BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes

By X. S. Liu, Douglas L. Brutlag, Jun S. Liu. Pacific Symposium on Biocomputing, 2000

935 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9044d58fd998d200e51b4e450bf23e9299088f5a

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Citations in the corpus

STAMP: a web tool for exploring DNA-binding motif similarities (2007, methodology): “Currently supported STAMP input formats include the output ﬁles from motif-ﬁnder programs like SOMBRERO (19), BioProspector (18), MDScan (20), AlignACE (21), MEME (22), Weeder (23), MotifSampler (24), YMF (25), ANN-Spec (26), Consensus (27), Improbizer and Co-Bind (28).”
RSAT: regulatory sequence analysis tools (2008, methodology): “edu/) combines a Gibbs-sampling pattern-discovery tool (22), with further adaptations to analyze phylogenetic footprints (CompareProspector) or chip-on-chip data (MDscan), respectively.”
An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments (2002, methodology): “We applied MDscan to both simulated and biological data sets and compared its performance with BioProspecto”
A survey of DNA motif finding algorithms (2007, background): “[47] developed the motif finding algorithm BioProspector that uses the promoter regions of coregulated genes.”
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny (2005, background): “, [8,9]) or that were bound by a common TF in ChIP-on-chip experiments (e.”
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression (2003, background): “In contrast, many approaches (e.g. Brazma et al., 1998; Liu et al., 2001; Roth et al., 1998; Sinha and Tompa, 2000; Tavazoie et al., 1999) use gene expression measurements to define clusters of genes that are potentially co-regulated, and then search for common motifs in the upstream regions of the ”
LOGOS: a modular Bayesian model for de novo motif detection (2003, methodology): “, 1995], splitting a “two-block” motif into two coupled sub-motifs [Liu et al., 2001; Bailey and Elkan, 1995], or imposing explicit “shape” [Helden et al.”
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE (2006, methodology): “We gathered the BioProspector and MDscan results from the original, published analyses, transformed them into PSSMs, and used them to predict DDG’s for the EMSA and lacZ experimentally tested sequences.”
ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. (2004, background): “Once the bound regulatory region is identified, the exact binding site can often be inferred by computational methods [32,33].”
A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes (2001, positive): “In parallel with our research, others (Liu et al. , 2001; McCue et al. , 2001; Workman and Stormo, 2000) have suggested the use of related higher-order background models to improve their motif-detection algorithms.”
Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators (2011, positive): “Denovomotifdiscoverywasperformed usingMEME(BaileyandElkan, 1994) or bioprospector (Liu et al., 2001) and motifs were compared with the JASPAR_CORE database (Bryne et al., 2008).”
Discovering Motifs in Ranked Lists of DNA Sequences (2007, methodology): “…REDUCE [3], YMF [4,5], ANN-SPEC [6], and a hypergeometric-based method [7]) or using a position weight matrix (PWM), which speciﬁes the probability of observing each nucleotide at each motif position (for example MEME [8], BioProspector [9], MotifBooster [10], DME-X [11], and AlignACE [12]).”
Discovering Sequence Motifs with Arbitrary Insertions and Deletions (2008, methodology): “These include A-GLAM [1], AlignACE [2], BioProspector [3], MDscan [4], RSA Tools [5,6], Weeder [7] and YMF [8].”
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling (2001, methodology): “Recently other researchers have also proposed the use of advanced background models in the Gibbs sampling algorithm (Liu et al., 2001; McCue et al., 2001).”
Lag Phase Is a Distinct Growth Phase That Prepares Bacteria for Exponential Growth and Involves Transient Metal Accumulation (2011, methodology): “using BioProspector (67), which is particularly suited to identifying”