Our lab is interested in leveraging OMICS, electronic medical records, and advanced machine learning methods to identify new therapeutics and biomarkers ( B. Chen, 2016, B. Chen, 2020). Three main research areas include: 1) OMICS-based drug discovery, 2) OMICS-based biomarker and target discovery, and 3) virtual platform development to support translational research. The data we primarily use include bulk/single cell transcriptomics, spatial transcriptomics, and EMR/EHR. In addition to traditional bioinformatics methods (e.g., sequence analysis), we actively develop and implement new machine learning models such as transfer learning and deep reinforcement learning to deal with the emerging big data. To achieve the goal of identifying new therapeutics, we closely collaborate with data mining experts, statisticians, bench scientists, medicinal chemists, and physicians. We are always looking for highly motivated students and postdocs to join the endeavor.
Upcoming events
News
We don't provide regular updates anymore, instead, we will only share our annual report and the most significant updates. Here is the one for the 2022-2023 academic year .
Our DIPG drug repurposing manuscript and our EHR LOINC mapping manuscript are accepted in Acta Neuropathologica Communications and JAMIA Open, respectively.
Our drug discovery work for SARS-COV-2 and its variants is accepted in principle by iScience (Cell publishing group), MSU today.
Our AI-drug discovery R01 finally gets started, MSU today.
Shan-Ju Yeh accepts a fixed-term assistant professor position at Taiwan National Tsing Hua University, congrats!
Welcome our high school summer interns Chris Chang, Jenny Qi, and Rohit Agarwal.
Rama submits the NIH Pathway to Independence Award (K99) proposal. Good luck.
Our MolSearch paper with the Zhou Lab wins the best paper award (first place) at the 2022 KDD Health Day. Well done.
Bin is promoted to Associate Professor with tenure at MSU. Excited to move to the next stage.
Welcome Xiaodan Zhang to join our lab as a data science specialist.
Mengying successfully defended. She joins Facebook(Meta) as a data scientist. Best wishes!
Welcome Dmitry Leshchiner, MD, to join our lab as a postdoc fellow.
Dr. Jing Xing accepts an offer to start her OWN group at Shanghai Institute of Materia Medica, Chinese Academy of Sciences soon. Cheers!
Dr. Ke Liu accepts an offer to start his OWN lab in Shandong University in China soon and is named Qilu Scholar (齐鲁青年学者). Cheers!
Dr. Eugene Chekalin finishes the postdoc training and joins Illumina as a senior computational biologist. Congrats and best wishes!
The lab receives an R01 Diversity Supplement award to support Dimitri for his racial disparity work. Cheers.
The lab first EMR/EHR data mining paper led by Dr. Ke Liu is accepted by AMIA 2022. A great collaboration with Spectrum Health.
Bin recieves the 2021 Early Career Research Excellence Award at CHM. Cheers!
Our AI-based virtual screening R01 recieves an outstanding score (7 percentile). Looking foward to the great science.
Our pipeline is also applied to find drugs to overcome resistance in melanoma (accepted by Molecular Pharmacology, on the cover)
Our drug repurposing pipeline is successfully applied to Alzheimer's disease (Nature Aging).
Welcome Han Meng to join our lab as a research assistant.
Bin has a new appointment at the Department of Computer Science and Engineering.
Welcome lab rotation student Jacob Zieba.
Chen lab co-leads an NIH T32 funded boot camp in big data and computational chemistry.
Welcome our summer intern Jeanne Yang from UM and undergraduate researcher Spancer Zhou.
The SARS-CoV-2 drug analysis manuscript led by Jing is accepted by Briefings in Bioinformatics (IF:11). link, News. Congrats.
Bin is invited to speak at the Frontline Genomics and the Sino-American Pharmaceutical Professionals Association (SAPA) Scientific Symposium.
Xiangyun Chen, our high school intern in 2020, will go to UPenn. Congrats!
Mengying and Jing's manuscript on contrastive learning in molecular representation is accepted by KDD. A great collaboration with Jiayu's lab.
Bin organizes the local biweekly Computational Biology Forum this spring. A great success!
Rama and Ke present their posters at the AACR annual meeting.
Jing's anti-SARS-CoV-2 drug analysis work is selected to present at the Pediatric Research Day and at the ISMB/ECCB 2021.
We are striving to use the best science to help patients suffering from COVID-19. Check out our three COVID projects.
The MODS biomarker work led by Dr. Rama Shankar is accepted by EBioMedicine(The Lancet) . First collaboration with Spectrum Health. Congrats!
Dr. Ke Liu becomes a research assistant professor at MSU, congrats Ke.
MSU ICER highlights lab COVID-19 research.
Bin joins the Journal of Cheminformatics Editorial Board (IF: 5.3).
Our collaborative work with Prof. Jiayu Zhou's lab gets accepted into ICDM. This work paves the way to perform large-scale novel compound screening.
Welcome new rotation PhD students Dimitri Joseph and Ruoqiao Chen.
OCTAD is accepted by Nature Protocols. Congrats!
Excited to organize one-week Translational Bioinformatics in R Workshop at MSU.
Delighted to join the effort led by Dr. Ying Ding to develop COVID dashboard funded by NSF Rapid.
Welcome summer intern Xiangyu Chen and new members Jeremy Haskins and John Fan. Wish the best to our medical students Rae, Cathy, and Krista.
Since late Jan, the lab has been working crazily on the COVID 19 research, we released our first work today ( MSU Today, WLNS, Detroit Business), we also welcomed twin medical students Austin and Tyler.
Lab research on biomarker discovery is featured at MSU Today
The lab receives an award from the NIH NCATS Translator program. Excited to be part of this program.
Welcome our new postdoc Dr. Evgeny Chekalin who received the PhD in both Genetics and Bioinformatics from the Vavilov Institute of General Genetics, Russian Academy of Sciences.
Bin Chen is one of the eight scientists featured on the C&EN Discovery Report on AI in drug discovery.
The video of our recent seminar big data in translational research is available here (watch).
Chen lab research is featured on the MSU Innovation Center Fall e-newsletter
Welcome Dr. Yingying Wu to join our lab as a postdoc. Dr. Wu received her PhD at UT Austin and MS at Harvard.
The snoRNAs work led by Davide Ruggero's lab is accepted by eLife. Glad to help with the bioinformatics analysis.
Bin is invited to speak at Moving Targets 2019 at USC.
The lab receives a 5-year R01 from the NIH to continue our exciting research.
Bin Chen presents lab research at Fudan University (China), Suzhou University (China), JSM 2019 (Denver), and Childhood Cancer Data Initiative (Washington DC).
The lab receives funding from the MSU-Spectrum Health Alliance to mine EMR data at Spectrum Health. We are hiring full-time data scientists to join this endeavor.
Patrick starts his residency, Best of luck! Welcome visiting student Shan-Ju Yeh from National Tsing Hua University and summer intern Suchir Gupta from the Central High school.
Ke, Rama and Bin present their work at ICIBM 2019 in Columbus, Ohio. Amazing 6h road trip together (Ke, Rama, Bin, Jing and Shreya).
The pan-cancer cell line comparison work led by Sirota's lab is accepted by Nature Communications. Glad to be part of it.
The lab receives a two-year industry-sponsored grant to work on immunotherapy target discovery. Excited to expand our drug discovery pipeline to cancer immunotherapy.
Welcome Christopher Chang, a medical student at COM/MSU, to work on the capstone project in the lab.
Our cell line evaluation paper is published in Nature Communications today (MSU Today, GEN). Cheers!
Bin is quoted in the MSU Global Impact Initiative story.
Welcome medical students Cathy Lee, Krista Young and Rae Felismino to work on their capstone projects in the lab.
Chen lab receives AWS Cloud Credits for Research Application to support OCTAD development, Thanks, Amazon!
Jing presents the work on the prediction of drug-induced gene expression change at the 2019 P4 Midwest Conference, well done!
Our collaborator Prof. Haiyan Huang at UC Berkeley is visiting the lab for a week, welcome!
Ke's cell line evaluation work is accepted by Nature Communiciations, Congrats!
Patrick presents the DIPG work and Rama presents the MODS work in the Pediatric Research Day, well done!
Patrick matched the competitive Radiation Oncology program at the University of Oklahoma! We are super happy for Patrick!
The book chapter with Ben, Li, Rong, Joel is online now. Great collaboration!
Patrick's DIPG work is chosen as one of the six oral presentations from over 50 submissions in the MSU Pediatrics Research Day 2019. Well done!
Albert Jiao presents his work on cholangiocarcinoma therapeutic discovery at MSU Graduate Academic Conference 2019. Well done!
Our review on big data in HCC therapeutic discovery is accepted by Nature Reviews Gastroenterology & Hepatology. Congrats!
Tom presents the AICM method and Bin presents the cell line evaluation work at PSB. Tom wins the travel award. Congrats!
Welcome medical students Albert Jiao, Kasim Fassia and rotation student Omar Kana to the lab.
Bin Chen speaks at the inaugural immunology and immunometabolism conference in Chongqing, China
Chen Lab work is reported in the Drug Discovery special issue at C&EN: Mining gene expression data for drug discovery.
Chen Lab organizes the computational drug discovery workshop for medical students at MSU.
Bin Chen speaks at the Big Data Ignite Conference in Grand Rapids.
Tom's manuscript entitled "AICM: A Genuine Framework for Correcting Inconsistency Between Large Pharmacogenomics Datasets" is accepted to PSB. Congrats!
Bin Chen is invited to speak at JSM 2018 in Vancouver, Canada.
Welcome new members. Check out our first lab party at MSU.
Bin Chen speaks at ICSA 2018 Applied Statistics Symposium in New Brunswick, NJ and at ICIBM 2018 in Los Angeles, CA.
Bin Chen attends the 2018 Data Science Innovation Lab: Mathematical Challenges of Single Cell Dynamics.
Ke submits his manuscript about cell line evaluation for metastatic cancer research. Way to go.
We will present the open cancer therapeutic discovery pipeline at AACR Annual Meeting 2018 in Chicago, Illinois, USA
Chen Lab moves to MSU from UCSF. Chen is recruited under the Global Impact Initiative program.
Billy's manuscript on using deep learning for reference normal tissue selection is accepted by ICIBM 2018, and will appear in BMC Genomics. Congrats!
Bin Chen is invited to speak at 2018 Breast Oncology Program Annual Retreat at UCSF
Billy submits his manuscript about using deep learning for reference normal tissue selection and Jenny submits her abstract about identifying breast cancer non-responder signatures.Well done.
Bin Chen organizes for the Chinese American Biopharmaceutical Society (CABS) workshop entitled BIG DATA FOR DRUG TARGET DISCOVERY
Bin Chen presents a poster about our drug discovery pipeline at PSB 2018 in The Big Island of Hawaii
Our liver cancer work is featured in the UCSF Magazine Winter 2018 and the UCSF Cancer Year in Review: 2017 . Well Done 2017!
Michael F. Sharpnack's paper on RNA editing is out and there is one commentary on this work. Congratulations!
We are joining the IDG (Illuminating the Druggable Genome ) Ion-Channel informatics team.
Bin Chen is invited to speak at Global Pharma R&D Informatics Congress 2017 in Lisbon, Portugal
Bin Chen is invited to speak at 2nd Strategic Partnerships for Drug Repurposing Forum in Boston MA
Bin Chen gives a talk for the DahShu Virtual Club and SFASA Monthly Seminar. Download slides and video here.
We are excited to participate the P01 grant entitled "I-SPY2 +: Evolving The I-SPY 2 Trial To Include MRI-Directed, Adaptive Sequential Treatment To Optimize Breast Cancer Outcomes". We will predict drugs to overcome drug resistance in breast cancer. Excited to join I-SPY.
The basal cell carcinoma repositioning work led by the Stanford researchers is accepted by JCI Insight.
We recieve a 2-year R21 ($570K in total) from NCATS to support our liver cancer drug repositioning work.
Our recent big data work is featured in KCBS.
Our paper on using big data to find out a new way of cancer treatment published in Nature Communications. (press release, paper link)
We, together with Butte Lab and Hadley Lab, recieve funds from L'Oreal to discover drugs for hyperpigmentation.
Welcome Reuben Sarwal, an undergraduate student from UC Berkeley, to join us this summer as an intern.
Bin Chen is invited to present at 2017 UCSF Hepatobiliary Cancers Research Symposium
Bin Chen receives the BD2K K01 Career Development Award (four years, $684,000 in total). He will use this award to develop novel methods for personalized cancer therapy.
Bin Chen is invited to present the work on using big data to combat cancer to UCSF donors at UCSF Cancer Showcase 2017.
our paper on using big data to identify new therapeutics for liver cancer is out ( press release)
Bin Chen gives a talk at AMIA 2017 TBI
Bin Chen is invited to participate the Big Data For Breast Cancer\West Coast Conference organized by Susan G. Komen
Summer student Tanisha Joshi presents her work at Dahshu 2017 Symposium
our paper on using big data to identify new therapeutics for Ewing Sarcoma is out.
Bin Chen and other members from Dahshu organize the conference Dahshu 2017: Data Science & Computational Precision Health. Paper submissions due: October 10, 2016 11:59PM PT!!!
Bin Chen gives an invited talk at DDW in San Diego, CA
Bin Chen gives an invited talk at the UCSF Precision Medicine Conference by PMSA at UCSF
Bin Chen and other members from Dahshu organize the Fourteenth Asia Pacific Bioinformatics Conference (APBC) in San Francisco, CA