A5023923164- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Algorithms and Data Compression
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- DNA and Biological Computing
- Enzyme Structure and Function
- Viral gastroenteritis research and epidemiology
- Amino Acid Enzymes and Metabolism
- Helicobacter pylori-related gastroenterology studies
- Bacillus and Francisella bacterial research
- Parasite Biology and Host Interactions
- CRISPR and Genetic Engineering
- Genetic diversity and population structure
- Photosynthetic Processes and Mechanisms
- Plant biochemistry and biosynthesis
- Antioxidant Activity and Oxidative Stress
- Microbial Metabolic Engineering and Bioproduction
- Evolutionary Algorithms and Applications
- Glycosylation and Glycoproteins Research
- Gene expression and cancer classification
- Modular Robots and Swarm Intelligence
- Biochemical and Molecular Research
- Innovative Microfluidic and Catalytic Techniques Innovation
- Single-cell and spatial transcriptomics
American Museum of Natural History
2013
Virginia Tech
2012
Oregon State University
2012
DSM (Switzerland)
2010
DSM (Netherlands)
2008
DKFZ-ZMBH Alliance
2006
German Cancer Research Center
2004-2006
We present an in silico approach for the reconstruction of complete mitochondrial genomes non-model organisms directly from next-generation sequencing (NGS) data-mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related or (ii) barcode sequences are available as starting-reference seeds, respectively. demonstrate efficiency case studies using real NGS data sets two monogenean ectoparasites species Gyrodactylus thymalli...
We present an EST sequence assembler that specializes in reconstruction of pristine mRNA transcripts, while at the same time detecting and classifying single nucleotide polymorphisms (SNPs) occuring different variations thereof. The uses iterative multipass strategies centered on high-confidence regions within sequences has a fallback strategy for using low-confidence when needed. It features special functions to assemble high numbers highly similar without prior masking, automatic editor...
ABSTRACT Bacillus subtilis is both a model organism for basic research and an industrial workhorse, yet there are major gaps in our understanding of the genomic heritage provenance many widely used strains. We analyzed 17 legacy strains dating to early years B. genetics. For three—NCIB 3610 T , PY79, SMY—we performed comparative genome sequencing. remainder, we conventional sequencing sample regions expected show sequence heterogeneity. Sequence comparisons showed that 168, its siblings...
Prokaryote genomes are the result of a dynamic flux genes, with increases achieved via horizontal gene transfer and reductions occurring through loss. The ecological selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is naturally competent bacterium occupies various environments, including plant-associated, soil, marine niches, gut both invertebrates vertebrates. Here, we quantify diversity B. infer genome dynamics explain high genetic phenotypic...
Using an oligonucleotide microarray, we searched for previously unrecognized transcription units in intergenic regions the genome of Bacillus subtilis, with emphasis on identifying small genes activated during spore formation. Nineteen were identified, 11 which shown to depend one or more sporulation-regulatory proteins their expression. A high proportion contained small, functional open reading frames (ORFs). One such newly identified ORF is a member family six structurally similar that are...
ABSTRACT Summary: The plain text Sequence Alignment/Map (SAM) file format and its companion binary form (BAM) are a generic alignment for storing read alignments against reference sequences (and unmapped reads) together with structured meta-data (Li et al. , 2009). Driven by the needs of 1000 Genomes Project which sequenced many individual human genomes, early SAM/BAM usage focused on pairwise reads to reference. However, through CIGAR P operator multiple sequence can also be preserved....
Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the of construction intermediates and final product a gene project is critical part workflow, yet one that has received least attention. Sequence validation equally important for other kinds curated clone collections. Ensuring physical sequence matches its published common quality control step performed at once over course research project. GenoREAD web-based application breaks verification...
Rhodoxanthin is a vibrant red carotenoid found across the plant kingdom and in certain birds fish. It member of atypical retro class carotenoids, which contain an additional double bond concerted shift conjugated bonds relative to more widely occurring pigments, whose biosynthetic origins have long remained elusive. Here, we identify LHRS (Lonicera hydroxylase rhodoxanthin synthase), variant β-carotene (BCH)-type integral membrane diiron enzyme that mediates conversion into rhodoxanthin. We...