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Genome-Wide Location and Function of DNA Binding Proteins

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Control of Pancreas and Liver Gene Expression by HNF Transcription Factors

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Assessing computational tools for the discovery of transcription factor binding sites

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Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitionsPreprint

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Tissue Classification with Gene Expression Profiles

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Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity

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The Core of the Polycomb Repressive Complex Is Compositionally and Functionally Conserved in Flies and Humans

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ANN-SPEC: A METHOD FOR DISCOVERING TRANSCRIPTION FACTOR BINDING SITES WITH IMPROVED SPECIFICITY

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CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure

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Discovery of novel transcription factor binding sites by statistical overrepresentation

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Identification and Characterization of Phenylpyruvate Decarboxylase Genes in Saccharomyces cerevisiae

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Modeling dependencies in protein-DNA binding sites

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A statistical method for finding transcription factor binding sites.

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Displaying the in formation contents of structural RNA alignments: the structure logos

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Practical Strategies for Discovering Regulatory DNA Sequence Motifs

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Transcriptional Induction by Aromatic Amino Acids in Saccharomyces cerevisiae

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De novo cis-regulatory module elicitation for eukaryotic genomes

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Met31p and Met32p, Two Related Zinc Finger Proteins, Are Involved in Transcriptional Regulation of Yeast Sulfur Amino Acid Metabolism

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Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA

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Oligonucleotide‐based microarray for DNA methylation analysis: Principles and applications

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Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation

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Computational Identification of Transcription Factor Binding Sites via a Transcription-factor-centric Clustering (TFCC) Algorithm

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A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites

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Mining ChIP-chip data for transcription factor and cofactor binding sites

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The ABACUS system for branch-and-cut-and-price algorithms in integer programming and combinatorial optimization

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UME6, a negative regulator of meiosis insaccharomyces cerevisiae, contains a C-terminal Zn2Cys6binuclear cluster that binds the URS1 DNA sequence in a zinc-dependent manner

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Macromolecular recognition

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Adaptively inferring human transcriptional subnetworks

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A boosting approach for motif modeling using ChIP-chip data

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GOLEM: an interactive graph-based gene-ontology navigation and analysis tool

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Scoring Genes for Relevance

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Regulatory element detection using correlation with expression (abstract only)

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Scoring functions for transcription factor binding site prediction

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Some guidelines for identification of recognition sequences: Regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A)

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Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs

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An improved map of conserved regulatory sites for Saccharomyces cerevisiae

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Cis-acting sequences that affect the expression of the human fetal gamma-globin genes.

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Human–Mouse Gene Searcher: a tool to assist discovery of malformation-associated genes by using phenotype databases

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Molecular and genetic properties of tumors associated with local immune cytolytic activity

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GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

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Host microbiota constantly control maturation and function of microglia in the CNS

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Microglia development follows a stepwise program to regulate brain homeostasis

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Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

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The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight

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Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span

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RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

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Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

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Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

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Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

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DC isoketal-modified proteins activate T cells and promote hypertension

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Abundant Pleiotropy in Human Complex Diseases and Traits

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Morphometric Similarity Networks Detect Microscale Cortical Organization and Predict Inter-Individual Cognitive Variation

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The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids

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A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

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A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging

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Developmental programming of CpG island methylation profiles in the human genome

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The air-liquid interface and use of primary cell cultures are important to recapitulate the transcriptional profile of in vivo airway epithelia

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Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

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A cellular and spatial map of the choroid plexus across brain ventricles and ages

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Artemisinins Target GABAA Receptor Signaling and Impair α Cell Identity

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The genomic landscape of nasopharyngeal carcinoma

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Treg Cells Promote the SREBP1-Dependent Metabolic Fitness of Tumor-Promoting Macrophages via Repression of CD8+ T Cell-Derived Interferon-γ

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