A5048857636- Protein Structure and Dynamics
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Genetic Mapping and Diversity in Plants and Animals
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Bacteriophages and microbial interactions
- Genetics, Bioinformatics, and Biomedical Research
- Probiotics and Fermented Foods
- Glycosylation and Glycoproteins Research
- Advanced Statistical Methods and Models
- Cancer-related molecular mechanisms research
- Animal Genetics and Reproduction
- Computational Drug Discovery Methods
- MicroRNA in disease regulation
- Plant Virus Research Studies
- Antifungal resistance and susceptibility
- Microbial Community Ecology and Physiology
- Ruminant Nutrition and Digestive Physiology
- Statistical Methods and Inference
- Milk Quality and Mastitis in Dairy Cows
- Fungal Infections and Studies
Natural Resources Institute Finland
2016-2025
Tieto (Finland)
2025
Equinor (United Kingdom)
2024
National Research Center for Applied Cybersecurity ATHENE
2024
Tampere University
2010-2020
Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)
2013-2020
Center for Clinical and Cosmetic Research
2020
Tampere University Hospital
2016
Airbus (Germany)
2016
Fimlab (Finland)
2016
Consensus structure prediction methods (meta-predictors) have higher accuracy than individual algorithms (their components). The goal for the development of 3D-Jury system is to create a simple but powerful procedure generating meta-predictions using variable sets models obtained from diverse sources. resulting protocol should help improve quality structural annotations novel proteins.The generates created methods. It not necessary know prior characteristics able utilize immediately new...
Abstract Motivation: Evaluating the accuracy of predicted models is critical for assessing structure prediction methods. Because this problem not trivial, a large number different assessment measures have been proposed by various authors, and it has already become an active subfield research (Moult et al. (1999) Critical methods protein (CASP): round III. Proteins , Suppl32–6). The CASP (1997) proteins II. Suppl3, Dedicated Issue, Moult Suppl32–6) CAFASP (Fischer CAFASP-1: fully automated...
Abstract In protein fold recognition, one assigns a probe amino acid sequence of unknown structure to library target 3D structures. Correct assignment depends on effective scoring the for its compatibility with each Here we show that, in addition probe, sequence‐derived properties (such as predicted secondary structure) are useful assignment. The additional measure between and is level agreement known fold. That is, recommend sequence‐structure function that combines previously developed...
Prediction of protein structures is one the fundamental challenges in biology today. To fully understand how well different prediction methods perform, it necessary to use measures that evaluate their performance. Every two years, starting 1994, CASP (Critical Assessment Structure Prediction) process has been organized ability predictors blindly predict structure proteins. capture features models, several have developed during processes. However, these not examined detail before. In an...
The Structure Prediction Meta Server offers a convenient way for biologists to utilize various high quality structure prediction servers available worldwide. meta server translates the results obtained from remote services into uniform format, which are consequently used request jury consensus Pcons.The is freely at http://BioInfo.PL/meta/, some have however restrictions non-academic users, respected by server.Results of several sessions CAFASP and LiveBench programs assessment performance...
The results of the second Critical Assessment Fully Automated Structure Prediction (CAFASP2) are presented. goals CAFASP to (i) assess performance fully automatic web servers for structure prediction, by using same blind prediction targets as those used at CASP4, (ii) inform community users about capabilities servers, (iii) allow human groups participating in CASP use and analyze while preparing their nonautomated predictions CASP, (iv) compare automated that human-expert CASP. More than 30...
Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated (bolus) faeces of dairy cattle to assess if non-invasive samples could be used as proxies for digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different supplements in a 5 x Latin square design. Extracted DNA analysed by qPCR sequencing 16S 18S rRNA genes the fungal ITS1 amplicons. Faeces...
The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet dietary additives in a complex way. aim this study was investigate the benefits increasing depth community analysis describing explaining responses changes. Quantitative PCR, ssu rRNA amplicon based taxa composition, diversity co-occurrence network analyses were applied digesta samples obtained from four multiparous Nordic Red dairy cows fitted with rumen cannulae. received...
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step technology analytical approaches available to define, manage conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR terms technological continuity, capacity integrative methodologies needed fully exploit new, multidimensional data. final conference the ESF program aimed address...
Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS...
To gain a better understanding of the biological role proteins encoded in genome sequences, knowledge their three-dimensional (3D) structure and function is required. The computational assignment folds becoming an increasingly important complement to experimental determination. In particular, fold-recognition methods aim predict approximate 3D models for bearing no sequence similarity any protein known structure. However, fully automated structure-prediction can currently produce reliable...
The results of the first Critical Assessment Fully Automated Structure Prediction (CAFASP-1) are presented. objective was to evaluate success rates fully automatic web servers for fold recognition which available community. This study based on targets used in third meeting Techniques Protein (CASP-3). However, unlike CASP-3, not a blind trial, as it held after structures were known. aim assess performance methods without user intervention that several groups their CASP-3 submissions....
Journal Article A computer vision based technique for 3-D sequence-independent structural comparison of proteins Get access Orly Bachar, Bachar 1Computer Science Department, School Mathematical Sciences Search other works by this author on: Oxford Academic PubMed Google Scholar Daniel Fischer, Fischer Sciences2Sackler Institute Molecular Medicine, Faculty Tel Aviv UniversityTel 69978, Israel Ruth Nussinov, Nussinov 4 2Sackler Israel3Laboratory BiologyPRI/Dynacorp, NCI-FCRF, Building 469,...
Genome-wide studies have already shed light into the evolution and enormous diversity of viral world. Nevertheless, one unresolved mysteries in comparative genomics today is abundance ORFans – ORFs with no detectable sequence similarity to any other ORF databases. Recently, attempting understand origin functions bacterial been reported. Here we present a first genome-wide identification analysis world, focus on bacteriophages. Almost one-third all 1,456 complete virus genomes correspond...
Abstract Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions such as Galaxy towards command-line Nextflow and Snakemake. We report on recent developments in nf-core frameworks that have led to widespread adoption across many scientific communities. describe how adopting standards enables faster development, improved interoperability, collaboration with >8,000...
Abstract We present a novel, continuous approach aimed at the large‐scale assessment of performance available fold‐recognition servers. Six popular servers were investigated: PDB‐Blast, FFAS, T98‐lib, GenTHREADER, 3D‐PSSM, and INBGU. The was conducted using as prediction targets large number selected protein structures released from October 1999 to April 2000. A target if its sequence showed no significant similarity any proteins previously in structural database. Overall, able produce...
A crucial step in exploiting the information inherent genome sequences is to assign each protein sequence its three-dimensional fold and biological function. Here we describe assignment for proteins encoded by small of Mycoplasma genitalium. The was carried out our computer server (http://www.doe-mbi.ucla.edu/people/frsvr/ frsvr. html), which assigns folds amino acid comparing sequence-derived predictions with known structures. Of total 468 ORFs, 103 (22%) can be assigned a high confidence,...
Journal Article Molecular surface recognition by a computer vision-based technique Get access Raquel Norel, Norel 1Computer Science Department, School of Mathematical SciencesTel Aviv 69978, Israel Search for other works this author on: Oxford Academic PubMed Google Scholar Daniel Fischer, Fischer Israel2Saclder Institute Medicine, Faculty Tel UniversityTel Haim J. Wolfson, Wolfson Israel3Robotics Research Laboratory, Courant Sciences, New York University715 Broadway, 12th Floor, York, NY...
We have developed a long-extension-PCR strategy which amplifies approximately half of the mitochondrial genome (6.3 kb)of Caenorhabditis elegans using an individual worm as target. analyzed three strains over their life span to assess number detectable deletions in genome. Two these are wild-type for while third is mutant age-1 gene, doubling its maximum span. At mean strains, there was significant difference between frequency detected compared with young animals. In addition, occur at...
We present the results of evaluation latest LiveBench-8 experiment. These provide a snapshot view state art in automated protein structure prediction, just before 2004 CAFASP-4/CASP-6 experiments begin. The last CAFASP/CASP demonstrated that meta-predictors entail significant advance field, already challenging most human expert predictors. corroborates superior performance meta-predictors, which are able to produce useful predictions for over one-half test targets. More importantly,...