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Using a complete set of budding-yeast mutants bearing deletions of all known open reading frames, a recent study has revealed multiple overlapping pathways that coordinately regulate cell-cycle progression wit...
Many essential transcription factors have conserved roles in regulating biological programs,...cis-regulatory sequences, rather than differences between the regulators or nuclear environments.
High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned?
A report on The Biology of Genomes meeting, Cold Spring Harbor, USA, 12-16 May 2004.
Immediate early genes are considered to play important roles in dynamic gene regulatory networks following exposure to appropriate stimuli. One of the immediate early genes, early growth response gene 1 (EGR-1), ...
ChIP-seq is a powerful method for obtaining genome-wide maps of protein-DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq...
Here, we introduce species-aware DNA language models, which we trained on more than 800 species spanning over 500 million years of evolution. Investigating their ability to predict masked nucleotides from context...
Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constr...
MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited ...
Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA ...
A report on the Keystone Symposium 'Comparative Genomics of Plants', Taos, USA, 4-9 March 2004.
A report on the Fifth International Workshop on Bioinformatics and Systems Biology, Berlin, Germany, 22-25 August 2005.
An elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors has been developed by Rhee and Pugh.
Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical p...
Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Ex...
The Erratum to this article has been published in Genome Biology 2005 6:403
Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PT...
Large-scale expression profiling has revealed distinct clusters of circadian clock-regulated genes and identified a phase-specific cis-regulatory element.
Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characterization and evolution of ...
This study analyzes the predictions of a number of promoter predictors on the ENCODE regions of the human genome as part of the ENCODE Genome Annotation Assessment Project (EGASP). The systems analyzed operate...
This article is part of a Supplement: Volume 7 Supplement 1
To address this limitation, we use a purposefully generated cellular model of colon cancer invasiveness to generate multi-omics data, including expression, accessibility, and selected histone modification profile...
Quantitative information on gene activity at single cell-type resolution is essential for the understanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specialized...
Single-cell RNA sequencing (scRNA-seq) plays a pivotal role in our understanding of cellular heterogeneity. Current analytical workflows are driven by categorizing principles that consider cells as individual ...
A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generate...
Promoters are sites of transcription initiation that harbour a high concentration of phenotype-associated genetic variation. The evolutionary gain and loss of promoters between species (collectively, termed tu...
Alcoholism is a complex disorder determined by interactions between genetic and environmental risk factors. Drosophila represents a powerful model system to dissect the genetic architecture of alcohol sensitivity...
Genome‐wide transcriptome analyses have given systems‐level insights into gene regulatory networks. Due to the limited depth of quantitative proteomics, however, our understanding of post‐transcriptional gene ...
Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the ...
Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes are the gold standard model for the assessment of drug efficacy, safety, and toxicity in the early phases of dru...
The development of novel approaches for reprogramming mouse and human somatic cells has enabled the generation of induced pluripotent stem cells that are free of exogenous genes.
Increasing evidence demonstrates that stem cells maintain their identities by a unique transcription network and chromatin structure. Opposing epigenetic modifications H3K27me3 and H3K4me3 have been proposed t...
T cells in the thymus undergo opposing positive and negative selection processes so that the only T cells entering circulation are those bearing a T cell receptor (TCR) with a low affinity for self. The mechan...
Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (C...
The largest sequence-based models of transcription control to date are obtained by predicting genome-wide gene regulatory assays across the human genome. This setting is fundamentally correlative, as those mod...
The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to iden...
Extensive studies have revealed the function and mechanism of lncRNAs in development and differentiation, but the majority have focused on those lncRNAs adjacent to protein-coding genes. In contrast, lncRNAs l...
DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the...
Cold stress can greatly affect plant growth and development. Plants have developed special systems to respond to and tolerate cold stress. While plant scientists have discovered numerous genes involved in resp...
Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of...
A major mechanism for the preservation of gene duplicates in the genome is thought to be mediated via loss or modification of cis-regulatory subfunctions between paralogs following duplication (a process known as...
Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source method...
Transposable elements are increasingly recognized as a source of cis...-regulatory variation. Previous studies have revealed that transposons are often bound by transcription factors and some have been co-opted i...
cERMIT is a computationally efficient motif discovery tool based on analyzing genome-wide quantitative regulatory evidence. Instead of pre-selecting promising candidate sequences, it utilizes information acros...
A report on the biannual Swiss Institute for Experimental Cancer Research (ISREC) Symposium on the Cell and Molecular Biology of Cancer, Lausanne, Switzerland, 19-22 January 2005.
A report on the Keystone Symposium 'Innate Immunity: Signaling Mechanisms', Keystone, USA, 24-29 February, 2008.
A report on the 44th Annual Drosophila Research Conference, Chicago, USA, 5-9 March, 2003.
A report on the 23rd Annual Lorne Conference on the Organization and Expression of the Genome, Lorne, Victoria, Australia, 17-21 February 2002.
The ENCODE gene prediction workshop (EGASP) has been organized to evaluate how well state-of-the-art automatic gene finding methods are able to reproduce the manual and experimental gene annotation of the huma...
This article is part of a Supplement: Volume 7 Supplement 1
RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in RBP expression and function are often observed in cancer and influence critical pathways implicated in tumor initiat...
Nucleosomes have position-specific functions in controlling gene expression. A complete systematic genome-wide reference map of absolute and relative nucleosome positions is needed to minimize potential confus...
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