Boris Lenhard
A5052661284- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
- Chromosomal and Genetic Variations
- Gene expression and cancer classification
- Medical Imaging Techniques and Applications
- Cancer-related gene regulation
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Animal Genetics and Reproduction
- CRISPR and Genetic Engineering
- Plant Molecular Biology Research
- MicroRNA in disease regulation
- Identification and Quantification in Food
- Pancreatic function and diabetes
- Aquaculture disease management and microbiota
- Genetic Mapping and Diversity in Plants and Animals
- Bacterial Genetics and Biotechnology
- T-cell and B-cell Immunology
- Immune Cell Function and Interaction
- Developmental Biology and Gene Regulation
MRC London Institute of Medical Sciences
2015-2024
Hammersmith Hospital
2015-2024
Imperial College London
2015-2024
Genomics (United Kingdom)
2017-2024
University of Edinburgh
2024
University of Bergen
2013-2022
NIHR Imperial Biomedical Research Centre
2020
MRC Clinical Trials Unit at UCL
2013-2018
Centre for Innovation in Regulatory Science
2016
Google (United States)
2015
This study describes comprehensive polling of transcription start and termination sites analysis previously unidentified full-length complementary DNAs derived from the mouse genome. We identify 5' 3' boundaries 181,047 transcripts with extensive variation in arising alternative promoter usage, splicing, polyadenylation. There are 16,247 new protein-coding transcripts, including 5154 encoding proteins. Genomic mapping transcriptome reveals transcriptional forests, overlapping on both...
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery all classes cis-regulatory elements including enhancers, promoters, insulators, silencers locus control regions. Here we present first extensive map human DHSs identified through genome-wide profiling in 125 diverse cell tissue types. We identify ∼2.9 million that encompass virtually known experimentally validated sequences expose a vast trove novel elements, most with highly cell-selective...
The analysis of regulatory regions in genome sequences is strongly based on the detection potential transcription factor binding sites. preferred models for representation specificity have been termed position-specific scoring matrices. JASPAR an open-access database annotated, high-quality, matrix-based site profiles multicellular eukaryotes. were derived exclusively from sets nucleotide experimentally demonstrated to bind factors. complemented by a web interface browsing, searching and...
Antisense transcription (transcription from the opposite strand to a protein-coding or sense strand) has been ascribed roles in gene regulation involving degradation of corresponding transcripts (RNA interference), as well silencing at chromatin level. Global transcriptome analysis provides evidence that large proportion genome can produce both strands, and antisense commonly link neighboring "genes" complex loci into chains linked transcriptional units. Expression profiling reveals frequent...
Abstract JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release JASPAR, the CORE collection has been expanded with 245 new PFMs (169 vertebrates, 42 plants, 17 nematodes, 10 insects, and 7 fungi), 156 were updated (125 28 plants 3 insects). These represent 18% expansion compared to previous...
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There an international collaborative effort to identify all full-length mRNA transcripts from mouse, and ensure that each represented in physical collection clones. Here we report manual annotation 60,770 complementary DNA sequences. These are clustered 33,409 'transcriptional units', contributing 90.1% newly established transcriptome database. Of these transcriptional units, 4,258 new...
Abstract JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new (148 plants, 101 vertebrates, 85 urochordates, and 7 insects), which corresponds to a 19% expansion over previous release. We added 298 Unvalidated when no orthogonal evidence was found in literature. All were clustered provide...
JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release JASPAR, CORE collection has been expanded with 322 new PFMs (60 vertebrates 262 plants) 33 were updated (24 vertebrates, 8 plants 1 insects). These represent a 30% expansion compared to 2016 release. addition, we...
JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the CORE collection with 494 new TF (315 vertebrates, 11 nematodes, 3 insects, 1 fungi and 164 plants) updated 59 (58 vertebrates fungi). The introduced represent 83% expansion 10% update when compared to previous release....
JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing binding preference transcription factors from multiple species. The fifth major release greatly expands heart JASPAR—the CORE subcollection, which contains curated, non-redundant profiles—with 135 new curated (74 in vertebrates, 8 Drosophila melanogaster, 10 Caenorhabditis elegans and 43 Arabidopsis thaliana; a 30% increase total) older updated (36 3 D. melanogaster 4 A. 9%...
JASPAR is a popular open-access database for matrix models describing DNA-binding preferences transcription factors and other DNA patterns. With its third major release, has been expanded equipped with additional functions aimed at both casual power users. The heart of the database-the CORE sub-database-has increased by 12% in size, three new specialized sub-databases have added. New include clustering similarity, generation random matrices sampling from selected sets existing...
JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing DNA-binding patterns transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release largest expansion core to date: now holds 457 non-redundant, curated profiles. The new entries include first batch derived from ChIP-seq ChIP-chip whole-genome binding experiments, 177 yeast TF introduction division brings convenience an active...
ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity increased by an order magnitude as compared to single-sequence analysis. offers several unique features, including interactive expert system...
We report evidence for a mechanism the maintenance of long-range conserved synteny across vertebrate genomes. found largest mammal-teleost chromosomal segments to be spanned by highly noncoding elements (HCNEs), their developmental regulatory target genes, and phylogenetically functionally unrelated “bystander” genes. Bystander genes are not specifically under control that drive expressed in patterns different from those Reporter insertions distal zebrafish pax6.1/2 , rx3 id1 fgf8 miRNA...
Abstract Summary: The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central computational studies of gene regulation. TFBSTools an R/Bioconductor package for the analysis and manipulation TFBSs their associated profile matrices. TFBStools provides a toolkit handling TFBS matrices, scanning sequences alignments including whole genomes, querying JASPAR database. functionality can be easily extended include advanced statistical analysis, data...
Chromosome conformation capture approaches have shown that interphase chromatin is partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized topological domains. This compartmentalization thought to facilitate the matching of genes regulatory elements, but its precise function mechanistic basis remain unknown. Cohesin controls chromosome topology enable DNA repair segregation in cycling cells. In addition, cohesin associates with active enhancers promoters CTCF form...
Genomes of animals as different sponges and humans show conservation global architecture. Here we that multiple genomic features including transposon diversity, developmental gene repertoire, physical order, intron-exon organization are shattered in the tunicate Oikopleura, belonging to sister group vertebrates retaining chordate morphology. Ancestral architecture animal genomes can be deeply modified may therefore largely nonadaptive. This rapidly evolving lineage thus offers unique...
Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing interspecies the transcriptional responses primary human and mouse macrophages Toll-like receptor (TLR)–4 agonist lipopolysaccharide (LPS). By using custom platform permitting cross-species interrogation coupled with deep sequencing mRNA 5′ ends, we identified extensive divergence LPS-regulated orthologous...
JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing provided orthogonal support 72 from previous release's UNVALIDATED collection. Altogether, 2024 update provides 20% increase in release. A trimming algorithm enhanced by...