Lab Members
Faculty
Li Shen, PhD, FAIMBE
Professor of Informatics and Radiology
li.shen@pennmedicine.upenn.edu
215-573-2956
Dr. Li Shen is Professor and Deputy 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 serves as the Associate Director for Bioinformatics at the IBI and the Faculty Director of the IBI Bioinformatics Core. 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.
Short Bio | PENN | DBEI | IBI | BGS (GCB, GGEB, NGG) | AMCS | BioEng | ITMAT | LDI | AI2D
AIMBE | ACM | IEEE-CS | Google Scholar | My Biblio | ORCID | DBLP | OpenReview | Scopus | LinkedIn
Senior Data Analysts
Ari Z. Klein, PhD
Senior Data Analyst (Co-mentor: Dr. Graciela Gonzalez Hernandez)
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
Senior Data Analyst (Co-mentor: Dr. Graciela Gonzalez Hernandez)
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
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.
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.
Davoud Ataee Tarzanagh, PhD
Postdoctoral Fellow (Co-mentor: Dr. Qi 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.
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
PhD Student (Co-mentor: Dr. Qi 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.
Jenna Ballard, BS
PhD Student (Co-mentor: Dr. Qi 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.
Jiong Chen, BS, ME
PhD Student
jiongc@seas.upenn.edu
Jiong Chen is a 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.
Travyse Edwards, BA
PhD Student (Rotation in Fall 2023)
Travyse.Edwards@Pennmedicine.upenn.edu
Travyse is a PhD student in the Genomics and Computational Biology program at Penn. He received his BA in Physics from Binghamton University. His research interests include genomics, biomedical data science, and machine learning.
Lina Takemaru, BS, MPS
PhD Student (Rotation in Fall 2023)
Lina.Takemaru@Pennmedicine.upenn.edu
Lina is a PhD student in the Genomics and Computational Biology program at Penn. She received her BS in Biometry and Statistics and her MPS in Applied Statistics from Cornell University. She is interested in applying machine learning methods and developing data analytics tools to multi-modal data to advance precision health.
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
PhD Student
zxwang@sas.upenn.edu
Zexuan Wang is a 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
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
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.
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
PhD Student (Co-mentor: Dr. Qi Long)
zhuopinz@sas.upenn.edu
Zhouping Zhou is a 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
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
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.
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.
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.
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.
Hanxiang Xu, BS
Master's Student (Co-mentor: Dr. Haochang Shou)
Hanxiang.Xu@pennmedicine.upenn.edu
Hanxiang is a master student in Biostatistics program. His research interests include mediation analysis, imaging genomics and biomedical data science.
Jia Xu, BS
Post Master Research Assistant
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.
Qiao Xu (Betty), BS
Master's Student
qiaoqiao@seas.upenn.edu
Betty is a graduate student at Penn studying Electrical Engineering. She is interested in applying machine learning and big data in healthcare and NLP.
Handi Zhang, BS, MA
Post Master Research Assistant
handi@sas.upenn.edu
Handi Zhang received her M.A. in Applied Mathematics and Computational Science at Penn, and her B.S. in Applied Mathematics and B.A. in Economics from the University of California, San Diego. She is interested in applied mathematics, machine learning and federated learning.
Undergraduate Students
Jae Young Baik
Undergraduate Student
Jae Young is an undergraduate student currently studying Computational Biology at Penn. He is interested in combining biological data and computer science to further our understanding in biological systems, diseases, and healthcare.
Lucy Blank
Undergraduate Student
Lucy is an undergraduate student at Penn studying Bioengineering and Data Science. She loves problem solving and is interested in using machine learning and data analytics to better understand and advance the field of medicine.
Michael Gao
Undergraduate Student
Michael is currently studying Computer and Information Science at UPenn. He is interested in biomedical applications of data science and machine learning.
Kenny Liou
Undergraduate Student
Kenny is a Neuroscience major with Chemistry and Data Science minors at Penn. He is interested in applying machine learning, data analysis, and developing algorithms to better understand Alzheimer's.
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.
Patrick Wu
Undergraduate Student
Patrick is studying CIS at Penn. He is interested in the intersection between healthcare and computer science and hopes to apply machine learning to better understand Alzheimer's disease.
ALUMNI (Recent since 2023)
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
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
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.
Aaron Chacko, BS
Master's Student (11/2020-05/2023)
Aaron.Chacko@uphs.upenn.edu
Aaron was 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.
Brian Lee, BA
Undergraduate and Master's Student (08/2019-05/2023)
leebn@sas.upenn.edu
Brian Lee was 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.
Yamei Lu, BA, MS
Master's Student and Post Master Research Assistant (12/2021-01/2023)
luyamei@upenn.edu
Yamei Lu was 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.
Yinfeng Lu, BA
Master's Student (09/2022-05/2023)
luyf@sas.upenn.edu
Yinfeng Lu was 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.
Jeffrey Qu
Undergraduate and Master's Student (05/2020-05/2023)
Jeffrey was an undergraduate and master's student in 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.
Jiahang Sha, BS, MA
Master's Student and Post Master Research Assistant (09/2021-05/2023)
jhsha@sas.upenn.edu
Jiahang Sha was 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
Master's Student (02/2022-05/2023)
wxinkai@sas.upenn.edu
Xinkai Wang was 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.
Yuezhi Xie, BA
Master's Student (04/2022-05/2023)
debxie@upenn.edu
Yuezhi was 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.
Wenxi Yang, BS
Master's Student (05/2022-05/2023)
ywenxi@sas.upenn.edu
Wenxi Yang was a master student in Applied Mathematics and Computational Science at Penn. His interests include theoretical analysis and applications Machine Learning and Optimization Methods.
Ruichen Zhang, MS
Post Master Research Assistant (07/2023-08/2023)
ruichenz@seas.upenn.edu
Ruichen completed his master’s degree in Computer and Information Technology at Penn. He has a background in chemistry from his undergraduate studies. He is passionate about creating web applications and software tools, and utilizing them to enhance research.
Yuqin Zhang, BS
Master's Student (07/2022-05/2023)
yuqinz@seas.upenn.edu
Yuqin Zhang was 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.
Justin Dong
Undergraduate Student (02/2021-05/2023)
Justin was 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.
Amanda Lee
Undergraduate Student (05/2022-05/2023)
Amanda is a Biology and CIS student at Penn. She is interested in the utilization of machine learning in healthcare.
Isabel Lopez
Undergraduate Student (05/2022-12/2022)
Isabel Lopez is a Neurobiology major and Computer Science minor at Georgetown University. She was an SUIP scholar at Penn. She is interested in how machine learning and big data analysis can advance treatments for neurodisorders.
Andrés Mondragón
Undergraduate Student (06/2023-08/2023)
Andrés is an Economics major with minors in Data Science and Statistics at Penn. His interests lie in applying Machine Learning, Big Data, and NLP techniques to a wide range of areas in research including healthcare.
Sandra Vo
Undergraduate Student (05/2023-08/2023)
Sandra is an undergraduate at Regis University majoring in biology and minoring in chemistry and writing. She is an intern from the Penn SUIP and interested in how technology and data analysis can broaden the current understanding of biology.
