A5023325161- Chemical Reactions and Isotopes
- DNA Repair Mechanisms
- Genomics and Phylogenetic Studies
- Mitochondrial Function and Pathology
- DNA and Nucleic Acid Chemistry
- ATP Synthase and ATPases Research
- Enzyme Structure and Function
- Influenza Virus Research Studies
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Mass Spectrometry Techniques and Applications
- Metabolism and Genetic Disorders
- Computational Drug Discovery Methods
- Magnetic and Electromagnetic Effects
- Diabetes and associated disorders
- Neurological Disorders and Treatments
- Diabetes Treatment and Management
- Metabolomics and Mass Spectrometry Studies
- Animal Disease Management and Epidemiology
- Bacteriophages and microbial interactions
- Mathematical Biology Tumor Growth
- Biofield Effects and Biophysics
- Protein Structure and Dynamics
- RNA Research and Splicing
- Adversarial Robustness in Machine Learning
SIB Swiss Institute of Bioinformatics
2013-2024
University of Geneva
2016-2024
Pirogov Russian National Research Medical University
2008-2024
Semenov Institute of Chemical Physics
2003-2024
University of Luxembourg
2024
Bielefeld University
2024
Robert Bosch (Germany)
2023
Scientific and Production Association. S.A. Lavochkin
2022
Russian Academy of Sciences
2008-2020
University of Lausanne
1996-2020
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...
Abstract An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) determination, design. The method uses develops a previously introduced approach model biomolecular structures in which bond lengths, angles, torsion angles are considered independent variables,...
OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up the resource coverage, sampling genomic diversity 1271 eukaryotes, 6013 prokaryotes 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, 404 archaeal genomes, picking best sequenced annotated representatives for each species or operational taxonomic unit. relies on concept hierarchy...
OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from single gene in their last common ancestor. In 2016 reached its 9th release, growing to over 22 million 5000 species, now adding plants, archaea and viruses. this update we focused on usability fast-growing wealth data: updating the user programmatic interfaces browse query data, further enhancing already extensive integration available functional annotations. Collating annotations 100 resources, enabled...
Abstract OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling eukaryotes, prokaryotes, viruses. Genomics continues to accelerate our exploration gene diversity orthology is the most precise way bridging knowledge with rapidly expanding universe genomic sequences. samples organisms best quality genomics data provide leading coverage species diversity. This update underlying over 18 000 prokaryotes almost 2000 eukaryotes 100 million propels another level....
Abstract OrthoDB provides evolutionary and functional annotations of orthologs, inferred for a vast number available organisms. is leading in the coverage genomic diversity sampling Eukaryotes, Prokaryotes Viruses, Bacteria further set to increase three-fold. The user interface has been enhanced response massive growth data. three views on data: (i) list orthologous groups related query, which are now arranged visualize their hierarchical relations, (ii) detailed view an group, featuring...
The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both user interface and back end server were improved. A number tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) added or updated improve usability service. MySQL schema associated API revamped database engine (HitKeeper) was separated from interface. This paper summarizes current status server, with emphasis on new services.
Motivation: Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage signaling. Cellular lipidomes may contain tens thousands structures, staggering degree complexity whose significance is not yet fully understood. High-throughput mass spectrometry-based platforms provide means to study this complexity, but the interpretation lipidomic data its integration prior knowledge lipid biology suffers from lack appropriate tools manage extract it.
Abstract Aims/hypothesis Five clusters based on clinical characteristics have been suggested as diabetes subtypes: one autoimmune and four subtypes of type 2 diabetes. In the current study we replicate cross-validate these in three large cohorts using variables readily measured clinic. Methods independent cohorts, total 15,940 individuals were clustered age, BMI, HbA 1c , random or fasting C-peptide, HDL-cholesterol. Clusters cross-validated against original HOMA measures. addition, between...
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues an unprecedented depth, thus documenting patterns expression almost 20,000 genes with high sensitivity and specificity. The data confirm widely held belief that differences in gene between cell tissue types are largely determined by transcripts derived from a limited number tissue-specific genes, rather than combinations more promiscuously expressed genes. Expression little...
Plants forming a rosette during their juvenile growth phase, such as Arabidopsis thaliana (L.) Heynh., are able to adjust the size, position and orientation of leaves. These responses under control plants circadian clock follow characteristic diurnal rhythm. For instance, increased leaf elongation hyponasty - defined here increase in elevation angle can be observed when shaded. Shading either caused by decrease fluence rate photosynthetically active radiation (direct shade) or red compared...
Type 2 diabetes is a multifactorial disease with multiple underlying aetiologies. To address this heterogeneity, investigators of previous study clustered people according to five subtypes. The aim the current investigate etiology these clusters by comparing their molecular signatures. In three independent cohorts, in total 15,940 individuals were based on clinical characteristics. subset, genetic (N = 12,828), metabolomic 2,945), lipidomic 2,593), and proteomic 1,170) data obtained plasma....
Modern commercial antivirus systems increasingly rely on machine learning (ML) to keep up with the rampant inflation of new malware. However, it is well-known that models are vulnerable adversarial examples (AEs). Previous works have shown ML malware classifiers fragile white-box attacks. used in (AV) products usually not available attackers and only return hard classification labels. Therefore, more practical evaluate robustness real-world AVs a pure black-box manner. We propose...
We identify biomarkers for disease progression in three type 2 diabetes cohorts encompassing 2,973 individuals across molecular classes, metabolites, lipids and proteins. Homocitrulline, isoleucine 2-aminoadipic acid, eight triacylglycerol species, lowered sphingomyelin 42:2;2 levels are predictive of faster towards insulin requirement. Of ~1,300 proteins examined two cohorts, GDF15/MIC-1, IL-18Ra, CRELD1, NogoR, FAS, ENPP7 associated with progression, whilst SMAC/DIABLO, SPOCK1 HEMK2...
The rate of ATP synthesis by creatine kinase extracted from V. xanthia venom was shown to depend on the magnetic field. yield produced enzymes with 24Mg2+ and 26Mg2+ ions in catalytic sites increases 7−8% at 55 mT then decreases 80 mT. For enzyme 25Mg2+ ion a site, 50% 70% fields mT, respectively. In Earth field enzyme, which Mg2+ has nucleus 25Mg, is 2.5 times higher than that enzymes, nonmagnetic, spinless nuclei 24Mg or 26Mg. Both effect isotope demonstrate an ion-radical process,...
Magnetic isotope and magnetic field effects on the rate of DNA synthesis catalysed by polymerases b with isotopic ions 24 Mg 2+ , 25 26 in catalytic sites were detected.No difference enzymatic activity was found between carrying spinless, non-magnetic nuclei Mg.However, nucleus shown to suppress two three times respect ions.Such an dependence directly indicates that mass-independent effect functions.Similar is exhibited Zn 67 64 nuclei, respectively.A new, ion-radical mechanism suggested...
Global disease suitability models are essential tools to inform surveillance systems and enable early detection. We present the first global model of highly pathogenic avian influenza (HPAI) H5N1 demonstrate that reliable predictions can be obtained at scale. Best using spatial predictor variables describing host distributions, rather than land use or eco-climatic variables, with a strong association domestic duck extensively raised chicken densities. Our results also support more systematic...
Abstract: Diabetic neuropathy (DN) is a debilitating disorder occurring in most diabetic patients without viable treatment yet. The present work examined the protective effect of 25 Mg-PMC 16 nanoparticle (porphyrin adducts cyclohexil fullerene-C60) rat model streptozotocin (STZ)-induced DN. (0.5 lethal dose 50 [LD ]) was administered intravenously two consecutive days before intraperitoneal injection STZ (45 mg/kg). 24 and MgCl 2 were used as controls. Blood 2,3-diphosphoglycerate...
In type 2 diabetes (T2D), pancreatic β cells become progressively dysfunctional, leading to a decline in insulin secretion over time. this study, we aimed identify key genes involved beta cell dysfunction by analyzing multiple mouse strains parallel under metabolic stress. Male mice from six commonly used non-diabetic were fed high fat or regular chow diet for three months. Pancreatic islets extracted and phenotypic measurements recorded at days, 10 30 90 days assess progression. RNA-Seq was...
OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling eukaryotes, prokaryotes, viruses, extending experimental gene function knowledge to newly sequenced genomes. We collect annotations, delineate hierarchical orthology annotate groups (OGs) with traits. is leading resource for species diversity, striving sample most diverse well-researched organisms highest quality genomic data. This update expands include 5827...
Although research on influenza lasted for more than 100 years, it is still one of the most prominent diseases causing half a million human deaths every year. With recent observation new highly pathogenic H5N1 and H7N7 strains, appearance pandemic caused by H1N1 swine-like lineage, collaborative effort to share observations evolution this virus in both animals humans has been established. The OpenFlu database (OpenFluDB) part effort. It contains genomic protein sequences, as well...
Combining epidemiological information, genetic characterization and geomapping in the analysis of influenza can contribute to a better understanding description epidemiology ecology, including possible virus reassortment events. Furthermore, integration information such as agroecological farming system characteristics provide new knowledge on risk factors emergence spread. Integrating viral into an animal disease is therefore expected unique tool trace-and-track particular strains; generate...