A5103270230- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- Immune Cell Function and Interaction
- Epigenetics and DNA Methylation
- Bacterial Genetics and Biotechnology
- T-cell and B-cell Immunology
- Immunotherapy and Immune Responses
- Chromosomal and Genetic Variations
- Cytokine Signaling Pathways and Interactions
- CRISPR and Genetic Engineering
- Protein Degradation and Inhibitors
- Chromatin Remodeling and Cancer
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Cell Adhesion Molecules Research
- Glycosylation and Glycoproteins Research
- NF-κB Signaling Pathways
- Lipid Membrane Structure and Behavior
- Wnt/β-catenin signaling in development and cancer
- Time Series Analysis and Forecasting
SIB Swiss Institute of Bioinformatics
2012-2024
Defence Scientific Information & Documentation Centre
2023
École Polytechnique Fédérale de Lausanne
2012-2021
Livestrong Foundation
2018
Swiss Group For Clinical Cancer Research
1994-2011
University of Lausanne
2007
Ludwig Cancer Research
2001-2002
University of Geneva
2001
Universidade Federal de São Paulo
2000
Universidade de São Paulo
2000
Computer analysis of a conserved domain, BRCT, first described at the carboxyl ter-minus breast cancer protein BRCA1, p53 binding (53BP1), and yeast cell cycle checkpoint RAD9 revealed large super- family domains that occur predominantly in proteins involved functions responsive to DNA damage. The BRCT domain consists ~95 amino acid residues occurs as tandem repeat terminus numerous proteins, but has been observed also or single copy. superfamily presently includes ~40 nonorthologous namely,...
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete components with high success rates but assembly complete isoform structures poses a major challenge even when all constituent elements identified. Expression-level estimates also varied widely across methods, based on similar models. Consequently,...
We describe several protein sequence statistics designed to evaluate distinctive attributes of residue content and arrangement in primary structure. Considered are global compositional biases, local clustering different types (e.g., charged residues, hydrophobic Ser/Thr), long runs or uncharged periodic patterns, counts distribution homooligopeptides, unusual spacings between particular types. The computer program SAPS (statistical analysis sequences) calculates all the for any individual...
A representative set of 168 eukaryotic POL II promoters has been compiled from the EMBL library and subjected to computer signal search analysis. Application this technique E. coli as a control ensemble revealed well known consensus sequences at -35 -10 which indicates that methods are adequate approach problems kind. The results obtained promoter can be summarised follows: (i) Common sequence features confined region between -50 +10 relative transcriptional initiation site, (ii) only...
Krüppel-associated box domain-zinc finger proteins (KRAB–ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing study of KRAB–mediated regulation at different units. By targeting a drug-controllable KRAB–containing gene-trapping lentiviral vectors, demonstrate that KRAB and its corepressor KAP1 can silence promoters located several...
We present an update of EPDNew (http://epd.vital-it.ch), a recently introduced new part the Eukaryotic Promoter Database (EPD) which has been described in more detail previous NAR Issue. EPD is old database experimentally characterized eukaryotic POL II promoters, are conceptually defined as transcription initiation sites or regions. EPDnew collection automatically compiled, organism-specific promoter lists complementing corpus manually compiled entries EPD. This exclusively derived from...
We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next generation sequencing (NGS) data. Thanks to abundant release new high-throughput transcript mapping data (CAGE, TSS-seq, GRO-cap) database could be extended plant and fungal species. further report expansion mass genome annotation (MGA) repository...
Noncoding variation and gene expression Natural genetic outside of protein coding regions affects multiple molecular phenotypes that can differ across individuals. To examine how genomic proximal (cis) or distal (trans) regulation, Delaneau et al. analyzed expression, chromatin, the three-dimensional conformation genome. Clustering regulatory elements activity individuals reveals structures termed cis-regulatory domains trans-regulatory hubs affect expression. Associations between these...
SNP2TFBS is a computational resource intended to support researchers investigating the molecular mechanisms underlying regulatory variation in human genome. The database essentially consists of collection text files providing specific annotations for single nucleotide polymorphisms (SNPs), namely whether they are predicted abolish, create or change affinity one several transcription factor (TF) binding sites. A SNP's effect on TF estimated based position weight matrix (PWM) model specificity...
STAT transcription factors are expressed in many cell types and bind to similar sequences. However, different gene knock-outs show very distinct phenotypes. To determine whether differences between the binding specificities of proteins account for these effects, we compared sequences bound by STAT1, STAT5A, STAT5B, STAT6. One sequence set was selected from random oligonucleotides recombinant or For another including weak sites, quantified relative affinities We results sites natural target...
We have analyzed conserved domains in t-SNAREs [soluble N -ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors the target membrane], proteins that are believed to be involved fusion of transport vesicles with their membrane. By using a sensitive computer method, generalized profile we were able identify new homology domain is common two families previously identified act as t-SNAREs, syntaxin and SNAP-25 (synaptosome-associated 25 kDa) families, which therefore...
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of experimentally characterised eukaryotic POL II promoters. underlying definition a promoter that transcription initiation site. All information presented in EPD results from independent evaluation primary experimental data shown the biological literature. Sequences flanking sites are indirectly given by pointers to EMBL sequences. annotation part entry includes description promoter-defining evidence,...
The use of comparative genomics to infer genome function relies on the understanding how different components change over evolutionary time1,2,3. aim such analysis is identify conserved, functionally transcribed sequences as protein-coding genes and non-coding RNA genes, other functional regulatory regions4,5, well genomic features. Here, we have compared entire human chromosome 21 with syntenic regions mouse genome, identified a large number conserved blocks unknown function. Although...
Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription–PCR using arbitrarily chosen primers will result in the preferential central portion transcript. Systematic, high-throughput sequencing such products would an sequence tag (EST) database consisting central, generally coding regions genes. Such a add significant value to existing public EST databases, which consist mostly sequences derived from extremities cDNAs, and facilitate...
Abstract Members of the discoidin (DS) domain family, which includes C1 and C2 repeats blood coagulation factors V VIII, occur in a great variety eukaryotic proteins, most have been implicated cell‐adhesion or developmental processes. So far, no three‐dimensional structure known example this extracellular module has determined, limiting usefulness identifying new sequence as member family. Here, we present results recent search protein database for DS domains using generalized profiles,...