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2004
Bailey, J.A., Baertsch, R.,
Kent, W.J., Haussler, D. and Eichler, E.E.
Hotspots of
mammalian chromosomal evolution.
Genome Biol. 5, R23 (2004).
Bejerano, G.
Algorithms for variable length Markov chain modeling.
Bioinformatics 20, 788-9 (2004).
Bejerano, G., Friedman, N. and Tishby, N.
Efficient Exact p-Value Computation for Small Sample, Sparse and Surprising Categorical Data.
J. Comp. Biol. (to appear) (2004).
Bejerano, G., Haussler, D., and Blanchette, M.
Into the heart of darkness: large-scale clustering of human non-coding DNA.
Bioinformatics 20, I40-I48 (2004).
Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S.
and Haussler, D.
Ultraconserved elements in the human genome.
Science 304, 1321-1325 (2004).
Click here for a free reprint.
Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.,
Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D.,
Haussler, D., Miller, W.
Aligning multiple genomic sequences with the threaded blockset aligner.
Genome Res. 14, 708-15 (2004).
The ENCODE Project Consortium.
The ENCODE (ENCyclopedia Of DNA Elements) Project.
Science 306, 636-640 (2004).
Furey, T.S., Diekhans, M., Lu, Y., Graves, T.A., Oddy, L., Randall-Maher, J.,
Hillier, L.W., Wilson, R.K., and Haussler, D.
Analysis of human mRNAs with the reference genome sequence reveals
potential errors, polymorphisms, and RNA editing.
Genome Res. 14, 2034-2040 (2004).
Grimwood, J. et al.
The DNA sequence and biology of human chromosome 19.
Nature 428, 529-535 (2004).
International Chicken Genome Sequencing Consortium.
Sequence and comparative analysis of the chicken provide unique perspectives on vertebrate evolution.
Nature (in press).
International Human Genome Sequencing Consortium.
Finishing the euchromatic sequence of the human genome.
Nature 431, 931-945 (2004).
Jensen-Seaman, M.I., Furey, T.S., Payseur, B.A., Lu, Y., Roskin, K.M., Chen, C.,
Thomas, M.A., Haussler, D. and Jacob, H.J.
Comparative recombination rates in the rat, mouse, and human genomes.
Genome Res. 14, 528-38 (2004).
Jojic, V., Jojic, N., Meek, C., Geiger, D., Siepel, A., Haussler, D.,
Heckerman, D.
Efficient approximations for learning phylogenetic HMM models from data.
Proc of ISMB 2004 and
Bioinformatics (to appear) (2004).
Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W.,
Haussler, D. and Kent, W.J.
The UCSC Table Browser data retrieval tool.
Nucl. Acids Res. 32, D493-D496 (2004).
Rat Genome Sequencing Project Consortium.
Genome sequence
of the brown Norway rat yields insights into mammalian evolution .
Nature 428, 493-521 (2004).
Roskin, K.M., Diekhans, M., and Haussler, D.
Score functions for determining regional conservation in two-species local alignments.
J Comput. Biol. 11, 395-411 (2004).
She, X., Horvath, J.E., Jiang, Z. Liu, G., Furey, T.S., Christ, L., Clark, R.,
Graves, T., Gulden, C., Alkan, C., Bailey, J.A., Sahinalp, C., Rocchi, M.,
Haussler, D., Wilson, R., Miller, W., Schwartz, S., Eichler, E.E.
The structure and evolution of centromeric transition regions within the human genome.
Nature 430, 857-864 (2004).
Siepel, A. and Haussler, D.
Combining phylogenetic and hidden Markov models in biosequence analysis.
J. Comput. Biol. 11, 413-28 (2004).
Siepel, A. and Haussler, D.
Computational
identification of evolutionarily conserved exons.
Proc. 8th Int'l Conf. on Research in
Computational Molecular Biology (RECOMB '04), pp. 177-186 (2004).
Siepel, A. and Haussler, D.
Phylogenetic estimation of context-dependent substitution rates
by maximum likelihood.
Mol. Bio. and Evol. 21, 468-488 (2004).
Siepel, A. and Haussler, D.
Phylogenetic hidden Markov models.
In Statistical Methods in Molecular Evolution (ed. Nielsen, R.)
(in press) (Springer, 2004).
Sugnet, C.W., Kent, W.J., Ares, M. Jr. and Haussler, D.
Transcriptome and genome conservation of alternative splicing events in humans
and mice.
Pacific Symposium on Biocomputing (PSB) 2004 Online Proceedings (2004).
Wolfsberg, T.G., Wetterstrand, K.A., Guyer, M.S., Collins, F.S., and
Baxevanis, A.D.
A user's guide to the human genome.
Nature Genet. 35(supplement), 1-79 (2004).
Yang, S., Smit, A.F., Schwartz, S., Chiaromonte, F., Roskin, K.M., Haussler, D.,
Miller, W. and Hardison, R.C.
Patterns of insertion and their covariation with substitutions in the rat, mouse and human genomes.
Genome Res. 14, 517-27 (2004).
2003
Blanchette, M.
A comparative analysis method for detecting binding sites in
coding regions.
Proc. 7th Int'l Conf. on Research in Computational Molecular Biology
(RECOMB '03), pp. 57-65 (2003).
Chiaromonte, F., Weber, R.J., Roskin, K.M., Diekhans, M., Kent, W.J., and
Haussler, D.
The share of human genomic DNA under selection estimated from human-mouse
genomic alignments.
Cold Spring Harbor Symp. Quant. Biol. 68, 245-254 (2003).
DeGuzman, V., Winters-Hilt, S., Solbrig, A., Sughrue, W., Deamer, D.,
Haussler, D., and Akeson, M.
Sequence-dependent fraying of single DNA molecules measured in real time
at 5 angstrom resolution using an ion channel.
Biophys. J. 84, 490A-490A Part 2 Suppl. (2003).
Furey, T.S. and Haussler, D.
Integration of the cytogenic map with the draft human genome sequence.
Hum. Mol. Genet. 12, 1037-1044 (2003).
Hardison, R.C., Chiaromonte, F., Kolbe, D., Hao Wang, Petrykowska, H., Elnitski,
L., Yang, S., Giardine, B., Zhang, Y., Riemer, C., Schwartz, S., Haussler, D.,
Roskin, K.M., Weber, R.J., Diekhans, M., Kent, W.J., Weiss, M.J., Welch, J.,
and Miller, W.
Global predictions and tests of erythroid regulatory regions.
Cold Spring Harbor Symp. Quant. Biol. 68, 335-44 (2003).
Hardison, R., Roskin, K.M., Yang, S., Diekhans, M., Kent, W.J., Weber, R.,
Elnitski, L., Li, J., O'Connor, M., Kolbe, D., Schwartz, S., Furey, T.S.,
Whelan, S., Goldman, N., Smit, A., Miller, W., Chiaromonte, F. and Haussler, D.
Covariation in frequencies of substitution, deletion, transposition and
recombination during eutherian evolution.
Genome Res. 13, 13-26 (2003).
Hillier, L.W. et al.
The DNA
sequence of human chromosome 7.
Nature 424, 157-64 (2003).
Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T.,
Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., Weber, R.J.,
Haussler, D. and Kent, W.J.
The UCSC Genome Browser database.
Nucl. Acids Res. 31, 51-54 (2003).
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W. and Haussler, D.
Evolution's cauldron:
duplication, deletion, and rearrangement in the mouse and human genomes.
P. Natl. Acad. Sci. USA 100, 11484-11489 (2003).
Margulies, E.H., Blanchette, M., NISC Comparative Sequencing Program,
Haussler, D., and Green, E.D.
Identification and characterization of multi-species conserved sequences.
Genome Res. 13, 2507-2518 (2003).
Roskin, K.M., Diekhans, M., and Haussler, D.
Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments.
Proc. 7th Int'l Conf. on Research in Computational Molecular Biology
(RECOMB '03), pp. 257-266 (2003).
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W.
Human-mouse alignments with BLASTZ.
Genome Res. 13, 103-107 (2003).
Siepel, A. and Haussler, D.
Combining phylogenetic and hidden markov models in biosequence analysis.
Proc. 7th Int'l Conf. on Research in Computational Molecular Biology
(RECOMB '03), pp. 277-286 (2003).
Thomas, J.W. et al.
Comparative analyses of multi-species
sequences from targeted genomic regions.
Nature 424, 788-793 (2003).
Wang, H., Hubbell, E., Hu, J., Mei, G., Cline, M., Lu, G., Clark, T., Siani-Rose,
M.A., Ares, M., Kulp, D.C., and Haussler, D.
Gene structure-based splice variant deconvolution using a microarray platform.
Proc. of ISMB 2003 and Bioinformatics 19, i315-i322 (2003).
Winters-Hilt, S., Vercoutere, W, DeGuzman, V., Deamer, D., Akeson, M., and
Haussler, D.
Highly accurate classification of Watson-Crick basepairs on termini of single
DNA molecules.
Biophys. J. 84, 967-976 (2003).
2002
Clark, T.A., Sugnet, C.W., Ares, M. Jr.
Genomewide analysis of mRNA processing in yeast using splicing-specific
microarrays.
Science 296, 907-910 (2002).
Cline, M., Karplus, K., Lathrop, R. Smith, T., Rogers, R., Haussler, D.
Information theoretic dissection of pairwise contact potentials.
Proteins: Structure, Function and Genetics 49, 7-14 (2002).
Karchin, R., Karplus, K., and Haussler, D.
Classifying G-protein coupled receptors with support vector machines.
Bioinformatics 18, 147-159 (2002).
Karolchik, D. and Kent, W.J.
The UCSC Genome Browser.
In Current Protocols in Bioinformatics (ed. Baxevanis, A.D.)
(John Wiley & Sons, Inc., 2002).
Kent, W.J.
BLAT - the BLAST-like alignment tool.
Genome Res. 12, 656-664 (2002).
Kent, W.J. and Brumbaugh, H.
autoSQL and autoXml: code generators from the Genome Project.
Linux Journal 99, 68-77 (2002).
Kent, W.J., Sugnet, C. W., Furey, T. S., Roskin, K.M., Pringle, T. H., Zahler,
A. M., and Haussler, D.
The human genome browser at UCSC.
Genome Res. 12, 996-1006 (2002).
Mouse Genome Sequencing Consortium.
Initial sequencing and comparative analysis of the mouse genome.
Nature 420, 520-562 (2002).
Roskin, K.M., Diekhans, M., Kent, W.J. and Haussler, D.
Score functions for assessing conservation in locally aligned
regions of DNA from two species.
UCSC Tech Report UCSC-CRL-02-30 Sep. 2002 (2002).
Wolfsberg, T.G., Wetterstrand, K.A., Guyer, M.S., Collins, F.S., and
Baxevanis, A.D.
A user's guide to the human genome.
Nature Genet. 32(supplement), 1-79 (2002).
2001
BAC Resource Consortium.
Integration of cytogenetic landmarks into the draft sequence of the human genome.
Nature 409, 953-958 (2001).
The Genome Sequencing Consortium.
Initial sequencing and analysis of the human genome.
Nature 409, 860-921 (2001).
International Human Genome Mapping Consortium.
A physical map of the human genome.
Nature 409, 934-941 (2001).
Kent, W.J. and Haussler, D.
Assembly of the working draft of the human genome with gigAssembler.
Genome Res. 11, 1541-1548 (2001).
Pavlidis, P., Furey, T.S., Liberto, M., Haussler, D., and Grundy, W.N.
Promoter region-based classification of genes.
Pacific Symposium on Biocomputing (PSB) 6, 151-164 (2001).
2000
Brown, M.P., Grundy, W.N., Lin D., Cristianini, N., Sugnet, C.W., Furey,
T.S., Ares, M. Jr., Haussler, D.
Knowledge-based analysis of microarray gene expression data using support vector machines.
PNAS 97, 262-267 (2000).
Furey, T.S., Duffy, N., Cristianini, N., Bednarski, D., Schummer, M., and
Haussler, D.
Support vector machine classification and validation of cancer tissue samples using microarray expression data.
Bioinformatics 16, 906-914 (2000).
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