Center Archives - Sanford Burnham Prebys

Page Type: Center

Center for Data Sciences

Center for Data Sciences group photo

From Data to Discovery

Unlocking the Power of Biomedical Information

The future of biomedical research depends on our ability to make sense of vast, complex datasets. At Sanford Burnham Prebys, the Center for Data Sciences brings together experts in AI, statistics, genetics and more to uncover patterns, generate insights and spark innovation. Their work turns raw information into knowledge that drives scientific breakthroughs and new possibilities for human health.

Mission Statement

To drive groundbreaking discoveries in biomedical research by harnessing the power of data science and artificial intelligence, transforming how we diagnose, treat, and prevent disease.

We achieve this mission by data-centric research, inter-disciplinary collaborations, development and sharing of reusable resources, and contemporary training.

Interim Center Director

Expertise and Research Interests

Common Themes

PICancerMuscleAgingDrug Discovery
Lukas Chavez✔️
Ani Deshpande✔️✔️
Susanne Heynen-Genel✔️✔️
Andrei Osterman✔️✔️
Giovanni Paternostro✔️
Lorenzo Puri✔️✔️✔️
Sanjeev Ranade✔️
Sanju Sinha✔️✔️✔️
Alessandro Vasciaveo✔️✔️
Will Wang✔️✔️✔️
Kevin Yip✔️✔️

Technical Highlights

PITechnical Highlight
Lukas ChavezGenomics
Ani DeshpandeFunctional Genomics
Susanne Heynen-GenelHigh-content imaging
Andrei OstermanResistomics
Giovanni PaternostroMetabolomics
Lorenzo PuriChromatin architecture
Sanjeev RanadeSingle-cell RNA-seq
Sanju SinhaAI: imaging
Alessandro VasciaveoAI: drugs
Will WangSpatial multiomics
Kevin YipAI: omics

Four Pillars Of Research

Reusable Resources

PERCEPTION AI cancer

PERCEPTION

We build a precision oncology computational approach capitalizes on recently published matched bulk and single-cell (SC) transcriptome profiles of large-scale cell-line drug screens to build treatment response models from patients’ SC tumor transcriptomics. The general objective of this project is to utilize single-cell omics from patients tumor to predict response and resistance. The following figure describe the architecture of PERCEPTION pipeline.

PERCEPTION
DNA with biological concept, 3d rendering

ecDNA

This portal provides a comprehensive catalog of circular extrachromosomal DNA (ecDNA) associated with childhood cancers, facilitating research and clinical insights. Explore detailed ecDNA profiles, patient information, and access valuable resources to advance scientific understanding and improve patient outcomes.

ecDNA

PERsonalized single-Cell Expression-based Planning for Treatments In ONcology

We build a precision oncology computational approach capitalizes on recently published matched bulk and single-cell (SC) transcriptome profiles of large-scale cell-line drug screens to build treatment response models from patients’ SC tumor transcriptomics. The general objective of this project is to utilize single-cell omics from patients tumor to predict response and resistance. The following figure describe the architecture of PERCEPTION pipeline.

PERCEPTION

Childhood Cancer Catalog of Circular Extrachromosomal DNA

This portal provides a comprehensive catalog of circular extrachromosomal DNA (ecDNA) associated with childhood cancers, facilitating research and clinical insights. Explore detailed ecDNA profiles, patient information, and access valuable resources to advance scientific understanding and improve patient outcomes.

ecDNA

Recent News

Center for Data Sciences

View All News

Programming in a Petri Dish

An AI Series

Programming in a Petri Dish - AI series graphic
Institute News

Acceleration by automation

Increases in the scale and pace of research and drug discovery are being made possible by robotic automation.

Sep 5, 2024
Programming in a Petri Dish - AI series graphic
Institute News

Scripting their own futures

At Sanford Burnham Prebys Graduate School of Biomedical Sciences, students embrace computational methods to enhance their research careers

Aug 8, 2024
Programming in a Petri Dish - AI series graphic
Institute News

Coding clinic

Rapidly evolving computational tools may unlock vast archives of untapped clinical information—and help solve complex challenges confronting healthcare providers

Aug 6, 2024

Papers of the Week

Recent Publications

Showing 3 of 3

Effective targeting of PDGFRA-altered high-grade glioma with avapritinib.

Mayr L, Neyazi S, Schwark K, Trissal M, Beck A, Labelle J, Eder SK, Weiler-Wichtl L, Marques JG, de Biagi-Junior CAO, Lo Cascio C, Chapman O, Sridhar S, Kenkre R, Dutta A, Wang S, Wang J, Hack O, Nascimento A, Nguyen CM, Castellani S, Rozowsky JS, Groves A, Panditharatna E, Cruzeiro GAV, Haase RD, Tabatabai K, Madlener S, Wadden J, Adam T, Kong S, Miclea M, Patel T, Bruckner K, Senfter D, Lämmerer A, Supko J, Guntner AS, Palova H, Neradil J, Stepien N, Lötsch-Gojo D, Berger W, Leiss U, Rosenmayr V, Dorfer C, Dieckmann K, Peyrl A, Azizi AA, Baumgartner A, Slaby O, Pokorna P, Clark LM, Cameron A, Nguyen QD, Wakimoto H, Dubois F, Greenwald NF, Bandopadhayay P, Beroukhim R, Ligon K, Kramm C, Bronsema A, Bailey S, Stucklin AG, Mueller S, Skrypek M, Martinez N, Bowers DC, Jones DTW, Jones C, Jäger N, Sterba J, Müllauer L, Haberler C, Kumar-Sinha C, Chinnaiyan A, Mody R, Chavez L, Furtner J, Koschmann C, Gojo J, Filbin MG

Cancer Cell 2025 Apr 14 ;43(4):740-756.e8

Synergistic RAS-MAPK and AKT Activation in MYC-Driven Tumors via Adjacent PVT1 Rearrangements.

Tiwari A, Paithane U, Friedlein J, Tashiro K, Saulnier O, Barbosa K, Trinh Q, Hall B, Saha S, Soni A, Nakashima T, Bobkov A, Fujimoto LM, Murad R, Maurya S, Saraswat M, Sarmashghi S, Lange JT, Wu S, Masihi MB, Ghosh S, Hemmati G, Chapman O, Hendrikse L, James B, Luebeck J, Eisemann T, Tzaridis T, Rohila D, Leary R, Varshney J, Konety B, Dehm SM, Kawakami Y, Beroukhim R, Largaespada DA, Stein L, Chavez L, Suzuki H, Weiss WA, Zhao J, Deshpande A, Wechsler-Reya RJ, Taylor MD, Bagchi A

bioRxiv 2025 Feb 22 ;():
View All Publications

Center for Therapeutics Discovery

Science Becomes Progress

Fundamental to the mission of Sanford Burnham Prebys is the translation of academic research into actionable drug discovery for the development of new therapeutics to remedy our most debilitating diseases.

The Center for Therapeutics Discovery (CTD) is where it happens, where the rubber meets the road and concepts become realities.

We use physical and computational screening to identify prototype drugs, then develop these into first-in-class therapeutics through medicinal chemistry-led optimization.

We deploy the latest technologies, including robotically enabled high-throughput screening, assay development, in vitro and in vivo pharmacology, medicinal and computational chemistry and cheminformatics — all enabled and enhanced by artificial intelligence and machine learning.

Concepts for these novel therapeutics originate with Sanford Burnham Prebys faculty and collaborators. Scientists at CTD translate these ideas and insights into actual drugs, primarily small molecule chemicals that comprise 90% of pharmaceutical drugs, typically administered as pills to patients

Director’s Statement

“Translational research defines Sanford Burnham Prebys, it’s central to our mission.The purpose of this center is to take new knowledge and shape it into novel therapeutics that  can positively impact the health and quality of life of patients with unmet medical needs.”

Portrait of Michael Jackson, PhD
Michael Jackson, PhD
 Center Director

Conrad Prebys Center for Chemical Genomics

From target validation to preclinical development, our ultramodern technologies accelerate pharmaceutical discovery, helping researchers rapidly identify and develop new molecules and compounds for next-generation drugs.

Learn More

Exterior shot of the Conrad Prebys Center for Chemical Genomics

Recent News

Center for Therapeutics Discovery

View All News

Center for Metabolic and Liver Diseases

liver cell

A Menace in the Multitudes

The rising prevalence of metabolic disorders in the United States and around the world is alarming, especially those conditions that affect the liver—central to metabolic health. 

One in three American adults has metabolic syndrome, a group of conditions that includes coronary heart disease, diabetes and stroke. Liver disease is equally prevalent. It’s estimated that 20-30% of adults in the U.S. have metabolic-dysfunction associated steatotic liver disease (MASLD) and 5-10% have the more severe form called metabolic-dysfunction associated steatohepatitis or MASH, which can lead to scarring (cirrhosis), liver cancer and organ failure. 

Worldwide, the estimated prevalence of MASLD is 38%.

Our goal is to identify and interpret the underlying causes and drivers of metabolic and liver diseases, a continuum of research that includes basic intracellular signaling, metabolic translational research, human physiological studies and clinical trials. 

Literally millions of people endure or face lives of chronic poor health, diminished well being and eventual death from metabolic diseases. Current therapeutic options are limited, ineffective or don’t exist at all. We want to change that. 

Recent News

Center for Metabolic and Liver Diseases

View All News

Center for Neurologic Diseases

Scientist looking into a microscrope

A Challenge for All Ages

The U.S. population is older than ever, with unprecedented and accelerating growth beyond age 65. 

With age comes the greater likelihood of age-related diseases. Six in 10 American adults have a chronic disease; 4 in 10 have two or more. The prevalence of chronic diseases mirrors the aging of America, with cases multiplying in everything from cardiovascular disease to type 2 diabetes to neurodegenerative conditions like Alzheimer’s disease that is expected to triple worldwide by 2050 to exceed 150 million individuals.

Director’s Statement

“Our mission is to gain a fundamental and therapeutically actionable understanding of aging-related diseases through molecular and systems-based approaches that can lead to novel treatments and improved quality of life.”

Portrait of Su-Chun Zhang
Su-Chun Zhang, MD, PhD Center Director

Programs

  • mouse brain with alz plaque ncats

    Degenerative Diseases Program

    Proteins are necessary to the construction, function and regulation of the body’s tissues and organs. But when a protein doesn’t have the correct shape and is ‘misfolded’, it can cause great harm. In fact, every degenerative disease is associated with misfolded proteins. We are unraveling their secrets.

    Learn More
  • Scientists collaborate at a microscope

    Development, Aging and Regeneration Program

    Aging is inevitable, but how it happens can be optimized. By parsing how biological processes change over time and under different conditions, we reveal how aging affects disease and how development and regeneration can be modified and improved to promote healthy aging.

    Learn More
  • A child and mother and toured through a lab with Duc Dong, PhD

    Human Genetics Program

    Our genes play critical, but often unseen or poorly understood roles, in our risk for certain diseases and in our general well being. We dig for the genetic roots of human health disorders, translating that unearthed knowledge into tangible treatments.

    Learn More
1 of 3

Recent News

Center for Neurologic Diseases

View All News

Center for Cardiovascular and Muscular Diseases

red blood cell clot

Heart of the Matter

Coronary heart disease (CAD) remains the leading cause of death in the United States. One in 20 adults age 20 and older in the United States have CAD; someone dies from cardiovascular disease every 33 seconds.

We want to get to the heart of the matter: What are the underlying mechanisms of organ formation, how are patterns generated and how do cells and tissue types assume their correct fates and functions. More specifically, how do proteins called transcription factors control the development and function of cardiac cells and how mutations in those factors can cause congenital heart defects, which impact 1 in 100 newborns.

The heart is one type of muscle. Skeletal muscle is another, These are the muscles of voluntary movement. They make up 30% to 40% of your total body mass, and when they begin to decay and decline, devastating conditions result, such as muscular dystrophies. Muscle wasting can also be a hallmark of aging. Muscle stem cells offer great promise as a therapeutic remedy. We are exploring the extrinsic and intrinsic factors that regulate muscle stem cells in vivo.

Director’s Statement

“The muscles of your heart and body make life possible. Our mission is to better understand how they are formed, grow, function and fail, and in those answers, find new treatments for millions of people.”

Portrait of Rolf Bodmer
Rolf Bodmer, PhD Center Director

Program

Scientists collaborate at a microscope

Development, Aging and Regeneration Program

Aging is inevitable, but how it happens can be optimized. By parsing how biological processes change over time and under different conditions, we reveal how aging affects disease and how development and regeneration can be modified and improved to promote healthy aging.

Learn More

Recent News

Center for Cardiovascular and Muscular Diseases

View All News

Conrad Prebys Center for Chemical Genomics

Exterior shot of the Conrad Prebys Center for Chemical Genomics

Conducting Drug Discovery Research

With our extensive pharmaceutical drug discovery experience, we drive projects toward the goal of drugs and therapies that benefit patients. We have projects in all stages of drug discovery, from target validation through investigational new drug application that enables preclinical development. 

We are the partner of choice for academic investigators pursuing translational studies, both within the Institute and at collaborating institutions, and serve as a bridge to biotechnology and pharmaceutical partners developing novel therapeutics.

The Prebys Center is fully equipped and staffed to conduct world-class drug discovery research. We are experts in assay development, high-throughput screening, pharmacology and medicinal chemistry, working as integrated teams to advance translational projects using industry best practices. We are nationally recognized as one of four comprehensive probe/drug discovery centers in the National Institutes of Health’s Molecular Libraries Probe Production Centers Network and one of seven comprehensive centers in the National Cancer Institute’s Chemical Biology Consortium.

Our mission is to effectively employ public and private grants, as well as philanthropy and other private gifts, to translate basic research conducted by faculty at Sanford Burnham Prebys and other academic and nonprofit research institutions into new medicines for unmet medical needs. We want to partner with biotechnology and pharmaceutical companies to help bring these new medicines through clinical development and into the market and clinical practice.

Our vision is to be the world’s leading academic drug discovery and development organization, an epicenter for innovative approaches to accelerate the discovery of new drugs that help save lives and treat disease.

Click to Play Video

Director’s Statement

“Our vision is to be the world’s leading academic drug discovery and development organization, an epicenter for innovative approaches to accelerate the discovery of new drugs that help save lives and treat disease.”

Michael Jackson, PhD, is the director of the Sanford Burnham Prebys Center for Therapeutics Discovery. He also is the senior vice president of drug discovery and development for the institute’s Conrad Prebys Center for Chemical Genomics.
Michael Jackson, PhD Senior Vice President of Drug Discovery and Development

Our History and Evolution

Established in 2009, the Prebys Center has evolved from a chemical biology and probe production center focused on projects originating in the NIH Molecular Libraries program (MLP) to a full-function drug discovery enterprise that develops “new chemical entities” ready for clinical development. 

The center’s early drug discovery capabilities were substantial, and included a state-of-the-art robotic platform assembled in 2008 and capable of performing ultra-high-throughput screening (uHTS) of very large chemical collections to identify chemical leads as starting points for new drugs. The uHTS enabled the center to operate as a Molecule Libraries Probe Production Center (MLPCN) for the National Institutes of Health. As a comprehensive center in this network, the center worked with investigators from more than 50 institutes throughout the United States,  successfully completing 132 high-throughput screens and generating 67 published chemical probes.

Since 2013, when the MLPCN program ended, the center has diversified its project portfolio by establishing collaborative alliances with pharmaceutical companies, health care organizations, disease foundations and through collaborations involving traditional grants and contracts from state and federal organizations. These translational collaborations and partnerships represent a fundamental shift for the center away from a core service operations model to partnership-collaboration model in which the center acts as a drug discovery engine, playing a central coordination and project management role in initiatives to discover novel therapeutics.

Over the past five years, the center has produced an outstanding track record of collaborations with Sanford Burnham Prebys investigators and beyond, attracting numerous, highly competitive translational science grants, including awards from the NIH totaling more than $90 million. 

These awards directly fund drug discovery activities, such as assay development, HTS screens, medicinal chemistry and molecular pharmacology, in the center and in the laboratories of collaborators. They provide Sanford Burnham Prebys scientists and collaborators with a unique opportunity to explore high-risk, game-changing innovations that, when successful, can lead to a leadership position in developing “first-in-class” therapeutics.

Core Values

Scientific excellence. We conduct the rigorous discovery research required to address difficult questions and provide objective, informative, actionable answers.

Technological development. We continuously develop and adopt the latest technologies needed to improve speed and probability of success for our drug discovery and translation efforts.

Focus on translation into medicines. Patients urgently need more effective or new drugs and treatments. We focus on diseases and therapeutic areas where the medical need is particularly and substantially unmet, seeking to create first-in-class, transformational medicines.

Stewardship and accountability. We are responsible stewards of the gifted, granted and partnered resources provided to us, and of the medical and scientific potential inherent in existing and new knowledge uncovered by researchers throughout the world.

Knowledge creation and sharing. We create new knowledge through our research, and through publications and sharing enable others to build upon and further progress, translating our combined work into new medicines that alleviate patient suffering and save and extend healthy lives.

Partnership. We constantly seek to combine our resources and talents with others to assemble the multidisciplinary teams necessary for successful drug discovery and development, helping to ensure our work ultimately benefits patients.

Conrad Prebys

Conrad Prebys (1933-2016)

Born in South Bend, Indiana, Conrad Prebys moved to San Diego in 1965 and quickly became a major public figure, first through his expansive construction and property management businesses and later through his philanthropy, which spanned diverse interests. 

In June 2009, Prebys made a generous $10 million pledge to help create the Conrad Prebys Center for Chemical Genomics at Sanford Burnham Prebys. The gift provided seed funding to catalyze the center’s transformation from a core service provider to a state-of-the-art drug discovery center whose driving mission is to translate scientific breakthroughs into the medicines of tomorrow.

In 2015, Prebys donated $100 million—his all-time largest gift—to the Institute to support its 10-year strategic vision to develop and implement innovative medical treatments that can have lasting, positive effects on the field of health care.

The Prebys Center and Institute honor the vision and responsibility that Prebys entrusted with his support, striving every day to make a difference in biomedical research and improved human health. 

Leadership and Team

Recent News

Conrad Prebys Center for Chemical Genomics

View All News

NCI-Designated Cancer Center

Marzia Scortegagna in lab coat walking past Cancer Center sign holding tray

Conquering Cancer

Our investigators collaborate to answer fundamental questions in cancer biology and to address unmet clinical needs by conducting translational studies. They partner with our dedicated core facilities, which provide state-of-the art technologies and expertise necessary to effectively to pursue modern cancer research.

These efforts involve many specialists, from immunologists to cell biologists and experts in epigenetics, metabolism, the microbiome and aging. As one of seven official basic research cancer centers designated by the National Cancer Institute—the highest federal rating a basic research cancer center can achieve—we help advance the field by leveraging the capabilities of the Conrad Prebys Center for Chemical Genomics, which offers unparalleled technical expertise in drug discovery.

We are committed to performing impactful translational multi-disciplinary research relevant to the diagnosis and treatment of cancer.

Director’s Statement

“We are committed to performing impactful translational multi-disciplinary research relevant to the diagnosis and treatment of cancer.”

Portrait of Cosimo Commisso
Cosimo Commisso, PhD Interim Center Director, Deputy Director

Programs

breast cancer cells

Cancer Metabolism and Microenvironment Program

Cancer is the consequence of highly organized cells and molecules, fueled by disinformation, that create abnormal tissues and deadly tumors. We seek to understand how cancer cells survive and thrive within their microenvironment, and how to intervene to combat them.

Learn More

Technology in Support of Cancer Research

Shared Resources

The nine shared resources of the cancer center feature specialized services that sustain and promote research by both faculty members and other nonprofit and for-profit investigators in cancer research.

Learn More

Recent News

NCI-Designated Cancer Center

View All News