Gene Regulatory Element . . .

Gene Regulatory Element . . . (2008)

Cached

Download Links

[www.comp.nus.edu.sg]

by Vipin Narang

BibTeX

@MISC{Narang08generegulatory,
    author = {Vipin Narang},
    title = {Gene Regulatory Element . . . },
    year = {2008}
}

Bookmark

OpenURL

Abstract

Citations

1923	Basic local alignment search tool - Altschul, Gish, et al. - 1990
960	T: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res - Thompson, Higgins, et al. - 1994
598	Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge Univ - Durbin, Eddy, et al. - 2000
451	Bayesian Network Classifiers - Friedman, Geiger, et al. - 1997
423	Bayesian Networks and Decision Graphs - Jensen - 2001
372	Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment - Lawrence - 1993
327	Fitting a Mixture Model by Expectation Maximization to Discover Motifs in Biopolymers - Bailey, Elkan - 1994
269	On-line construction of suffix trees - Ukkonen - 1995
253	Beyond independence: conditions for the optimality of the simple bayesian classifier - Domingos, Pazzani - 1996
207	DNA binding sites: representation and discovery - Stormo - 2000
196	Identifying DNA and protein patterns with statistically significant alignments of multiple sequences - Hertz, Stormo - 1999
181	TRANSFAC: transcriptional regulation, from patterns to profiles - Matys, Fricke, et al. - 2003
174	Finding motifs using random projections - Buhler, Tompa - 2002
164	Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation - Roth, Hughes, et al. - 1998
162	Assessing computational tools for the discovery of transcription factor binding sites - Tompa, Li, et al. - 2005
152	A statistical method for evaluating systematic relationships - RR, CD - 1958
142	JASPAR: an open-access database for eukaryotic transcription factor binding profiles - Sandelin, Alkema, et al. - 2004
132	Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies - Helden, Andre, et al. - 1998
114	CLOSET+: Searching for the Best Strategies for Mining Frequent Closed Itemsets”, in proceeding of the SIGKDD ’03 - Wang, Han, et al. - 2003
101	An algorithm for finding protein–DNA binding sites with applications to chromatinimmunoprecipitation microarray experiments - Liu, Brutlag, et al. - 2002
82	Discovering regulatory elements in non-coding sequences by analysis of spaced dyads - Helden, Rios, et al. - 2000
82	Identification of regulatory regions which confer muscle-specific gene expression - Wasserman, Fickett - 1998
81	Gene regulatory networks for development - Levine, Davidson - 2005
80	A statistical method for finding transcription factor binding sites - Sinha, Tompa - 2000
79	The hardwiring of development: organization and function of genomic regulatory systems. Development 124 - MI, EH - 1997
75	Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome - Berman, Nibu, et al. - 2002
71	Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification - Marsan, Sagot - 2000
69	Identification of consensus patterns in unaligned DNA sequences known to be functionally related - Hertz, Hartzell, et al. - 1990
66	GD: ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput - CT, Stormo
63	Pesole G: An algorithm for finding signals of unknown length - Pavesi, Mauri
59	Finding composite regulatory patterns in DNA sequences - Eskin, Pevzner - 2002
57	Pevzner P: Finding motifs in the twilight zone - Keich
56	An exact method for finding short motifs in sequences, with application to the ribosom binding site problem. ISMB - Tompa
55	Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences - Bucher - 1990
54	T: Modeling dependencies in protein-DNA binding sites - Barash, Elidan, et al. - 2003
54	YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation - Sinha, Tompa - 2003
53	Hatzigeorgiou A: Eukaryotic Promoter Recognition. Genome Res - Fickett - 1997
53	Detection of cis-element clusters in higher eukaryotic DNA - Frith, Hansen, et al. - 2001
53	A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes - Thijs, Marchal, et al. - 2002
51	A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling - Thijs, Lescot, et al. - 2001
51	Extracting protein alignment models from the sequence database - Neuwald, Liu, et al. - 1997
50	DS: Predicting Pol II promoter sequences using transcription factor binding sites - Prestridge - 1995
48	Gene expression during the life cycle of Drosophila melanogaster - Arbeitman, Furlong, et al. - 2002
45	Algorithms for phylogenetic footprinting - Blanchette, Schwikowski, et al. - 2002
44	Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis - Bussemaker, Li, et al. - 2000
40	Models for prediction and recognition of eukaryotic promoters. Mamm Genome - Werner - 1999
39	De novo cis-regulatory module elicitation for eukaryotic genomes - Gupta, Liu - 2005
39	Pattern recognition in several sequences: consensus and alignment - Waterman, Galas, et al. - 1984
35	Computational identification of promoters and first exons in the human genome - Davuluri, Grosse, et al. - 2001
34	Computational analysis of core promoters in the Drosophila genome - Ohler, Liao, et al. - 2002