sensors that stick to the skin and monitor vital signs, such as the brain activity of a newborn. They also developed injectable hydrogels that can help muscle tissues heal after a heart attack.

Researchers celebrated their achievements over the past five decades and looked to the future during a three-day 50th anniversary celebration May 19 to 21. … Read the Full Story from the UC San Diego Newsroom

Shu Chien, PhD

Shu Chien, PhD

The founding chair of the UC San Diego Department of Bioengineering is Shu Chien, PhD, Distinguished Professor of Medicine in the Division of Physiology and Professor of Bioengineering. He is founding director of the UC San Diego Institute of Engineering in Medicine.

Dr. Chien is an elected Fellow of the National Academy of Inventors and the American Association for the Advancement of Science, among many honorific societies, and he received the Franklin Institute Award in November 2015.

Melissa Gymrek, PhD, Speaks This Friday, Feb. 26: “Dissecting the Contribution of Complex Genetic Variation to Human Traits”

Computer Science and Engineering Colloquium Talk / Winter 2016

Melissa Gymrek, PhD
Massachusetts General Hospital and the Broad Institute

Friday, February 26, 2016
12 – 1 p.m.

Computer Science and Engineering Building EBU-3B, Room CSE 1202

Title: Dissecting the Contribution of Complex Genetic Variation to Human Traits

Recent studies have made substantial progress in identifying genetic variants associated with disease and molecular phenotypes in humans. However, these studies have primarily focused on single nucleotide polymorphisms (SNPs), ignoring more complex variants that have been shown to play important functional roles. Here, I focus on short tandem repeats (STRs), one of the most polymorphic and abundant classes of genetic variation. I will first present lobSTR, a novel algorithm for genotyping STRs from whole-genome sequencing datasets. Next, I will describe insights into population-wide trends of STR variation revealed by applying lobSTR to thousands of sequencing datasets to generate the largest and highest-quality STR catalog to date. I will then show how we used this catalog to conduct a genome-wide analysis of the contribution of STRs to gene expression in humans. This survey revealed that STRs explain 10-15% of the heritability of expression mediated by all common cis variants and potentially play an important role in clinically relevant conditions. Finally, I will discuss preliminary analyses incorporating functional genomics data with high-quality complex variant genotypes to predict and validate the function of non-coding variants driving common human diseases. Altogether, these results highlight the putative phenotypic contribution of complex variants and the opportunity for a wealth of genetic discoveries to be gained by expanding analyses to less-understood regions of the genome.

I am currently a post-doctoral fellow at Massachusetts General Hospital and the Broad Institute. I recently received my PhD in Bioinformatics and Integrative Genomics from the Harvard/MIT Division of Health Sciences and Technology under the supervision of Yaniv Erlich and Mark Daly. Prior to my PhD, I received my B.S. in Computer Science and Mathematics at MIT.

My major research interest is to understand complex genetic variants that underlie phenotypic changes, ultimately leading to human disease. My recent work focuses on repetitive DNA variants known as short tandem repeats (STRs) as a model for complex variation. I develop computational methods for analyzing and visualizing complex variation from large-scale sequencing data. These tools allow us for the first time to answer many questions regarding STRs and other variant types, including their contribution to complex human phenotypes. In future work, I aim to build on my experience dissecting challenging regions of the genome to develop and test predictive models of the regulatory effects of complex sequence variation.

Faculty Host:
Vineet Bafna, PhD
Professor of Computer Science and Engineering
Jacobs School of Engineering
UC San Diego

CAR Trials Drive Leukemia and Lymphoma Treatment in New Direction

Experimental cellular-immunotherapy may boost body’s ability to find and destroy specific cancers —

Cancer immunology is based upon boosting the body’s own immune system to vanquish malignancies. It is among the fastest growing areas of oncology research. Researchers at UC San Diego Moores Cancer Center have launched three clinical trials to test the safety and efficacy of a novel cellular-immunotherapy that uses modified T cells – one of the immune system’s primary weapons – to treat three different types of blood cancer that often defy existing therapies.

“Lymphomas and leukemias affect thousands of Americans every year and unfortunately a good number of them die as a direct consequence of the disease progression or toxicity from existing treatments,” said Januario E. Castro, MD … Read the Full Story from the UC San Diego Newsroom

Januario E. Castro, MDDr. Januario E. Castro is the principal investigator of the three ZUMA clinical trials of the potential treatment, KTE-C19. Dr. Castro is Professor of Medicine in the Division of Bone Marrow Transplantation.
For more information about the trials, contact Amy Guzdar at (858) 822-6843 or

Drs. Shu Chien, Shaochen Chen Report Creation of in Vitro Liver Tissue Model Using Novel Bioprinting Technology

A team led by engineers at the University of California, San Diego has 3D-printed a tissue that closely mimics the human liver’s sophisticated structure and function. The new model could be used for patient-specific drug screening and disease modeling. The work was published the week of Feb. 8 in the online early edition of Proceedings of the National Academy of Sciences. … Read the Full Story from the UC San Diego Newsroom

Shu Chien, MD, PhD

Shu Chien, MD, PhD. Photo courtesy of Jacobs School of Engineering/UC San Diego.

Shu Chien, MD, PhD, co-senior author of the study report in PNAS, is founding chair of the UC San Diego Department of Bioengineering and director of the Institute of Engineering in Medicine.

In the Department of Medicine, he is Distinguished Professor of Medicine in the Division of Physiology.

Dr. Chien is a world-renowned researcher and inventor who has conducted pioneering investigations in atherosclerosis and hypertension. His work has brought about significant advances in the diagnosis and treatment of cardiovascular disease.

Read the abstract of the PNAS report

Read more about the biofabrication technology used to create the liver model

GenomeSpace “Recipes” Help Biologists Interpret Genomic Data

Data analysis platform will enlist the user community to streamline use of multiple bioinformatics tools —

Many biomedical researchers are striving to make sense of the flood of data that has followed recent advances in genomic sequencing technologies. In particular, researchers are often limited by the challenge of getting multiple bioinformatics tools to “talk” to one another. To help address this need, researchers at University of California, San Diego School of Medicine, in collaboration with labs at the Broad Institute of MIT and Harvard, Stanford University, Weizmann Institute and Pennsylvania State University, developed GenomeSpace, a cloud-based, biologist-friendly platform that connects more than 20 bioinformatics software packages and resources for genomic data analysis.

The team is now developing and crowdsourcing “recipes” — step-by-step workflows — to better enable non-programming researchers to interpret their genomic data … Read the full story from the UC San Diego Newsroom

Dr. Jill Mesirov

Dr. Jill Mesirov

Jill Mesirov, PhD, is senior investigator on the GenomeSpace project. Dr. Mesirov joined UC San Diego in 2015 as Associate Vice Chancellor for Computational Health Sciences and Professor of Medicine in the Division of Medical Genetics.

Trey Ideker, PhD, Professor of Medicine, is a coauthor.

The article citation: Qu K, Garamszegi S, Wu F, et al. Nature Methods. 2016 Jan 18. doi: 10.1038/nmeth.3732.