Human-mouse genome comparisons to locate regulatory sites

No abstract is available for this paper.

• Publication year

  2000

• Venue

  Nature Genetics

• Publication date

  2000-10-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1038/79965PMID 11017083
• 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.

• Discovery and modeling of transcriptional regulatory regions.

  2000cited by this paper
• Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach.

  2000cited by this paper
• Genomic sequence comparison of the human and mouse adenosine deaminase gene regions

  1999cited by this paper
• Systematic determination of genetic network architecture

  1999cited by this paper
• Bayesian inference on biopolymer models

  1999cited by this paper
• An action plan for mouse genomics

  1999cited by this paper
• Models for prediction and recognition of eukaryotic promoters

  1999cited by this paper
• Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene.

  1998cited by this paper
• Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines.

  1998cited by this paper
• Bayesian adaptive sequence alignment algorithms

  1998cited by this paper
• Molecular characterization of the creatine kinases: and some historical perspectives

  1998cited by this paper
• Identification of regulatory regions which confer muscle-specific gene expression.

  1998cited by this paper
• Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

  1998cited by this paper
• Specificity, free energy and information content in protein-DNA interactions.

  1998cited by this paper
• Eukaryotic Transcription : An Interlaced Review Network of Transcription Factors and Chromatin-Modifying Machines

  1998cited by this paper
• Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes

  1997cited by this paper
• Eukaryotic promoter recognition.

  1997cited by this paper
• Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome.

  1997cited by this paper
• Searching for regulatory elements in human noncoding sequences.

  1997cited by this paper
• Transcriptional regulation by the Sp family proteins.

  1997cited by this paper
• Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome.

  1997cited by this paper
• A Bayesian Evolutionary Distance for Parametrically Aligned Sequences

  1996cited by this paper
• Analysis of compositionally biased regions in sequence databases.

  1996cited by this paper
• A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.

  1995cited by this paper
• Regulation of globin gene expression in erythroid cells.

  1995cited by this paper
• Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution.

  1995cited by this paper
• Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies

  1995cited by this paper
• Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.

  1993cited by this paper
• A space-efficient algorithm for local similarities

  1990cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• A test for nucleotide sequence homology.

  1973cited by this paper

• Genetic effects of sequence-conserved enhancer-like elements on human complex traits

  2024cites this paper
• Predicting genome‐wide tissue‐specific enhancers via combinatorial transcription factor genomic occupancy analysis

  2024cites this paper
• Conserved non-coding elements evolve around the same genes throughout Metazoan evolution.

  2024cites this paper
• Sex and gender perspectives in colorectal cancer

  2023cites this paper
• Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density

  2023cites this paper
• Hep3Gel: A Shape-Shifting Extracellular Matrix-Based, Three-Dimensional Liver Model Adaptable to Different Culture Systems

  2022cites this paper
• Genetic effects of sequence-conserved enhancer-like elements on human complex traits

  2022cites this paper
• On the importance of evolutionary constraint for regulatory sequence identification.

  2021cites this paper
• Pathogen Inducible cis-acting Elements of Synthetic Promoters in Plants-review

  2020cites this paper
• The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

  2020influential citation
• Comparative sequence analysis across Brassicaceae, regulatory diversity in KCS5 and KCS6 homologs from Arabidopsis thaliana and Brassica juncea, and intronic fragment as a negative transcriptional regulator.

  2020cites this paper
• DNA sequence-specific recognition by transcriptional factors

  2020cites this paper
• Transcription factors-DNA interactions in rice: identification and verification

  2020cites this paper
• The Ap-2α/Elk-1 axis regulates Sirpα-dependent tumor phagocytosis by tumor-associated macrophages in colorectal cancer

  2020cites this paper
• Modeling of hypertrophic cardiomyopathy and assessment of gene therapy in human iPSC-derived cardiomyocytes

  2018cites this paper
• High-contrast differentiation resolution 3D imaging of rodent brain by X-ray computed microtomography

  2018cites this paper
• Human Behavior Under Emergency and Its Simulation Modeling: A Review

  2018cites this paper
• The Role of Chromosome Deletions in Human Cancers.

  2018cites this paper
• Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq.

  2017cites this paper
• Functional Divergence of the Nuclear Receptor NR2C1 as a Modulator of Pluripotentiality During Hominid Evolution

  2016cites this paper
• Genomic features of human limb specific enhancers.

  2016cites this paper
• Mechanism of allele specific assembly and disruption of master regulator transcription factor complexes of NF-KBp50, NF-KBp65 and HIF1a on a non-coding FAS SNP.

  2016cites this paper
• Evolutionary Analysis of Regulatory Sequences in Promoter of Senecence-induced Glutamine Synthetase cytosolic isozyme GS1;5 in Arabidopsis thaliana

  2016cites this paper
• The Identification of Cis-Regulatory Sequence Motifs in Gene Promoters Based on SNP Information.

  2016cites this paper
• Gene regulation in the ventral midbrain of the developing chick embryo

  2016cites this paper
• Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis

  2015cites this paper
• CONDITION-SPECIFIC DIFFERENTIAL SUBNETWORK ANALYSIS FOR BIOLOGICAL SYSTEMS

  2015cites this paper
• Exploiting high-throughput data for establishing relationships between genes

  2015cites this paper
• Cis‐regulatory control of human GLI2 expression in the developing neural tube and limb bud

  2015cites this paper
• Development of novel software tools and methods for investigating the significance of overlapping transcription factor genomic interactions

  2015cites this paper
• ERF-VII transcription factors bind to an evolutionarily conserved cis-motif to 1 regulate hypoxia-responsive gene expression in Arabidopsis 2 3

  2015cites this paper
• Histone Acetylation Accompanied with Promoter Sequences Displaying Differential Expression Profiles of B-Class MADS-Box Genes for Phalaenopsis Floral Morphogenesis

  2014cites this paper
• Computational Methods for Analysis of Transcriptional Regulation

  2014cites this paper
• Evolution of transcription factor binding in metazoans — mechanisms and functional implications

  2014cites this paper
• Functional analysis of human enhancers using the zebrafish embryo

  2014cites this paper
• Computationa 21. Computational Methods for Analysis of Transcriptional Regulation

  2014cites this paper
• A bioinformatic and computational study of myosin phosphatase subunit diversity.

  2014cites this paper
• Promoter analysis of the gene encoding GDNF in murine Sertoli cells.

  2014cites this paper
• In silico prediction of

  2014cites this paper
• Position Weight Matrix of Transcription Factor Binding Sites

  2014cites this paper
• The start of systems biology in Ukraine

  2014cites this paper
• Identification and characterization of ERFIb transcription factor binding motifs and their target genes

  2013cites this paper
• CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data

  2013cites this paper
• Profiling of Androgen Response in Rainbow Trout Pubertal Testis: Relevance to Male Gonad Development and Spermatogenesis

  2013cites this paper
• Characterization and Identification of cis-Regulatory Elements in Arabidopsis Based on Single-Nucleotide Polymorphism Information[W][OPEN]

  2013cites this paper
• Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers

  2013cites this paper
• Characterization and identification of cis-regulatory elements in Arabidopsis thaliana based on SNP information.

  2013cites this paper
• Plant Signaling Peptides

  2012cites this paper
• Distance and Helical Phase Dependence of Synergistic Transcription Activation in cis-Regulatory Module

  2012cites this paper
• PPARG Binding Landscapes in Macrophages Suggest a Genome-Wide Contribution of PU.1 to Divergent PPARG Binding in Human and Mouse

  2012cites this paper
• Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets.

  2012cites this paper
• Computational-Based Analysis to Associate the Function of Plant Signaling Peptides with Distinct Biological Processes

  2012cites this paper
• Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites

  2012cites this paper
• A new algorithm for quantifying binding site pattern similarity with applications for Next Generation Sequencing

  2012cites this paper
• Regulatory Annotation of Human Genome Huy Vu

  2012cites this paper
• In Silico and Deletion Analysis of Upstream Promoter Fragment of S-Adenosyl Homocysteine Hydrolase (SAHH1) Gene of Arabidopsis Leads to the Identification of a Fragment Capable of Driving Gene Expression in Developing Seeds and Anthers

  2012cites this paper
• A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

  2012cites this paper
• The cis-regulatory dynamics of the Drosophila CNS determinant castor are controlled by multiple sub-pattern enhancers.

  2012cites this paper
• Genome annotation of the 1.2MB Region on chromosome 8p22-p23.1 harbouring the gene for Keratolytic Winter Erythema (KWE)

  2012cites this paper
• Sequence Pattern Discovery with Applications to Understanding Gene Regulation and Vaccine Design

  2012influential citation
• The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3′ UTR

  2012cites this paper
• Improving Computational Predictions of Cis-regulatory Binding Sites in Genomic Data

  2011cites this paper
• Interspecies Heterogeneity in the Hepatic Transcriptomic Response to AHR Activation by Dioxin

  2011cites this paper
• Investigating the Biological Significance of Metallointercalators with cDNA Microarrays

  2011cites this paper
• Computational Methods for Analysis of Transcriptional Regulations

  2011cites this paper
• Cross species comparison of C/EBPa and PPAR¿ profiles in mouse and human adipocytes reveals interdependent retention of binding sites Cross species comparison of C/EBP a and PPAR g profiles in mouse and human adipocytes reveals interdependent retention of binding sites

  2011cites this paper
• Statistical Applications in Genetics and Molecular Biology Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data

  2011cites this paper
• Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices

  2011cites this paper
• Identifying a transcriptional signature for cell sensitivity to the cancer chemotherapy agent, BCNU

  2011cites this paper
• Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

  2011cites this paper
• Mapping the sequences of potential guanine quadruplex motifs

  2011cites this paper
• Distant cis-regulatory elements in human skeletal muscle differentiation.

  2011cites this paper
• Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana

  2011cites this paper
• Species-specific strategies underlying conserved functions of metabolic transcription factors.

  2011cites this paper
• High - throughput bioinformatic approaches to study tumorigenesis in mammalian cells

  2011cites this paper
• Cistrome: an integrative platform for transcriptional regulation studies

  2011cites this paper
• Algorithms for genome comparison applied to bacterial genomes. (Algorithmes de comparaison de génomes appliqués aux génomes bactériens)

  2010cites this paper
• Emergence of mammals by emergency: exaptation

  2010cites this paper
• Proteome analysis and genome-wide regulatory motif prediction identify novel potentially sex-hormone regulated proteins in rat efferent ducts.

  2010cites this paper
• Computational Biology of Transcription Factor Binding

  2010cites this paper
• The role of highly conserved non-coding DNA sequences in vertebrate development and evolution

  2010cites this paper
• Genome‐wide maps of transcription regulatory elements

  2010cites this paper
• Systematic identification of conserved motif modules in the human genome

  2010cites this paper
• Co-occurrence of transcription factor binding sites (Gemeinsames Auftreten von Transkriptionsfaktor-Bindungsstellen)

  2010cites this paper
• Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress

  2010cites this paper
• Sequence analysis of chromatin immunoprecipitation data for factors

  2010cites this paper
• A systems approach to mapping transcriptional networks controlling surfactant homeostasis

  2010cites this paper
• Sequence analysis of chromatin immunoprecipitation data for transcription factors.

  2010cites this paper
• Genome design in eukaryotes.

  2010cites this paper
• Novel sequence variations in LAMA2 andSGCG genes modulating cis-acting regulatory elements and RNA secondary structure

  2010cites this paper
• Transcription Factor Binding Site Identification by Phylogenetic Footprinting

  2010cites this paper
• Expression analysis of the Adam21 gene in mouse testis.

  2010cites this paper
• Genome-wide proximal promoter analysis and interpretation.

  2010cites this paper
• Context-specific methods for sequence homology searching and alignment

  2010cites this paper
• Bayesian Model Based Approaches In The Analysis Of Chromatin Structure And Motif Discovery

  2010cites this paper
• Computational prediction and experimental verification of gene regulatory elements in neuronal development

  2010cites this paper
• Gene Expression Analysis of Forskolin Treated Basilar Papillae Identifies MicroRNA181a as a Mediator of Proliferation

  2010cites this paper
• A Systems Biology Approach to Transcription Factor Binding Site Prediction

  2010cites this paper
• Evolution of cis-regulatory sequences in Drosophila.

  2010cites this paper
• Identification of promoter regions and regulatory sites.

  2010cites this paper