Bjarne Knudsen

Evidence for Faster X Chromosome Evolution in Spiders

Jesper Bechsgaard, Mads F. Schou, Bram Vanthournout, Frederik Hendrickx et autres

In species with chromosomal sex determination, X chromosomes are predicted to evolve faster than autosomes because of positive selection on recessive alleles or weak purifying selection. We investigated X chromosome evolution in Stegodyphus spiders that differ in mating system, sex ratio, and …

dk, se, be (code pays fourni par la source)

Variability Handling for Mobile Banking Apps on iOS and Android

Jens Bæk Jørgensen, Bjarne Knudsen, Lennert Sloth, Johan Rugager Vase et autres

During the last four years, Mjølner Informatics has developed mobile banking apps for 11 Danish banks on the two major platforms iOS and Android, in total 22 apps. We make two contributions with this industrial practice paper. In the first place, we …

dk (code pays fourni par la source)

Abstract 4181: Accurate and fast detection and comparison of larger clinically relevant insertions and deletions

Anne-Mette K. Hein, Patrick Dekker, Anika Joecker, Cecilie Boysen et autres

Abstract Larger somatic insertions and deletions in tumor samples are often of significant clinical impact. Many of them are cancer driver mutations and play an important role in drug treatment1. Detecting the accurate breakpoints of larger insertions and deletions is often problematic …

dk (code pays fourni par la source)

Abstract 2227: An automatic pipeline to find and annotate rare subclonal somatic variants in a paired tumor/normal sample

Anika Joecker, Nathan Pearson, Cecilie Boysen, Naomi Thomson et autres

Abstract Identifying and characterizing somatic variants in deep genome sequence data from tumor samples remains challenging and time-consuming. Of special interest in cancer research and diagnostics is the detection and annotation of rare subclonal somatic variants found only in a small proportion …

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Abstract 2334: Identification of differentially expressed genes and somatic mutations in esophageal adenocarinoma cancer patients

Bodil Øster, Anika Joecker, Anne-Mette K. Hein, Patrick Dekker et autres

Abstract High throughput sequencing technologies are currently revolutionizing the cancer research area with rapid improvements in sequencing capacity and time consumption. As a result the most time consuming step has moved from being the sequencing process itself to being the bioinformatic data …

gb, cz, us (code pays fourni par la source)

Abstract 5332: Comparison of variant calling from whole exome and transcriptome sequencing using CLC Cancer Research Workbench

Anne I.J. Arens, Anne-Mette K. Hein, Uwe Appelt, Anika Joecker et autres

Abstract The now commonplace application of whole exome and genome sequencing in cancer research and diagnostics has allowed for rapid identification of SNPs and InDels in protein coding regions, but neither method is able to reveal situations of incomplete penetrance. That is, …

dk (code pays fourni par la source)

Handling design-level requirements across distributed teams: Developing a new feature for 12 Danish mobile banking apps

Lars K. Bruun, Mikkel Bovbjerg Hansen, Jorgen Bondergaard Iversen, Jens Bæk Jørgensen et autres

Bankdata and Mjølner have cooperated in the development of a new feature for 12 Danish mobile banking apps. Bankdata is the main system provider and Mjølner is subcontractor. Different teams from Bankdata have collected requirements, developed the necessary backend and middleware software, …

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools

Andrey Alexeyenko, Björn Nystedt, Francesco Vezzi, Ellen Sherwood et autres

BACKGROUND: Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between sequencing costs and assembly quality. RESULTS: In order to sequence the …

se, us (code pays fourni par la source)

Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue

Jakob Hedegaard, Kasper Thorsen, Mette K. Lund, Anne-Mette K. Hein et autres

Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for clinical research. However, nucleic acids extracted from FFPE tissues are fragmented and chemically modified making them challenging to use in molecular studies. We analysed 23 fresh-frozen (FF), 35 FFPE and 38 paired FF/FFPE …

dk (code pays fourni par la source)

Draft genome sequence of the rubber tree Hevea brasiliensis

Ahmad Yamin Abdul Rahman, Abhilash O Usharraj, Biswapriya B. Misra, Gincy P. Thottathil et autres

BACKGROUND: Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. RESULTS: …

my, cn, us, dk, ca, Afrique du Sud (code pays fourni par la source)

Characterising RNA secondary structure space using information entropy

Zsuzsanna Sükösd, Bjarne Knudsen, James W. Anderson, Adam M. Novak et autres

Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how …

dk, gb (code pays fourni par la source)

First draft genome sequence of the Japanese eel, Anguilla japonica

Christiaan V. Henkel, Ron P. Dirks, Daniëlle L. de Wijze, Yuki Minegishi et autres

The Japanese eel is a much appreciated research object and very important for Asian aquaculture; however, its genomic resources are still limited. We have used a streamlined bioinformatics pipeline for the de novo assembly of the genome sequence of the Japanese eel …

nl, jp, no, fr (code pays fourni par la source)