Research Scientist

BEIBEI HUANG

AREA OF INTEREST

Data Science and Computational Chemistry

Machine Learning and Artificial Intelligence

CAMPUS ADDRESS

Department of Experimental Therapeutics,

The University of Texas M. D. Anderson

Cancer Center, 1881 East Road, Houston,

TX 77054, USA

EM ads926@r.postjobfree.com

ads926@r.postjobfree.com

TELE: 1-713-***-****(office)

Mobile: 713-***-****

EDUCATION

2011-2015.7 PH.D IN CHEMICAL ENGINEERING (CUM LAUDE) DEPARTMENT OF CHEMICAL ENGINEERING,

UNIVERSITAT ROVIRA I VIRGILI SPAIN

2006-2009 Ph.D in Software theory,

School of computer science,

Wuhan Uni, Wuhan, China

2003-2006 Master in Software theory,

Jinan Uni, Guangzhou, China

1999-2003 Bachelor in Computer Science and Technology, Wuhan Uni, Wuhan, China

APPOINTMENTS

2016/7 – Now: MD Anderson Cancer Center

Experimental Therapeutics

Research Scientist

2009/7 - 2011/07: Chinese Academy of Sciences

Institute of Computational Mathematics

Postdoctoral Researcher

2017/07 – 2017/12: Vice Chair Responsible Conduct of Research Subcommittee RESEARCH & PROJECT EXPERIENCE

2016/7 -Now

• Research Scientist High Performance Computing and Big data analytics. The unique expertise in combining mathematics with computer science and chemistry makes me huge asset for multiple projects in the AI technique applications, such as drug discovery and development field. I specializes in modeling large-scale data and computer simulation, has successfully developed software systems for predicting drug activity, which are the basis for understanding complex chemical and biological systems that have led to drug discovery and development.

2011/1 - 2013/12

• Principal Investigator: Computer simulation of the electrostatic potential of biological macromolecules. China National Science Foundation for Young Scholars (170,000RMB).

• PI Coordinator: Responsible for the application based on PB models, studying the theory of the phenomenon caused by the electrostatic interaction, and developing efficient mathematical solver and tools. The software “IPEC” has been downloaded >1,000 times to date.

TEACHING

2004/09--2006/06: JINAN UNI. COLLEGE OF LIFE SCIENCE Teaching Assistant

Teaching "computational molecular biology"

2012/09--2014/06: UNIVERSITAT ROVIRA I VIRGILI Department of Chemical Engineering (DEQ) Supervisory Teaching

Teaching "Statistics & Operation on PC"

AWARDS

Crowd for Good - Cancer ML Benchmarking Challenge version 1.0 The overall goal is to leverage Topcoder members' technical skills in order make progress in the field of Oncology/Cancer. Top3 Rank4 6/20/2022

Poster presentation “IPEC Solver: Numerical simulation tool to study inter-polyelectrolyte complexation”, during “9-th Poster Exhibition of Doctoral Students of Department d’Enginyeria Química” in the Universitat Rovira i Virgili (Spain) won the First Place Award. PUBLICATIONS

JOURNAL ARTICLES

1. Huang, Beibei, et al. "Sequence-based Optimized Chaos Game Representation and Deep Learning for Peptide/Protein Classification." bioRxiv (2022). 2. L Zhang, J Qu, Y Qi, Y Duan, YW Huang, Z Zhou, P Li, J Yao, B Huang, Ping Li, Shuxing Zhang EZH2 Engages TGFβ Signaling to Promote Breast Cancer Bone Metastasis via Integrin β1-FAK Activation Nature Commun. 13 (1), 1-16, 2022 3. Huang, B., et al., JavaDL: a Java-based Deep Learning Tool to Predict Drug Responses. bioRxiv, 2020: p. 2020.05.04.077701.

4. Chaudhari, R., et al., An up-to-date overview of computational polypharmacology in modern drug discovery. Expert Opin Drug Discov, 2020. 15(9): p. 1025-1044. 5. Monroig-Bosque, P.D.C., et al., OncomiR-10b hijacks the small molecule inhibitor linifanib in human cancers. Sci Rep, 2018. 8(1): p. 13106. 6. Huang, B., et al., Interaction between nanoparticles and charged phospholipid membranes. Phys Chem Chem Phys, 2018. 20(46): p. 292**-*****. 7. Xu, Z., Y. Yang, and B. Huang, A teaching approach from the exhaustive search method to the Needleman-Wunsch algorithm. Biochem Mol Biol Educ, 2017. 45(3): p. 194-204. 8. Huang, B., S. Maset, and K. Bohinc, Interaction between Charged Cylinders in Electrolyte Solution; Excluded Volume Effect. J Phys Chem B, 2017. 121(38): p. 9013-9023. 9. Chaudhari, R., et al., Computational polypharmacology: a new paradigm for drug discovery. Expert Opin Drug Discov, 2017. 12(3): p. 279-291. 10. Huang, B. and V.A. Baulin, IPEC Solver: Numerical simulation tool to study inter- polyelectrolyte complexation. Computer Physics Communications, 2013. 184(9): p. 9. 11. Huang, B., B. Tu, and B. Lu, A fast direct solver for a class of 3-D elliptic partial differential equation with variable coefficient. Communications in Computational Physics, 2012. 12(4): p. 14.

CONFERENCE PROCEEDINGS

12. Li, H., B. Huang, and J. Lu, Dynamical evolution analysis of the object-oriented software systems. IEEE Congress on Evolutionary Computation, 2008: p. 5. 13. Huang, B., G. Zhang, and P.C.-Y. Sheu, A Natural Language Database Interface Based on a Probabilistic Context Free Grammar. IEEE International Workshop on Semantic Computing and Systems, 2008: p. 7.

14. Huang, B., Z. Guo, and X. Cao, An Algorithm Based on Fast Walsh Transform for Multiple Sequence Alignment. Bioinformatics and Biomedical Engineering, 2007: p. 4. POSTER PRESENTATIONS

15. 2013 Feb 24-26 Poster presentation at the “Workshop on biomaterials and their interactions with biological and model membranes 2013”, Salou (Spain) 16. 2013 July 1-3 Poster presentation at workshop “Computational Electrostatics for Biological Application (CEBA'13)”, Genoa(Italy)

17. 2007 6-8 July Poster presentation at conference “International Conference on Bioinformatics and Biomedical Engineering”, Wuhan, China 18. 2005. Poster presentation at workshop “The third International Forum on Post-Genome Technologies(3’ IFPT)”, Guilin, China

BOOK CHAPTERS

19. Beibei Huang, Vladimir A. Baulin. Efficient and stable method to solve Poisson-Boltzmann equation with steep gradients Computational Electrostatics for Biological Applications (book chapter) 2014,Springer

20. Beibei Huang, Zhongneng Xu, etc. Bioinformation chapter 4 Tinghua University Press, 2008.5

21. Lon W. R. Fong, Beibei Huang, Rajan Chaudhari, Shuxing Zhang Computational and Pharmacoinformatic Approaches to Oral Bioavailability Prediction (in press) TO BE SUBMITTED SOON

22. Luo Song, Rajan R. Chaudhari, Beibei Huang, Gabriel Lopez, George A. Calin, Edward Nikonowicz, Shuxing Zhang miRmo: a web server for non-paired pre-miRNA motif screening BMC Bioinformatics

23. Beibei Huang, Lon Wolf Fong, Rajan Chaudhari,Zhi Tan, Shuxing Zhang Supervised Autoencoders and Classification of Phosphoinositide-binding proteins BMC Bioinformatics JOURNAL REVIEWER:

13. Reviewer, Bioinformatics, Oxford University Press, 2018 14. Reviewer, ACS Sustainable Chemistry & Engineering, ACS, 2018 15. Reviewer, Expert Opinion on Drug Discovery, Informa Healthcare, 2020 16. Reviewer, BMC Pharmacology and Toxicology, BMC, 2019 to now 17. Reviewer, Mathematical Biosciences and Engineering, AIMS Press, 2021 to now

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