Published in Genome Biology
We present CSDeconv, a computational method that determines locations of transcription factor binding from ChIP-seq data. CSDeconv differs from prior methods in that it uses a blind deconvolution approach that allows closely-spaced binding sites to be called accurately. We apply CSDeconv to novel ChIP-seq data for DosR binding in Mycobacterium tube...
Published in Analytical Biochemistry
NAD(P)H oxidoreductases of the outer mitochondrial membrane (OMM) are able to activate various xenobiotics and stimulate the production of reactive oxygen species and the opening of the mitochondrial permeability transition pore. However, the role of these systems in the cell damage by xenobiotics and chemotherapeutic drugs is poorly understood bec...
Published in Investigational New Drugs
The number of patients treated at each dose-level in dose seeking phase I trials is arbitrarily established. The most frequently used design is the “classical 3 + 3 design (3 + 3D)”. Recently, Simon et al. had introduced several “accelerated titration designs (ATD)”. In the present analysis, we compared the performance of these two types of designs...
Published in Intensive Care Medicine
PurposeTo compare inter-laboratory and inter-assay measurements of total cortisol in patients with septic shock and to evaluate current recommendations for diagnosis of corticosteroid insufficiency in septic shock.MethodsIn the multinational CORTICUS study duplicate serum samples were taken before and after corticotropin stimulation tests in patien...
Published in Genome Biology
We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of ...
Published in Applied Microbiology and Biotechnology
Although researchers can access information on the entire genomic DNA sequence of typical research organisms, convenient genome walking methods in the laboratory are still needed. For the analysis of microorganisms, these methods are especially useful because the available genetic information is often scarce or limited. Many genomic walking methods...
Published in Evolutionary Biology
Biogeography deals with the combined analysis of the spatial and temporal components of the evolutionary process. To this purpose, biogeographical analysis should consider two extra steps: a reciprocal illumination step, and a consilience step. Even if the traditional challenges of biogeography were successfully handled, the obtained hypothesis is ...
Published in Securitas Vialis
Este trabajo apunta la necesidad de un nuevo modelo sobre el siniestro vial. Se formula un modelo secuencial de eventos, denominado MOSES. El primer paso consiste en definir los conceptos fundamentales que establecen el marco de aplicación del modelo. A continuación se expone un esquema de la metodología de aplicación de MOSES a un hipotético supue...
Published in Genome Biology
To exploit fully the potential of current sequencing technologies for population-based studies, one must enrich for loci from the human genome. Here we evaluate the hybridization-based approach by using oligonucleotide capture probes in solution to enrich for approximately 3.9 Mb of sequence target. We demonstrate that the tiling probe frequency is...
Published in Genome Biology
Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by hybridization to oligonucleotide probes specific for 467 cancer-related genes, this method showed high selectivity, improved mutation detection enabling discovery ...
