Computational Systems Biology in Biomedicine

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Engineering Science Hall (bldg.9), Level 2, Lecture Hall 2


We are pleased to host the KAUST Research Conference: Computational Systems Biology in Biomedicine.

Rapid progress in many areas of information technology and computer science has resulted in an unprecedented development of many areas of science and technology. Amongst the greatest beneficiaries of this information era is certainly life science, particularly in the form of computational biology. Entirely new computational methodologies are emerging as a result of the latest, powerful computational methods. Computational Systems Biology (CSB), with its focus on mathematical and computational modeling of complex biological systems, provides new insights into the functioning of organisms at different scales. Properties and interactions of entities within cells, tissues, and organs, together with associated biological networks, can now be studied in ever-increasing detail through multi-scale methods. Advances in CSB can offer many promises for life science. One of the most prominent of these is certainly in the field of biomedicine. Understanding the relationships between the entities studied in CSB and their impact on human health is a subject of great interest in medicine. Many methods in diagnostics, genetics, gene therapy, immunology, and others are developed through the application of CSB. There is no doubt that many more will be developed in the future.

A considerable part of our work here at the Computational Bioscience Research Center (CBRC) at KAUST is related to CSB, and its applications. Organizing this conference presents a great opportunity for leading researchers in the field of systems biology to survey the state of the field and discuss the latest developments, trends, and applications in biomedicine. We hope that the conference and its achievements would be of interest to a wider audience.

On behalf of CBRC and the Conference Organizing Committee, we welcome all our participants and hope for a productive and enjoyable stay at KAUST and the Kingdom of Saudi Arabia.

Vladimir Bajic, Director, CBRC and Conference Co-Chair

Takashi Gojobori, Associate Director, CBRC and Conference Co-Chair

Brief Biography

Michael Waterman holds an Endowed Associates Chair at USC. He came to USC in 1982 after positions at Los Alamos National Laboratory and Idaho State University. He has a bachelor’s degree in Mathematics from Oregon State University and a Ph.D. in Statistics and Probability from Michigan State University. He has held visiting positions at the University of Hawaii (1979-80), the University of California at San Francisco (1982), Mt. Sinai Medical School (1988), Chalmers University (2000), and in 2000-2001 he held the Aisenstadt Chair at University of Montreal.

Michael Waterman was named a Guggenheim Fellow (1995). He is an elected member of the American Academy of Arts and Sciences (1995), the National Academy of Sciences (2001) and the National Academy of Engineering (2012). Also, he is an elected Fellow of the American Association for the Advancement of Science (1990), Institute of Mathematical Statistics (1991), Society of Industrial and Applied Mathematics (2009) and International Society of Computational Biology (2009). In fall 2000 he became the first Fellow of Celera Genomics. Waterman received a Gairdner Foundation International Award (2002), the Friendship Award from the Chinese government (2013) and the Dan David Prize (2015). He is an elected Foreign Member of the French Académie des Sciences (2005) and the Chinese Academy of Sciences (2013). He received Doctor Philosophiae Honors Causa from Tel Aviv University (2011) and Southern Denmark University (2013).

During 2003-2008, Professor Waterman held a 5-year term as Faculty Master of Parkside International Residence College at USC. PIRC is a residential college that is home to over 600 undergraduates and serves as a center for internationally oriented cultural, academic and social events.

From May 2008 to May 2014, in addition to his USC appointment, Michael Waterman became Chair Professor at Tsinghua University in Beijing.  He led a team of distinguished scientists which collectively worked to enhance Tsinghua's programs in bioinformatics and computational biology. Currently, he is Cao Xingcheng Chair Professor at Tsinghua University and Distinguished Professor at Fudan University in Shanghai.

Michael Waterman is a founding editor of the Journal of Computational Biology and is on the editorial board of several journals. He is the author of Introduction to Computational Biology: Maps, Sequences and Genomes and is a co-author of the text Computational Genome Analysis: An Introduction. Also with Istrail and Pevzner in 1997, he began the international conference Research in Computational Biology (RECOMB).

Professor Waterman works in the area of Computational Biology and Bioinformatics, concentrating on the creation and application of mathematics, statistics and computer science to molecular biology, particularly to DNA, RNA and protein sequence data. He is the co-developer of the Smith-Waterman algorithm for sequence comparison and of the Lander-Waterman formula for physical mapping. His paper with Idury in 1995 introduced the use of Eulerian and De Bruijn graphs for sequence assembly.

Statistical Issues of Sequence Comparison: Analysis by Position and Analysis by Pattern​

Comparison of DNA and protein sequences is often done by calculation of an optimal alignment between two sequences. This talk will briefly survey statistical issues for global and local alignment, including Smith-Waterman and BLAST. In the last few years analysis by pattern or word counts has become important. A careful analysis of the relevant count summaries is crucial to increasing the statistical power of this approach.​


  • Michael Waterman, Professor of Biological Sciences, Mathematics, Computer Science University of Southern California, USA, Special guest and speaker
  • Adeeb Noor, Assistant Professor King Abdulaziz University, Saudi Arabia
  • Alyaa Mohammed, Ph.D. Student, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Saudi Arabia
  • Arwa Bin Raies, Ph.D. Student, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Saudi Arabia
  • Charlotte Hauser, Professor, King Abdullah University of Science and Technology, Saudi Arabia
  • Dan Cook, Research Professor, Dept. of Physiology & Biophysics, and Biomedical & Health Informatics University of Washington, USA
  • Fa Zhang, Professor, Institute of Computing Technology, Chinese Academy of Sciences, China
  • Fengzhu Sun, Professor, University of Southern California, USA
  • Hiroto Maeda, Director of Marine Research Center, Faculty of Fisheries, Kagoshima Univeristy, Japan
  • Imene Boudellioua, Ph.D. Student, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Saudi Arabia
  • Intikhab Alam, Senior Software Developer Bioinformatician, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Saudi Arabia
  • Jesper Tegner, Professor, King Abdullah University of Science and Technology, Saudi Arabia
  • Jysoo Lee, Director, Supercomputing Lab, Core Labs, King Abdullah University of Science and Technology, Saudi Arabia
  • Katsuhiko Mineta, Senior Research Scientist, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Saudi Arabia
  • Martin Noble, Professor of Structural Biology and Anticancer Drug Discovery, Northern Institute for Cancer Research, Newcastle University, UK
  • Masashi Mizokami, Director, Genome Medical Sciences Project, National Center for Global Health and Medicine, Japan
  • Naruya Saitou, Professor, National Institute of Genetics, Japan
  • Peer Bork, Senior Group Leader, Head of Unit and Strategic Head of Bioinformatics, European Molecular Biology Laboratory (EMBL), Germany
  • Peter Hunter, Professor, Auckland Bioengineering Institute, New Zealand
  • Pierre Magistretti, Distinguished Professor, Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Saudi Arabia
  • Rashid Mehmood, Professor of Big Data Systems, Director of Research, Training and Consultancy High Performance Computing Center, King Abdulaziz, Saudi Arabia
  • Stefan Arold, Professor, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Saudi Arabia
  • Stefan Knapp, Professor  of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany and University of Oxford, UK 
  • Takehiko Kobayashi, Lab Head Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan
  • Tao Jiang, Professor, University of California, Riverside, USA
  • Wei Wang, Director of Scalable Analytics Institute, University of California, Los Angeles, USA



1- Out-of-Kingdom Entries (Closed)

The winners will have an all-expenses-paid trip to attend the CBRC conference at KAUST, Kingdom of Saudi Arabia.

The Computational Bioscience Research Center (CBRC) will cover travel and accommodation for a number of students to attend and exhibit their posters at the Conference.

The Student Poster Competition is open for any graduate student to present work from projects that they have carried out at their university or during internships. All submitted posters will become public information, so it is the student’s responsibility to make sure that there are no confidentiality issues or other conflicts arising from the submission.

In order to enter the competition, applicants must be currently in a masters, doctoral or first-year postdoctoral level status. Submissions will be evaluated based on novelty and applicability of Computational Systems Biology in Biomedicine.

The applicants must ensure that they are in possession of a passport valid for at least six months after the intended date of departure from Saudi Arabia in order to be able to apply for a Saudi visa in a timely manner. We will guide and assist the chosen students in their visa application. Proposals should be submitted via email to or with Computational Systems Biology in Biomedicine Competition in the subject line to whom further inquiries should be made.

2- KAUST Entries (Deadline November 20, 2016)


The Student Poster Competition is open to all students of KAUST who have research in the field of Computational Systems Biology in Biomedicine.

Proposals should be submitted via email to or with Computational Systems Biology in Biomedicine Competition in the subject line to whom further inquiries should be made.


Follow the simple steps to register:


Please send your:

  • Full name
  • Email address
  • Position
  • Institution

To Ms. Ann Bauwens, Executive Secretary: or Ms. Sarah Salhi, Administrative Assistant:


Frequently Asked Questions


Q: Where is the conference located?

A:  KAUST Research Conference: Computational Systems Biology in Biomedicine will take place at King Abdullah University of Science and Technology (KAUST), in the Engineering Science Hall (Building 9) Level 2, Lecture Hall 2.

Q: I would like to present at the conference. How can I do that?​

A: Presenting at the conference is by invitation only, except for a limited number of Ph.D. students whose poster session applications are accepted.

Q: I would like to attend the conference. How do I register?

A: Due to Saudi visa requirements, we can accept out-of-Kingdom attendees only in highly exceptional cases. In-Kingdom applicants will be considered subject to logistics availability. 

Q: How can I register for the conference?

A: You can register or unregister:

 (1) by sending an email to   or or
 (2) in person, before a session starts.

Q: I'm not in KAUST. How do I join the student poster competition? (CLOSED)

A: The deadline for external submissions is October 31, 2016. The deadline is early because we need time to process visas and other documents. Send your submissions to   or

Q: I'm in KAUST. How do I join the student poster competition?

A: The deadline for internal submissions is November 20, 2016. This is open to all KAUST students with research relevant to the conference title (Computational Systems Biology in Biomedicine). Send your submissions to   or​.​

Q: What is the guideline for the student poster competition?


  • The poster should be sent in PDF format, portrait layout and A0 size (841mm x 1189mm or 33.11" x 46.81").
  • Authors are expected to be by their posters during the poster session to answer questions from judges and attendees.
  • Participants are responsible to remove and collect their posters after the conference. Unclaimed posters will be discarded.

Q: What costs will be paid for the out-of-Kingdom winners of the student competition?

A: Airfare (economy class), hotel, taxi (to and from the airport in KSA) and visa fees.

Q: What are the student poster competition prizes?​


  •     1st Prize - Ipad Air
  •     2nd Prize - BOSE Sound Link System
  •     3rd Prize - PHOTO CUBE Compact Photo Printer

Additionally, there will be a "KICP Innovation Award" trophy for a student who presents an innovative research project with a high potential for market application. This may be awarded in conjunction with the 1st, 2nd or 3rd prize.

Q: Is there any business center around the conference venue?

A: Yes, KAUST Library is open 24 hours and offers workstations and a quiet space for work and study. Wi-Fi is also accessible everywhere on the KAUST campus. 

Q: What should I wear at KAUST?

A: December at KAUST will be warm and likely pleasantly breezy with the possibility of a chance of rain. Smart casual attire is required at the conference. Women do not have to wear abaya but should be dressed in conservative clothing (neck, arms, and legs covered with loosely fitted clothing). 

Q: What are the recreation options available at KAUST?

A: Many recreation options are available at KAUST. To find out more, visit this link.

Contact Person