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The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (2)

Ramp sequences occur when the average translational efficiency of codons near the 5 ' end of highly expressed genes is significantly lower than the re......

Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (4)

Protein-DNA binding is of a great interest due to its importance in many biological processes. Previous studies have presented many factors responsibl......

Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (1)

Whole-genome sequencing has facilitated genome-wide analyses of association, prediction and heritability in many organisms. However, such analyses in ......

Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (1)

BRCA1 germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variation......

A bioinformatic-assisted workflow for genome-wide identification of ncRNAs

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (3)

With the upcoming of affordable Next-Generation Sequencing technologies, the number of known non-protein coding RNAs increased drastically in recent y......

Targeted DNA methylation from cell-free DNA using hybridization probe capture

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (4)

Cell-free (cf)DNA signatures are quickly becoming the target of choice for non-invasive screening, diagnosis, treatment and monitoring of human tumors......

Optocoder: computational decoding of spatially indexed bead arrays

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (2)

Advancing technologies that quantify gene expression in space are transforming contemporary biology research. A class of spatial transcriptomics metho......

PDBspheres: a method for finding 3D similarities in local regions in proteins

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (4)

We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres compr......

MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (4)

DNA methylation is an epigenetic mark implicated in crucial biological processes. Most of the knowledge about DNA methylation is based on bulk experim......

HKG: an open genetic variant database of 205 Hong Kong cantonese exomes

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (1)

HKG is the first fully accessible variant database for Hong Kong Cantonese, constructed from 205 novel whole-exome sequencing data. There has long bee......

Inferring the contribution of small RNAs to changes in gene expression in response to stress

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (1)

A main strategy of bacteria adapting to environmental changes is the remodeling of their transcriptome. Changes in the transcript levels of specific g......

Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (1)

Effective embedding is actively conducted by applying deep learning to biomolecular information. Obtaining better embeddings enhances the quality of d......

Nano2NGS-Muta: a framework for converting nanopore sequencing data to NGS-liked sequencing data for hotspot mutation detection

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (2)

Nanopore sequencing, also known as single-molecule real-time sequencing, is a third/fourth generation sequencing technology that enables deciphering s......

mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (3)

Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, e......

Thermodynamic and structural characterization of an EBV infected B-cell lymphoma transcriptome

期刊: NAR GENOMICS AND BIOINFORMATICS, 2022; 4 (4)

Epstein-Barr virus (EBV) is a widely prevalent human herpes virus infecting over 95% of all adults and is associated with a variety of B-cell cancers ......

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