相关论文: Starr: Simple Tiling Array Analysis of Affymetrix …

Tiling arrays make possible a large scale exploration of the genome thanks to probes which cover the whole genome with very high density until 2 000 000 probes. Biological questions usually addressed are either the expression difference…

Affymetrix Genechip microarrays are used widely to determine the simultaneous expression of genes in a given biological paradigm. Probes on the Genechip array are atomic entities which by definition are randomly distributed across the array…

We present the design and performance analysis of a new integrated track reconstruction code developed for the STAR experiment at RHIC. The code is meant to replace multiple previous tracking codes written in FORTRAN many years ago, and to…

Motivation: Proteomic mass spectrometry analysis is becoming routine in clinical diagnostics, for example to monitor cancer biomarkers using blood samples. However, differential proteomics and identification of peaks relevant for class…

Microarray technology is still an important way to assess gene expression in molecular biology, mainly because it measures expression profiles for thousands of genes simultaneously, what makes this technology a good option for some studies…

Motivation: Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing…

The ability of oligonucleotide microarrays to measure gene expression has been hindered by an imperfect understanding of the relationship between input RNA concentrations and output signals. We argue that this relationship can be understood…

Aims. We present pyUPMASK, an unsupervised clustering method for stellar clusters that builds upon the original UPMASK package. Its general approach makes it plausible to be applied to analyses that deal with binary classes of any kind, as…

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…

Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…

A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…

The Worldwide spread of the Omicron lineage variants has now been confirmed. It is crucial to understand the process of cellular life and to discover new drugs need to identify the important proteins in a protein interaction network (PPIN).…

Predicting guide RNA (gRNA) activity is critical for effective CRISPR-Cas12 genome editing but remains challenging due to limited data, variation across protospacer adjacent motifs (PAMs-short sequence requirements for Cas binding), and…

We announce ChromaStarPy, an integrated general stellar atmospheric modeling and spectrum synthesis code written entirely in python V. 3. ChromaStarPy is a direct port of the ChromaStarServer (CSServ) Java modeling code described in earlier…

Motivation: The three-dimensional (3D) organization of the genome plays a critical role in regulating gene expression and maintaining cellular homeostasis. Disruptions in this spatial organization can result in abnormal chromatin…

We present the R package stellaR, which is designed to access and manipulate publicly available stellar evolutionary tracks and isochrones from the Pisa low-mass database. The procedures of the extraction of important stages in the…

We would like to find a way to improve the determination of galaxy star formation history from integrated light spectroscopy. To this end, several classes of chemically peculiar (CP) stars arise during the course of normal evolution in…

Gene expression data is widely used in disease analysis and cancer diagnosis. However, since gene expression data could contain thousands of genes simultaneously, successful microarray classification is rather difficult. Feature selection…

Clinical 12-lead ECG classification remains difficult because of diverse recording conditions, overlapping pathologies, and pronounced label imbalance hinder generalization, while unconstrained augmentations risk distorting diagnostically…

Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…