Yang Shen

Associate Professor

Department of Electrical and Computer Engineering
Department of Computer Science and Engineering (Affiliated)
Texas A&M University
3128 TAMU, College Station, TX 77843

E-mail:  YShen <AT> tamu.edu
Phone: +1-979-862-1694
YouTube: https://www.youtube.com/@ML-AI-Bioinf

Current/Prospective EE(Bio/ISLS)/CS/CE students seeking mentored and funded research opportunities: please feel free to email with CV, transcript, and a brief research statement.

Selected publications in 2024:   ICLR , Human Genetics , NeurIPS

Selected publications in 2023:   ICLR , Bioinformatics , JCI

Selected publications in 2022:   WSDM , ICLR , Bioinformatics , NeurIPS

Selected publications in 2021:   JCIM , Bioinformatics , ICML-1 , ICML-2

Selected publications in 2020:   JCTC , Proteins , Bioinformatics , CVPR , ICML , NeurIPS , JCIM

12/2024  Congratulations to Shaowen on passing the Ph.D. defense! A great Ph.D. journey dedicated to generative protein design.

10/2024  Congratulations to Qiang on passing the Ph.D. defense and bringing his data science expertise to finance!

06/2024  Congratulations to Yuning on passing the Ph.D. defense! TAMU Ph.D. ... Caltech Postdoc ... CUHK-SZ Faculty

05/2024  Congratulations to Shreeman who graduated with a B.S. in Computer Engineering! As an undegraduate research scholar, Shreeman completed a thesis "Molecular Discovery Chatbot".

10/2023  Congratulations to Yuanfei on passing the Ph.D. defense!

08/2023  Yang gave two talks on protein docking and chemical discovery at the American Chemical Society 2023 Fall National Meeting.

06/2023  Congratulations to Wuwei on passing the Ph.D. defense!

04/2023  Congratulations to Yuning who received a Quality Graduate Student Award from the Department of Electrical and Computer Engineering!

11/2022  Congrats to Yuanfei and Wuwei for their posters accepted to the Biophysical Society Annual Conference. Yuanfei was also selected for a travel award.

10/2022  Congrats to Arghamitra, Yuning, Rujie, and Yuanfei whose paper on multi-modal and multi-task learning for protein-protein interactions was accepted to MLSB @ NeurIPS.

10/2022  We welcome Dr. Jiwoong Park to join us with great expertise in graph learning and great interest in molecular discovery.

09/2022  Yang presented cross-modality and self-supervised protein embedding at ECCB, which is now published in Bioinformatics.

08/2022  Congratulations to Arghamitra who received a CSGrad4US Fellowship from the National Science Foundation!

06/2022  We welcome new Ph.D. student Shuying Zhu who joined us with a department merit fellowship.

06/2022  Yang attended an NSF-funded Network Biology Workshop at Notre Dame.

12/2021  Yang is thankful to be a co-recipient of the 2021 ECE Outstanding Faculty Award.

10/2021  Congratulations to Yue who passed the Ph.D. defense!

09/2021  Congratulations to Yuning who received a Chevron Scholarship from the Department of Electrical and Computer Engineering!

06/2021  Welcome, Andrew and Nithin, to join us for a summer of full-time mentored research under the USRG (Undergraduate Summer Research Grant) Program!
(Update: 08/2021) Check out their project presentation videos: here and here!

05/2021  Congratulations to Yuning and Yue on their two papers accepted to ICML'2021 (graph contrastive learning automated and joint text-image embedding-based generative protein design)! Congratulations to Yuning on his paper accepted as a long talk (3% acceptance rate)!

05/2021  Congratulations to Arghamitra and Maxwell for accomplishing their Undergraduate Research Scholars Theses after > two semesters of excellent work! Check out their project presentations: video 1 and video 2.
Arghamitra's project was selected to present to the ECEN board of directors and won a Second Prize. She will graduate with a B.S. in Electrical Engineering this May and start her career!
Max's project won both the First Place Award for Senior Capstone Design in ECEN and the First Place for Overall Capstone (across all Engineering departments) at 2021 Engineering Project Showcase featuring more than 150 team projects by over 1000 engineering students!

04/2021  Mostafa has been selected for a 2021 Association of Former Students Distinguished Graduate Student Award for Excellence in Research - Doctoral, one of the Texas A&M’s highest levels of recognition. (News 1 and 2 ). Congratulations, Mostafa!

12/2020  Our paper on guided conditional Wasserstein GAN for de novo protein design was featured on the cover of JCIM.

08/2020  Mostafa defended his Ph.D. thesis -- the first Ph.D. graduate from our group, Whoop! -- and will start his career with Microsoft. Congrats and best wishes!

06/2020  Di finished his chapter at TAMU with us (first M.S. then research associate) and will start his Ph.D. program at Penn. Congrats and best wishes!

05/2020  Fangtong graduated with M.S. and will start her Ph.D. program at NCSU. Congrats and best wishes!

02--05/2020  Congrats to Yuning's first and second papers (CVPR and ICML) here. Way to go!

03/2020  Yang attended an NSF-funded Cell Modeling Hackathon in San Francisco.

01/2020  Yang is thankful to receive a CAREER Award from NSF.

12/2019  Five of us attended the CAGI* Workshop in San Francisco. Yue was invited for a flash talk. Mostafa and Yue both received NIH-funded travel fellowships to present their latest work in posters.

09/2019  Our work "Learning to optimize in swarms" is accepted to NeurIPS 2019. (Update: Nov. 2019)

08/2019  Vishnu completed his 10-week program with us as an undergraduate research intern. Next stop ... Grad Program ... Good luck!

07/2019  Yang gave a talk "Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking" at ISMB 2019. Video

05/2019  Our paper "Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas" was selected among the Best of 2018 by Cell Reports.

05/2019  A group of our graduate and undergraduate students published in Human Mutation: "Predicting Pathogenicity of Missense Variants with Weakly Supervised Regression". Congratulations to all!

04/2019  Yang gave an invited talk "Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking" at the 7th CAPRI Meeting. He also gave a talk on "Interpretable Deep Learning for Compound-Protein Affinity Prediction" at the University of Cambridge.

04/2019  Our collaboration with the Ward and Ober Lab on pH-specific antibody-drug conjugate published in Nature Biotechnology. TAMU Research Bulletin.

02/2019  Mostafa and Di's DeepAffinity was published in Bioinformatics: "DeepAffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks" (code). Congratulations!

12/2018  Di has defended his M.S. thesis.

08/2018  Haoran and Tianliang have received their Master's degrees and Seyi has completed his USRG program. Congratulations!

06/2018  Mostafa's paper on exact combinatorial optimization for multistate protein design is accepted to ECCB and will appear in Bioinformatics. Congratulations, Mostafa!

05/2018  Shen lab graduates the first M.S. student. Congratulations to Yi!

03/2018  Call for papers: 3rd BOOM - Joint AAMAS-ICML-IJCAI Workshop EasyChair CFP.

09/2017  Thankful to receive a MIRA Award from NIGMS of NIH. TAMU ECE News.

06/2017  Invited talk at the 18th Yale Workshop on Adaptive and Learning Systems.

12/2016  Tied the 3rd (with Kihara and Seok) among 48 groups in The Second CASP-CAPRI. (source: Marc Lensink's latest CASP12-CAPRI paper in Proteins)

11/2016  Haoran and Yuanfei published their first paper on Proteins, titled "Predicting Protein Conformational Changes for Unbound and Homology Docking: Learning from Intrinsic and Induced Flexibility". Congratulations, Haoran and Yuanfei!

10/2016  Invited talk at MPI 2016 titled "Predicting protein conformational changes upon binding and mutation".

08/2016  Mostafa was selected to receive an NSF Award for Young Professionals Contributing to Smart and Connected Health and invited to give a lightning talk at IEEE EMBC 2016. Congratulations, Mostafa!

04/2016  Selected and invited talk at the 6th CAPRI Evaluation Meeting titled "Modeling protein conformational changes during protein interactions with cNMA – encounter complex-based Normal Mode Analysis".

01/2016 CALL FOR PAPERS: First International Workshop on Biomedical Informatics with Optimization and Machine Learning (BOOM2016; in conjunction with IJCAI) and EURASIP Journal on Bioinformatics and System Biology: Special Issue on Biomedical Informatics with Optimization and Machine Learning. Update(10/2016): The special issue is now released and being updated.

06/2015  "cNMA: A Framework of Encounter Complex-based Normal Mode Analysis to Model Conformational Changes in Protein Interactions" published in Bioinformatics.

01/2015  Ranked 4th among 29 groups for performances predicting 25 oligomeric protein structures in CAPRI Round 30. See an official summary (page 72).

01/2015  Assistant professor at TAMU.

11/2014  "Molecular Mechanisms and Design Principles for Promiscuous Inhibitors to Avoid Drug Resistance: Lessons Learned from HIV-1 Protease Inhibition" published in PROTEINS.

11/2013  "ESR1 Ligand-binding Domain Mutations in Hormone-resistant Breast Cancer" published in Nature Genetics. (Highlighted in Nature Reviews Clinical Oncology and Nature Reviews Cancer.)

10/2013  Dr. Tomasz Oliwa joins as a postdoctoral scholar. Welcome, Tomasz!

10/2013  "Improved Flexible Refinement of Protein Docking in CAPRI Rounds 22–27" published in PROTEINS.

09/2013  "Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds" published in ACS Chemical Biology.

05/2013  Antiandrogen paper highlighted in Nature Reviews Cancer and Science-Business eXchange (Cover Story).

04/2013  Selected talk at the 5th CAPRI Evaluation Meeting, titled "Improved flexible refinement of protein docking in CAPRI rounds 22–27".

04/2013  Invited talk at the 245th ACS, titled "Designing and unraveling promiscuous inhibitors against drug-resistant target mutations".

04/2013 "Overcoming Mutation-Based Resistance to Antiandrogens with Rational Drug Design" published in eLife. (Editor's Choice, eLife Insight)

02/2013  Awarded 2M CPU hours in total (2012-13) at Argonne Leadership Computing Facility.

11/2012 "Charge Optimization Theory for Induced-Fit Ligands" published in JCTC.

06/2012  Visiting assistant professor at MIT.

01/2012  Best performance in CAPRI Round 26 (1st out of 42 worldwide teams).

01/2012  Started the appointment of research assistant professor at TTI-C.

07/2011  Produced one fair and two medium predictions for three protein–protein targets and ranked No. 2 among 37 worldwide teams in CAPRI Round 23.

03/2011  Oral presentation at the 241st American Chemical Society (ACS) National Meeting.

Bio

Yang Shen is an associate professor in the Department of Electrical and Computer Engineering at Texas A&M University.  He is also affiliated with the Department of Computer Science and Engineering and the Institute of Biosciences and Technology.

He received his B.E. in Automatic Control from the University of Science and Technology of China in 2002 and his Ph.D. in Systems Engineering from Boston University in 2008.  In 2008–2011 he had been a postdoctoral associate with Bruce Tidor in the Department of Biological Engineering and the Computer Science & Artificial Intelligence Laboratory (CSAIL) at Massachusetts Institute of Technology where he remains a research affiliate. In 2012–2014 he had been a research assistant professor at Toyota Technological Institute at Chicago, a philanthropically endowed academic computer science institute with a close affiliation with the University of Chicago.

His research interests are in modeling, simulating, and engineering of biomolecules and biomolecular networks, with the goal of probing molecular mechanisms and modulating emergent behavior.  Specific topics include protein docking, protein engineering, drug design, systems and synthetic biology, and bioinformatics.  Central to these ends are the development and application of computational methods in molecular modeling, network simulation, optimization, machine learning, graph theory, and system and control theory.