相关论文: Starr: Simple Tiling Array Analysis of Affymetrix …
Registration of serial whole-slide histopathological images (WSIs) is critical for enabling direct comparison across diverse stains and for preparing paired datasets in artificial intelligence (AI) workflows such as virtual staining and…
Background: Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely used technique to investigate the function of chromatin-related proteins in a genome-wide manner. ChIP-Seq generates large quantities of…
The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large…
ChIP-seq, which combines chromatin immunoprecipitation with massively parallel short-read sequencing, can profile in vivo genome-wide transcription factor-DNA association with higher sensitivity, specificity and spatial resolution than…
Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) provides insights into both the genomic location occupied by the protein of interest and the difference in DNA occupancy between experimental states. Given that…
This R package evaluates main and pair-wise interaction effect of single nucleotide polymorphisms (SNPs) via the W-test, scalable to whole genome-wide data sets. The package provides fast and accurate p-value estimation of genetic markers,…
DNA microarrays are devices that are able, in principle, to detect and quantify the presence of specific nucleic acid sequences in complex biological mixtures. The measurement consists in detecting fluorescence signals from several spots on…
The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory processes, such as gene splicing, gene…
The STAR experiment at the Relativistic Heavy Ion Collider RHIC studies the new state of matter produced in relativistic heavy ion collisions and the spin structure of the nucleon in collisions of polarized protons. In order to improve the…
Biomarker discovery and gene ranking is a standard task in genomic high throughput analysis. Typically, the ordering of markers is based on a stabilized variant of the t-score, such as the moderated t or the SAM statistic. However, these…
In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was…
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
In this work, we propose a novel centrality metric, referred to as star centrality, which incorporates information from the closed neighborhood of a node, rather than solely from the node itself, when calculating its topological importance.…
Protein tagging with CRISPR-Cas9 enables the investigation of protein function in its native environment but is limited by low homology-directed repair (HDR) efficiency causing low knock-in rates. We present a detailed pipeline using HDR…
CLIP-seq methods are valuable techniques to experimentally determine transcriptome-wide binding sites of RNA-binding proteins. Despite the constant improvement of such techniques (e.g. eCLIP), the results are affected by various types of…
Multiple data views measured on the same set of participants is becoming more common and has the potential to deepen our understanding of many complex diseases by analyzing these different views simultaneously. Equally important, many of…
The newly installed Silmaril beam combiner at the CHARA array is designed to observe previously inaccessible faint targets, including Active Galactic Nuclei and T-Tauri Young Stellar Objects. Silmaril leverages cutting-edge optical design,…
Accurate information about protein content in the organism is instrumental for a better understanding of human biology and disease mechanisms. While the presence of certain types of proteins can be life-threatening, the abundance of others…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
RNA polymerase (RNAP) elongates RNA by walking along a DNA template and selectively incorporating ribonucleoside triphosphates (rNTPs). Rather than mechanically replicating the base sequence, RNAP conditions binding and chemistry on the…