Biology Reference
In-Depth Information
[16]
M. Kellis, N. Patterson, M. Endrizzi, B. Birren, and E. Lander. Sequencing and com-
parison of yeast species to identify genes and regulatory elements.
Nature
, 423:241-
254, 2003.
[17]
C. Kingsford, E. Zaslavsky, and M. Singh. A compact mathematical programming
formulation for dna motif finding. In
Proceedings of the Seventeenth Annual Sympo-
sium on Combinatorial Pattern Matching (CPM), Barcelona, Spain
, pages 233-245.
Springer, 2006.
[18]
C. Lawrence, S. Altschul, M. Boguski, J. Liu, A. Neuwald, and J. Wootton. Detecting
subtle sequence signals: a gibbs sampling strategy for multiple alignment.
Science
,
262:208-214, 1993.
[19]
C. Lawrence and A. Reilly. An expectation maximization (em) algorithm for the iden-
tification and characterization of common sites in unaligned biopolymer sequences.
Proteins: Structure, Function, and Genetics
, 7:41-51, 1990.
[20]
T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Han-
nett, C.T. Harbison, C.M. Thompson, I. Simon, J. Zeitlinger, E.G. Jennings, H.L.
Murray, D.B. Gordon, B. Ren, J.J. Wyrick, J.B. Tagne, T.L. Volkert, E. Fraenkel,
D.K. Gifford, and R.A. Young. Transcriptional regulatory networks in saccharomyces
cerevisiae.
Science
, 298(5594):799-804, 2002.
[21]
H.C. Leung and F.Y. Chin. Finding exact optimal motifs in matrix representation by
partitioning.
Bioinformatics
, 21 (Suppl. 2):ii86-ii92, 2005.
[22]
N. Li and M. Tompa. Analysis of computational approaches for motif discovery.
Al-
gorithms for Molecular Biology
, 1:8, 2006.
[23]
S. Liang, M.P. Samanta, and B.A. Biegel. Cwinnower algorithm for finding fuzzy
DNA motifs.
J. Bioinform. Comput. Biol.
, 2(1):47—60, 2004.
[24]
X. Liu, D.L. Brutlag, and J.S. Liu. Bioprospector: discovering conserved dna motifs
in upstream regulatory regions of co-expressed genes. In
Proceedings of the Sixth
Pacific Symposium on Biocomputing
, pages 127-138. International Society for Com-
putational Biology, 2001.
[25]
K. MacIsaac and E. Fraenkel. Practical strategies for discovering regulatory dna se-
quence motifs.
PLoS Computational Biology
, 2(4):e36, 2006.
[26]
T. K. Man and G. D. Stormo. Non-independence of mnt repressor-operator interac-
tion determined by a new quantitative multiple fluorescence relative affinity (qumfra)
assay.
Nucl. Acids Res.
, 29:2471-2478, 2001.
[27]
L. Marsan and M. F. Sagot. Algorithms for extracting structured motifs using a suffix
tree with an application to promoter and regulatory site consensus identification.
J.
Comput. Biol.
, 7:345-362, 2000.
[28]
H. Matsuda. Detection of conserved domains in protein sequences using a maximum-
density subgraph algorithm.
IEICE Trans. Fund. Elec. Comm. Comp. Sci.
, E83-
A(4):713-721, 2000.
[29]
L. McCue, W. Thompson, C. Carmack, M. Ryan, J. Liu, V. Derbyshire, and
C. Lawrence. Phylogenetic footprinting of transcription factor binding sites in pro-
teobacterial genomes.
Nucleic Acids Res.
, 29(3):774-782, 2001.
[30]
A. McGuire, J. Hughes, and G. Church. Conservation of dna regulatory motifs and
discovery of new motifs in microbial genomes.
Genome Res.
, 10(6):744-757, 2000.
[31]
S. Mukherjee, M.F. Berger, G. Jona, X.S. Wang, D. Muzzey, M. Snyder, R.A. Young,
and M.L. Bulyk. Rapid analysis of the dna-binding specificities of transcription fac-
Search WWH ::
Custom Search