[By Category] [By Topic] [By Year]

Journal Publications

  1. Dan He , Abudullah N. Aslan, Alan C.H. Ling: A fast Algorithm for the Constrained Multiple Sequence Alignment problem, Accepted by Acta Cybernetica, 2006.

  2. Dan He, Abdullah Aslan: A space-efficient algorithm for the constrained pairwise sequence alignment problem. Genome Informatics 2005，Genome Informatics Vol. 16, No. 1. ISBN 4-946443-93-2. Universal Academy Press, Inc.

Conference Publications

  1. new paper Dan He, Xingquan Zhu, Xindong Wu: Approximate Repeating Pattern Mining with Gap Requirements , 21st IEEE Int'l Conference on Tools with Artificial Intelligence, (ICTAI 2009)(one of the 8 final list best papers out of 205 submissions). Newark, New Jersey, Nov. 2-4, 2009.

  2. new paper Dan He, Xingquan Zhu, Xindong Wu: Error Detection and Uncertainty Modeling for Imprecise Data, 21st IEEE Int'l Conference on Tools with Artificial Intelligence, (ICTAI 2009) (short paper) Newark, New Jersey, Nov. 2-4, 2009.

  3. new paper Nick Furlotte, Dan He, Eleazar Eskin: Detection and reconstruction of copy number variations , The 59th Annual Meeting, the American Society of Human Genetics, (ASHG 2009) (Poster), Honolulu, Hawaii, Oct. 20-24, 2009.

  4. Dan He, Eleazar Eskin: Optimal Algorithm for Haplotype Assembly from Whole-Genome Sequence Data , Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009) (Poster), Tucson, Arizona, May 18-21, 2009.

  5. Xingquan Zhu, Peng Zhang, Xindong Wu, Dan He, Chengqi Zhang, and Yong Shi: Cleansing Noisy Data Streams , Proceedings of the IEEE International Conference on Data Mining (ICDM 2008), Pisa, Italy, December 15-19, 2008.

  6. Dan He, Abdullah N. Arslan, Yu He and Xindong Wu:Iterative Refinement of Repeat Sequence Specification Using Constrained Pattern Matching, Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE 2007), Harvard Medical School Conference Center, Cambridge - Boston, Massachusetts, USA, October 14-17, 2007.

  7. Dan He,Xindong Wu and Xingquan Zhu:SAIL-APPROX: An Efficient On-line Algorithm for Approximate Pattern Matching with Wildcards and Length Constraints, Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM'07) (acceptance rate: 60/133), San Jose, CA, USA, November 2-4, 2007.

  8. Dan He : BMA*: an efficient algorithm for one-to-some shortest paths problem on road maps, Proceeding of the 3rd International Conference on Algorithmic Aspects in Information and Management，AAIM'07，Lecture Notes in Computer Science. 6-8 June 2007，Portland, USA

  9. Dan He: A Novel Greedy Algorithm for the Minimum Common String Partition Problem, Proceeding of the 2007 International Symposium on Bioinformatics Research and Applications, ISBRA 2007, Lecture Notes in Computer Science. May 7-10, 2007, Atlanta, Georgia, USA

  10. Dan He , Xindong Wu : An Efficient Algorithm for Finding Approximate Complex Repetitive Patterns, Proceeding of the International Conference on Computational and Systems Biology, CASB 2006, November 13-15, 2006, Dallas, Texas, USA

  11. Abdullah Aslan, Dan He: An Improved Algorithm for the regular expression constrained multiple sequence alignment problem, Proceeding of IEEE the 6th Symposium on Bioinformatics and Bioengineering, BIBE 2006, Oct 16-18, 2006, Washington DC, USA

  12. Dan He, Xindong Wu : Ontology-Based Feature Weighting for Biomedical Literature Classification, Proceeding of the 2006 IEEE International Conference on Information Reuse and Integration, IEEE IRI 2006, Sep 16-18, 2006, Waikoloa, Hawaii, USA

  13. Dan He: Using Suffix Tree to Discover Complex Repetitive Patterns in DNA Sequences, The 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEEE EMBC 2006, New York City, New York, USA, August 30 - September 3, 2006

  14. Dan He, Abdullah Aslan: Space-efficient Parallel Algorithms for the Constrained Multiple Sequence Alignment Problem, The 2006 International Conference on Bioinformatics & Computational Biology, BIOCOMP 2006, Las Vegas, Nevada, USA, June 26-29, 2006 (Acceptance rate: 46 out of 141)

  15. Dan He, Abdullah Aslan: A* Algorithms for the Constrained Multiple Sequence Alignment Problem, The 2006 International Conference on Artificial Intelligence, ICAI 2006, Las Vegas, Nevada, USA, June 26-29, 2006 (Acceptance rate: 73 + 32 out of 230)

  16. Dan He, Abdullah Aslan: FastPCMSA: An improved parallel algorithm for the constrained multiple sequence alignment problem , The 2006 International Conference on Foundations of Computer Science, FCS 2006, Las Vegas, Nevada, USA, June 26-29, 2006 (Acceptance rate: 31 out of 83)

  17. Dan He, Abdullah Aslan: A space-efficient algorithm for the constrained pairwise sequence alignment problem, The 16th International Conference on Genome Informatics, GIW 2005, PACIFICO YOKOHAMA, Japan, December 19-21, 2005 (Acceptance rate: 26 out of around 60)

  18. Dan He, Abdullah Aslan: A parallel algorithm for the constrained multiple sequence alignment problem , IEEE the 5th Symposium on Bioinformatics and Bioengineering, BIBE 2005, Minneapolis, Minnesota, October, 19-21, 2005 (Acceptance rate: 29 + 18 out of 120)

  19. Dan He, Abdullah Aslan: A fast algorithm for the constrained multiple sequence problem , 11th International Conference on Automata and Formal Languages, AFL 2005, Dobogoko, Hungary, May, 17-20, 2005 (Acceptance rate: 21 out of 37)

Technical Reports

Conference Presentations

  1. Dan He: Using Suffix Tree to Discover Complex Repetitive Patterns in DNA Sequences, The 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEEE EMBC 2006, New York City, New York, USA, August 30 - September 3, 2006

  2. Dan He : Space-efficient Parallel Algorithms for the Constrained Multiple Sequence Alignment Problem, The 2006 International Conference on Bioinformatics & Computational Biology, BIOCOMP 2006, Las Vegas, Nevada, USA, June 26-29, 2006

  3. Dan He : A* Algorithms for the Constrained Multiple Sequence Alignment Problem , The 2006 International Conference on Artificial Intelligence, ICAI 2006, Las Vegas, Nevada, USA, June 26-29, 2006

  4. Dan He : FastPCMSA: An improved parallel algorithm for the constrained multiple sequence alignment problem , The 2006 International Conference on Foundations of Computer Science, FCS 2006, Las Vegas, Nevada, USA, June 26-29, 2006

  5. Dan He: A space-efficient algorithm for the constrained pairwise sequence alignment problem, The 16th International Conference on Genome Informatics, GIW 2005, PACIFICO YOKOHAMA, Japan, December 19-21, 2005