Bin Chen, PhD

Principal Investigator, Assistant Professor (CV)

Dept. of Pediatrics and Human Development

Dept. of Pharmacology and Toxicology

Dept. of Computer Science and Engineering (adjunct)

Bin was recruited to MSU through the Global Impact Initiative. Prior to this position, Bin was a faculty member (instructor, assistant professor) at UCSF for three years. Bin trained as a chemist in college, worked as a software engineer before graduate school, trained as a chem/bioinformatician in graduate school, worked as a computational scientist at Novartis, Pfizer and Merck. He received his PhD in informatics at Indiana University, Bloomington and pursued his postdoctoral training in Dr. Atul Butte's lab at Stanford University. Bin co-founded DahShu, a non-profit organization to promote research and education in data sciences. As a PI, he has received >$4.5 million research funding. He has also contributed to a number of big grants (e.g., P01 and U24) as a co-investigator. During weekends, Bin plays soccer or coaches kids to play soccer.

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Ke Liu, PhD

Postdoctoral Scholar (2018-2020), Assistant Professor (2020-)

Ke received the BA in computer science at Shandong University in 2008 and the PhD in biology at Tsinghua University in 2014. He then pursued his postdoctoral training at UC Berkeley before joining Chen lab in 2018. He is interested in integrating multiple omics data (e.g., RNA-Seq, Chip-Seq) to discover new therapeutics for complex diseases (especially lung cancer). He is also interested in bioinformatics tool development. Since 2020, he became a research assistant professor, leading the EMR big data program between MSU and Spectrum Health.

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Rama Shankar, PhD

Postdoctoral Scholar (2018-)

Rama completed the M.Sc. Biotechnology from the University of Hyderabad, India in 2010 and the PhD in computational biology from Jawaharlal Nehru University, India in 2018. He joined Dr. Bin Chen group in 2018. He is interested to apply single cell transcriptomic data into therapeutic discovery and integrate omics data to identify novel biomarkers.

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Jing Xing, PhD

Postdoctoral Scholar (2018-)

Jing received her BS in Pharmaceutical Sciences from Sun Yat-sen University in 2013 and the PhD in Drug Design from Shanghai Institute of Materia Medica, Chinese Academy of Sciences in 2018. She joined Dr. Bin Chen group in 2018. Her research interests include drug hit optimization using omics data and employing deep learning algorithms to solve pharmaceutical problems.

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Shreya Paithankar, MS

Technical Assistant (2018-)

Shreya received the MS in health informatics from GVSU. She provides bioinformatics support to lab researchers and collaborators. Her main tasks include developing and maintaining our RNA-Seq processing pipeline, expanding the OCTAD RNA-Seq database, and developing web portals.

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Mengying Sun

CS PhD student (co-supervised by Dr. Jiayu Zhou)(2018-)

As a PhD student in computer science, Mengying is interested in machine learning method development. In Chen lab, she develops machine learning methods (e.g., collaborative learning, contrastive learning, deep reinforcement learning) in drug-induced gene expression prediction and lead optimization.

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Evgenii (Evgeny) Chekalin, PhD

Postdoctoral Scholar (2019-)

Evgeny joins us from the Vavilov Institute of General Genetics, Russian Academy of Sciences, where he received the PhD in both Genetics and Bioinformatics. He has extensive experience with immune systems, gene networks and ancient DNA analysis. In Chen lab, he leads the effort in cancer immunotherapy and bispecific target discovery (DIPG and melanoma). His hobbies are hiking, rock-climbing and archery.

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Austin VanVelsen

CHM Medical Student

Austin works on biomarker data analysis while taking a leave of absence from medical school.

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Tyler VanVelsen

CHM Medical Student

Tyler works on biomarker data analysis while taking a leave of absence from medical school.

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Jeremy Haskins

Research Assistant (2020-)

Jeremy received an MS in cancer biology from Colorado State University. He spends half of his time in Chen lab running biological experiments and learning bioinformatics and another half in Dr. Copple's lab assisting the bench work.

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Dimitri Joseph

DO/PhD student (2020-)

Dimitri is a DO/PhD candidate pursuing a graduate degree in Pharmacology and Toxicology. He received his MSc in Biochemistry and Cell Biology from Stony Brook University. He is interested in connecting bioinformatics & Drug Discovery to identify novel mechanisms and validation in clinical models. His favorite organ/system is the brain and central nervous system.

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Ruoqiao Chen

BMS PhD student (2021-)

Ruoqiao received the BS in medical science from Huazhong University of Science & Technology in China. Her current research focuses on surface protein expression prediction using transfer learning and deep learning.

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Han Meng

Research Assistant (2021-)

Han received the MS in material science from MSU. She assists with the lab computational drug discovery effort.

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We always welcome highly motivated trainees to join the lab. For postdoc candidates, please send your CV and research interests to Dr. Chen. For graduate students, please apply through the BioMolecular Science program or the Genetics and Genome Sciences Program. Feel free to approach Dr. Chen if you plan to apply. Chen lab has the tradition to host high-school summer interns every year. Please contact Dr. Chen before April if you are interested. We occasionally recruit undergraduate and medical students. For all the trainees, before the application, please ensure you have some experience with programming (R and Python are preferred) and statistics. The Resource page will direct you to some great sources to learn programming and statistics.


Alumni

Jeanne Yang Summer intern Undergraduate at UM
Shan-Ju Yeh 2019-2020 Visiting Scholar PhD student in Taiwan National Tsinghua University
Christopher Chang 2019-2020 capstone Medical student at COM
Krista Young 2019-2020 capstone Medical student at COM
Xiangyu Chen 2020 Summer Intern East Grand Rapids High School, admitted to UPenn
Yingying Wu 2019 Postdoc postdoc at Harvard
Rae Felismino 2019 capstone Medical student at COM
Cathy Lee 2019 capstone Medical student at COM
Suchir Gupta 2019 summer intern Grand Rapids Central High School, admitted to UM
Billy Zeng UCSF medical student 2017-2019 UCSF medical student
Albert Jiao Medical student 2018 matched Radiology at Harvard
Kasim Fassia Medical student 2018 Medical student at MSU
Patrick Newbury, MD Postdoc from 2018-2019 Radiation oncology resident at University of Oklahoma
Anthony Sciarini Intern from GVSU in 2018 summer and fall GVSU undergraduate
Keith Schmitt Intern from GVSU in 2018 summer and fall GVSU undergraduate
Anita Wen Summer intern from UC Davis in 2018 UC Davis
Before we moved to MSU in 2018
Jordan Spatz Medical student UCSF
Michael F. Sharpnack Medical student, volunteer Ohio State University
Reuben Sarwal Summary Intern Undergraduate, UC Berkeley
Tanisha Joshi Summary Intern High school
Jane Wei Summary Intern Undergraduate, Cornell University
Rachel (Menghua) Wu Summary Intern High school, accepted into MIT
Charles Pei Summary Intern High school, accepted into Harvard, co-mentored by Marina Sirota

Collaborators

  • Samuel So, MD (Asian Liver Center, Stanford): HCC drug validation
  • Haiyan Huang, PhD (Department of Statistics, UC Berkeley): statistical model development
  • Jiayu Zhou, PhD (Department of Computer Science, MSU): deep learning model development
  • Theodore Nicolaides, MD,PhD (New York University): DIPG validation
  • Richard Neubig, MD,PhD (MSU): Melanoma validation
  • Rajasekaran Surender, MD (Spectrum Health): MODS biomarker discovery
  • Xiaohong Li, PhD (VARI): cancer metastasis
  • Nick Duesbery, PhD (Spectrum Health): EMR mining
  • Andrei Goga, MD, PhD (Department of Medicine, UCSF)
  • ISPY team (Breast cancer, UCSF)
  • John Gordan, MD, PhD (Gastrointestinal Oncology, UCSF)
  • Katie Kelley, MD (Liver cancer, Department of Medicine, UCSF)
  • Ben Glicksberg, PhD (Institute for Computational Health Sciences, UCSF)
  • Marina, Sirota, PhD (Institute for Computational Health Sciences, UCSF)
  • Dexter Hadley, MD, PhD (Institute for Computational Health Sciences, UCSF)