[2013]
- Motif Discovery through Memetic Computing
[Invited Speaker]
In:
2013 X-GEN Congress & Expo: Cambridge Healthtech Institute's Fourth Annual Genomic Data Analysis: Sequencing's Strategic Step
, San Diego, CA USA, March 18-20, 2013.
- Central nervous system lymphoma in immunocompetent patients: The North Shore-Long Island Jewish Health System experience.
J Clin Neurosci.
2013 Jan;20(1):75-9
[ PubMed ]
** Co-authored with
Zhang X, Chen QH, Farmer P, Nasim M, Demopoulos A, Devoe C, Ranjan T, Eisenberg MB, Schulder M, Li JY.
[2012]
- Identifying CYP2D6 endogenous biomarkers using metabolomics.
2012 Annual Pediatric Pharmacogenomics and Personalized Medicine Conference, Kansas City, Missouri USA (Abstract)
** Co-authored with Y.S. Lin, J.C. Tay, K. Thummel, D. Beyer, T. Bammler, R. Pearce, N. Ahlers, K. Wright, A. Gaedigk and J.S. Leeder
- Large-scale computation of pediatric growth percentiles with fuzzy logic justification of parameter selection.
Proceedings of The 2012 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB).
IEEE Press, Piscataway, NJ, pages 43-46 (2012).
[
IEEE Xplore
]
** Joint work with Steve Leeder
- Memetic algorithms for de novo motif-finding in biomedical sequences.
Artificial Intelligence in Medicine
56 (1), 1-17 (2012). [
PubMed |
ScienceDirect
]
[2011]
- The Xla (X-linked anemia) mouse: A transient neonatal anemia caused by a Gata1 splicing mutation.
Blood,
118, 1366-1367 (2011) [ PubMed ]
** Joint work with K Miller, M Silvey, D Logsdon, F Balch, N Nsumu, I Sokolovsky, M Gibson, D Heruth, and RA White
- Derivation of minimum best sample size from microarray data
Sets: A Monte Carlo approach.
Proceedings of The 2011 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB).
IEEE Press, Piscataway, NJ, pp. 129-134 (2011).
[
IEEE Xplore
]
** Joint work with Mara Becker and Steve Leeder.
- Tackling the challenging motif problem through hybrid particle
swarm optimized alignment clustering.
Proceedings of The 2011 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB).
IEEE Press, Piscataway, NJ, pp. 84-89 (2011)
[
IEEE Xplore
]
***Winner of Best Paper Award received from The 2011 IEEE Symposium Series on Computational Intelligence
(IEEE SSCI 2011, Paris, France).
[2010]
-
Allele drop-out in the MECP2 gene due to G-quadruplex and
i-motif sequences when using PCR-based diagnosis for Rett syndrome.
Genetic Testing and Molecular Biomarkers,
14 (2), 241-247 (2010).
[
PubMed
]
-
Determinisitc local alignment methods improved by a simple genetic algorithm.
Neurocomputing, 73, 2394-2406 (2010).
[
ScienceDirect
| ACM Digital Library
]
-
Supervised learning of maternal cigarette-smoking signatures from placental gene expression data: A case study.
Proc. 2010 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB), Montreal, Canada, pp. 1-6 (2010). (with Carrie Vyhlidal and Steve Leeder)
[
IEEEXplore
]
-
Comparison of optimization techniques for sequence pattern discovery by maximum-likelihood.
Pattern Recognition Letters, 31, 2147-2160 (2010).
[
ScienceDirect
| ACM Digital Library
]
[2009]
-
A Monte Carlo EM algorithm for motif discovery in biomolecular sequences.
IEEE/ACM Transactions on Computational Biology and Bioinformatics,
6 (3), 370-386 (2009).
[
PubMed
]
-
DNA motif alignment by evolving a population of Markov chains.
BMC Bioinformatics, 10, S13 (2009).
[
PubMed |
PDF
]
-
Genome-wide screening SNPs with arginine vs tryptophan change associated with allergy.
Journal of Allergy and Clinical Immunology, 123, S167 (2009).
** Joint work with J Meng and LJ Rosenwasser
-
DNA motif alignment by evolving a population of Markov chains.
Proc. the 7th Asia-Pacific Bioinformatics Conference
,vol 7, pp. 126-137. Tsinghua University Press, Beijing, CHINA (2009) [book chapter]
[2008]
-
Data augmentation algorithms for detecting conserved domains in protein sequences: A comparative study.
Journal of Proteome Research, 7 (1), 192-201 (2008)
[
PubMed
]
-
A comparative study on structured motif detection: algorithms and applications.
Molecular Pharmaceutics, 5 (1), 3-16 (2008)
[
PubMed
]
-
Computational intelligence in multiple sequence alignment.
Intl. J. Intelligent Computing and Cybernetics, 1 (1), 8-24 (2008)
-
Evolutionary Metropolis sampling in sequence alignment space.
Proc. 2008 IEEE Congress on Evolutionary Computation (CEC), Hong Kong, CHINA, pp. 189-194 (2008)
[
IEEEXplore
]
-
Neuro-Fuzzy classification of the Rhagoletis pomonella species group using digitized wing structure.
Proc. 2008 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB), Idaho, USA, pp. 159-165 (2008)
[
IEEEXplore
]
[2007]
-
SEAM: A stochastic EM-type algorithm for motif-finding in biopolymer sequences.
Journal of Bioinformatics and Computational Biology, 5 (1), 47-77 (2007)
[
PubMed
]
-
Wing pattern-based classification of the Rhagoletis pomonella species complex using genetic neural networks.
Intl J. Computer Sci. & Appl., 4 (3), 1-14 (2007)
[
PDF
]
-
A genetic-based EM motif-finding algorithm for biological sequence analysis.
Proc. 2007 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB), pp. 275-282, Hawaii, USA (2007)
[
IEEEXplore
]
*** Winner of Best Overall Paper Award received from IEEE SSCI'2007.
-
A survey of in silico motif discovery and computational intelligence applications.
Proc. 2007 International Conference on Artificial Intelligence, pp. 147-153. Las Vegas, USA. CSREA Press
-
Multiple sequence local alignment using Monte Carlo EM algorithm.
Lecture Notes in Bioinformatics, vol 4463, pp. 465-476,
Springer-Verlag (2007)
[
Book Chapter
]
[2006]
-
Correlation between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex Destabilization energy.
Journal of Molecular Biology, 358 (2), 597-613 (2006)
[
PubMed
]
-
BIPAD: A web server for modeling bipartite sequence elements.
BMC Bioinformaitcs, 7:76 (2006)
[
PubMed |
PDF
]
-
Computational model of the antioxidant response element.
ISSX-2006 (abstract)
-
A Monte Carlo EM algorithm for motif discovery problem.
Proceedings of 2006 ISMB Bioinformatics Rocky Conference, Snowmass/Aspen, CO, USA (abstract)
[2005]
-
Information theory as a model of genomic sequences.
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics,
vol 7, pp. 2868-2880, John Wiley & Sons Ltd. (2005)
[
Book Chapter
]
-
Determining thresholds for binding site sequence models using information theory.
Proc. 6th International Symposium on Computational Biology and Genome Informatics,
pp. 1285-1290. Utah, USA (2005)
[2004]
-
The analysis of stress-induced duplex destabilization in long genomic DNA sequences.
Journal of Computational Biology, 11 (4), 519-543 (2004)
[
PubMed |
PDF
]
-
Bipartite pattern discovery by entropy minimization-based multiple local alignment.
Nucleic Acids Research, 32 (17), 4979-4991 (2004)
[
PubMed |
PDF
]
-
WebSIDD: Server for prediction of the stress-induced duplex destabilized (SIDD) sites in superhelical DNA.
Bioinformatics, 20 (9), 1477-1479 (2004)
[
PubMed |
PDF
]
-
A minimization entropy-based bipartite algorithm with application to PXR/RXRa binding sites.
Proc. 8th Ann. Conference on Research in Computational Molecular Biology (RECOMB) , San Diego, California USA, pp. 453-454 (2004)
[2003]
-
The approximate algorithm for analysis of the strand separation transition in superhelical DNA using nearest neighbor energetics.
Proc. IEEE Computer Society for Bioinformatics,
pp. 460-461. Stanford University, California USA. IEEE Publisher. (2003)
[
IEEEXplore
]
[2002]
-
Pattern Classification of the Rhagoletis pomonella Species Complex.
Ph.D. Dissertation: Graduate School of The Pennsylvania State University, University Park, PA, USA.