Weng In SIU, Shirley蕭詠然
Assistant Professor

 

Academic Qualifications | Teaching | Research | Selected Publications | Professional Affiliations | Contact Details


Academic Qualification

  • B.Sc. in Software Engineering, University of Macau, Macau (1997)
  • M.Sc. in Software Engineering, University of Macau, Macau (2001)
  • M.Sc. in Bioinformatics, Saarland University, Germany (2006)
  • Ph.D. in Natural Sciences (Computational Biology), Saarland University, Germany (August 2010)

Related Working Experience

  • 1997-2001 Teaching Assistant, Faculty of Science and Technology, UM
  • 2001-2003 Lecturer, Faculty of Science and Technology, UM
  • 2009-2012 Senior Instructor, Faculty of Science and Technology, UM
  • 2010-2011 Postdoctoral research fellow, the Computational Biology Group, University of Erlangen-Nuernberg, Germany

Teaching

B.Sc. Courses

  1. Programming Languages Architecture I (SFTW241)
  2. Bioinformatics (Special Topics in CIS) (SFTW454)
  3. Information Security and Privacy (CISG113)
  4. Human-Computer Interaction (CISB250)
  5. Information Systems Analysis and Design (CISB359)

Research

Research Interests

  • Computer-aided drug design
  • Membrane protein structure prediction
  • Molecular dynamics simulations
  • Machine learning in bioinformatics

Recent Research Projects

  • “Protein-Ligand Binding Affinity Prediction for Structure-Based Drug Design”, funded by the Research Committee of University of Macau, MOP100,000, January 2013 – December 2013, PI.
  • “Computational Modeling of Electric Field in Digital Microfluidic Technologies and its Application on Simulating Droplets and Protein Adsorption on Device Surfaces”, funded by the Research Committee of University of Macau, MOP 835,000, April 2014 – March 2017, PI.
    Student positions available

Academic Activities

(1) Invited Seminar Talks:

  • The 9th Interational Conference on Advanced Data Mining and Applications (2013)
    Speech Title: Comparison of cutoff strategies for geometrical features in machine learning-based scoring functions
  • The 10th workshop on Computer Simulation and Theory of Macromolecules, Hünfeld, Germany (2011)
    Speech Title: Parameterization of hydrocarbons for OPLS-AA force fields
  • Workshop for Graduate school of the Physics department, Saarbrcken, Germany (2008)
    Speech Title: Low energy barrier of ion permeation through double helical gramicidin
  • Workshop on Computer Simulation and Theory of Macromolecules, Hnfeld, Germany (2008)
    Speech Title: Biomolecular simulations of membranes: Physical properties from different force fields
  • PhD Seminar, Center for Bioinformatics, Universitt des Saarlandes (2007)
    Speech Title: Free energy study of ion permeation through Gramidicin
  • Workshop on Computer Simulation and Theory of Macromolecules, Hnfeld, Germany (2006)
    Speech Title: Electric Fields & Membranes: Gramicidin A as a Test Ground

(2) Participated Conferences with Poster Presentation:

2010

  • Annual Meeting of the German Biophysical Society, Oct. 03-06, Bochum, Germany

2009

  • European Biophysics Congress, Jul. 11-15, Genoa, Italy
  • VIII European Symposium of the Protein Society, Jun. 14-18, Zurich, Switzerland
  • Workshop on Computer Simulation and Theory of Macromolecules, Apr. 17-19, Hnfeld, Germany

    2008

  • The 5th symposium on “Interplay between Molecular Conformations and Biological Function”, Oct. 6-8, Bad Kissingen, Germany
  • German Biophysical Society meeting, Sep 28-Oct 1, Berlin, Germany
  • Workshop for Graduate school of the Physics department, Sep. 24-26, Saarbrcken, Germany
  • Symposium on “From Computational Biophysics to Systems Biology” (CBSB), May 19-21, Jlich, Germany
  • Workshop on Computer Simulation and Theory of Macromolecules, Apr. 18-20, Hnfeld, Germany
  • Int. Workshop of Mechanical and Electrical Properties of Artificial & Cellular membranes, Mar. 31- Apr. 02, Gomadingen, Germany
  • Joint Meeting of the Biophysical Society 52nd Annual Meeting & 16th Intl. Biophysics Congress (UIPAB), Feb. 2-6, Long beach, US

    2007

  • Workshop for Graduate school of the Physics department, Sep. 11-13, Saarbrcken, Germany
  • European Biophysics Congress, Jul. 14-19, London, UK
  • Workshop on Computer Simulation and Theory of Macromolecules, Apr. 20-21, Hnfeld, Germany

    2006

  • German Biophysical Society meeting, Sep. 24-27, Mainz, Germany
  • Workshop for Graduate school of the Physics department, Sep. 11-13, Bostalsee, Germany
  • WE-Heraeus-Seminar: Biomolecular Simulation: From Physical Principles to Biological Function, May 22-24, Bad Honnef, Germany
  • Workshop on Computer Simulation and Theory of Macromolecules, Hnfeld, Germany, May 19-21.

Awards & Titles Received

  • 2008 Poster prize for “Free energy study of ion permeation through Gramicidin” in Workshop on Computer Simulation and Theory of Macromolecules, Hnfeld, Germany
  • 2006-2009 Scholarship from the Graduate school of the Physics department, Saarland University, Germany
  • 2003-2005 Scholarship from the International Max Planck Research School for Computer Science (IMPRS), Germany
  • 2003 The 2nd prize of IEEE (Macau Branch) Project Competition for “Mobile Ticket System”
  • 1997 Macau Foundation Prize for First Honor Degree graduates, UM

Selected Publications

For the copyright reason, some papers cannot be distributed online. Please email me if you are interested to obtain a copy of them.

Computational Biology related

2013

  1. Shirley W. I. Siu, Thomas K. F. Wong, and Simon Fong. Comparison of Cutoff Strategies for Geometrical Features in Machine Learning-Based Scoring Functions. Proceedings of the 9th International Conference on Advanced Data Mining and Applications (ADMA2013), Hangzhou, China, December 14-16, 2013, LNAI 8347, 336-347, Springer. (Read online)

2012

  1. Maria Borisovska, Yvonne N. Schwarz, Madhurima Dhara, Antonio Yarzagaray, Sandra Hugo, Daniele Narzi, Shirley W. I. Siu, Jaideep Kesavan, Ralf Mohrmann, Rainer A. Böckmann, and Dieter Bruns. Membrane-Proximal Tryptophans of Synaptobrevin II Stabilize Priming of Secretory Vesicles. J. Neurosci. 32 (2012), 15983-15997. (Read online)
  2. Shirley W. I. Siu, Kristyna Pluhackova, Rainer A. Böckmann. Reparameterization of the OPLS-AA force field for hydrocarbons. J. Chem. Theory Comput. 8 (2012), 1459-1470 (Read online).

2010

  1. Ling Wang, Shirley W. I. Siu, Wei Gu, and Volkhard Helms. Downhill binding energy surface of the barnase-barstar complex. Biopolymers 93 (2010), 977–985 (Read online).
  2. Siti A. Jusoh, Christoph Welsch, Shirley W. I. Siu, Rainer A. Böckmann, and Volkhard Helms. Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus. J. Mol. Modeling 16 (2010), 1625-1637 (Read online).

2009

  1. Shirley W. I. Siu and Rainer A. Böckmann. Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin. J. Phys. Chem. B 113 (2009), 3195-3202 (Read online).
  2. Robert Vácha, Shirley W.I. Siu, Michal Petrov, Rainer A. Böckmann, Justyna Barucha- Kraszewska, Piotr Jurkiewicz, Martin Hof, Max L. Berkowitz, Pavel Jungwirth. Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane. J. Phys. Chem. A 113 (2009), 7235-7243 (Read online).
  3. Rui Wang, Shirley W.I. Siu, Rainer A. Böckmann. Fine-Grained Protein Mutation Extraction from Biological Literature. Proceedings of International Conference on Electronic Computer Technology 2009 401-405, Macau, China, IEEE Computer Society, 2009.2 (Read online, pdf).

2008

  1. Daniele Narzi, Shirley W.I. Siu, Christian U. Stirnimann, John P.A. Grimshaw, Rudi Glockshuber, Guido Capitani, Rainer A. Böckmann. Evidence for proton shuffling in a thioredoxinlike protein during catalysis. J. Mol. Biol. 382 (2008), 978-986 (Read online).
  2. Shirley W. I. Siu, Robert Vácha, Pavel Jungwirth, Rainer A. Böckmann. Biomolecular simulations of membranes: Physical properties from different force fields. J. Chem. Phys. 128 (2008), 125103 (Read online, pdf).
    Selected for April issue of Virtual Journal of Biological Physics Research.

2007

  1. Shirley W. I. Siu and Rainer A. Böckmann. Electric Field Effects on Membranes: Gramicidin A as a Test Ground. J. Struc. Biol. 157 (2007), 545-556 (Read online).

2006

  1. Iris Antes, Shirley W. I. Siu, and Thomas Lengauer. DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics 22 (14): e16-e24 (Read online, pdf).

Software Engineering related

2004

  1. Antonio Leung, Simon Fong, Shirley W. I. Siu. Smart Card-based Irregular Access Patterns Detection System. IEEE International Conference on e-Technology, e-Commerce and e-Service (EEE 2004), Tapei, Taiwan, 28-31 March 2004, pp.546-553 (Read online).
  2. Simon Fong, Shirley W. I. Siu. An Integrative Framework of Predictive Mining Methods for Medical Prognosis. IASTED The 2nd International Conference on Biomedical Engineering (BioMED 2004), Innsbruck, Austria, 16-18 February 2004 (Read online).
  3. Simon Fong, Shirley W. I. Siu, Aixin Sun. Market Watcher Agent for E-Commerce. IASTED The International Conference on Artificial Intelligence and Applications (AIA 2004), Innsbruck, Austria, 16-18 February 2004 (Read online).
  4. Antonio Leung, Simon Fong, Shirley W. I. Siu. Smart Card-based Identification and Access Control Model with Real-time Suspicious Action Detection Mechanism. IASTED The International Conference on Artificial Intelligence and Applications (AIA 2004), Innsbruck, Austria, 16-18 February 2004 (Read online).

2003

  1. Shirley W. I. Siu, C. C. Fong, Z. S. Guo, K. F. Si Tou. Context-aware for Service Discovery in Ad Hoc Environment, The IASTED Intl. Conf. on Wireless and Optical Communication (WOC-2003), Banff, Canada, Jul. 14-16, 2003 (Read online, pdf).

2002

  1. Shirley W. I. Siu, H. M. Au. Solution for Electronic Ticket in Mobile Media. Proceedings of Macau IT Week 2002 Seminar Series, Macau, Oct 4-6 2002 (pdf).
  2. Shirley W. I. Siu, Z. S. Guo, C. C. Fong, Y. Zhuang, Extending E-Ticketing Service with Mobile Transactions. Proceedings of the 1st International Conference on Information Technology and Applications (ICITA-2002), Bathurst, Australia, Nov. 25-29, 2002 (pdf).
  3. C. C. Fong, Shirley W. I. Siu, and Aixin Sun, WebSpy: Retrieving Web Contents for e-Business Intelligence. Proceedings of the 1st International Conference on Information Technology and Applications (ICITA-2002), Bathurst, Australia, Nov. 25-29, 2002 (pdf).
  4. Z. S. Guo, Shirley W. I. Siu, C. T. Wong. Full-scale Online Event Ticketing System – The Design and Implementation. Proceeding of the 13th Chinese Process Control Conference, Macau and ZhuHai, China, Jul 29-Aug 2, 2002 (pdf).

2001

  1. Shirley W. I. Siu, Z. S. Guo. Application of Electronic Ticket to Online Trading with Smart Card Technology. Proceedings of the 6th INFORMS Conference on Information Systems and Technology (CIST-2001), Miami Beach, Florida, U.S., Nov.3-4 2001, pp.222-239 (pdf).

Professional Affiliations


Contact Details

Faculty of Science and Technology
University of Macau, E11
Avenida da Universidade, Taipa,
Macau, China

Room: E11-4025
Telephone: (853) 8822-4452
Fax: (853) 8822-2426 or (853) 3974285
Email: shirleysiu or siu_weng_in[at]gmail_[dot]_com (remove all the underscores)
Personal Homepage: http://www.cis.umac.mo/~shirleysiu