MY RESEARCH  Interests   Projects  Skills Resources Awards Acknowledgement

Interests

• Optimization, Graph Theory and its Applications
• Data Mining, Computation Intelligence
• Parallel and Distributed computing
• Scientific Computing, Bioinformatics
• Applied dynamical systems and complex networks

Projects (papers and softwares)

• AlignNets : Network alignment and motif finding( Recomb Satellite'07 paper,  BIBE'07 paper , BIBE'07 slides  , ISBRA'07 ,  CSBS 2007  ) ( It is still going on.......)
   
• iC2mpi : A Platform for Parallel Execution of Graph-Structured Iterative Computations (Paper in PDSEC'07  )  (CSc6310)
  - Studying static and dynamic load balancing in distributed computing;                                                      - Battlefield simulation based on iC2mpi;
   
• MANET : Self Management Routing of Mobile Sensor Network (Paper in SpringSim'06  Slides in SpringSim'06   Paper in Studies in Computational Intelligence'06    ) (Executable Codes).
  - Designing and implementing the self management routing for mobile sensor network
  - Agent based simulation
   
• CrayfishSim : A behavior-model simulation based on DEVSJAVA ( Poster in SECABC05 ) (Executable Codes);
  - Designing and implementing behavior-model oriented Heapsimulation
  - Designing and implementing a controller for the behavior-model simulation
   
• Task Allocation in Real Team and Multi Robots  (CSc8350) (.doc)

SKills

• Distributed application designing and programming with WebLogic, TOMCAT, JAVA, SERVLET, JSP, Java script, EJBs, JNDI, Java RMI, XML. (J2EE architecture, three years)
• Familiar with the digital security protocols: PKCS, X.509, SSL, HTTPS
• Experiences with
  Programming packages: JDK, EJBs, WebLogic, VC, VB, JDOM, JDBC, ODBC, SQL
  Operating Systems: Linux, Solaris, Windows 95/98/2000/XP
  Database Environment: SQL Server, Oracle
  Languages: C, Java
   

RESOURCES

• Research skills: Advice on Research and Writing , Paper Reading Check List , How to Read a Research Paper , Advice collection , You and Your Research by Richard Hamming
   
• Biological Network Research Groups: Systems Biodynamics Lab,      Systems Biology,      Gil Alterovitz,      Prof. Luonan Chen   UGA_CSBL   Srinivasan  BS : Algorithms for Bioinformatics in Stanford Univ CMU_AlgInComputationBiology   Olegro(Technion_Dr Pinter),     Mehmet Koyuturk in Purdue,     Ron Shamir,     Roded Sharan,     Darren Wilkinson ,     Serafim Batzoglou,     Jason Flannick,     Benny Chor,     UCSD_GCRC,     Dan Gusfield in UCDavis,      Peter D Karp in SRI ,      Eberhard O. Voit (GIT) ,      Sebastian Wernicke jeffrey heer (UC Berkeley)
 
 
• Data Mining Groups: Jiawei Han,      SUDUE,      Hiroshi Motoda,      Karsten M. Borgwardt(UC),      Michel Neuhaus,      Wojciech Szpankowski(Purdue),      Dennis Shasha(NYU),      Horst Bunke(GED),      George Karypis - FSG: Frequent Subgraph Miner,     
• Parallel Computing Groups: Vipin Kumar,     
• Applied Dynamical Systems and Complex Networks: Chai Wah Wu,      Uri Alon's lab,      Igor Belykh,     
• Scientific Computing Groups: Richard M. Fujimoto,     
• Focused Organization: SIGKDD   ISCB   BIOINFORMATICS
   InstituteOfSystemBiology
• Reading List:  Role of  Modeling in System Biology (pdfs)
   
• Tools for System Biology: EBI   BioCyc  Yeast  SBML  NCBI  ExPasy   KEGG
   
• Focused Events:
  10th Int. Conference on Data Warehousing :Data mining applications[March 28, 2008]
  8th ICDM Industrial Conference on Data Mining[1-21-2008] 
  ISMB 2008 [01-16-2008]  
  21th CBMS IEEE International Symposium on Computer-Based Medical Systems
  14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining[2-28-2008]
  2007 RECOMB Satellite Conference on Systems Biology [September 1, 2007]  
  12th International Conference on Research in Computational Molecular Biology (RECOMB2008)[24 September 2007]
  22nd IEEE International Parallel & Distributed Processing Symposium[8 October 2007]
  BioInfoSummer 2007[5 October 2007]
  IEEE/ACM Transactions on Computational Biology and Bioinformatics; [...]  
  IEEE Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)[Mar. 2008]  
  WABI: Workshop on Algorithms in Bioinformatics ICECCS: IEEE Intl Conf on Eng. of Complex Computer Systems (0.88) WG: Workshop on Graph Theory (0.86) AMIA: American Medical Informatics Annual Fall Symposium (0.96) ICSC2: International Computer Symposium Conference (0.87) ECAIM: European Conf on AI in Medicine (0.85) APAMI: Asia Pacific Assoc for Medical Informatics Conf (0.85) BIOCOMP/METMBS: Intl Conf on Bioinformatics and Computational Biology (0.62) ICATPN: International conference on application and theory of Petri nets (0.54) http://www.cs-conference-ranking.org/conferencerankings/topicsiv.html
 http://www.kmining.com/info_conferences.html
• Computing: Java Reference(Sun) , ANSI C Manual , The Open Group Base Specifications Issue , C/C++ Reference, Thinking in Java, C++ resource , C++ STL , SQL Tutorial, LaTeX Reference , Latex Tutorial, Matlab Function , Cliff Zou's Notes on Linux , Algorithm Repository , A compendium of NP optimization problems , Math World , ns-2 , Engineering Statistic , Some Computing Resources , Queueing Books Online , MIT Open Courseware , Cryptology Pointers ,  GNUPLOT, GNUPLOT 2, GAWK, Bash, Learning KShell, Perl, Learning PERL, Programming PERL, Mastering VI, Python Tutorial, Sed & AWK, java, HTML 4.0 Standard ,  HTML Tutorial,   XML Tutorials [XML]
   
• DB: SUN's JDBC tutorial, MySQL Database Manual, MySQL Connector-J
   
• Dictionary: TigerNT , Merriam-Webster's , Mathworld , math tables , Wikipedia