• Big Data

    Big data is a term for data sets that are so large or complex that traditional data processing applications are inadequate. We use deep learning to analyze multi-modal Big Data such as genomics or clinical imaging from patients to reveal patterns, trends, and associations with disease. We strive to ultimately translate Big Data from the clinics into useful medical intelligence to impact clinical decisions.

    Precision Medicine

    Precision medicine is an innovative approach to disease prevention and treatment that takes into account individual differences in people’s genes, environments, and lifestyles. We are building precision medicine tools for doctors and their patients to better understand the complex mechanisms underlying disease and to better predict which clinical or surgical interventions will be optimally effective.

    Digital Health

    Digital health is the convergence of the digital and genomic revolutions with health, healthcare, living, and society. Digital health is empowering people to better track, manage, and improve their own and their family's health, live better, more productive lives, and improve society. We develop medical intelligence to power digital health applications in the clinics to improve the precision of medicine for doctors and their patients.

  • Media

    We hope you enjoy our productions.

    Bloomberg The Year Ahead

    November 8, 2017

    Emma Chandra interviews Mike Cordano and Dexter Hadley at Bloomberg The Year Ahead on how Western Digital and UCSF will team up for breast cancer research. Delivered at Bloomberg headquarters in New York City.

    From Bits to Bedside™

    February 22, 2017.

    Keynote at LabRoots Precision Medicine 2017 virtual event keynote presentation on translating big data into precision medicine and digital health at University of California, San Francisco.

    Precision Screening and Diagnosis of Melanoma

    November 7th, 2016

    Three minute pitch at Science Match Future Medicine to use deep learning and smartphones for precision screening and diagnosis of skin cancer delivered in Berlin, Germany.

  • We Translate Big Data into Clinical Intelligence!

    Practicing medicine involves first screening patients towards making definitive diagnoses and ultimately therapeutic interventions. We leverage big data and digital health to realize precision medicine for doctors and their patients. We are building the infrastructure to collect, connect, and apply vast amounts of scientific research data and information about our health. Our goal is to understand how individuals respond differently to interventions to help guide more precise and predictive medicine worldwide.

    PRECISION SCREENING

    We develop digital health applications to improve screening for disease. We use data from mobile health apps and medical imaging to monitor large numbers of patients in the clinics. Our goal is to save lives by improving digital surveillance that can alert physicians and their patients earlier about the risks of disease.

    PRECISION DIAGNOSIS

    We develop models of medical intelligence to improve diagnosis and management of disease. We leverage deep learning technologies to translate big data into diagnostic and prognostic intelligence. Our goal is to develop medical intelligence models that perform at the level of a specialist physician.

    PRECISION THERAPY

    We mine open data to understand defective patterns of genomics disease signatures. We integrate genomic signatures of drug response to select optimal agents that directly reverse disease genomics. Our goal is to develop more personalized therapeutic options to fight disease.

  • The Search Tag Analyze Resource (STARGEO)

    is an open genomics discovery web platform to annotate digital samples housed within NCBI Gene Expression Omnibus (GEO) and to find robust genomic signatures of disease. We enlist the help of medical students without coding experience to generate genomic signatures of disease which we integrate with other large databases to discover novel biomarkers to diagnose or more optimal therapeutic interventions to treat disease. STARGEO is an NCI funded project through the NIH BD2K NIH initiative to characterize the functional genomics of disease with open data.

  • Secure login

    Skin is a digital health imaging app for tracking of moles and skin lesions. The platform is targeted towards academic researchers, physicians and patients looking to integrate a robust sharing platform for the management and surveillance of dermatological conditions. This app gives medical institutions and physicians a secure option to create scalable studies with hundreds of patient participants. The tool is intended to help support the creation of an intelligent model for the accurate diagnosis of skin diseases.

    Patient profiles

    Skin is a digital health imaging app for tracking of moles and skin lesions. The platform is targeted towards academic researchers, physicians and patients looking to integrate a robust sharing platform for the management and surveillance of dermatological conditions. This app gives medical institutions and physicians a secure option to create scalable studies with hundreds of patient participants. The tool is intended to help support the creation of an intelligent model for the accurate diagnosis of skin diseases.

    Body map

    Skin is a digital health imaging app for tracking of moles and skin lesions. The platform is targeted towards academic researchers, physicians and patients looking to integrate a robust sharing platform for the management and surveillance of dermatological conditions. This app gives medical institutions and physicians a secure option to create scalable studies with hundreds of patient participants. The tool is intended to help support the creation of an intelligent model for the accurate diagnosis of skin diseases.

    Anatomic mapping

    Skin is a digital health imaging app for tracking of moles and skin lesions. The platform is targeted towards academic researchers, physicians and patients looking to integrate a robust sharing platform for the management and surveillance of dermatological conditions. This app gives medical institutions and physicians a secure option to create scalable studies with hundreds of patient participants. The tool is intended to help support the creation of an intelligent model for the accurate diagnosis of skin diseases.

    Image capture

    Skin is a digital health imaging app for tracking of moles and skin lesions. The platform is targeted towards academic researchers, physicians and patients looking to integrate a robust sharing platform for the management and surveillance of dermatological conditions. This app gives medical institutions and physicians a secure option to create scalable studies with hundreds of patient participants. The tool is intended to help support the creation of an intelligent model for the accurate diagnosis of skin diseases.

    Image library

    Skin is a digital health imaging app for tracking of moles and skin lesions. The platform is targeted towards academic researchers, physicians and patients looking to integrate a robust sharing platform for the management and surveillance of dermatological conditions. This app gives medical institutions and physicians a secure option to create scalable studies with hundreds of patient participants. The tool is intended to help support the creation of an intelligent model for the accurate diagnosis of skin diseases.

  • Executive Profiles

    We've got the best people running the show!

    Dexter Hadley,

    MD, PhD

    Principal Investigator

    Dr. Hadley focused on genomics and computational biology during his medical education at Penn. His early work focused identifying genomic risk factors for pediatric neuropsychiatric disease such as autism and ADHD. After completing medical school and a surgical internship, he led a translational bioinformatics team at the Center For Applied Genomics at CHoP where his research contributed to an ongoing precision medicine clinical trial for ADHD. He trained in pathology at Stanford where he mined the open data for biomarkers of severe dengue hemorrhagic fever infection. His research now focuses on digital health to generate, annotate and ultimately reason over big data stores to improve the precision of medicine across the disease spectrum.

    Ben Franc,

    MD, MS

    Clinical Collaborator

    Dr. Franc, is a Professor of Clinical Radiology in the Nuclear Medicine subspecialty at UCSF, and he served as Chairman of Nuclear Medicine from 2009-2014 and concomitantly served in multiple leadership positions in professional societies and health policy entities. Dr. Franc established a research program at UCSF focusing on the development of new molecular imaging techniques including novel small molecule exploration and development techniques. He has developed programs for the early adoption and implementation of nuclear-based imaging and therapeutic technologies including the continued development of technologies for molecular imaging, His research leverages UCSF's expansive EMRs and imaging repository to explore the implications of molecular imaging in healthcare.

    John Shepherd,

    PhD

    Radiology Collaborator

    Dr. Shepherd is a Professor in the Department of Radiology and the Director of the Breast and Bone Density Imaging Group at the University of California, San Francisco. He is an expert in quantitative breast imaging as well as musculoskeletal imaging using x-ray absorptiometry techniques. Dr. Shepherd’s research interests involve quantitative imaging methods for tissue composition using x-rays. His mammographic methods are used extensively for research around the world and in the San Francisco Mammography Registry Program. Dr. Shepherd’s efforts are focused on the technical imaging aspects of the measurements of the body composition and the translation of these measurements into different fields of study.

    Faiq Shaikh,

    MD

    Radiomics Consultant

    Dr. Shaikh is a Molecular imaging physician, Informatician and a Radiomics/ML consultant. He trained in Imaging Informatics and Applied QIA/Radiomics at UPMC and currently does translational research in Immuno-oncology and Precision medicine at UCSF, Mayo and Stanford. Dr. Shaikh’s contribution to our lab includes expertise in cloud-based data sharing, informatics analytics, medical-IT liaison and Imaging genomics.

  • Trainee Profiles

    We've got a top notch team behind the production!

    Hari Trivedi, MD

    Post-doctoral clinical fellow

    Dr. Trivedi is currently a clinical fellow at UCSF, trained in radiology. Dr. Trivedi's expertise is in applying artificial intelligence to radiology through deep learning techniques for image analysis, language processing, and decision support. His current projects include automated MRI protocoling, automated cancer detection in mammography, and classification of free text clinical reports.

    Maryam Panahiazar, PhD

    Postdoctoral Fellow

    Dr. Panahiazar’s is an expert in natural language processing (NLP). Her background is in text mining approaches to extract, predict, and share metadata. She has earned two PhDs, one in computer science and the other in bioinformatics, and she was a former postdoc at the Center for Expanded Data Annotation and Retrieval (CEDAR) at Stanford as well as the Mayo Clinic. She implemented the ContextAware recommendation engine for meta data submission in CEDAR for GEO, and is extending it to BioSpecimens. Her NLP work today focuses on deep learning clinical contexts from EMR data and medical reports.

    Dmytro Lituiev, PhD

    Postdoctoral Fellow

    Dr. Lituiev is an expert in deep learning. He is the only certified NVIDIA Deep Learning Ambassador at UCSF, and he also teaches advanced data science courses at UC Berkeley. He hosts the weekly SF Deep Learning Study Group at UCSF where a community of deep learning practitioners across SF Bay Area, from both academia and industry, meet to review state-of-the-art DL approaches and tackle novel projects. He has earned a PhD in computational biology, and his passion is to develop machine learning and visualization tools, for Life Sciences, and other applications. Dr, Lituiev strives to turn demands of experimentalists into automatized solutions by applying statistical, image and signal processing and statistical tools.

    Andrew Wong

    Pre-doctoral Medical student

    Andrew is a UCSF medical student with a background in computer science berkeley. He is an avid computer programmer and software engineer and his interested lie in deep learning delirium screening from routine medical care and building optimal models for medical image recognition from siloed data. Andre won the prestigious Short Term Deans Prize in 2017 for his work predicting a patients risk for delirium from electronic medical records.

    April Liang

    Pre-doctoral Medical student

    April is a UCSF medical student who majored in Computer Science at Princeton University. Her goal is to apply computational tools to improve health care quality, accessibility, and efficiency. Her research interests include automating the extraction of key information from narrative clinical documents, using computer vision to improve breast cancer screening, and applying machine learning to the prediction of preeclampsia risk.

    Abhishek Bhattacharya 

    UNDERGRADUATE student

    Abhishek is an undergraduate honors student at UCSB majoring in Computer Science and Biology. He is a member of the prestigious College of Creative Studies at his campus which recognizes a select group of students for their excellence in academics and research. In the last few years, he has worked with leading scientists at Stanford, UCSF and UCSB to uncover the potential of big data in computational biology. He is an avid computer programmer and software engineer, and his interests lie in deep learning precision interpretation of medical imaging for the clinics. He is involved with a number of ongoing projects in skin and breast cancer quantitative image analysis.

    Henry Zhu

    UNDERGRADUATE student

    Henry is an undergraduate student at UC Berkeley majoring in Electrical Engineering and Computer Science (EECS) and Mechanical Engineering. He joined the lab through a collaboration with the Berkeley Institute of Data Science and is currently working on image recognition and classification of breast screenings, specifically on extracting information from pathology reports to efficiently generate large datasets.

     

  • Alumni Profiles

    Our alumni go on to do great things!

    Jordan Spatz, PhD

    Post-doctoral medical Student

    Dr. Spatz is a medical student at UCSF with a focus on practicing medicine and biomedical scientific inquiry in space. Dr. Spatz trained at MIT in bioastronautics and worked for Northrop Grumman to design aeronautical transportation. Dr. Spatz is mining the open data with STARGEO to find novel approaches to treat refractory breast cancer.

    James Pan

    Pre-doctoral medical Student

    James is a neurosurgery bound medical student at Stanford University. He studied design at Carnigie Mellon University and performed research in neurosurgery. James' interests lie in brain cancer and he is actively using STARGEO to mine the open data to reposition drugs for medulloblastoma.

  • We need superstars to help us do awesome work!

    We are looking for passionate and motivated candidates who think Big Data can change everything about the delivery of medicine and healthcare. We work closely with clinicians to test hypotheses that we formulate in the laboratory. To apply for any of these positions, please send your CV, a brief statement of research interests, and contact information for three references in one PDF document to dexter.hadley@ucsf.edu.

    Postdoctoral Fellows

    Our laboratory is particularly geared to recruiting combined MD, PhD candidates who seek to make a translational impact in the clinic. We are ideally looking for candidates who have already earned a MD and/or PhD degree with a strong background in bioinformatics, computational biology, biostatistics, and genomics. A great publication record is not required, but a strong desire to publish is. Strong problem-solving skills, creative thinking, and the ability to build new software tools as needed are required. Applicants must possess good communication skills and be fluent in both spoken and written English. A background in molecular biology or medicine or pharmacology will be a strong plus. Prior experience with genetic, genomic, clinical imaging, biomarker discovery, drug repositioning is recommended but not mandatory. Familiarity with machine learning, text-mining, knowledge representation, and high performance parallel computing platforms and building web and mobile applications is a definite plus.

    Medical Students

    We love med students and offer ample opportunities for them to get involved with our translational research. No coding required! We have medical students using STARGEO to estimate robust signatures of disease genomics from which we propose novel biomarkers or drug repositioning strategies for disease. We have medical students in the clinics that collect patient data with apps that feed our self-learning models of clinical intelligence. As a medical student, we will help to devise a computational project that aligns with you clinical interests. Your expected effort will be variable and contingent on your clinical commitments. We will provide you with many opportunities to publish your clinical and / or basic science research in peer-reviewed journals, and we encourage medical students to present their work at medical/scientefic conferences around the world. Finally. we offer you ample opportunities for mentoring and professional networking that may illustrate alternative careers in medicine for you to pursue that drive innovation in health care and embrace translational research.

    Predoctoral Students

    We are looking for graduate rotation students to commit 50% of their time working on our research projects. Rotating students will be provided space in our shared office-space in Mission Hall. You will meet with the PI on a bi-weekly basis. You will interact with our Post-doctoral Fellows and graduate students. You are expected to attend our weekly laboratory meetings where your will present your rotation work. You are strongly encouraged to submit a paper on your work, even though it is just a rotation projectWe will expose you to a variety of computational frameworks and techniques that include:

    • Python for open-source machine learning
    • R for open-source statistical software
    • Postgres for open-source relational database management..
  • Contact Us

    Don't be afraid to reach out. You + us = awesome.

    550 16th St
    San Francisco CA 94158
    415-514-0513