Biomedical Informatics  

Biomedical Informatics Program Students

Having problems updating your address book every year as new students enroll, senior students graduate and alumni move around the country? Join the "Biomedical Informatics Stanford School of Medicine" on Linkedin. This is a moderated group dedicated to anyone with an affiliation with this training program.

PhD & MS

 
 

Class of 2014/15
1st year

Jorge Caballero
Entered MS program: 2014
Research interest: To empower physicians to deliver personalized care before, during, and after surgery by developing tools based on existing clinical data.
Undergraduate affiliation: Stanford University
Research Advisor: Atul Butte

 
Emily Flynn
Entered PhD program: 2014
Research interest: Designing and developing computational methods and tools that improve biological understanding and have potential to impact medicine
Undergraduate affiliation: Smith College
Research Advisor:

Lichy Han
Entered PhD program: 2014
Research interest: Pharmacogenomics, personalized medicine, computational genomics
Undergraduate affiliation: Johns Hopkins University
Research Advisor: Russ Altman

Maulik Kamdar
Entered PhD program: 2014
Research interest: Intuitive and interactive Knowledge Discovery and Exploration, Semantic Web Technologies, Data Integration and Visualization
Undergraduate Affiliation : Indian Institute of Technology (IIT) Kharagpur, India
Research Advisor:
Albee Ling
Entered PhD program: 2014
Research interest: Utilizing statistical methods and computational tools for genomics data analysis
Undergraduate affiliation: Johns Hopkins University
Research Advisor:
Vinnie Liu
Entered MS program: 2014
Research interest: Informatics platforms to leverage real-time electronic medical records in hospitalized populations
Undergraduate affiliation: Univ of Pennsylvania (BA), New York University (MD), Stanford University (MS), Kaiser Permanente
Research Advisor: Mark Musen
 
Michelle Longmire
Entered MS program: 2014
Research interest:
Undergraduate affiliation:
Research Advisor:
 
Marcos Prunello
Entered MS program: 2014
Research interest: Application of statistical methods in the field of Bioinformatics
Undergraduate affiliation: National Universtiy of Rosario, Argentina (Universidad Nacional de Rosario, Argentina)
Research Advisor:
 
Alejandro Schuler
Entered PhD program: 2014
Research interest: Applications of unsupervised learning to functional genomics, drug repositioning, predictive modeling of complex biological systems
Undergraduate affiliation: BS Mechanical Engineering / UC Berkeley
MS Control Systems / UCLA
Research Advisor:
David Stark, MD
Entered MS program: 2014
Research interest: Developing methods and tools for integrating heterogeneous data to improve diagnostics, therapeutics, and wellness; biomarker discovery; wearable devices and mobile health; applications within neuroscience, clinical neurology, and behavioral health.
Undergraduate affiliation: BS Yale College; MD Harvard Medical School; Pediatrics and Pediatric Neurology Residency/Fellowship; New York Presbyterian Hospital
Research Advisor:
 

Jessica Torres
Entered PhD program: 2014
Research interest: Personalized Medicine, Algorithm Development, Clinical Informatics, and Data Mining.
Undergraduate affiliation: BS Cell and Molecular Biology: San Diego State University, MS in Bioinformatics: San Diego State University  
Research Advisor:

Michelle Wu
Entered PhD program: 2014
Research interest: Structural biology, systems biology, machine learning
Undergraduate affiliation: Princeton University
Research Advisor:
 
Darvin Yi
Entered PhD program: 2014, MOM Program 2014, Deferred BMI to 2015
Research interest: Computer Vision, Image Data Mining, Machine Learning, and Medical Imaging.  
Undergraduate affiliation: Princeton University
Research Advisor:


2nd year

Vibhu Agarwal
Entered MS program: 2013
Research interest: Data driven medicine, application of machine learning techniques to diagnostics, personal genomics
Undergraduate affiliation: Indian Institute of Technology, Kanpur
Research Advisor: Rotating
Diego Calderon
Entered PhD program: 2013
Research interest: Utilizing computational methods to improve our personal genomics capabilities and to study other biologically interesting datasets.
Undergraduate affiliation: Wesleyan University
Research Advisor: Rotating
Peyton Greenside
Entered PhD program: 2013
Research interest: Computational Biology, Functional Genomics, Cancer Genomics
Undergraduate affiliation: Harvard University
Research Advisor: Rotating
Winston Haynes
Entered PhD program: Summer 2013
Research interest: Bringing advanced computational analysis to problems of biological interest, with the ultimate goal of alleviating disease.
Undergraduate affiliation: Hendrix College
Research Advisor: Rotating
Daniel Kim
Entered PhD program: Autumn 2013 MSTP
Research interest: Integrative omics, particularly for cancer and differentiation, and network biology.
Undergraduate affiliation: MIT
Research Advisor: Dr. Paul Khavari and Dr. Anshul Kundaje
David Odgers
Entered MS program: 2013
Research interest: Data mining and knowledge discovery with actionable clinical applications
Undergraduate affiliation: Johns Hopkins (MS)
Research Advisor: Michel Dumontier
Tanya Podchiyska
Entered MS program: Summer 2013
Research interest: data mining, knowledge representation, cohort building.
Undergraduate affiliation: Stanford University
Research Advisor: Rotating
Sarah Poole
Entered PhD program: 2013
Research interest: Clinical Informatics, including personalisation of medicine and analysis of hospital record data.
Undergraduate affiliation: Mechatronics Engineering at Canterbury University, New Zealand
Research Advisor: Nigam Shah, Primary; Chris Longhurst, Co-Advisor.
Tim Sweeney, MD, PhD
Entered MS program: Summer 2013
Research interest: Learning to use omics to understand, diagnose, and eventually treat critical illness.
Past affiliation: Undergrad: University of Chicago. MD/PhD: Duke University. Surgery resident (current): Stanford.
Research Advisor: Rotating
Natalie Telis
Entered PhD program: 2013
Research interest: Computational evolutionary biology, comparative genomics, cancer biology
Undergraduate affiliation: University of California, Davis
Research Advisor: Rotating


3nd year

Emily Doughty
Entered PhD program: 2012
Research interests: Personalized medicine, particularly in pharmacogenomics; natural language processing; semantic web technology
Undergraduate affiliation: University of Maryland Baltimore County
Research Advisor: Russ Altman

 

Rachel Goldfeder
Entered PhD program: 2012
Research interests: Next-Generation Sequencing, Personal Genomic Medicine
Undergraduate affiliation: Washington University in St. Louis (Biomedical Engineering)
Research Advisor: Euan Ashley

Jerome Ku
Entered MS program: Winter 2012-13
Research interest:
Undergraduate affiliation: Stanford
Research Advisor: Rotating

Kimberly McManus
Entered MS program: Spring 2013
Research interest: Population genetics, Applying machine learning techniques to genetic data
Undergraduate affiliation: Massachusetts Institute of Technology
Research Advisor: Carlos Bustamante

David Moskowitz
Entered PhD program: 2012
Research Interests: Next-generation sequencing, functional domain prediction, systems biology, cancer genomics
Undergraduate affiliation: Brown University
Research Advisor: William Greenleaf

Erika Strandberg
Entered PhD program: 2012
Research interests: machine learning and statistical methods for large data sets and personalized medicine.
Undergraduate affiliation: Harvey Mudd College (BS) - Mathematical Biology
Graduate affiliation: University of California, San Diego (MS) - Statistics
Research Advisor: Mohsen Bayati

Emily Tsang
Entered PhD program: 2012
Research interests: proteomics, developmental biology, cellular networks, machine learning.
Undergraduate affiliation: McGill University
Research Advisor: Stephen Montgomery

Wei Wang, MBBS and PhD
Entered MS program: 2012
Research interests: next generation sequencing, functional genomics
Undergraduate affiliation: Beijing Medical University (Bachelor of Medicine)
Graduate affiliation: University of Southern California (PhD)
Research Advisor: Mike Snyder and Atul Butte

Kun-Hsing Yu, MD
Entered PhD program: 2012
Research interests: Biomarker discovery, decision support, machine learning, molecular modeling, natural language processing, and translational bioinformatics.
Undergraduate affiliation: MD, National Taiwan University
Research Advisor: Mike Snyder and Russ Altman


4th year

Tomer Altman
Entered HCP Masters program 2009;
Entered PhD program: Winter 2012
Research interests: Computational biology, bioinformatics, knowledge representation, flux-balance analysis, metabolomics, machine learning, healthcare informatics.
Undergraduate affiliation: UC Berkeley - Bioengineering
Research Advisor: David Dill

Mike Januszyk, MD
Entered MS program: Summer 2011; PhD Program 2013
Research interest: Characterizing the heterogeneity inherent in adult stem cell populations in order to improve their clinical efficacy
Undergraduate affiliation:University of Chicago, MD
Research Advisor: Atul Butte

Jonathan Mortensen
Entered PhD program: 2011
Research interest: Leveraging ontologies and other sources of biomedical knowledge to assist in solving clinical problems
Undergraduate affiliation: Case Western Reserve (BE)
Research Advisor: Mark Musen
Diego Munoz
Entered PhD program: 2011
Research interest: Development of stochastic simulation models of the natural history of cancer that use clinical data to estimate and predict cancer progression, as well as the effectiveness and cost-effectiveness of treatment and screening technologies. 
Undergraduate affiliation: MS (Stanford)
Research Advisor: Sylvia Plevritis

Katie Planey
Entered PhD program: 2011
Research interest: Integrative breast cancer diagnostic models that combine disparate data sets such as gene microarrays, tissue samples and medical images to optimize treatment plans for patients. (Long term: mixing my MBA and PhD in entrepreneurship.)
Affiliation: MBA (Stanford)
Research Advisor: Atul Butte

Rebecca Sawyer
Entered PhD program: 2011
Research interest: Medical image analysis, computer-aided diagnosis
Undergraduate Affiliation: UNC Charlotte - Electrical Engineering Graduate.
Affiliaton: Stanford - MSEE
Research Advisor: Daniel Rubin

Vanessa Sochat
Entered PhD program: Summer 2011
Research Interest: Application of computational methods to multimodal neuroimaging data to better understand, quantify, and visualize the human brain.  
Research Advisor: Daniel Rubin, Dennis Wall

Linda Szabo
Entered PhD program: Fall 2011
Research Interest: Developing new methods for the identification of cancer driver genes which will facilitate improved patient treatment and survival.
Research Advisor: Atul Butte

Luke Yancy, Jr.
Entered PhD program: Fall 2011
Research interest: Functional genomics and the study of diseases adversely affecting minority populations.
Research Advisor: Atul Butte

 

5th year

Francisco Gimenez
Entered PhD program: Fall 2010
Research Interest: Medical image analysis with a focus on improving radiological reporting.
Undergraduate affiliation: UC Berkeley
Research Advisor: Daniel Rubin

Sara Hillenmeyer
Entered PhD program: 2010
Research interest: Systems Pharmacology & Pharmacogenomics
Undergraduate affiliation: Brown University
Research Advisor: Russ Altman

Haruka Itakura, MD
Entered PhD program: 2010
Research interest: My primary research interest revolves around developing models for prediction as it relates to diagnosis, treatment response, monitoring, and survival in oncologic and cardiovascular diseases.
Research Advisor: Olivier Gevaert and Mark Musen

Ken Jung
Entered PhD program: 2010
Research interests: Structured probabilistic models such as Bayes Nets.  
Undergraduate affiliation: MS (Stanford)
Research Advisor: Nigam Shah

Yi Liu
Entered PhD program: 2010
Research interest: Empirical bayes, B cell hylogenetics
Undergraduate affiliation: University of Waterloo
Research Advisor: Daphne Koller and Scott D. Boyd

Brian Maples
Entered PhD program: 2010
Research interest: Statistical Genetics
Research Advisor: Carlos Bustamante

Bethany Percha
Entered PhD program: 2010; LOA Autumn 2014
Current: VP of Research and Development at Kyron, Inc
Research interest: Biomedical natural language processing and text mining.
Research Advisor: Russ Altman

David Poznik
Entered PhD program: September 2010
Research Interest: Human population genetics and computational genomics
Undergraduate affiliation: Sc.B. Biophysics, Brown University
Research Advisor: Carlos Bustamante

6th year & above

Rob Bruggner
Entered PhD program: 2008
Research and Interests:  Flow Cytometry Informatics, Automated Cell Population Discovery, Semantic Web Technologies, Machine Learning
Undergraduate / Masters affiliation: University of Notre Dame
Research Advisor: Garry Nolan

Tiffany Ting Liu
Entered PhD program: 2009
Research interest: integrated data analysis for clinical disease applications
Undergraduate affiliation: University of Waterloo, Canada
Research Advisors: Daniel Rubin

Daniel Newburger
Entered PhD program: 2008
Interests: Applications of machine learning to human genomic data. Sequencing algorithms and technologies.
Undergraduate affiliation: Yale University
Research Advisor: Serafim Batzoglou

Pablo Sanchez Cordero
Entered PhD program: 2009
Research interest: Studying combining biology and computers.
Research Advisors: Rhiju Das and Euan Ashley

Co-Terms

Lauren Edelson
Entered Coterminal Masters program: Winter 2014
Research interest: Neuroscience, personalized medicine, genetics.
Undergraduate affiliation: Stanford

Eric Kofman
Entered Coterminal Masters program: Winter 2014
Research interest:
Undergraduate affiliation: Stanford

Chelsea Lewis
Entered Coterminal Masters program: Spring 2014
Research interest: The interplay between computer science and genomics: personalized medicine, data-driven medicine, etc.
Undergraduate affiliation: Stanford

Elliott Lui
Entered Coterminal Masters program: Spring 2013
Research interest: Processing large clinical data sets, genomics, personalized medicine. 
Undergraduate affiliation: Stanford

Isaac Madan
Entered Coterminal Masters program: Winter 2014
Research interest: Translational bioinformatics, data-driven medicine, and pharmacogenomics.
Undergraduate affiliation: Stanford

Danielle Rasooly
Entered Coterminal Masters program: Spring 2012
Research interest: Applying mathematics to clinical problems, in order to further understand disease progression and discover the most effective treatment methods.
Undergraduate affiliation: Stanford

Aaditya Shidham
Entered Coterminal Masters program: Winter 2014
Research interest: Deriving new clinical insights from public data.
Undergraduate affiliation: Stanford

Sanjay Siddhanti
Entered Coterminal Masters program: Fall 2014
Research interest: Genomics, Pharmacology, Machine Learning, Electronic Medical Records. 
Undergraduate affiliation: Stanford

Dana Wyman
Entered Coterminal Masters program: Winter 2014
Research interest: Personal genomics. 
Undergraduate affiliation: Stanford

HCP

Sam Adhikari
Entered HCP Masters program: Fall 2013
Research interest: Application of Machine Learning and Data Mining in clinical and Biomedical Informatics
Undergraduate affiliation: MS, Bioengineering, Temple University
Current affiliation: Software engineer at Sysoft Corporation.

Alon Ben-Ari
Entered HCP Masters program: Fall 2014
Research interest: Clinical data mining, data visualization, network analysis, machine learning.
Undergraduate affiliation: Technion, Israel Institute of Technology.
Current affiliation: Staff Anesthesiologist, Assistant Professor and Director Medical Informatics Fellowship Program, University of Washington - Seattle VA Medical Center.

Anthony Chang, MD
Entered HCP Masters program: Winter 2012
Research interest: Artificial intelligence use in medicine
Undergraduate affiliation: Johns Hopkins University; MD, Georgetown University; MBA, University of Miami, MPH was UCLA 
Current affiliation: Medical Director Heart Institute at Children's Hospital of Orange County and Medical Director of the Medical Intelligence and Innovation Institute.

Ken Ferrell
Entered HCP Masters program: Winter 2014
Research interest: Genetic Evolution, Big Data and Health Care, real-time EHR decisioning, biosensors
Undergraduate affiliation: Arizona State University
Current affiliation: Data Scientist / Statistician at Dignity Health

Ivan Ip, MD
Entered HCP Masters program: Winter 2014
Research interest: Transforming big data into personalized clinical practice in medicine
Undergraduate affiliation: MD, Cornell University Weill Medical College; MPH, University of California at Berkeley
Current affiliation: Physician, health service researcher at Brigham and Women's Hospital, Harvard Medical School.

Peter Lamb
Entered HCP Masters program: 2013
Research interest: Biomedical image analysis, linking radiographic biomarkers to genomic biomarkers
Undergraduate affiliation: MIT
Current affiliation: Research scientist at General Electric's Global Research Center.

Evan Minty , MD
Entered HCP Masters program: Fall 2013
Research interest: Clinical Research Informatics: Analytics that can define and refine process of care, clinical ontologies, reasoning in conditions of uncertainty.
Undergraduate affiliation: BSc hon. Biophysics (University of British Columbia, Canada), MSc Physics (University of Alberta, Canada), MD (University of Calgary, Canada)
Current affiliation: Internal Medicine Specialist - Alberta Health Services, University of Calgary. Clinical Scholar in Medical Informatics, U of C / Stanford

Manoj Sharma, PhD
Entered HCP Masters program: Fall 2013
Research interest: Data Mining (Assessing and understanding large datasets for chronic disease states to research for meaningful solutions)
Undergraduate affiliation: BS (Mathematics, Physics, Chemistry) and MS (Statistics), University of Rajasthan; PhD (Statistics), University of Maryland Baltimore County
Current affiliation: Health Care-Med Prod/Instrumnt / Research Fellow at LifeScan Inc., a J&J Co.

Craig Smail
Entered HCP Masters program:  Winter 2014
Research interest: Pharmacogenomics; drug repurposing; methods to deal with biases in large-scale clinical datasets
Undergraduate affiliation: University of Edinburgh
Current affiliation: Senior Research Project Coordinator at American Academy of Family Physicians

Eric Wong, MBBS
Entered HCP Masters program: Fall 2011
Research interest: Healthcare Informatics' Concepts and Development
Undergrad and affiliation: National University of Singapore (MBBS), Royal College of Surgeon, Edinburgh (MRCSAE), Academy of Medicine Singapore (FAMS Emergency Medicine), Tan Tock Seng Hospital Singapore (Emergency Physician / Deputy Chief Medical Informatics Officer)
Current affiliation: Consultant at Tan Tock Seng Hospital, Singapore

PhD Minor

Lee, Yunqin
Entered PhD Minor program: Spring 2013
Research interest: Data mining, translational bioinformatics. Undergraduate affiliation: Imperial College London - Bioengineering
and John Sunwoo

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