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Most Recent Articles: Genome Biology
Updated: 4 hours 58 min ago

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

Mon, 01/03/2021 - 5:30am
Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the true complexity of processing. However, the relatively high erro...
Categories: Bioinformatics Trends

MEDALT: single-cell copy number lineage tracing enabling gene discovery

Tue, 23/02/2021 - 5:30am
We present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles, and a statistical routine...
Categories: Bioinformatics Trends

scSorter: assigning cells to known cell types according to marker genes

Mon, 22/02/2021 - 5:30am
On single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact expression levels a...
Categories: Bioinformatics Trends

Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase

Mon, 22/02/2021 - 5:30am
The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. However, there is currently no ...
Categories: Bioinformatics Trends

ReSeq simulates realistic Illumina high-throughput sequencing data

Fri, 19/02/2021 - 5:30am
In high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions at each step of a project. Simulations are a critical part of method comparis...
Categories: Bioinformatics Trends

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

Fri, 19/02/2021 - 5:30am
The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we presen...
Categories: Bioinformatics Trends

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

Thu, 18/02/2021 - 5:30am
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving bio...
Categories: Bioinformatics Trends

iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks

Thu, 18/02/2021 - 5:30am
The integration of single-cell RNA-sequencing datasets from multiple sources is critical for deciphering cell-to-cell heterogeneities and interactions in complex biological systems. We present a novel unsuperv...
Categories: Bioinformatics Trends

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

Thu, 18/02/2021 - 5:30am
To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals.
Categories: Bioinformatics Trends

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues

Sun, 14/02/2021 - 5:30am
Single-cell and bulk genomics assays have complementary strengths and weaknesses, and alone neither strategy can fully capture regulatory elements across the diversity of cells in complex tissues. We present C...
Categories: Bioinformatics Trends

Author Correction: Assembly of hundreds of novel bacterial genomes from the chicken caecum

Fri, 12/02/2021 - 5:30am
An amendment to this paper has been published and can be accessed via the original article.
Categories: Bioinformatics Trends

Data bias

Wed, 10/02/2021 - 5:30am
Categories: Bioinformatics Trends

The data-hypothesis conversation

Wed, 10/02/2021 - 5:30am
Categories: Bioinformatics Trends

The data-hypothesis relationship

Wed, 10/02/2021 - 5:30am
Categories: Bioinformatics Trends

3 ′-5 ′ crosstalk contributes to transcriptional bursting

Thu, 04/02/2021 - 5:30am
Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different n...
Categories: Bioinformatics Trends

GeneWalk identifies relevant gene functions for a biological context using network representation learning

Tue, 02/02/2021 - 5:30am
A bottleneck in high-throughput functional genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Gene Ontology (GO) enrichment methods provide insi...
Categories: Bioinformatics Trends

A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

Fri, 29/01/2021 - 5:30am
Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiv...
Categories: Bioinformatics Trends

My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype

Fri, 29/01/2021 - 5:30am
Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerat...
Categories: Bioinformatics Trends

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March 2021