[HTML][HTML] Multiple reference genomes and transcriptomes for Arabidopsis thaliana

X Gan, O Stegle, J Behr, JG Steffen, P Drewe… - Nature, 2011 - nature.com
Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive
phenotypic variation, and until now these have been interpreted largely in the context of the
annotated reference accession Col-0. Here we report the sequencing, assembly and …

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

KL McNally, KL Childs, R Bohnert… - Proceedings of the …, 2009 - National Acad Sciences
Rice, the primary source of dietary calories for half of humanity, is the first crop plant for
which a high-quality reference genome sequence from a single variety was produced. We
used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference …

rQuant. web: a tool for RNA-Seq-based transcript quantitation

R Bohnert, G Rï¿ ½tsch - Nucleic acids research, 2010 - academic.oup.com
We provide a novel web service, called rQuant. web, allowing convenient access to tools for
quantitative analysis of RNA sequencing data. The underlying quantitation technique rQuant
is based on quadratic programming and estimates different biases induced by library …

Accurate detection of differential RNA processing

P Drewe, O Stegle, L Hartmann, A Kahles… - Nucleic acids …, 2013 - academic.oup.com
Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of
cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling
data enable identification of novel isoforms, quantification of known isoforms and detection …

Bioinformatory‐assisted analysis of next‐generation sequencing data for precision medicine in pancreatic cancer

L Malgerud, J Lindberg, V Wirta… - Molecular …, 2017 - Wiley Online Library
Pancreatic ductal adenocarcinoma (PDAC) is a tumor with an extremely poor prognosis,
predominantly as a result of chemotherapy resistance and numerous somatic mutations.
Consequently, PDAC is a prime candidate for the use of sequencing to identify causative …

Statistical tests for detecting differential RNA-transcript expression from read counts

O Stegle, P Drewe, R Bohnert, K Borgwardt… - Nature …, 2010 - nature.com
As a fruit of the current revolution in sequencing technology, transcriptomes can now be
analyzed at an unprecedented level of detail. These advances have been exploited for
detecting differential expressed genes across biological samples and for quantifying the …

Reliability of algorithmic somatic copy number alteration detection from targeted capture data

N Rieber, R Bohnert, U Ziehm, G Jansen - Bioinformatics, 2017 - academic.oup.com
Motivation Whole exome and gene panel sequencing are increasingly used for oncological
diagnostics. To investigate the accuracy of SCNA detection algorithms on simulated and
clinical tumor samples, the precision and sensitivity of four SCNA callers were measured …

[HTML][HTML] Comprehensive benchmarking of SNV callers for highly admixed tumor data

R Bohnert, S Vivas, G Jansen - PloS one, 2017 - journals.plos.org
Precision medicine attempts to individualize cancer therapy by matching tumor-specific
genetic changes with effective targeted therapies. A crucial first step in this process is the
reliable identification of cancer-relevant variants, which is considerably complicated by the …

Transcript quantification with RNA-Seq data

R Bohnert, J Behr, G Rätsch - BMC bioinformatics, 2009 - Springer
Methods To approach this problem, we have developed a new technique, called rQuant,
based on quadratic programming. Given a gene annotation and position-wise exon/intron
read coverage from read alignments, we determine the abundances for each annotated …

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

VT Sreedharan, SJ Schultheiss, G Jean… - …, 2014 - academic.oup.com
We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that
is integrated in Galaxy. Its distinguishing features include customizable computational
workflows and a modular pipeline architecture that facilitates comparative assessment of …