Lab Members


Faculty

Li Shen, PhD, FAIMBE

Li Shen, PhD, FAIMBE

Professor of Informatics / Interim Director, Division of Informatics
 li.shen@pennmedicine.upenn.edu
 215-573-2956

Dr. Li Shen is Professor and Interim Director of Division of Informatics in the Department of Biostatistics, Epidemiology and Informatics at the Perelman School of Medicine in the University of Pennsylvania. He obtained his Ph.D. degree in Computer Science from Dartmouth College. His research interests include medical image computing, biomedical informatics, machine learning, network science, imaging genomics, multi-omics and systems biology, Alzheimer’s disease, and big data science in biomedicine. He is a fellow of AIMBE, a distinguished member of ACM, and a distinguished contributor of IEEE Computer Society.

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Senior Data Analysts

Ari Z. Klein, PhD

Ari Z. Klein, PhD

Senior Data Analyst, co-mentored by G Gonzalez-Hernandez and L Shen
 ariklein@pennmedicine.upenn.edu

Dr. Ari Z. Klein is a Senior Data Analyst in the Division of Informatics in the Department of Biostatistics, Epidemiology, and Informatics at the University of Pennsylvania. He obtained his Ph.D. in Rhetoric from Carnegie Mellon University and his postdoctoral training from the University of Pennsylvania. His research interests are at the intersection of natural language processing, social media mining, corpus linguistics, and health informatics.


Senior Data Analysts

Karen O'Connor, MS

Karen O'Connor, MS

Senior Data Analyst, co-mentored by G Gonzalez-Hernandez and L Shen
 karoc@pennmedicine.upenn.edu

Ms. Karen O'Connor is a Senior Data Analyst in the Division of Informatics in the Department of Biostatistics, Epidemiology, and Informatics at the University of Pennsylvania. She obtained her M.S. degree in Biomedical Informatics from Arizona State University. Her research interests are at the intersection of natural language processing, social media mining, and health informatics.


Postdoctoral Fellows

Sumita Garai, PhD

Sumita Garai, PhD

Postdoctoral Fellow
 Sumita.Garai@pennmedicine.upenn.edu

Dr. Sumita Garai obtained her Ph.D. degree in Mathematics with a specialization in Algebraic Number Theory from the Penn State University. Her research interests include applied mathematics, machine learning, and biomedical data science.

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Bojian Hou, PhD

Bojian Hou, PhD

Postdoctoral Fellow
 Bojian.Hou@pennmedicine.upenn.edu

Dr. Bojian Hou obtained his Ph.D. degree in Computer Science and Technology at Nanjing University. His research interests include machine learning with feature evolvable streams, interpretability study for deep learning models,  semi-supervised learning, natural language processing, medical image analysis, and survival analysis.

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Davoud Ataee Tarzanagh, PhD

Davoud Ataee Tarzanagh, PhD

Postdoctoral Fellow, co-mentored by L Shen and Q Long
 Davoud.AtaeeTarzanagh@Pennmedicine.upenn.edu

Dr. Davoud Ataee Tarzanagh is a Postdoctoral Researcher in the DBEI, hosted by Profs. Li Shen and Qi Long. Previously, he was a Postdoctoral Research Fellow in the Department of EECS at the University of Michigan, hosted by Prof. Laura Balzano. He received his Ph.D. in Mathematics from the University of Florida in 2020 under the supervision of Profs. William Ward Hager and George Michailidis. His research interests include Optimization for Machine Learning, High Dimensional and Network Data Analysis, Fairness in Machine Learning, and Tensor Analysis. 

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Shu Yang, PhD

Shu Yang, PhD

Postdoctoral Fellow
 Shu.Yang@pennmedicine.upenn.edu

Dr. Shu Yang obtained his Ph.D. degree in Computer Science at the University of British Columbia. His research interests include computational biology, bioinformatics algorithm, data mining, and machine learning.


PhD Students

Jingxuan Bao, BS, MA

Jingxuan Bao, BS, MA

PhD Student, co-mentored by L Shen and Q Long
 Jingxuan.Bao@Pennmedicine.upenn.edu

Jingxuan Bao is a PhD student in Genomics and Computational Biology at Penn. He received his MA degree in Applied Mathematics and Computational Science from University of Pennsylvania. His research interests include machine learning, applied mathematics, imaging genomics, biomedical data science.

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Jenna Ballard, BS

Jenna Ballard, BS

PhD Student, co-mentored by L Shen and Q Long
 Jenna.Ballard@Pennmedicine.upenn.edu

Jenna Ballard is a PhD student in Genomics and Computational Biology at Penn. She received her BS degree in Biomedical Engineering from the Johns Hopkins University. Her research interests include developing machine learning methods to extract predictive insights from imaging data in conjunction with multi-omics and clinical data to enable more precise and effective medical diagnosis and treatment.

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Jiong Chen, BS, ME

Jiong Chen, BS, ME

PhD Student (incoming)
 jiongc@seas.upenn.edu

Jiong Chen is an incoming PhD student in Bioengineering at Penn. He received his BS degree in Biomedical Engineering from the University of Wisconsin Madison, and ME degree in Bioengineering from Penn. His research interests include genomics, neuroimaging, and cytometric analysis.

Boning Tong, BS, ME

Boning Tong, BS, ME

PhD Student
 boningt@seas.upenn.edu

Boning Tong is a PhD student in Bioengineering at Penn. She received her ME degree from the same program. She joined the Shen lab in January, 2021. She is interested in applying machine learning method to detect Alzheimer’s disease using multimodal brain imaging data.

Zexuan Wang, BS, MA

Zexuan Wang, BS, MA

PhD Student (Incoming)
 zxwang@sas.upenn.edu

Zexuan Wang is an incoming PhD student in Applied Mathematics and Computational Science at Penn. He received his BS degree in Mathematics and Physics from the University of Virginia, and his MA degree in Applied Mathematics and Computational Science at Penn. He is interested in the intersection of statistical methods and machine learning.

Zixuan Wen, BS, MA

Zixuan Wen, BS, MA

PhD Student
 Zixuan.Wen@pennmedicine.upenn.edu

Zixuan Wen is a PhD student in Applied Mathematics and Computational Science at PhD. She received her MA degree from the same program. Her research interests include applied mathematics, machine learning, and biomedical data science.

Frederick Xu, BS

Frederick Xu, BS

PhD Student
 fredxu@seas.upenn.edu

Frederick Xu is a PhD student in Bioengineering at Penn. He received his BS degree from the Johns Hopkins University with major in Biomedical Engineering and minor in Computer Science and Math. His research interests include medical image computing, machine learning, biomedical engineering, and biomedical data science.

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Qipeng Zhan, BS, MS

Qipeng Zhan, BS, MS

PhD Student
 qipengz@sas.upenn.edu

Qipeng Zhan is a PhD student in Applied Mathematics and Computational Science at Penn. He received his MS degree in Applied Mathematics from ETH Zürich. His research interests include applied mathematics, deep learning and related statistical and computational problems.

Zhuoping Zhou, BS, MA

Zhuoping Zhou, BS, MA

PhD Student (Incoming), co-mentored by L Shen and Q Long
 zhuopinz@sas.upenn.edu

Zhouping Zhou is an incoming PhD student in Applied Mathematics and Computational Science at Penn. She received her MA degree in Applied Mathematics and Computational Science from Penn, and her BS degree in Mathematics from UC Irvine. Her research interests include applied mathematics, machine learning and deep learning.


Master's Students

Aaron Chacko, BS

Aaron Chacko, BS

Master's Student
 Aaron.Chacko@uphs.upenn.edu

Aaron is a Biomedical Informatics student who is passionate about the intersection of medicine and technology. He received his BS degree in Biology and Public Health from Temple University. His research interests include machine learning, precision medicine, and data mining.

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Yanbo Feng, BS, ME

Yanbo Feng, BS, ME

Post Master Research Assistant
 yanbof@seas.upenn.edu

Yanbo Feng is post master research assistant in the Shen Lab. He received his BS degree in Biomedical Engineering and Neurobiology from University of Wisconsin Madison, and his ME degree in Bioengineering from Penn. He joined the Shen lab in November, 2021. He is interested in machine learning, deep learning, and brain-computer-interface.

Weiqing He, BS

Weiqing He, BS

Master's Student
 weiqingh@sas.upenn.edu

Weiqing He is a master's student in Applied Mathematics and Computational Science at Penn. His interests include applied mathematics, machine learning and deep learning.

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Brian Lee, BA

Brian Lee, BA

Master's Student
 leebn@sas.upenn.edu

Brian Lee is a master’s student in the Bioengineering program. He received his BS degree from the Biology department at Penn. He was a CASURG scholar in 2020. He is broadly interested in using computational techniques to make sense of biological/biomedical data; currently, he studies multi-omics and genetic data to better understand biological contributors to Alzheimer’s disease.

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Yamei Lu, BA, MS

Yamei Lu, BA, MS

Post Master Research Assistant
 luyamei@upenn.edu

Yamei Lu is a research assistant in the Shen lab. She received her MS degree in the Data Analytics Master of Science in Social Policy program in the School of Social Policy & Practice from Penn. She is interested in applying machine learning and big data techniques to real-world biomedicine problems.

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Yinfeng Lu, BA

Yinfeng Lu, BA

Master's Student
 luyf@sas.upenn.edu

Yinfeng Lu is a master's student in pure mathematics at Penn. He received his BA degrees in mathematics and physics from UC Berkeley in May 2021. His research interests include machine learning, deep learning, and their applications in medical image analysis.

Shizhuo Mu, BS

Shizhuo Mu, BS

Post Master Research Assistant
 shizhuo@seas.upenn.edu

Shizhuo Mu is an MS student in Bioengineering at Penn. She received her BS degree in Theoretical and Applied Mechanics from Fudan University. She joined the Shen lab in August, 2022. She is interested in biomedical engineering, biomedical data science and biomedical modeling.

Jeffrey Qu

Jeffrey Qu

Master's Student

Jeffrey is currently studying Computer and Information Science at Penn. He joined the Shen Lab as part of the PURM program in May 2020. He is interested in applying machine learning for outcome prediction within healthcare.

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Jiahang Sha, BS, MA

Jiahang Sha, BS, MA

Post Master Research Assistant
 jhsha@sas.upenn.edu

Jiahang Sha is a research assistant in the Shen Lab. He received his MA degree in Applied Mathematics and Computational Science from Penn, and his BS degree in Mathematics – Computer Science from UCSD. His research interests include applied mathematics, machine learning, and biomedical computing.

Xinkai Wang, BS

Xinkai Wang, BS

Master's Student
 wxinkai@sas.upenn.edu

Xinkai Wang is a master's student in Applied Mathematics and Computational Science at Penn. He received his BS degree in Mathematics, Computer Science, Cognitive Science and Machine learning from UCSD. He joined the Shen lab in February, 2022. He is interested in computer science, machine learning, cognitive science, and biomedical data science.

Tianyi Wei, BS

Tianyi Wei, BS

Master's Student
 tywei@seas.upenn.edu

Tianyi Wei is a Master's student in Data Science at Penn Engineering. She received her BS in Mathematics from the University of Minnesota. She is interested in machine learning strategies for Alzheimer's disease research.

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Ruiming Ray Wu, BS

Ruiming Ray Wu, BS

Post Master Research Assistant
 wuru@seas.upenn.edu

Ray is a master’s student in the Data Science program and undergraduate in the Bioengineering and Computer and Information Science programs at Penn. His research interests include machine learning, network analysis, and brain interface.

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Yuezhi Xie, BA

Yuezhi Xie, BA

Master's Student
 debxie@upenn.edu

Yuezhi is an MS student of Social Policy and Data Analytics in the School of Social Policy & Practice. She received her BA degree in Literature and Economics from Hamilton College. Her interest lies in the area of machine learning, data ethics, and big data analytics.

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Jia Xu, BS

Jia Xu, BS

Master's Student
 jiaxu7@upenn.edu

Jia Xu is a master's student in the Data Analytics Master of Science in Social Policy program in the School of Social Policy & Practice. She is passionate about applying machine learning and big data science in biomedicine. Her research interests include machine learning, data mining, and biomedical data science.

Wenxi Yang, BS

Wenxi Yang, BS

Master's Student
 ywenxi@sas.upenn.edu

Wenxi Yang is a master student in Applied Mathematics and Computational Science at Penn. His interests include theoretical analysis and applications Machine Learning and Optimization Methods.

Yuqin Zhang, BS

Yuqin Zhang, BS

Master's Student
 yuqinz@seas.upenn.edu

Yuqin Zhang is an MSE student in Data Science at Penn. She received her BS degree in Applied Mathematics from UCLA. She is interested in data mining, machine learning, and biomedical data science.


Undergraduate Students

Justin Dong

Justin Dong

Undergraduate Student

Justin is a Biochemistry student at Penn, and in the Vagelos program. He is interested in machine learning, brain imaging genomics, drug study, and Alzheimer's research.

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Daniel Rohacs

Daniel Rohacs

Undergraduate Student

Daniel is an undergraduate studying Computer and Information Science at Penn. He is interested in applying machine learning and data science to genetics and Alzheimer’s research.

Amanda Lee

Amanda Lee

Undergraduate Student

Amanda is a Biology and CIS student at Penn. She is interested in the utilization of machine learning in healthcare.

Isabel Lopez

Isabel Lopez

Undergraduate Student

Isabel Lopez is a Neurobiology major and Computer Science minor at Georgetown University. She is an SUIP scholar at Penn. She is interested in how machine learning and big data analysis can advance treatments for neurodisorders.

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Austin Wang

Austin Wang

Undergraduate Student

Austin is a sophomore majoring Computer Science and minoring in Data Science, originally from Taiwan. He is very interested in the potential applications of AI and big data in medicine, especially in the area of better understanding Alzheimer's Disease right now. In his free time, Austin enjoys going to the gym, playing basketball, and hanging out with friends.

Richard Zhang

Richard Zhang

Undergraduate Student

Richard is an undergraduate studying math and CIS at Penn. He is interested in the application of machine learning to medicine to improve disease diagnosis and prognosis.


ALUMNI (Recent since 2023)

Duy Duong-Tran, PhD

Duy Duong-Tran, PhD

Postdoctoral Fellow (07/2022-01/2023)
 duyanh.duong-tran@pennmedicine.upenn.edu

Dr. Duy Duong-Tran is an Assistant Professor in the Department of Mathematics at The United States Naval Academy. He obtained his Ph.D. in Computational Neuroscience in the School of Industrial Engineering at Purdue University. His research interest is in the intersection of applied mathematics and computational neuroscience. During his Ph.D., he was the recipient of Ross Doctorate Research Fellowship, Magoon Teaching Excellence Award, and Bilsland Dissertation Fellowship.

Daniele Pala, PhD

Daniele Pala, PhD

Postdoctoral Fellow (04/2022-04/2023)
 Daniele.Pala@pennmedicine.upenn.edu

Dr. Daniele Pala is an Assistant Professor the University of Pavia. He obtained his Ph.D. degree in Technologies for Health, Bioengineering and Bioinformatics at the University of Pavia, Italy. His research interests include machine learning, biomedical data science and bioinformatics

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Joseph D. Romano, PhD

Joseph D. Romano, PhD

Postdoctoral Fellow (11/2021-12/2022)
 Joseph.Romano@pennmedicine.upenn.edu

Dr. Joe Romano is an Assistant Professor of Informatics at the University of Pennsylvania. He was a postdoctoral researcher in Penn's Institute for Biomedical Informatics and Center of Excellence in Environmental Toxicology. His research focuses on using translational bioinformatics and artificial intelligence to make new discoveries in toxicology and systems pharmacology.

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