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

Patents

  1. Dan He, David Haws, Irina Rish, Laxmi Parida: Mutual Information based Transductive Feature Selection, Patent YOR920120919US1

  2. Dan He, David Haws, Laxmi Parida: A Dynamic Programming Algorithm for Mutual Information based Feature Selection, Patent YOR920120921US1

  3. Dan He, David Haws, Laxmi Parida: Mutual Information based Epistasis Model, Patent YOR920120930US1

  4. Dan He, David Haws, Laxmi Parida: A Hill-climbing Algorithm for Mutual Information based Feature Selection, Patent YOR920120929US1

  5. Dan He, Irina Rish, Laxmi Parida: Transductive HSIC Lasso, Patent YOR920120931US1

  6. David Haws, Dan He, Laxmi Parida: Modeling Multiple Interactions Between Multiple Loci, Patent YOR920120932US1

Book Publications

  1. Dan He, Noah Zaitlen, Bogdan Pasaniuc, Eleazar Eskin, Eran Halperin: Genotyping common and rare variation using overlapping pool sequencing , Bioinformatics: The Impact of Accurate Quantification on Proteomics, Genomics and Genetic Analysis and Research, Apple Academic Press, 2013.

Journal Publications

  1. new paper Dan He, Zhanyong Wang, Laxmi Parida: Data-driven Encoding for Genetic Trait Prediction , BMC Bioinformatics, 2015.

  2. new paper Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin: IPED2: Inheritance path based pedigree reconstruction algorithm for complicated pedigrees , Invited to TCBB, 2015.

  3. new paper Dan He, Eleazar Eskin: IPED2X: A robust pedigree reconstruction algorithm for complicated pedigrees , Journal of bioinformatics and computational biology, 2014.

  4. Dan He, Nicholas A. Furlotte, Rafail Ostrovsky, Amit Sahai, Eleazar Eskin: Identifying Genetic Relatives without Compromising Privacy , Genome Research, 2014.

  5. Dan He, Stott Parker: SemInf: A burst-based semantic model for topic influence. the IEEE Journal of Biomedical and Health Informatics Accepted, 2013

  6. Wen-Yun Yang, Farhad Hormozdiari, Zhanyong Wang, Dan He,Bogdan Pasaniuc, Eleazar Eskin: Leveraging Multi-SNP Reads from Sequencing Data for Haplotype Inference, Bioinformatics, 2013

  7. Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin: IPED: An efficient algorithm for pedigree reconstruction based genotype data. To appear in the Journal of Computation Biology2013

  8. Dan He, Eleazar Eskin: Hap-seqX: An Expedite Algorithm for Haplotype Phasing with Imputation using Sequencing Data The journal of Gene (Impact Factor: 2.314) 2012

  9. Xingquan Zhu, Bin Li, Xindong Wu, Dan He and Chengqi Zhang: CLAP: Collaborative Pattern Mining for Distributed Information Systems , Decision Support Systems, 2011, accepted.

  10. Dan He, Noah Zaitlen, Bogdan Pasaniuc, Eleazar Eskin, Eran Halperin: Genotyping common and rare variation using overlapping pool sequencing , BMC Bioinformatics to appear, 2011.

  11. Dan He, Farhad Hormozdiari, Nick Furlott, Eleazar Eskin: Efficient Algorithms for Tandem Copy Number Variation Reconstruction in Repeat-rich Regions , Bioinformatics to appear, 2011.

  12. Jae Hoon Sul, Buhm Han, Dan He, Eleazar Eskin: An Optimal Weighted Aggregated Association Test for Identification of Rare Variants Involved in Common Diseases, Genetics, 2010, to appear.

  13. Dan He, Nick Furlotte, Eleazar Eskin: Detection and reconstruction of copy number variations , BMC Bioinformatics. 2010, to appear.

  14. Dan He, Xindong Wu, Xingquan Zhu: Approximate Repeating Pattern Mining with Gap Requirements, The Jounral of Computational Intelligence. 2010, to appear.

  15. Dan He, Arthur Choi, Knot Pipatsrisawat, Adnan Darwiche and Eleazar Eskin: Optimal Algorithms for Haplotype Assembly From Whole-Genome Sequence Data, Bioinformatics , to appear.

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

  17. 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, Zhanyong Wang, Laxmi Parida: Data-driven Encoding for Genetic Trait Prediction , The Thirteenth Asia Pacific Bioinformatics Conference (APBC), Taiwan, 2015.

  2. new paper Dan He, Eleazar Eskin: IPED2X: A robust pedigree reconstruction algorithm for complicated pedigrees , GIW/ISCB-Asia, Tokyo, Japan, 2014.

  3. new paper Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin: IPED2: Inheritance path based pedigree reconstruction algorithm for complicated pedigrees , Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACMBCB), Long Beach, LA, 2014.

  4. Dan He, Irina Rish, Laxmi Parida: Transductive HSIC Lasso, , SIAM Data Mining (SDM), Philadelphia, USA, 2014.

  5. Dan He, Eleazar Eskin: IPEDX: An Exact Algorithm for Pedigree Reconstruction using Genotype Data, , The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shanghai, China, 2013.

  6. Dan He,Douglas S. Parker: Optimized Retrieval Algorithms for Personalized Content Aggregation, The 14th IEEE Conference on Information Reuse and Integration, San Francisco, USA, August 14-16, 2013

  7. Dan He,Irina Rish, David Haws, Simon Teyssedre, Zivan Karaman, Laxmi Parida: MINT: Mutual Information based Transductive Feature Selection for Genetic Trait Prediction, The Seventh International Workshop on Machine Learning in Systems Biology (MLSB 2013), Berlin, Germany, July 21 - 23, 2013

  8. Dan He: IBD-Groupon: An Efficient Method for Detecting Group-wise Identity-by-Descent regions simultaneously in Multiple Individuals based on Pairwise IBD relationships, The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2013), Berlin, Germany, July 21 - 23, 2013

  9. Dan He, Stott Parker: SemInf: A burst-based semantic model for topic influence. the 13th SIAM International Conference on Data Mining (SDM 2013)May 2-4, Texas, Austin, 2013

  10. Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin: IPED: An efficient algorithm for pedigree reconstruction based genotype data. the 17th Annual International Conference on Research in Computational Molecular Biology (Recomb 2013), April 7-12, Beijing, China, 2013

  11. Dan He, Eleazar Eskin: Hap-seqX: An Expedite Algorithm for Haplotype Phasing with Imputation using Sequencing Data The 23rd International Conference on Genome Informatics (GIW2012) Tainan, Taiwan, 2012

  12. Dan He: Modeling Semantic Influence for Biomedical Research Topics using MeSH Hierarchy IEEE International Conference on Bioinformatics and Biomedicine (BIBM2012) Philadelphia, 2012

  13. Dan He: CPAM: Effective Composite Regulatory Pattern Miner. ISBRA, Dallas, Texas, 2012

  14. Dan He, Buhm Han, Eleazar Eskin: Optimal Algorithm for Haplotype Phasing with Imputation using Sequencing Data , the 16th Annual International Conference on Research in Computational Molecular Biology (Recomb 2012), April. 21-24, Barcelona, Spain, 2012.

  15. Dan He, Xingquan Zhu, Douglas S. Parker: How Does Research Evolve? Pattern Mining for Research Meme Cycles , the 2011 IEEE International Conference on Data Mining (ICDM2011), Dec. 11-14, Vancouver, Canada, 2011.

  16. Dan He: Mining Research Topic-related Influence between Academia and Industry , European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD2011) (Acceptance rate: 20% out of 599 submissions), Athens, Greece, Sep 5-9, 2011.

  17. Dan He, Pratima Kunwar, Helen Horton, Eleazar Eskin, Peter Gilbert, Tomer Hertz: Using HLA binding prediction algorithms for epitope mapping in HIV vaccine clinical trials , Second Immunoinformatics and Computational Immunology Workshop (ICIW 2011), Aug 1, 2011 - Aug 3, 2011, Chicago.

  18. Dan He, Farhad Hormozdiari, Nick Furlott, Eleazar Eskin: Efficient Algorithms for Tandem Copy Number Variation Reconstruction in Repeat-rich Regions , HiTSeq 2011 (Joint with ISMB 2011), July 15-19, 2011, Vienna, Austria.

  19. Dan He, Noah Zaitlen, Bogdan Pasaniuc, Eleazar Eskin, Eran Halperin: Genotyping common and rare variation using overlapping pool sequencing , RECOMB Satellite Workshop on Massively Parallel Sequencing (Recomb 2011), 2011, March 26-27 2011, Vancouver, BC, Canada.

  20. Dan He: Mining Research Cycles with Adapted Hierarchical Clustering , Text Mining workshop of the Eleventh SIAM International Conference on Data Mining (SDM 2011), 2011, Mesa, Arizona, April 30, 2011.

  21. Dan He: Learning the Funding Momentum of Research Projects , The 15th Pacific-Asia Conference on Knowledge Discovery and Data Mining(PAKDD 2011) (Acceptance for long presentation: 9.7%) May 24 - Mar 27, 2011, Shenzhen, China.

  22. Pratima Kunwar, Dan He, Ann Collier, Tomer Hertz and Helen Horton: Analysis of epitope-specific HIV T cell Responses during early HIV Infection and their association with viral control , Keystone Symposia: Protection from HIV: Targeted Intervention Strategies, (Poster, selected for oral presentation and travel scholarship) Mar 20 - Mar 25, 2011, Whistler, British Columbia

  23. Dan He, Nick Furlotte, Eleazar Eskin: Efficient Algorithm for Reconstruction of Tandemly organized copy number variations in repeat-rich regions. , The 60th Annual meeting of the American Society of Human Genetics, (ASHG2010) (Poster) Washington DC, Nov. 2-6, 2010.

  24. Michael Welch, Uri Schonfeld, Dan He, Junghoo Cho: Topical Semantics of Twitter Links , Fourth ACM International Conference on Web Search and Data mining (WSDM 2011) (Acceptance rate: 32 (8.6%) + 51 (13.7%) out of 372 submissions) Hong Kong, China, February 9-12, 2011.

  25. Dan He, Nick Furlotte, Eleazar Eskin: Detection and reconstruction of copy number variations , The 21st International Conference on Genome Informatics (GIW 2010) Hangzhou, China, December 16-18, 2010.

  26. Dan He, Eleazar Eskin: Effective Algorithms for Fusion Gene Detection, 10th Workshop on Algorithms in Bioinformatics (WABI2010) , September 6-8, University of Liverpool, United Kingdom.

  27. Dan He, Douglas S. Parker: Topic Dynamics: an alternative model of `Bursts' in Streams of Topics, The 16th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, (SIGKDD 2010) (Acceptance rate: 13% out of 578 submissions) , July 25-28, 2010, Washington DC.

  28. Dan He, Arthur Choi, Knot Pipatsrisawat, Adnan Darwiche and Eleazar Eskin: Optimal Algorithms for Haplotype Assembly From Whole-Genome Sequence Data, The 18th Annual International Conference on Intelligent Systems for Molecular Biology, (ISMB 2010) (Acceptance rate: 19% out of over 240 submissions) , July 11-13, 2010, Boston.

  29. Dan He, Xindong Wu, Xingquan Zhu: Rule Synthesizing from Multiple Related Databases, The 14th Pacific-Asia Conference on Knowledge Discovery and Data Mining, (PAKDD 2010) (Acceptance rate: 10.2% out of 412 submissions). 21-24 June, 2010 - Hyderabad, India.

  30. 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.

  31. 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.

  32. 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.

  33. 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.

  34. 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.

  35. 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.

  36. 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.

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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)

  44. 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)

  45. 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)

  46. 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)

  47. 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)

  48. 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