UCSD Jacobs School of Engineering

UC San Diego Bioengineering Department Makes Strong Showing in List of Highly Cited Researchers Around the World

San Diego, Calif., Nov. 25, 2019 -- Eleven faculty members and affiliates of the Department of Bioengineering at the University of California San Diego are among the world’s most influential in their fields, according to a new research citation report from the Web of Science Group.

UC San Diego played key roles in launching the discipline of bioengineering over 50 years ago, and the new report is yet another indicator that the Department of Bioengineering at the UC San Diego Jacobs School of Engineering continues to shape the future of bioengineering.

These eleven individuals with ties to bioengineering are among the 52 UC San Diego researchers named to the 2019 Highly Cited Researchers list.

The UC San Diego bioengineering professors are Ludmil Alexandrov, Shu Chien, Rob Knight, Prashant Mali, Bernhard O. Palsson and Kun Zhang. UC San Diego professors affiliated with bioengineering and have primary affiliations across campus are Trey Ideker, Julian Schroeder, Joseph Wang, Gene Yeo and Liangfang Zhang.

“The UC San Diego bioengineering department has been pushing the field of bioengineering over the past 50 years and is continuing to take the field in new and exciting directions. If you look at the research areas being pursued by our Highly Cited faculty, a few non-traditional directions emerge, including Systems and Network Biology, Genome Engineering, Microbiome and Nanomedicine,” said UC San Diego professor and chair of bioengineering Kun Zhang.

“This campus has an incredible open and vibrant environment, which has been catalyzed by a number of strategic recruitments. This enables us to continue exploring the next frontiers and embracing non-traditional research directions in the realm of bioengineering.”

2019 Highly Cited Researchers List

Each year the Web of Science Group, an information and technology provider for the global scientific research community, compiles its Highly Cited Researchers list. In 2019, just over 6,000 scientists from around the world made the list. Their studies were among the top 1% of most-cited publications in their field over the past 11 years.

The number of highly cited researchers from UC San Diego totaled 52 this year, an increase of 13% over last year’s number of 46.

“UC San Diego has world-leading researchers at the forefront of bioengineering and related disciplines that encompass the whole range of seniority, including young starting faculty, who presage the magnificent future of the department,” said Shu Chien, the department’s founding chair and a professor emeritus who recently retired after serving 31 years at UC San Diego.

“The outstanding work by our bioengineering faculty is facilitated and enhanced by a campus-wide ecosystem that fosters highly effective interdisciplinary interactions for engineering principles and technologies to be applied to clinical medicine to enhance the diagnosis, treatment and prevention of diseases and to improve human health.”

The UC San Diego Department of Bioengineering is ranked 1st in the nation for biomedical engineering by the National Research Council at the National Academies. The department has been consistenly ranked among the top five programs in the nation every year for more than a decade.

The department is proud to have two junior faculty named among this year’s Highly Cited list: Ludmil Alexandrov and Prashant Mali.

“This is an incredible list with Shu Chien still maintaining highly active research six decades into his research career, as well as two assistant professors leading some of the most exciting fields: Mali being among the first who demonstrated mammalian genome editing with CRISPR-Cas9, and Alexandrov who first discovered mutational signatures in cancers and linked them to specific exposure such as tobacco and UV sun light. UC San Diego’s bioengineering department has been on a hiring spree of junior investigators working on the next-big things. Bringing in brilliant young investigators into this department is transforming our research and education programs,” Zhang said.    

Researchers and Research

The eleven Highly Cited UC San Diego bioengineering researchers and affiliates, along with one of their highly cited papers over the last 11 years, are listed below.    

Ludmil Alexandrov, assistant professor of bioengineering. Alexandrov maps the mutational processes in cancer and devises better strategies for preventing it.

Most cited paper: “Signatures of mutational processes in human cancer,” published in Nature, 2013.

Shu Chien, professor emeritus of bioengineering and medicine, founding chair of the Department of Bioengineering and founding director of the Institute of Engineering in Medicine. Chien is a world leader in the study of how blood flow and pressure affect blood vessels. His research has led to new understanding about the medical and biological mechanisms of atherosclerosis and hypertension, and to the development of better diagnostic tests and treatments for cardiovascular disease.

Most cited paper: “Effects of disturbed flow on vascular endothelium: pathophysiological basis and clinical perspectives,” published in Physiological Reviews, 2011.

Trey Ideker, professor of genetics and bioengineering. Ideker seeks to comprehensively map connections between the many genes and proteins in a cell and how these connections trigger or prevent disease. His current work focuses on DNA mutations that cause cancer.

Highly cited papers: “Network-based stratification of tumor mutations,” published in Nature Methods, 2013.

A NEW APPROACH TO DECODING LIFE: Systems Biology,” published in Annual Review of Genomics and Human Genetics, 2001.

Rob Knight, professor of pediatrics, bioengineering, computer science and engineering, and director of the Center for Microbiome Innovation. Knight studies the human microbiome—the totality of microorganisms living in and on us—and how they can be manipulated to benefit human health and the environment.

Most cited paper: “QIIME allows analysis of high-throughput community sequencing data,” published in Nature Methods, 2010.

Prashant Mali, assistant professor of bioengineering. Mali’s expertise is in the fields of genome engineering and regenerative medicine. He has helped pioneer the development of CRISPR/Cas9, a powerful genome editing tool derived from microbial systems, with wide applications in both basic biology and human therapeutics. More recently, he is focused on the development of RNA and protein targeting tools derived from endogenous human systems.

A recent paper from his lab: “In vivo RNA editing of point mutations via RNA-guided adenosine deaminases,” published in Nature Methods, 2019.

Bernhard O. Palsson, Galletti Professor of Bioengineering and professor of pediatrics. Palsson’s research focuses on developing experimental and computational models in systems biology. He has focused on the red blood cell, E. coli, CHO cells, and several human pathogens to study cellular life. His Systems Biology Research Group leverages high-power computing to build vast interactive databases of biological information.

Most cited paper: ”What is flux balance analysis?” published in Nature Biotechnology, 2010.

Julian Schroeder, distinguished professor of biology and faculty affiliate of bioengineering. Schroeder pioneered the characterization of ion channels in higher plants. His laboratory's research now focuses on identifying the basic molecular mechanisms by which plants respond to and mount resistance to climate change-linked environmental stresses, in particular drought and salinity.  

A highly cited paper: "Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins," published in Science, 2009.

Joseph Wang, Distinguished Professor of Nanoengineering, director of the Center for Wearable Sensors and co-director of the Center of Mobile Health at the UC San Diego Institute of Engineering in Medicine. Wang’s research focuses on developing micro- and nanorobots and wearable biosensors for medical, military, security and environmental applications.

A highly cited paper: “Electrochemical glucose biosensors,” published in Chemical Reviews, 2008.

Gene Yeo, professor of cellular and molecular medicine and faculty affiliate of bioengineering. Yeo focuses on understanding how gene expression is controlled at the RNA level to maintain proper functioning of cells during development and aging. In particular, his group studies how a class of proteins, called RNA binding proteins, influence RNA processing.

A highly cited paper: “Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP),” published in Nature Methods, 2016.

Kun Zhang, professor and chair of bioengineering. Zhang develops technologies for ultra-accurate genome sequencing and imaging of single human cells. These technologies enable Zhang and colleagues to build 3D, digital single-cell maps of the human brain and organs in the respiratory and urinary systems. His work aims to provide a deeper understanding of the functions and malfunctions of organs in the human body at the level of individual cells.

A highly cited paper: ”Somatic coding mutations in human induced pluripotent stem cells,” published in Nature, 2011.

Liangfang Zhang, professor of nanoengineering, affiliated professor of bioengineering and faculty member of the Institute of Engineering in Medicine. Zhang’s revolutionary work in the field of nanomedicine focuses on developing nanoparticles that perform therapeutic tasks in the body without being rejected by the immune system. He invented a technology to disguise synthetic nanoparticles in the skins of natural cells (i.e. red blood cells, white blood cells, cancer cells and others). These cell membrane-coated nanoparticles have shown promise in fighting drug-resistant bacterial infections; training the immune system to fight cancer; and treating rheumatoid arthritis and other diseases.

Most cited paper: “Nanoparticles in medicine: therapeutic applications and developments,” published in Clinical Pharmacology & Therapeutics, 2008.

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