A5039131441- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Metabolomics and Mass Spectrometry Studies
- Genetics, Bioinformatics, and Biomedical Research
- Biofuel production and bioconversion
- Scientific Computing and Data Management
- Insect symbiosis and bacterial influences
- Genetic diversity and population structure
- Insect and Arachnid Ecology and Behavior
- Neurobiology and Insect Physiology Research
- Evolution and Genetic Dynamics
- Microbial Natural Products and Biosynthesis
- Developmental Biology and Gene Regulation
- Cancer-related molecular mechanisms research
- Glycosylation and Glycoproteins Research
- Machine Learning in Bioinformatics
- Protein Structure and Dynamics
- Semantic Web and Ontologies
- Cell Image Analysis Techniques
- RNA modifications and cancer
University of Lausanne
2012-2025
SIB Swiss Institute of Bioinformatics
2013-2024
University College London
2013
CSCS - Swiss National Supercomputing Centre
2013
ETH Zurich
2013
University of Basel
2012
Centre National de la Recherche Scientifique
2006
Laboratoire Information Génomique et Structurale
2006
École Polytechnique Fédérale de Lausanne
2006
Institut de Biologie Structurale
2006
ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases software tools in different areas life sciences. Scientists can henceforth access seamlessly a wide range domains, such proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual (databases, web-based...
This article introduces a new interface for T-Coffee, consistency-based multiple sequence alignment program. provides an easy and intuitive access to the most popular functionality of package. These include default T-Coffee mode protein nucleic acid sequences, M-Coffee that allows combining output any other aligners, template-based modes deliver high accuracy alignments while using structural or homology derived templates. three available template are Expresso with known 3D-Structure,...
Expresso is a multiple sequence alignment server that aligns sequences using structural information.The user only needs to provide sequences.The runs BLAST identify close homologues of the within PDB database.These structures are used as templates guide original structure-based methods like SAP or Fugue.The final result based on information templates.An advanced mode makes it possible either upload private specify which should be model each sequence.Providing suitable available, delivers...
Abstract Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating data types (RNA-Seq, Affymetrix, situ hybridization, EST data). It based exclusively on curated healthy wild-type (e.g., no knock-out, treatment, disease), provide comparable reference of normal expression. Curation includes very large datasets such as GTEx (re-annotation samples ‘healthy’ or not) well many small ones. Data are integrated made between species...
The M-Coffee server is a web that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user simultaneously run all his of choice without having arbitrarily choose them. delivered along with local estimation its consistency individual MSAs was derived from. computation consensus alignment carried out using special mode T-Coffee package [Notredame, Higgins Heringa (T-Coffee: novel...
MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from number major resources imported into common namespace chemical compounds, reactions, cellular compartments—namely MNXref—and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well variety tools that allow users import their own GSMNs, map them the MNXref reconciliation, manipulate, compare, analyze, simulate (using flux balance analysis)...
The evolution of ants is marked by remarkable adaptations that allowed the development very complex social systems. To identify how ant-specific are associated with patterns molecular evolution, we searched for signs positive selection on amino-acid changes in proteins. We identified 24 functional categories genes which were enriched positively selected ant lineage. also reanalyzed genome-wide data sets bees and flies same methodology to check whether was specific or present other insects....
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora databases tools deployed, technically complex diverse implementations, across spectrum disciplines. The corpus documentation resources is fragmented Web, with much redundancy, has lacked common standard information. outcome scientists must often struggle find, understand, compare use best for...
Abstract MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality reconciliation, particular attention dedicated preserving intrinsic properties GSMN models. MetaNetX website (https://www.metanetx.org/) provides access full database online services. A improvement for mapping user-provided GSMNs...
Abstract Summary: MetaNetX.org is a website for accessing, analysing and manipulating genome-scale metabolic networks (GSMs) as well biochemical pathways. It consistently integrates data from various public resources makes the accessible in standardized format using common namespace. Currently, it provides access to hundreds of GSMs pathways that can be interactively compared (two or more), analysed (e.g. detection dead-end metabolites reactions, flux balance analysis simulation reaction...
Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These suggested be strongest during either early or mid-embryogenesis, which corresponds conservation model hourglass model, respectively. Conflicting results reported, but in recent studies transcriptomes has favored. Studies usually report descriptive statistics calculated for all genes over developmental time points. This introduces dependencies between sets compared...
Selectome (http://selectome.unil.ch/) is a database of positive selection, based on branch-site likelihood test. This model estimates the number nonsynonymous substitutions (dN) and synonymous (dS) to evaluate variation in selective pressure (dN/dS ratio) over branches sites. Since original release Selectome, we have benchmarked implemented thorough quality control procedure multiple sequence alignments, aiming provide minimum false-positive results. We also improved computational efficiency...
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation enzymes description metabolic networks. describes enzyme-catalyzed covering IUBMB Enzyme Nomenclature list as well additional reactions, including spontaneously occurring using entities from ChEBI (Chemical Entities Biological Interest) ontology small molecules. Here we describe developments in since our last report database issue Nucleic...
The Experimental Natural Products Knowledge Graph (ENPKG) framework combines a sample-centric approach with semantic enrichment to organize large heterogeneous metabolomics data sets as knowledge graph. Harmonization of experimental publicly available and federated queries mechanisms enable efficient information extraction the contextualization studies, thereby offering exciting opportunities for drug discovery global chemodiversity characterization.
Gene set enrichment approaches have been increasingly successful in finding signals of recent polygenic selection the human genome. In this study, we aim at detecting biological pathways affected by positive more ancient evolutionary history. Focusing on four branches primate tree that lead to modern humans, tested all available protein coding gene trees Primates clade for adaptation these branches, using likelihood-based branch site test selection. The results locus-specific tests were then...
ABSTRACT Although it is well established that certain stages of development are more conserved than others, the reasons for this phenomenon remain largely unknown. We study molecular conservation in an organ, molar, by comparing temporal profiles expression mice and hamsters. find molar characterized a rarely observed pattern level coding sequences forming inverse hourglass, with at beginning end morphogenesis intermediate stages. As rodent described, we were able to link properties...
The R-Coffee web server produces highly accurate multiple alignments of noncoding RNA (ncRNA) sequences, taking into account predicted secondary structures. uses a novel algorithm recently incorporated in the T-Coffee package. works along same lines as T-Coffee: it pairwise or sequence alignment (MSA) methods to compute primary library input alignments. program then computes an MSA consistent with both contained and structures associated sequences. are using RNAplfold. provides two modes....
Genome wide scans have shown that positive selection is relatively frequent at the molecular level. It of special interest to identify which protein sites and phylogenetic branches are affected. We present Selectome, a database provides results rigorous branch-site specific likelihood test for selection. The Web interface presents mapped both onto trees alignments. allows rapid access by keyword, gene name, or taxonomy based queries. Selectome freely available http://bioinfo.unil.ch/selectome/.
Aquaporins (AQPs) are membrane channels belonging to the major intrinsic proteins family and known for their ability facilitate water movement. While in Populus trichocarpa, AQP form a large encompassing fifty-five genes, most of experimental work focused on few genes or subfamilies. The current was undertaken develop comprehensive picture whole gene species by delineating expression domain distinguishing responsiveness developmental environmental cues. Since duplication events amplified...
Abstract Summary: The Quest for Orthologs (QfO) is an open collaboration framework experts in comparative phylogenomics and related research areas who have interest highly accurate orthology predictions their applications. We here report highlights discussion points from the QfO meeting 2015 held Barcelona. Achievements recent years established a basis to support developments improved prediction explore new approaches. Central effort proper benchmarking of methods services, as well design...
Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integrated made comparable between species thanks consistent annotation processing. In the past years, we have single-cell RNA-sequencing into through careful curation of public datasets We fully this new technology along with wealth other existing Bgee. As result, can now provide one definitive answer all way cell resolution about gene's pattern,...
Abstract Motivation: We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments proteins with known structures. Results: demonstrate that iRMSD is equivalent to standard RMSD although much simpler compute we also show it comparing benchmarking multiple alignment methods. tested score on 6 established packages found results be consistent those obtained using an reference collection like Prefab. Availability: The...
Modern natural products (NPs) research relies on untargeted liquid chromatography coupled with mass spectrometry metabolomics. Together cutting-edge processing and computational annotation strategies, such approaches can yield extensive spectral structural information. However, current workflows require feature-alignment steps based retention time which hinders the comparison of samples originating from different batches or analyzed using instrumental setups. In addition, there is currently...