A5018565194- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Genomic variations and chromosomal abnormalities
- Chromosomal and Genetic Variations
- Genetic Associations and Epidemiology
- Gene expression and cancer classification
- Antibiotic Resistance in Bacteria
- Genomics and Rare Diseases
- Genomics and Chromatin Dynamics
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Genetic Mapping and Diversity in Plants and Animals
- Chemical Synthesis and Analysis
- Forensic and Genetic Research
- RNA modifications and cancer
- Bacterial Identification and Susceptibility Testing
- Nicotinic Acetylcholine Receptors Study
- Machine Learning in Bioinformatics
- Prenatal Screening and Diagnostics
- Genetic diversity and population structure
- Photosynthetic Processes and Mechanisms
- Antimicrobial Peptides and Activities
- Vibrio bacteria research studies
- Microbial Community Ecology and Physiology
University of Tartu
2015-2024
Estonian Biocentre
2008-2019
Central Bank of Luxembourg
2015
Université de Lorraine
2015
National Center for Biotechnology Information
2012
Bioinformatics Institute
2012
DKFZ-ZMBH Alliance
2012
Institute of Molecular and Cell Biology
2012
Heidelberg University
2012
SIB Swiss Institute of Bioinformatics
2012
Polymerase chain reaction (PCR) is a basic molecular biology technique with multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis genes, diagnosis diseases, genotyping discovery genetic variants. Reliable primer design crucial for successful PCR, over decade, the open-source Primer3 software has been widely used design, often in high-throughput genomics applications. It also incorporated into numerous publicly available packages web services....
Abstract Summary: The determination of annealing temperature is a critical step in PCR design. This parameter typically derived from the melting primers, so for successful work it important to determine primer accurately. We introduced several enhancements widely used design program Primer3. improvements include formula calculating and salt correction formula. Also, new version can take into account effects divalent cations, which are included most buffers. Another modification enables using...
It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, date the Y-chromosomal most recent common ancestor (MRCA) Africa at 254 (95% CI 192–307) kya and detect cluster major founder haplogroups narrow time interval 47–52 kya,...
Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the contain large number repeat sequences and other unsuitable amplification by PCR. We have developed novel k-mer based masking method that uses statistical model to detect mask failure-prone on DNA template prior primer design. implemented software as standalone primer3_masker integrated it into design program Primer3.The version in C. The source code freely available at...
Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with Illumina Infinium platform. In cohorts where sample size was >100, one hundred randomly chosen samples were used for analysis to minimize effect, resulting in a total 1,564 samples. This revealed that structure European population correlates closely geography. The first two PCs highlight diversity...
The geographic origin and time of dispersal Austroasiatic (AA) speakers, presently settled in south southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. first these places speakers Asia with later during Neolithic, whereas second hypothesis advocates pre-Neolithic origins this family from Asia. To test two alternative models, study combines analysis uniparentally inherited markers 610,000 common single...
Significance Translation arrest regulated by nascent peptides and small cofactors controls expression of important genes, including medically relevant macrolide antibiotic resistance genes. The role the cofactor for triggering this mechanism has remained enigmatic. Previous studies suggested that extensive interactions between chain molecule juxtaposed in ribosomal exit tunnel were critical halting translation. However, here we show induces stalling, even without significant contacts with...
The Haplotype Map (HapMap) project recently generated genotype data for more than 1 million single-nucleotide polymorphisms (SNPs) in four population samples. main application of the is selection tag (tSNPs) to use association studies. usefulness this process needs be verified populations outside those used HapMap project. In addition, it not known how well represent general population, as only 90–120 chromosomes were each and since genotyped SNPs selected so have high frequencies. study, we...
Abstract Background Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of – neighboring nucleotides and can have certain patterns. The codon context influence both translational accuracy elongation rates. However, it is known how strong or conserved preferences in different organisms are. We analyzed 138 (bacteria, archaea eukaryotes) to find patterns pairs. Results After removing effects single usage dipeptide biases we discovered a set for which...
The mRNA translation initiation region (TIR) comprises the initiator codon, Shine-Dalgarno (SD) sequence and translational enhancers. Probably most abundant class of enhancers contains A/U-rich sequences. We have tested influence SD length presence on efficiency initiation. found that during bacterial growth at 37°C, a six-nucleotide (AGGAGG) is more efficient than shorter or longer enhancer contributes strongly to initiation, having greatest stimulatory effect in exponential phase bacteria....
Abstract Background Translational GTPases are a family of proteins in which GTPase activity is stimulated by the large ribosomal subunit. Conserved sequence features allow members this to be identified. Results To achieve accurate protein identification and grouping we have developed method combining searches with Hidden Markov Model profiles tree based grouping. We found all genes for translational 191 fully sequenced bacterial genomes. The sequences were grouped into nine subfamilies....
Plant gas exchange is regulated by guard cells that form stomatal pores. Stomatal adjustments are crucial for plant survival; they regulate uptake of CO2 photosynthesis, loss water, and entrance air pollutants such as ozone. We mapped ozone hypersensitivity, more open stomata, CO2-insensitivity phenotypes the Arabidopsis thaliana accession Cvi-0 to a single amino acid substitution in MITOGEN-ACTIVATED PROTEIN (MAP) KINASE 12 (MPK12). In parallel, we showed mutant cis (CO2-insensitive) were...
Background Plasmids play an important role in the dissemination of antibiotic resistance, making their detection task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make a complex problem. Results We developed tool named PlasmidSeeker that enables plasmids from WGS data without assembly. The algorithm based on k -mers uses -mer abundance distinguish between sequences. tested performance set simulated real...
Abstract Endophytes are microbes and fungi that live inside plant tissues without damaging the host. Herein we examine dynamic changes in endophytic bacterial community potato ( Solanum tuberosum ) tuber response to pathogenic infection by Pectobacterium atrosepticum, which causes soft rot numerous economically important crops. We quantified using both cultivation next-generation sequencing of 16S rRNA gene found that, despite observing significant variability mass macerated tissue structure...
Background Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility identifying from unassembled next-generation sequencing reads using custom-made guide trees. Results A tool named StrainSeeker developed that constructs a list specific k -mers for each node any given Newick-format tree enables 1–2 min. It uses novel algorithm, which analyses observed expected fractions node-specific test...
We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) identifies phenotype-specific k-mers, (b) generates a k-mer-based statistical model for predicting given phenotype (c) predicts the from sequencing data of bacterial isolate. The was validated on 167 Klebsiella pneumoniae isolates (virulence), 200 Pseudomonas aeruginosa (ciprofloxacin resistance) 459 Clostridium difficile (azithromycin resistance). prediction models trained these datasets obtained...