Methods for calculating the probabilities of finding patterns in sequences

No abstract is available for this paper.

• Publication year

  1989

• Venue

  Comput. Appl. Biosci.

• Publication date

  1989-04-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/5.2.89PMID 2720468
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Methods to define and locate patterns of motifs in sequences

  1988cited by this paper
• Selection of DNA binding sites by regulatory proteins.

  1988cited by this paper
• A simple statistical significance test of window scores in large dot matrices obtained from protein or nucleic acid sequences

  1987cited by this paper
• Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

  1987cited by this paper
• Information content of binding sites on nucleotide sequences.

  1986cited by this paper
• Promoter-specific activation of RNA polymerase II transcription by Sp1

  1986cited by this paper
• Confidence limits for homology in protein or gene sequences. The c-myc oncogene and adenovirus E1a protein.

  1985cited by this paper
• The TGGCA protein binds to the MMTV-LTR, the adenovirus origin of replication, and the BK virus enhancer.

  1985cited by this paper
• Computer Methods to Locate Genes and Signals in Nucleic Acid Sequences

  1985cited by this paper
• Activation of heat-shock genes in eukaryotes

  1985cited by this paper
• Computer methods to locate signals in nucleic acid sequences

  1984cited by this paper
• Graphic methods to determine the function of nucleic acid sequences

  1984cited by this paper
• The nucleotide sequence of the human beta-globin gene.

  1980cited by this paper
• Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 .

  1971cited by this paper

• REV-ERBα regulates brain NAD+ levels and tauopathy via an NFIL3–CD38 axis

  2025cites this paper
• MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks

  2023cites this paper
• Digital Commons@Becker Digital Genome ‑ wide chromatin accessibility analyses provide a map for Genome wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration enhancing optic nerve regeneration

  2022cites this paper
• Genome-wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration

  2021cites this paper
• RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach

  2020cites this paper
• Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism

  2020cites this paper
• Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for axon regeneration

  2020cites this paper
• Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

  2019cites this paper
• Fast and Accurate Genome-Scale Identification of DNA-Binding Sites

  2018cites this paper
• Fast sequence analysis based on diamond sampling

  2018cites this paper
• 0 Motif Discovery with Compact Approaches-Design and Applications

  2018cites this paper
• Fast Significant Matches of Position Weight Matrices Based on Diamond Sampling

  2017cites this paper
• Un'indagine su larga scala dell'interazione Enhancer-Promotore mediata da fattori di trascrizione

  2017cites this paper
• Development of bioinformatics methods for the analysis of large collections of transcription factor binding motifs : positional motif enrichment and motif clustering

  2017cites this paper
• Transcriptional and Post-transcriptional Regulation of Gene Expression

  2016cites this paper
• TEMPLE: analysing population genetic variation at transcription factor binding sites

  2016cites this paper
• Fast motif matching revisited: high‐order PWMs, SNPs and indels

  2016cites this paper
• Computational Methods in Bioinformatics

  2015cites this paper
• Unsupervised Learning in Genome Informatics

  2015cites this paper
• Discriminative Learning for Probabilistic Sequence Analysis

  2015cites this paper
• MINING DNA ELEMENTS INVOLVED IN TARGETING OF CHROMATIN MODIFIERS

  2014cites this paper
• Discrimination of Mammalian GPI-Anchored Proteins by Hydropathy and Amino Acid Propensities

  2013cites this paper
• A primer on thermodynamic-based models for deciphering transcriptional regulatory logic.

  2013cites this paper
• NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data

  2013cites this paper
• Sugar Type Discrimination in O-glycosylation Based on Protein Primary Sequences

  2013cites this paper
• Topics in Computational Genomics

  2013cites this paper
• Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors

  2013cites this paper
• Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites

  2012cites this paper
• Detection and evolutionary analysis of functional conserved non-coding sequences in higher plants by integrating evolutionary and functional conservation

  2012cites this paper
• A statistical model to determine multiple binding sites of a transcription factor on DNA using ChIP-seq data

  2012cites this paper
• Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics1[C][W]

  2012cites this paper
• Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor

  2012cites this paper
• Genomic approaches towards finding cis-regulatory modules in animals

  2012cites this paper
• Parallel implementation of DNA sequences matching algorithms using PWM on GPU architecture

  2011cites this paper
• coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data

  2011cites this paper
• Finding Significant Matches of Position Weight Matrices in Linear Time

  2011cites this paper
• Manycore High-Performance Computing in Bioinformatics

  2011cites this paper
• Discrimination of Golgi Type II Membrane Proteins Based on Their Hydropathy Profiles and the Amino Acid Propensities of Their Transmembrane Regions

  2011cites this paper
• daptation of AmtR-controlled gene expression by modulation of AmtR binding ctivity in Corynebacterium glutamicum ristin Hasselt

  2011cites this paper
• Motif Discovery with Compact Approaches - Design and Applications

  2011cites this paper
• Mixture models for analysing high throughput sequencing data

  2011cites this paper
• Association Based Prioritization of Genes

  2011cites this paper
• Adaptation of AmtR-controlled gene expression by modulation of AmtR binding activity in Corynebacterium glutamicum.

  2011cites this paper
• Identification of mammalian GPI-anchored proteins based on amino acid propensities in their GPI attachment signal sequences

  2010cites this paper
• Theoretical and empirical quality assessment of transcription factor-binding motifs

  2010cites this paper
• A discrimination method for Golgi type II membrane proteins based on the hydropathy alignment and the position-specific score matrix around their transmembrane regions

  2010influential citation
• A Comparison Study of Transcription Factor – DNA Binding Models

  2010influential citation
• Towards a theoretical understanding of false positives in DNA motif finding

  2010cites this paper
• Sequence Alignment Statistics

  2010influential citation
• Counting of oligomers in Sequences Generated by Markov Chains for DNA Motif Discovery

  2009cites this paper
• Inferring Binding Energies from Selected Binding Sites

  2009cites this paper
• Exact Calculation of Distributions on Integers, with Application to Sequence Alignment

  2009cites this paper
• Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes

  2009cites this paper
• Promoter analysis: gene regulatory motif identification with A-GLAM.

  2009cites this paper
• Improved algorithms for string searching problems

  2009cites this paper
• Biological insights of transcription factor through analyzing ChIP-Seq data

  2009cites this paper
• Parallel Position Weight Matrices Algorithms

  2009cites this paper
• Prediction and Experimental Validation of Novel STAT3 Target Genes in Human Cancer Cells

  2009cites this paper
• Gene-set analysis identifies master transcription factors in developmental courses.

  2009cites this paper
• Self-overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching

  2009cites this paper
• Context-specific independence mixture models for cluster analysis of biological data (Kontext-spezifische Unabhängigkeits-Mischmodelle für die Cluster-Analyse von biologischen Daten)

  2009cites this paper
• Regulatory Motif Analysis

  2009cites this paper
• Bioinformatics : Tools and Applications

  2009cites this paper
• Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.

  2009cites this paper
• Methods for discovery and characterization of DNA sequence motifs

  2009cites this paper
• GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery

  2009cites this paper
• MOODS: fast search for position weight matrix matches in DNA sequences

  2009cites this paper
• Stochastic Models for Biological Patterns

  2009cites this paper
• Integrating sequence, evolution and functional genomics in regulatory genomics

  2009cites this paper
• Computational Systems Biology

  2009cites this paper
• Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development.

  2009cites this paper
• Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

  2008cites this paper
• Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands

  2008cites this paper
• Sequence length limits for controlling false positives in discovering nucleotide sequence motifs

  2008cites this paper
• Fast profile matching algorithms - A survey

  2008cites this paper
• Algorithmes pour la comparaison de génomes et la recherche de signaux cis-régulateurs

  2008cites this paper
• Discovery and Analysis of Genomic Patterns: Applications to Transcription Factor Binding and Genome Rearrangement

  2008cites this paper
• Matrices score-position, algorithmes et propriétés

  2008cites this paper
• Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions

  2008cites this paper
• Natural similarity measures between position frequency matrices with an application to clustering

  2008cites this paper
• Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia

  2008cites this paper
• Index-based algorithms for motif search and their integration in a system for differential genome analysis

  2007cites this paper
• Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

  2007cites this paper
• Efficient and accurate P-value computation for Position Weight Matrices

  2007cites this paper
• Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements

  2007cites this paper
• An efficient method for statistical significance calculation of transcription factor binding sites

  2007cites this paper
• Identification of muscle-specific regulatory modules in Caenorhabditis elegans.

  2007cites this paper
• Algorithms for Weighted Matching

  2007cites this paper
• PhyloScan: identification of transcription factor binding sites using cross-species evidence

  2007influential citation
• A new approach to the assessment of the quality of predictions of transcription factor binding sites

  2007cites this paper
• Fast Search Algorithms for Position Specific Scoring Matrices

  2007cites this paper
• Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

  2007cites this paper
• Reverse engineering mammalian transcriptional regulatory networks

  2007cites this paper
• Statistical significance of cis-regulatory modules

  2007cites this paper
• Computational identification of transcriptional regulatory elements in DNA sequence

  2006cites this paper
• Statistical significance in biological sequence analysis

  2006influential citation
• Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes

  2006cites this paper
• Context-specific independence mixture modeling for positional weight matrices

  2006cites this paper
• Calculating PSSM probabilities with lazy dynamic programming

  2006cites this paper
• Contribution of the Histone H3 and H4 Amino Termini to Gcn4p- and Gcn5p-mediated Transcription in Yeast*

  2006cites this paper