Dan He  Dan He photo       

contact information

Computational Genomics
Thomas J. Watson Research Center, Yorktown Heights, NY USA
  +1dash914dash945dash2315

links

Professional Associations

Professional Associations:  ACM  |  IEEE Member  |  International Society for Computational Biology


2016

Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction
He, Dan and Kuhn, David and Parida, Laxmi
Bioinformatics 32(12), i37--i43, Oxford Univ Press, 2016

Mint: Mutual information based transductive feature selection for genetic trait prediction
He, Dan and Rish, Irina and Haws, David and Parida, Laxmi
IEEE/ACM Transactions on Computational Biology and Bioinformatics 13(3), 578--583, IEEE, 2016


2015

Does encoding matter? A novel view on the quantitative genetic trait prediction problem
He, Dan and Parida, Laxmi
Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on, pp. 123--126

SAME: a sampling-based multi-locus epistasis algorithm for quantitative genetic trait prediction
He, Dan and Parida, Laxmi
Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, pp. 286--295, 2015

Performance evaluation of different encoding strategies for quantitative genetic trait prediction
Ogundijo, Oyetunji E and He, Dan and Parida, Laxmi
Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on, pp. 1--6

Mined: An efficient mutual information based epistasis detection method to improve quantitative genetic trait prediction
He, Dan and Wang, Zhanyong and Parada, Laxmi
International Symposium on Bioinformatics Research and Applications, pp. 108--124, 2015

Variable-Selection Emerges on Top in Empirical Comparison of Whole-Genome Complex-Trait Prediction Methods
Haws, David C and Rish, Irina and Teyssedre, Simon and He, Dan and Lozano, Aurelie C and Kambadur, Prabhanjan and Karaman, Zivan and Parida, Laxmi
PloS one 10(10), e0138903, Public Library of Science, 2015

Data-driven encoding for quantitative genetic trait prediction
He, Dan and Wang, Zhanyong and Parida, Laxmi
BMC bioinformatics 16(Suppl 1), S10, BioMed Central Ltd, 2015


2014

IPED2: Inheritance path based pedigree reconstruction algorithm for complicated pedigrees
He, Dan and Wang, Zhanyong and Parida, Laxmi and Eskin, Eleazar
Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 202--210, 2014


2013

IPEDX: An exact algorithm for pedigree reconstruction using genotype data
He, Dan and Eskin, Eleazar
Bioinformatics and Biomedicine (BIBM), 2013 IEEE International Conference on, pp. 517--520

Optimized retrieval algorithms for personalized content aggregation
He, Dan and Parker, Douglass S
Information Reuse and Integration (IRI), 2013 IEEE 14th International Conference on, pp. 270--277

Leveraging multi-SNP reads from sequencing data for haplotype inference
Yang, Wen-Yun and Hormozdiari, Farhad and Wang, Zhanyong and He, Dan and Pasaniuc, Bogdan and Eskin, Eleazar
Bioinformatics, btt386, Oxford Univ Press, 2013

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data
Yang, Wen-Yun and Hormozdiari, Farhad and Wang, Zhanyong and He, Dan and Pasaniuc, Bogdan and Eskin, Eleazar
Bioinformatics 29(18), 2245--2252, Oxford Univ Press, 2013


IPED: inheritance path-based pedigree reconstruction algorithm using genotype data
He, Dan and Wang, Zhanyong and Han, Buhm and Parida, Laxmi and Eskin, Eleazar
Journal of Computational Biology 20(10), 780--791, Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA, 2013


2012


Modeling semantic influence for biomedicai research topics using MeSH hierarchy
D. He
Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on, pp. 1--6

Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data
D. He, B. Han, E. Eskin
Research in Computational Molecular Biology, pp. 64--78, 2012


2011

Mining research topic-related influence between academia and industry
D. He
Machine Learning and Knowledge Discovery in Databases, 17--31, Springer, 2011

CLAP: Collaborative pattern mining for distributed information systems
X. Zhu, B. Li, X. Wu, D. He, C. Zhang
Decision Support Systems, Elsevier, 2011

How Does Research Evolve? Pattern Mining for Research Meme Cycles
D. He, X. Zhu, D.S. Parker
Data Mining (ICDM), 2011 IEEE 11th International Conference on, pp. 1068--1073

Genotyping common and rare variation using overlapping pool sequencing
D. He, N. Zaitlen, B. Pasaniuc, E. Eskin, E. Halperin
BMC Bioinformatics 12(Suppl 6), S2, BioMed Central Ltd, 2011

MINING APPROXIMATE REPEATING PATTERNS FROM SEQUENCE DATA WITH GAP CONSTRAINTS
D. He, X. Zhu, X. Wu
Computational Intelligence 27(3), 336--362, Wiley Online Library, 2011

Using HLA binding prediction algorithms for epitope mapping in HIV vaccine clinical trials
D. He, P. Kunwar, E. Eskin, H. Horton, P. Gilbert, T. Hertz
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 594--601, 2011

Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions
D. He, F. Hormozdiari, N. Furlotte, E. Eskin
Bioinformatics 27(11), 1513--1520, Oxford Univ Press, 2011

Learning the funding momentum of research projects
D. He, D. Parker
Advances in Knowledge Discovery and Data Mining, 532--543, Springer, 2011

An optimal weighted aggregated association test for identification of rare variants involved in common diseases
J.H. Sul, B. Han, D. He, E. Eskin
Genetics 188(1), 181--188, Genetics Soc America, 2011

Topical semantics of twitter links
M.J. Welch, U. Schonfeld, D. He, J. Cho
Proceedings of the fourth ACM international conference on Web search and data mining, pp. 327--336, 2011


2010

Rule synthesizing from multiple related databases
D. He, X. Wu, X. Zhu
Advances in Knowledge Discovery and Data Mining, 201--213, Springer, 2010

Effective algorithms for fusion gene detection
D. He, E. Eskin
Algorithms in Bioinformatics, 312--324, Springer, 2010

Detection and reconstruction of tandemly organized de novo copy number variations
D. He, N. Furlotte, E. Eskin
BMC bioinformatics 11(Suppl 11), S12, BioMed Central Ltd, 2010

Optimal algorithms for haplotype assembly from whole-genome sequence data
D. He, A. Choi, K. Pipatsrisawat, A. Darwiche, E. Eskin
Bioinformatics 26(12), i183--i190, Oxford Univ Press, 2010

Topic dynamics: an alternative model of bursts in streams of topics
D. He, D.S. Parker
Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining, pp. 443--452, 2010


2009

Approximate repeating pattern mining with gap requirements
D. He, X. Zhu, X. Wu
Tools with Artificial Intelligence, 2009. ICTAI'09. 21st International Conference on, pp. 17--24

Error detection and uncertainty modeling for imprecise data
D. He, X. Zhu, X. Wu
Tools with Artificial Intelligence, 2009. ICTAI'09. 21st International Conference on, pp. 792--795


2008

Cleansing noisy data streams
X. Zhu, P. Zhang, X. Wu, D. He, C. Zhang, Y. Shi
Data Mining, 2008. ICDM'08. Eighth IEEE International Conference on, pp. 1139--1144


2007

Iterative Refinement of Repeat Sequence Specification Using Constrained Pattern Matching
D. He, A.N. Arslan, Y. He, X. Wu
Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on, pp. 1199--1203

A novel greedy algorithm for the minimum common string partition problem
D. He
Bioinformatics Research and Applications, 441--452, Springer, 2007

SAIL-APPROX: An efficient on-line algorithm for approximate pattern matching with wildcards and length constraints
D. He, X. Wu, X. Zhu
Bioinformatics and Biomedicine, 2007. BIBM 2007. IEEE International Conference on, pp. 151--158


2006

Ontology-Based FeatureWeighting for Biomedical Literature Classification
D. He, X. Wu
Information Reuse and Integration, 2006 IEEE International Conference on, pp. 280--285

Using suffix tree to discover complex repetitive patterns in DNA sequences
D. He
Engineering in Medicine and Biology Society, 2006. EMBS'06. 28th Annual International Conference of the IEEE, pp. 3474--3477

A fast algorithm for the Constrained Multiple Sequence Alignment problem
D. He, A.N. Arslan, A.C.H. Ling
Acta Cybernetica 17(4), 701--717, Acta Cybernetica, 2006


2005

A parallel algorithm for the Constrained Multiple Sequence Alignment problem
D. He, A.N. Arslan
Bioinformatics and Bioengineering, 2005. BIBE 2005. Fifth IEEE Symposium on, pp. 258--262



Year Unknown

Space-efficient Algorithms for the Constrained Multiple Sequence Alignment Problem
D. He, A.N. Arslan
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