Yang Shen

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Assistant Professor

Department of Electrical and Computer Engineering
TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering
Texas A&M University
3128 TAMU, College Station, TX 77843

E-mail:  YShen <AT> tamu.edu
Phone: +1-979-862-1694


 

News


Recruiting postdocs in sequence analysis, protein modeling, systems biology, omics, or machine learning. Please see an ad here.

Recruiting excellent Ph.D. students all the time! (CS/OR/Engineering (Algorithms)/Applied Maths background preferred). Please see an older ad here.

Teaching: ECEN489/ECEN689 Algorithms in Structural Bioinformatics Spring 2016 Syllabus, Fall 2015 Final Projects and Spring 2016 Final Projects. (Will be offered as ECEN 766 once a year from 2017-18).

Check out a video about our research.

I am organizing ECEN Bio-Group Seminar.

Current TAMU students: please feel free to email with CV, transcript, and a brief research statement.



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 proteinprotein 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 assistant professor in the Department of Electrical and Computer Engineering at Texas A&M University.  He is also affiliated with the TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering.

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 20082011 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 20122014 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.