S. Briesmeister, T. Blum, S. Brady, Y. Lam, O. Kohlbacher and H. Shatkay.
SherLoc2: A High-Accuracy Hybrid Method for Predicting Subcellular Localization of Proteins}. Journal of Proteome Research. 2009. (To appear).
H. Shatkay, N. Chen and D. Blostein.
Integrating Image Data into Biomedical Text Categorization. Bioinformatics. 22(11). Special issue: Proc. of the Int. Conf. on Intelligent Systems for Molecular Biology (ISMB'06). August, 2006. (pp. e446-e453).
H. Shatkay, J. Miller, C. Mobarry, M. Flanigan, S. Yooseph and G. Sutton.
ThurGood: Evaluating Assembly-to-Assembly Mapping,
Journal of Computational Biology (JCB), V.11, #5, (pp. 800-811), October, 2004.
S. Istrail, G.G. Sutton,
L. Florea, A.L. Halpern, C.M. Mobarry, R. Lippert,
B. Walenz, H. Shatkay, I. Dew, J.R. Miller,
M.J. Flanigan, N.J. Edwards, R. Bolanos, D. Fasulo,
B.V. Halldorsson, S. Hannenhalli, R. Turner, S. Yooseph,
F. Lu, D.R. Nusskern, B.C. Shue, X.H. Zheng,
F. Zhong, A.L. Delcher, D.H. Huson, S.A. Kravitz,
L. Mouchard, K. Reinert, K.A. Remington, A.G. Clark,
M.S. Waterman, E.E. Eichler, M.D. Adams,
M.W. Hunkapiller, E.W. Myers, and J.C. Venter.
Whole-Genome Shotgun
Assembly and Comparison of Human Genome Assemblies,
PNAS, V.101, #7, (pp. 1916-1921), February, 2004.
H. Shatkay and L.P. Kaelbling,
Learning Geometrically-Constrained Hidden Markov Models for
Robot Navigation: Bridging the Geometrical-Topological Gap,
Journal of AI Research (JAIR), (pp. 167-207), April, 2002.
PDF.
H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski,
Genes, Themes and Microarrays, Proc. of the Int. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2000. (pp. 317-328).
Compressed Postscript,PDF, (10 pages).
H. Shatkay and W.J. Wilbur.
Finding Themes in Medline Documents:
Statistical Similarity Search,
IEEE Conference on Advances in Digital Libraries (ADL), 2000.
(pp. 183-192).
Compressed Postscript,PDF, (10 pages).
H. Shatkay.
Learning Hidden Markov Models with Geometrical Constraints,
Proc. of the Int. Conf. on Uncertainty in Artificial Intelligence
(UAI),1999. (pp. 602-611).
Compressed Postscript,PDF, (10 pages).
H. Shatkay and L.P. Kaelbling.
Heading in the Right Direction, Proc. of the Int. Conf. on Machine
Learning (ICML), 1998. (pp. 531-539).
Compressed Postscript,PDF, (9 pages).
H. Shatkay and L.P. Kaelbling,
Learning Topological Maps
with Weak Local Odometric Information, Proc. of the Int. Joint Conf.
on Artificial Intelligence (IJCAI), 1997. (pp. 920-929).
Compressed Postscript,PDF, (8 pages).
H. Shatkay and S.B. Zdonik.
Approximate Queries and
Representations for Large Data Sequences, Proc. of the
Int. Conf. on Data Engineering (ICDE), 1996. (pp. 536-545)
Compressed Postscript, PDF, (11 pages).
Other Publications, Workshop Papers, Posters and Abstracts
H. Shatkay and L. Zheng. BLIMP: Biomedical Literature (and text) Mining Publications Forum:
A Web-Based Resource.
Poster and Abstract.
The International Conference on Intelligent Systems for Molecular, ISMB, June, 2005.
H. Shatkay and L. Zheng.
BLIMP: Biomedical Literature (and text) Mining Publications Forum:
A Web-Based Resource, Poster and Abstract.
BioLINK SIG Workshop
on Linking Literature, Information and Knowledge for Biology, ISMB,
June, 2005.
H. Shatkay, J. Miller, C. Mobarry, M. Flanigan, S. Yooseph and G. Sutton,
{\it ThurGood: Evaluating Assembly-to-Assembly Mapping},
Poster and Abstract,
The International Conference on Intelligent Systems for Molecular
Biology (ISMB), August, 2004.
H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski,
Using Information Retrieval for Large Scale Gene Analysis.
Abstract and invited talk at the Dagstuhl Seminar
on Bioinformatics, Schloss Dagstuhl, Wadern Germany, December 2000.
H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski,
Information Retrieval Meets Gene Analysis. Abstract and poster.
The Fourth TIGR Annual Symposium
on Computational Genomics, Baltimore MD, November, 2000.
H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski,
{\it Genes, Themes and Microarrays: Automated Genome-Wide
Extraction of Gene Function from PubMed},
Abstract and poster at the NIH Research Festival, Bethesda MD,
October, 2000.
H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski.
Genes, Themes and Microarrays: Automated Genome-Wide Extraction of
Gene Function from PubMed.
Selected for Oral presentation (selection ratio: 1 out of 5 abstracts)
at the Genome Sequencing and Biology meeting at Cold Spring Harbor,
May, 2000.
H. Shatkay.
Learning Models for Robot Navigation,
Ph.D. dissertation and Technical Report cs-98-11, Brown University,
Department of Computer Science, Providence, RI, December, 1998.
Abstract. Complete pdf.