Institution
Bielefeld University
Education•Bielefeld, Nordrhein-Westfalen, Germany•
About: Bielefeld University is a education organization based out in Bielefeld, Nordrhein-Westfalen, Germany. It is known for research contribution in the topics: Population & Quantum chromodynamics. The organization has 10123 authors who have published 26576 publications receiving 728250 citations. The organization is also known as: University of Bielefeld & UNIVERSITAET BIELEFELD.
Topics: Population, Quantum chromodynamics, Gene, Context (language use), Quark
Papers published on a yearly basis
Papers
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TL;DR: A program is presented, RNA-hybrid, that predicts multiple potential binding sites of miRNAs in large target RNAs and applied this method to the prediction of Drosophila miRNA targets in 3'UTRs and coding sequence.
Abstract: MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a few targets are known. In contrast to plant miRNAs, which usually bind nearly perfectly to their targets, animal miRNAs bind less tightly, with a few nucleotides being unbound, thus producing more complex secondary structures of miRNA/target duplexes. Here, we present a program, RNA-hybrid, that predicts multiple potential binding sites of miRNAs in large target RNAs. In general, the program finds the energetically most favorable hybridization sites of a small RNA in a large RNA. Intramolecular hybridizations, that is, base pairings between target nucleotides or between miRNA nucleotides are not allowed. For large targets, the time complexity of the algorithm is linear in the target length, allowing many long targets to be searched in a short time. Statistical significance of predicted targets is assessed with an extreme value statistics of length normalized minimum free energies, a Poisson approximation of multiple binding sites, and the calculation of effective numbers of orthologous targets in comparative studies of multiple organisms. We applied our method to the prediction of Drosophila miRNA targets in 3′UTRs and coding sequence. RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/).
2,236 citations
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Cornell University1, Middle Tennessee State University2, Bielefeld University3, University of California, San Diego4, University of Chicago5, University of Florida6, Sanford-Burnham Institute for Medical Research7, San Diego State University8, Argonne National Laboratory9, Portland State University10, University of Illinois at Urbana–Champaign11, Russian Academy of Sciences12
TL;DR: The subsystem approach is described, the first release of the growing library of populated subsystems is offered, and the SEED is the first annotation environment that supports this model of annotation.
Abstract: The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.
1,896 citations
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Joint Genome Institute1, Bielefeld University2, University of California, Davis3, University of Technology, Sydney4, Bigelow Laboratory For Ocean Sciences5, University of British Columbia6, University of Nevada, Las Vegas7, University of Patras8, Woods Hole Oceanographic Institution9, University of Illinois at Urbana–Champaign10, University of Queensland11
TL;DR: This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet.
Abstract: Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
1,856 citations
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Civil Aviation Authority of Singapore1, University of Copenhagen2, Rothamsted Research3, Beijing Institute of Genomics4, Rural Development Administration5, John Innes Centre6, North China University of Science and Technology7, University of Georgia8, University of California, Berkeley9, University of Missouri10, University of Queensland11, Australian Research Council12, National Research Council13, Bielefeld University14, Australian Centre for Plant Functional Genomics15, University of Rennes16, Wageningen University and Research Centre17, Agriculture and Agri-Food Canada18, Huazhong Agricultural University19, French Alternative Energies and Atomic Energy Commission20, Chungnam National University21, Norwich Research Park22
TL;DR: The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
Abstract: We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
1,811 citations
Authors
Showing all 10375 results
Name | H-index | Papers | Citations |
---|---|---|---|
Stefan Grimme | 113 | 680 | 105087 |
Alfred Pühler | 102 | 658 | 45871 |
James Barber | 102 | 642 | 42397 |
Swagata Mukherjee | 101 | 1048 | 46234 |
Hans-Joachim Werner | 98 | 317 | 48508 |
Krzysztof Redlich | 98 | 609 | 32693 |
Graham C. Walker | 93 | 381 | 36875 |
Christian Meyer | 93 | 1081 | 38149 |
Muhammad Farooq | 92 | 1341 | 37533 |
Jean Willy Andre Cleymans | 90 | 542 | 27685 |
Bernhard T. Baune | 90 | 608 | 50706 |
Martin Wikelski | 89 | 420 | 25821 |
Niklas Luhmann | 85 | 421 | 42743 |
Achim Müller | 85 | 926 | 35874 |
Oliver T. Wolf | 83 | 337 | 24211 |