A5047727399- vaccines and immunoinformatics approaches
- Pneumonia and Respiratory Infections
- Genomics and Phylogenetic Studies
- Microbial infections and disease research
- Bacteriophages and microbial interactions
- Microbial Community Ecology and Physiology
- RNA and protein synthesis mechanisms
- Probiotics and Fermented Foods
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- SARS-CoV-2 and COVID-19 Research
- Mycorrhizal Fungi and Plant Interactions
- SARS-CoV-2 detection and testing
- Plant Pathogens and Fungal Diseases
- Reproductive tract infections research
- Influenza Virus Research Studies
- Fuzzy Logic and Control Systems
- Enzyme-mediated dye degradation
- Toxin Mechanisms and Immunotoxins
- Milk Quality and Mastitis in Dairy Cows
- Vector-borne infectious diseases
- Computational Drug Discovery Methods
- Click Chemistry and Applications
- Biofuel production and bioconversion
- Aquaculture disease management and microbiota
University of Potsdam
2020-2024
Hasso Plattner Institute
2020-2024
Universidade Federal de Minas Gerais
2018-2021
Universidade Federal do Pará
2014-2020
Freie Universität Berlin
2020
Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative Critical Assessment Metagenome Interpretation (CAMI). The CAMI II challenge engaged community to assess methods on realistic complex datasets with long- short-read sequences, created computationally from around 1,700 new known genomes, as well 600 plasmids viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due...
Pneumonia is an infectious disease caused by bacteria, viruses or fungi that results in millions of deaths globally. Despite the existence prophylactic methods against some major pathogens disease, there no efficient prophylaxis atypical agents such as Mycoplasma pneumoniae, a bacterium associated with cases community-acquired pneumonia. Because morphological peculiarity M. which leads to increased resistance antibiotics, studies prospectively investigate development vaccines and drug...
The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase the number complete genomes available biological databases. This advance allowed development several computational tools enabling analyses large amounts data each various steps, from processing and quality filtering to gap filling manual curation. developed for closure are very useful as they result more genomes, which will influence downstream genomic plasticity comparative genomics. However,...
Lactococcus lactis subsp. NCDO 2118 is a nondairy lactic acid bacterium, xylose fermenter, and gamma-aminobutyric (GABA) producer isolated from frozen peas. Here, we report the complete genome sequence of L. 2118, strain with probiotic potential activity.
Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative Critical Assessment Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged community to assess their methods on realistic complex datasets with long short reads, created from ∼1,700 novel known microbial genomes, as well ∼600 plasmids viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in...
HiClass is an open-source Python library for local hierarchical classification entirely compatible with scikit-learn. It contains implementations of the most common design patterns machine learning models found in literature, that is, classifiers per node, parent node and level. Additionally, package metrics, which are more appropriate evaluating performance on data. The documentation includes installation usage instructions, examples within tutorials interactive notebooks, a complete...
Abstract Background Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, internal transcribed spacer (ITS) region was adopted universal marker for classifying fungi. Hence, an accurate robust method ITS classification is not only desired purpose of better diversity estimation, but it...
Abstract Summary The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand evolution virus, monitor viral population, and plan epidemiological responses. Detailed analysis, easy visualization intuitive filtering latest sequences are powerful for this purpose. We present CovRadar, a tool Spike protein. CovRadar consists an analytical pipeline web application that enable analysis hundreds thousand sequences. First, extracts regions interest using...
Herein, we present the draft genome of Trametes villosa isolate CCMB561, a wood-decaying Basidiomycota commonly found in tropical semiarid climate. The assembly was 57.98 Mb size with an L50 691. A total 16,711 putative protein-encoding genes predicted, including 590 coding for carbohydrate-active enzymes (CAZy), directly involved decomposition lignocellulosic materials. This is first this species high interest bioenergy research. CCMB561 will provide important resource future investigations...
Lactobacillus crispatus is the dominant species in vaginal microbiota associated with health and considered a homeostasis biomarker. Interestingly, some strains are even used as probiotics. However, genetic mechanisms of L. involved control microbiome protection against bacterial vaginosis (BV) not entirely known. To further investigate these mechanisms, we sequenced characterized first four genomes from samples Brazilian women genome-wide association study (GWAS) comparative analyses to...
Pertussis is a highly contagious respiratory disease caused by Bordetella pertussis, Gram-negative bacterium described over century ago. Despite broad vaccine coverage and treatment options, the remerging as public health problem especially in infants older children. Recent data indicate re-emergence of related to bacterial resistance immune defences decreased effectiveness, which obviously suggests need new effective vaccines drugs. In an attempt contribute with solutions this great...
Vibrio fluvialis is a halophilic bacterium found in many environments and mainly associated with sporadic cases outbreaks of gastroenteritis humans. Here, we describe the genome sequences environmental strains V. 560 (Vf560) 539 (Vf539) possessing variant integrative conjugative element (ICE) SXT for first time Brazil South America.
The genus Rickettsia belongs to the Proteobacteria phylum and these bacteria infect animals humans causing a range of diseases worldwide. is divided into 4 groups despite public health threat knowledge accumulated so far, mandatory intracellular behaviour limitation for in vitro culture makes it difficult create new vaccines drug targets bacteria. In an attempt overcome limitations, pan-genomic approaches has used 47 genomes Rickettsia, order describe species similarities genomics islands....
Abstract Assembling metagenomic data sequenced by NGS platforms poses significant computational challenges, especially due to large volumes of data, sequencing errors, and variations in size, complexity, diversity abundance organisms present a given metagenome. To overcome these problems, this work proposes an open-source, bioinfor-matic tool called GCSplit, which partitions sequences into subsets using computationally inexpensive metric: the GC content. Experiments performed on real show...
ABSTRACT The SARS-CoV-2 pandemic underlined the importance of molecular surveillance to track evolution virus and inform public health interventions. Fast analysis, easy visualization convenient filtering latest sequences are essential for this purpose. However, access computational resources, lack bioinformatics expertise, sheer volume in databases complicate efforts. CovRadar combines an analytical pipeline a web application designed spike gene SARS-CoV-2, important vaccine target....