Search results for "sequence"

ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads

2019

Abstract Motivation Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, the real-world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. Results Here, we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore, can be applied to any RNA-seq dataset wit…

RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing

2012

Abstract Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving. Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression pr…

Structure Learning in Nested Effects Models

2007

Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs of phenotyping studies, e.g., the effects showing in gene expression profiles or as morphological features of the perturbed cell. In this paper we expand the statistical basis of NEMs in four directions. First, we derive a new formula for the likelihood function of a NEM, which generalizes previous results for binary data. Second, we prove model identifiability under mild assumptions. Third, we show that the new formulation of the likelihood allows efficiency in traversing model space. Fourth, we…

Efficient change point detection in genomic sequences of continuous measurements

2010

Abstract Motivation: Knowing the exact locations of multiple change points in genomic sequences serves several biological needs, for instance when data represent aCGH profiles and it is of interest to identify possibly damaged genes involved in cancer and other diseases. Only a few of the currently available methods deal explicitly with estimation of the number and location of change points, and moreover these methods may be somewhat vulnerable to deviations of model assumptions usually employed. Results: We present a computationally efficient method to obtain estimates of the number and location of the change points. The method is based on a simple transformation of data and it provides re…

Mapping accretion and its variability in the young open cluster NGC 2264: A study based on u-band photometry

2014

We aim at characterizing the accretion properties of several hundred members of the star-forming cluster NGC 2264 (3 Myr). We performed a deep u,g,r,i mapping and a simultaneous u+r monitoring of the region with CFHT/MegaCam in order to directly probe the accretion process from UV excess measurements. Photometric properties and stellar parameters are determined homogeneously for about 750 monitored young objects, spanning the mass range 0.1-2 Mo. About 40% are classical (accreting) T Tauri stars, based on various diagnostics (H_alpha, UV and IR excesses). The remaining non-accreting members define the (photospheric+chromospheric) reference UV emission level over which flux excess is detecte…

The Gaia-ESO survey: Discovery of a spatially extended low-mass population in the Vela OB2 association

2015

The nearby (distance~350-400 pc), rich Vela OB2 association, includes $\gamma^2$ Velorum, one of the most massive binaries in the solar neighbourhood and an excellent laboratory for investigating the formation and early evolution of young clusters. Recent Gaia-ESO survey observations have led to the discovery of two kinematically distinct populations in the young (10-15 Myr) cluster immediately surrounding $\gamma^2$ Velorum. Here we analyse the results of Gaia-ESO survey observations of NGC 2547, a 35 Myr cluster located two degrees south of $\gamma^2$ Velorum. The radial velocity distribution of lithium-rich pre-main sequence stars shows a secondary population that is kinematically distin…

Synthesis and Characterization of Adducts Derived from the syn-Diastereomer of Benzo[a]pyrene 7,8-Dihydrodiol 9,10-Epoxide and the 5‘-d(CCTATAGATATCC…

1996

5'-d(CCTATAGATATCC) was reacted with each syn-enantiomer of trans-7,8-dihydroxy 9,10-epoxy 7,8,9,10-tetrahydrobenzo[a]pyrene (syn-BPDE). The (-)-enantiomer yielded one dominating adduct, whereas the (+)-enantiomer resulted in two major adducts. As indicated by optical spectroscopic methods, the major adduct derived from both (-)- and (+)-syn-BPDE involves cis addition of the C-10 position of the diol epoxide to the exocyclic amino group of deoxyguanosine [(-)-syn-BPDEc-N2-dG and (+)-syn-BPDEc-N2-dG, respectively], whereas the minor (+)-syn-BPDE adduct is identical to a trans adduct [(+)-syn-BPDEt-N2-dG]. The cis adducts as well as the (+)-syn-BPDEt-N2-dG adduct are chemically stable for sev…

Beyond Pseudo‐natural Products: Sequential Ugi/Pictet‐Spengler Reactions Leading to Steroidal Pyrazinoisoquinolines That Trigger Caspase‐Independent …

2021

In this work, we describe how stereochemically complex polycyclic compounds can be generated by applying a synthetic sequence comprising an intramolecular Ugi reaction followed by a Pictet-Spengler cyclization on steroid-derived scaffolds. The resulting compounds, which combine a fragment derived from a natural product and a scaffold not found in nature. are both structurally distinct and globally similar to natural products at the same time, and interrogate an alternative region of the chemical space. One of the new compounds showed significant antiproliferative activity on HepG2 cells through a caspase-independent cell-death mechanism, an appealing feature when new antitumor compounds are…

ChemInform Abstract: Synthesis of Glycopeptides with Lewisa Antigen Side Chain and HIV Peptide T Sequence Using the Trichloroethoxycarbonyl/Allyl Est…

2010

Mononuclear heterocyclic rearrangements. Part 12. Rearrangement of 1,2,4-oxadiazoles into indazoles

1979

The first example of a mononuclear heterocyclic rearrangement involving an XYZ = CCN side-chain sequence is reported. The 3-(o-aminophenyl)-, and 3-(o-methylaminophenyl)-5-methyl-1,2,4-oxadiazoles (3a,b) gave a thermally induced rearrangement into 3-acylaminoindazoles (4a,b). On the other hand, the 3-(o-acetylaminophenyl)-5-methyl-1,2,4-oxadiazole (3c) produced a base induced rearrangement into 3-acetylaminoindazole (4a).