People

Faculty

Daniel L. Rubin, M.D., M.S.

Assistant Professor of Radiology and of Medicine (Biomedical Informatics Research)
Member, Stanford Cancer Center; Member, Bio-X

Daniel Rubin is Assistant Professor in the Department of Radiology at Stanford University. Work in the lab lies at the intersection of biomedical informatics and imaging science. His NIH-funded research program focuses on developing informatics methods of knowledge representation, natural language processing, and decision support to improve the quality and consistency of radiology practice. Major projects include (1) developing methods to extract information and meaning from images for data mining, (2) developing statistical natural language processing methods to extract and summarize information in radiology reports and published articles, (3) resources to integrate images with related clinical and molecular data to discover novel image biomarkers of disease, and (4) translating these methods into practice by creating decision support applications that relate radiology findings to diagnoses and that will improve diagnostic accuracy and clinical effectiveness.

Postdoctoral Fellows and Postgraduate Trainees

Luis de Sisternes

Postdoctal Fellow

Luis de Sisternes is a Postdoctoral Scholar in the Department of Radiology at the Laboratory of Quantitative Imaging. His main research interests include image processing, quantitative imaging, 3-D modeling and CAD. He received his Ph. D. in Electrical Engineering at Illinois Institute of Technology, where he investigated the application of novel Phase-Contrast X-Ray imaging methods in breast diagnosis while researching at the Medical Imaging Research Center. An important part of his previous research work includes the development of a versatile mathematical model that enables the generation of a large number of realistic three-dimensional breast tumor simulations. His current projects are focused on the development and evaluation of novel quantitative imaging features of disease both in retinal imaging using optical coherence tomography and for cancer characterization in computed tomography images.

Daniel Golden

Postdoctal Fellow

Daniel Golden received his B.S. in Electrical and Computer Engineering from Cornell University in 2005 and his Ph.D. in Electrical Engineering from Stanford University in 2011. Daniel's interests involve using machine learning and statistics in order to predict response to therapy for patients with known cancerous lesions. His current project is focused on using quantitative measures from dynamic contrast-enhanced MRI images to predict the response of triple-negative breast cancer patients to neoadjuvant chemotherapy. This predictive capability will allow patients and physicians to more effectively tailor custom therapies to individual patients.

Camille Kurtz

Postdoctal Fellow

Camille Kurtz received respectively M.Sc. and the Ph.D. degrees in Computer Sciences from the University of Strasbourg (France) in 2009 and 2012. His main research interests include image analysis, hierarchical segmentation, classification, pattern recognition, mathematical morphology, medical imaging and remote sensing. His current project focuses on developing new methodologies that can be used to search large databases of radiological images based on different types of image features: (1) semantic features coded by radiologists using a controlled terminology, and (2) computer-generated features of pixels characterizing the lesion’s texture as well as the sharpness of its boundary. The main objective is to develop software tools to facilitate the retrieval of radiological images containing similar lesions.

Adrien Depeursinge

Postdoctal Fellow

Adrien Depeursinge received the B.Sc. and M.Sc. degrees in electrical engineering from the Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland, in 2003 and 2005, respectively, with a specialization in signal and image processing. From 2006 to 2010, he performed his Ph.D. thesis on medical image analysis with a focus on texture analysis and content-based image retrieval at the University Hospitals of Geneva (HUG). He then spent two years as a Postdoctoral Fellow at the University of Applied Sciences Western Switzerland, Sierre (HES-SO), Switzerland and the HUG. Dr. Depeursinge was the recipient of the 2011 German Association for Medical Informatics, Biometry and Epidemiology Award in medical informatics for his Ph.D. thesis. His research interests include (1) N-dimensional texture analysis with control of scales and orientations, (2) automated detection of semantic visual concepts (e.g. Radlex terms), and (3) clinical workflows of image-based computer-aided diagnosis systems.

Graduate Students

Tiffany Ting Liu

Graduate Student - Biomedical Informatics

Tiffany Ting Liu is a Ph.D. student in Biomedical Informatics. She received her Bachelor of Computer Science with Bioinformatics Option at the University of Waterloo in Canada. She is interested in integrated analysis of molecular and imaging data using methods in machine learning and image analysis. Her thesis project is on analyzing multiscale glioblastoma data to identify molecular and imaging biomarkers for personalized cancer treatment.

Francisco Gimenez

Graduate Student - Biomedical Informatics

Francisco Gimenez is a Ph.D. student in Biomedical Informatics. He received his B.S. in Electrical Engineering and Computer Sciences at UC Berkeley, and was a researcher at UCSF for 2 years. He is interested in providing decision support for radiologists using methods in computer vision, natural language processing, and machine learning. His current projects are focused on developing validation systems for radiological reporting to increase accuracy and reproducibility.

Vanessa Sochat

Graduate Student - Biomedical Informatics

Vanessa Sochat is a PhD student in Biomedical Informatics. She received a BA in Psychology and Neuroscience from Duke University, and was head RA in a neuropsychology lab at Duke for two years before coming to Stanford. She aims to use multimodal neuroimaging data and methods from machine learning and natural language processing to identify patterns of structure and function that predict disorder. She is currently working on feature extraction methods to better define subtypes of neurological disease.

Rebecca Sawyer

Graduate Student - Biomedical Informatics

Rebecca Sawyer is a M.S. student in Electrical Engineering and a PhD student in Biomedical Informatics. She received her B.S. in Electrical Engineering at UNC Charlotte. She is interested in image processing and machine learning for content-based image retrieval and computer-aided diagnosis. She is currently working on mammography feature extraction methods for computer-aided diagnosis of breast cancer.

Jocelyn Barker

Doctoral Student - Biophysics

Jocelyn Barker is a graduate student in Biophysics. Her main research interests are image analysis of medical data for biological and medical relevance. Previously in her undergraduate career, she did research in genomic bioinformatics while getting her degrees in Biochemistry and Molecular Biology and Mathematics. For her thesis project, she is working on the analysis of pathological data for cancers for correlation with molecular, radiological, and survival outcomes data.

Abra Jeffers

Doctoral Student - Management Science & Engineering

Abra Jeffers is a PhD student in Management Science & Engineering. She received an MPhil in Management Science from Cambridge University. She received her BA and BS in Chemistry and Economics from Michigan State University. Her research interests are decision and risk analysis and probabilistic modeling. She is current researching a breast cancer risk assessment model."

Selen Bozkurt

Doctoral Student - Biostatistics and Medical Informatics

Selen Bozkurt is a Ph.D. student and research assistant in Department of Biostatistics and Medical Informatics at Akdeniz University, Turkey. She received her M.Sc. degree in Medical Informatics at same department and B.S. in Statistics at 9 Eylul University, Turkey. She is also a member of RSNA Radiology Reporting Committee since 2009. Her interests are Structured Reporting in Radiology and providing decision support for radiologists using methods in natural language processing and machine learning. Her dissertation proposal title is entitled "A Real Time Decision Support System for Mammography Interpretations."

Hakan Bulu

Doctoral Student - Computer Engineering

Hakan recieved his M.Sc. degree in computer engineering from 9 Eylul University, Turkey in 2007. Currently, he is a Ph.D. student, and a Research Assistant at the same department. He is working on developing an ontology based medical image annotation and retrieval system for mammographic examinations. In this way, he aims to make possible case-based retrieval for mammography.

Mustafa Safdari

Graduate Student - Computer Science

Mustafa has a Bachelor's in Computer Science from Birla Institute of Technology and Science - Goa Campus. At Stanford, he is pursuing Master's in Computer Science in the Artificial Intelligence Track. His areas of interest include probabilistic topic models, and his current work includes implementing these models for classification and semantic searching in images.

Radiology Residents and Medical Students

Irene Liu

Radiology Resident

Irene received her MD and PhD at Stanford. Her PhD is in biomedical informatics, and she is interested in creating decision support applications to improve the consistency in radiology interpretation. She is developing Bayesian Network models of thyroid imaging to help radiologists evaluate thyroid nodules and improve decision making about when to biopsy these lesions.

Aaron Abajian

Medical Student

Aaron is a medical student at Yale University. He earned a B.S. in Computer Science & Engineering, a B.S. in Mathematics, and a B.S. in Biological Sciences from the University of California, Irvine. He spent two years following graduation as a full-time high school chemistry teacher as part of Teach for America. He previously worked as a PACS software engineer with Candelis, Inc. His research interests include the development of automated algorithms for the segmentation and extraction of metadata from solid tumor images. His current project entails the comparative analysis of novel response to treatment criteria.

Undergraduate Students

Dana Yeo

College Student

Dana Yeo is currently a Senior at Stanford University majoring in BioMedical Computation. She is interested in increasing the efficacy and precision of medical diagnostics using computational methods. Her previous research project focused on using zinc finger technology to target the sickle cell mutation in patient-derived IPS lines. In her spare time she enjoys a pint of green tea ice cream and a good game of Settlers of Catan.

William Du

College Student

William Du is a freshman at Stanford University who recently took part in the Stanford Institute of Medical Research Summer Program (SIMR). He is interested in radiogenomic analysis as a way to expand his understanding of biomedical informatics as a whole. He is currently working on radiogenomic analysis of glioblastoma patients in order to gain insights into medical features.

High School Students

Sadhika Malladi

High School Student

Sadhika Malladi is a rising sophomore in high school and enjoys working to use Computer Science in medical applications. In particular, her interests include building a plugin to ePad's environment and modeling patient responses to chemotherapy.

Daniela Lee

High School Student

Daniela Lee is a high school student at The Harker School. Her research interests are centered around the medicine field as a whole, but especially the imaging aspect. She is currently working on the standardization of image data into AIM files as well as on the analysis of image features to create a treatment response model to neoadjuvant chemotherapy.

Research Staff

Debra Willrett

Scientific Research Developer

AlDebra received her BS in mathematics and BS in computer science from Iowa State University. She received her MS in electrical engineering from Stanford University. She has designed and built web applications for business and education. These sites sell services and products, manage memberships, offer member services, publish online member directories, manage group calendars, and process online event registration and payments. In addition, she has provided litigation support to law firms for software intellectual property cases. Debra designed and developed the award-winning project management application MacProject which was awarded the Readers Choice Software of the Year Award for many years running by MacWorld magazine, and was the first third-party application to be release for the Macinotsh. MacProject was the follow on product to Debra's LisaProject, the first graphical project management software, which was distributed by Apple for the Lisa. Debra is working on the ePad project (http://epad.stanford.edu), using cutting-edge features of GWT-P and HTML5 to create Web application-based front ends for image viewing and semantic image annotation.

SIIM Mentees

Michael Shah

College Student

Michael Shah is an undergraduate at The Ohio State University studying Computer Science Engineering with interests in visualization. He is involved with a research project at The Oregon Health and Sciences University in tracking and visualizing the motion of tumors on the lung. The project will help radiation therapists better create radiation treatment plans for accurately targeting tumors in motion on the lung. Michael is also currently involved in volume visualizations with The Ohio Supercomputer Center developing a simulator to train future veterinarian surgeons in performing a dog knee arthroscopy.

Ichiro Ikuta, MD

Fellow and Masters Student

Ichiro Ikuta earned his B.S. in physiology and B.A. in Spanish from Michigan State University, M.D. at SUNY Upstate Medical University, and did a transitional year internship at Columbia University/Mary Imogene Bassett Hospital. He is currently a fellow at Brigham and Women's Hospital in the Center for Evidence-Based Imaging, working on a masters in biomedical informatics from Harvard Medical School. His research interests are the development of decision support for neuroradiology, critical care/pulmonary re-evaluations, and patient radiation exposures from medical imaging.

Mohamed Muthiullah, MD

Clinical Assistant Professor of Cardiology and Masters Student

IcMohamed Muthiullah earned his M.B.B.S. from the Madras Medical College,The Tamil Nadu Dr.MGR Medical University,Chennai in 2000.Subsequently he completed his residency in Internal Medicine and Fellowship in Cardiovascular Medicine from the same University in 2007.After three years of clinical cardiology experience in non academic tertiary level medical centers,he is now a clinical assistant professor of Cardiology at Sri Ramchandra Medical College Hospital and Research Institute / Sri Ramachandra Hospital-Sri Ramachandra University,Chennai since November 2010.His subspecialization in cardiovascular Imaging is underway and he is also a part time student of Masters in Information Systems and Technology at the University of Liverpool.His interest areas are Image processing,Image compression,Image distribution,Connectivity-IT Infrastructure and Computer aided diagnosis.

Collaborating Faculty

Jafi Lipson

Clinical Instructor

BDr. Lipson is an Assistant Professor of Radiology in the Breast Imaging Division at Stanford. Her current research includes the classification and quantification of dynamic contrast enhanced breast MRI patterns of response to poly ADP-ribose polymerase (PARP) inhibitor therapy in the neoadjuvant treatment of triple-negative and BRCA-associated breast cancer; the evaluation of mammographic breast density and breast cancer risk; and the creation and evaluation of an Annotated Breast Map, an automated, WIKI-form visual summarization of a patient's breast history.

Bao Do

Clinical Instructor

Bao is interested in leveraging radiology image and report data to drive discovery and improve patient care. He is currently developing natural language processing methods to detect uncertainty in radiology reports and to extract findings. He has developed a searchable database of radiology reports.

Mia Levy

Faculty in Biomedical Informatics and Medicine, Vanderbilt University

Mia Levy received her PhD in Biomedical Informatics at Stanford in 2010. She is currently Assistant Professor in Biomedical Informatics and Medicine at Vanderbilt University and Cancer Clinical Informatics Officer at Vanderbilt Ingram Cancer Center. She is developing generalizable methods of representing treatment response to disease. She continues to collaborate with our laboratory in developing methods for using quantitative imaging to evaluate cancer treatment response and tool development to automate these tasks.

Administrative Staff

Kimberly Maclaren

Administrative Assistant

Kimberly Maclaren is an Administrative Assistant for the Department of Radiology supporting Dr. Rubin. She can be reached at phone: (650) 724-4752 or email kmaclare@stanford.edu.

Lab Alumni

Jiajing Xu

Doctoral Student - Electrical Engineering

Jiajing Xu completed his PhD in the Department of Electrical Engineering at Stanford University in 2013. His research interests include machine learning and content-based image retrieval for medical applications. He received his bachelor's and master's degree in EE from California Institute of Technology and Stanford University in 2006 and 2008. His work is in methods for content-based image retrieval (CBIR) in radiology for decision support, automated segmentation, and computerized methods to evaluate temporal imaging studies to quantify tumor response to treatment.

Raghav Pasari

Graduate Student - Computer Science

Raghav Pasari received his B. Tech in Information Technology from Indian Institute of Information Technology, Allahabad. Currently he is a first year Masters student in the Computer Science program at Stanford. He has worked as a intern at Google India for about 5 months and will be interning at eBay San Jose this summer. Currently he is working on liver lesion classification and detection using a novel visual dictionary of words approach. His interests include Image Processing and application of Machine Learning approaches to solve biomedical problems.

Witi Sachchamarga

Graduate Student - Management Science & Engineering

Witi is a Ph.D. student in Management Science & Engineering at Stanford University. He received his BS in Mechanical Engineering and his MS in Industrial and System Engineering from Texas A&M University. His research interests are in decision and risk analysis, probabilistic modeling and artificial intelligence. He is currently researching how to aggregate a number of expert opinions (network structure, probability and evidence) for decision support systems in medical diagnostic domains.

Mina Ghaly

Medical Student

Mina Ghaly is a medical student at Dartmouth Medical School. He received his B.S. in Biochemistry and Molecular Biology/Biological Sciences from the University of Massachusetts-Amherst. His current interests include bioinformatics, radiology decision support and machine learning capabilities.

Alan Snyder

Scientific Research Developer

Alan Snyder received his Bachelors from the University of Illinois in Engineering Physics. He previously did lithography research for Intel, where patented work related to phase-shifted reticles. Since then he has been a software developer working at start-ups, working on distributing video in the Internet. He has worked at worked at Live365, Macrovision, Azureus/Vuze among others. At Macrovision he received a patent for "Techniques for Watermarking and Distributing Content" using a peer-to-peer network protocol. While at Azureus he wrote the Network Monitor plug-in, which is used to determine which ISP is throttling connections, in addition to working on the client and writing the data-center management applications. Alan is currently working on the ePad project (http://epad.stanford.edu) using the latest features of HTML5 for semantically annotating medical images for clinical and research purposes.

Lior Weizman

Graduate Student - Computer Science

Lior Weizman received his B.Sc and M.Sc. degrees in Electrical Engineering from the Ben-Gurion University of the Negev, Israel in 2002 and 2004, respectively. He is currently a Ph.D. student in the School of Engineering and Computer Science in the Hebrew University of Jerusalem, and a summer intern at Stanford University. His main research interests are image segmentation, biomedical image processing and statistical signal processing.

Christina Hung

High School Student

Christina Hung is a student at Piedmont Hills High School. She has a strong interest in graphical models and computerized decision support, as well as the uses of imaging in the field of radiology. She worked on a project involving decision support with mammography during a summer rotation project.

Ihsan Djomehri

Medical Student

Ihsan received the BA in physics and BS in electrical engineering from UC Berkeley, and the MS and then PhD in electrical engineering from MIT. He has worked on both experimental development and computational physics research of nanotechnology devices and imaging. Now as a medical student at Stanford University, he is interested in bioinformatics and using the semantic web for radiology decision support of focal liver disease as an example.

Rohan Bansal

College Student

Rohan Bansal is currently a student at Princeton University. He is a pre-medical Computer Science major. His major interests lie in imaging and its uses in medicine, as well as other computer-science related technologies in medicine. He is working to create distinguish and split regions in an MRI to subregions and superpixels. His previous and current research includes peak-picking and analyzing mass spectrometry data, and creating a user friendly viewer for the plasmodium genome based off of PlasmDB.

Chaitanya Malladi

High School Student

Chaitanya Malladi is a high school graduate from the Harker School. He will be a member of the Class of 2016 at Caltech. He is interested in bioimaging analysis, decision support tools, and other bioinformatics applications. He is working on improving the functionality of the biomedical image metadata manager (BIMM) by expanding the available features. One such enhancement is allowing BIMM to interface with PACS.

Qiang Chen

Faculty – Computer Science

Qiang Chen received his B.Sc. degree in computer science and Ph.D. degree in Pattern Recognition and Intelligence System from Nanjing University of Science and Technology, China, in 2002 and 2007, respectively. Currently, he is an associate professor with the School of Computer Science and Technology at the Nanjing University of Science and Technology. His main research interests are image segmentation, object tracking, image restoration, image enhancement, and image quality assement.

Mia Levy

Faculty in Biomedical Informatics and Medicine, Vanderbilt University

Mia Levy received her PhD in Biomedical Informatics at Stanford in 2010. She is currently Assistant Professor in Biomedical Informatics and Medicine at Vanderbilt University and Cancer Clinical Informatics Officer at Vanderbilt Ingram Cancer Center. Her dissertation was entitled "Rule-Based Response Assessment Framework" in which she developed generalizable methods of representing treatment response to disease. She continues to collaborate with our laboratory in developing methods for using quantitative imaging to evaluate cancer treatment response and tool development to automate these tasks.

Pooja Naik

Undergraduate Student

Pooja Naik is a final year student at Birla Institute of Technology and Science, Pilani- Goa Campus pursuing Msc (Tech.) Information Systems. Her research interests include Artificial Intelligence, Machine Learning, Quantitative Imaging and Decision Support. She is currently working on using DCE-MRI to discover imaging biomarkers that predict response to PARP inhibitor therapy in Triple Negative Breast Cancer.

Neeraj Agrawal

Graduate Student - Computer Science

Neeraj received a bachelor's degree in computer science from the Indian Institute of Technology Roorkee. He is currently working on image analysis to characterize liver legions for content based image retrieval in radiology.

Ankit Gupta

Graduate Student – Computer Science

Ankit received a bachelor's degree in computer science from the Indian Institute of Information Technology and is completing a masters in Computer Science at Stanford. While in the lab, he worked on image analysis to characterize the margin of lesions for content based image retrieval in radiology. He produced a manuscript on his work and accepted submissions to major meetings.

Allika Walvekar

College Student

Allika Walvekar is an undergraduate at Caltech. She is interested in electronic encoding of medical knoweledge, and she is working on building a prototype decision support system that will use the knowledge in the Semantic Media wiki to help doctors access current medical knowledge more effectively to make the best diagnostic decisions.

Daniel Korenblum

Scientific Research Developer

Daniel Korenblum obtained a B.A. in Biochemistry and Molecular Biology (BMB) from Reed College, an M.S. in Biophysics from Cornell University, and an M.S. in Computational and Mathematical Engineering at Stanford University. His interests include biomedical image and signal processing, biomedical informatics, molecular modeling, and computational biophysics. Daniel is part of the Image Feature effort of the Information Science in Imaging at Stanford (ISIS) group. He was the primary architect and developer of the biomedical image metadata manager (BIMM) and co-developer of the Aim Template Manager (pre-release version only) applications. He is currently working at Genia Technologies Inc., developing protein nanopore single-molecule measurement devices.

Cesar Rodriguez

Research Programmer

Cesar received his bachelor’s degree in Biological Science from Florida State University and his MD from Howard University College of Medicine. He created the initial version of iPAD, an application to use ontologies to annotate radiology images to make the semantic content machine-accessible. While he has now moved on to puruse systems biology, he continues to remain engaged in the iPAD project to support its continued development.

Katie Hsih

College Student

Katie Hsih received her BSE degree Operations Research & Financial Engineering from Princeton University in 2010. She is interested in a multidisciplinary approach to medical problems and global health policy. Katie currently running a pilot study for iPAD, a computerized tool for annotation of radiological images.

Krithin Sitaram

Princeton Student

Krithin Sitaram is a undergraduate student at Princeton interested in Natural Language Processing.

Meeta Arora

Graduate Student - Management Science & Engineering

Meeta is pursuing her Master's in Management Science and Engineering at Stanford University. Prior to this, she received her undergraduate degree in Computer Engineering from Mumbai University and worked as a Software Engineer developing web applications. She is developing Web-based applications to enable viewing large pre-coordinated terminologies for radiology and to create integrated data warehouses linking clinical data (through the I2B2 platform) to radiology data (in BIMM).

Brett Lullo

College Student

Brett Lullo is a senior at Princeton University where he is a Computer Science major on the Pre Med track. Brett's Junior Independent Work has examined the crossroads of medicine and technology. In the Fall he worked on the AphasiaFox extension for firefox, a picture, sound and video pop-up dictionary for people suffering from the language disorder aphasia. In the Spring he worked on the MotifDigger project in order to identify let-7 miRNA target sequences in the 3'UTR region of the human genome. Currently he is working at the American College of Radiology Imaging Network, updating the iPAD annotation tool for radiological images.

Jithun Nair

Graduate Student - Electrical Engineering

Jithun Nair received his B. Tech in Electronics and Electrical Engineering from Indian Institute of Technology Kharagpur. He's pursuing his Masters in Electrical Engineering at Stanford. He is currently working on developing a web-based version of the iPad, a computerized tool for annotation of radiological images. His interests include developing Rich Internet Applications (RIA) and Computer Graphics.

Abhik Lahiri

Graduate Student - Computer Science

Abhik Lahiri is pursuing a Master's in Computer Science at Stanford. He received his Bachelor's in Computer Science from Birla Institute of Technology and Science, Pilani - Goa Campus. He recently worked for 5.5 months in HP Labs, Bangalore. His interests are in AI, Machine Learning, Information Retrieval. Abhik is currently working on information extraction of semantic information from radiology reports to enable publishing and computerized reasoning over these data on the Semantic Web.

Stephanie Chan

Radiology Resident

Stephanie received her MD from Stanford and is currently a radiology resident at UCSF. She is interested in creating models to help physicians integrate diverse data in decision making. She is currently developing a probabilistic model of breast imaging that incorporates the results of biopsy to help radiologists evaluate whether negative biopsy is due to sampling error.