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Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum
Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum
Despite having been extensively studied, it remains largely unclear why humans bear a particularly high risk of c...
METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets
METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets
DNA N6-methyldeoxyadenosine (6mA) is rarely present in mammalian cells and its nuclear role remains elusive. Here we show ...
SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data
SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data
We present SIEVE, a statistical method for the joint inference of somatic variants and cell phylogeny under the finite-sit...
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computationa...
The genetic and biochemical determinants of mRNA degradation rates in mammals
The genetic and biochemical determinants of mRNA degradation rates in mammals
Degradation rate is a fundamental aspect of mRNA metabolism, and the factors governing it remain poorly characterized. Und...
m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis
m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis
Heat-imposed crop failure is often attributed to reduced thermotolerance of floral tissues; however, the underlying mechan...
Parallel evolution of amphioxus and vertebrate small-scale gene duplications
Parallel evolution of amphioxus and vertebrate small-scale gene duplications
Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic...
metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies
metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies
Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and d...
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in ca...
Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads
Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads
There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software t...
A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships
A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships
Chromatin contacts are essential for gene-expression regulation; however, obtaining a high-resolution genome-wide chromati...
Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples
Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples
The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a re...
Gene flow and introgression are pervasive forces shaping the evolution of bacterial species
Gene flow and introgression are pervasive forces shaping the evolution of bacterial species
Although originally thought to evolve clonally, studies have revealed that most bacteria exchange DNA. However, it remains...
Deciphering the impact of genetic variation on human polyadenylation using APARENT2
Deciphering the impact of genetic variation on human polyadenylation using APARENT2
3′-end processing by cleavage and polyadenylation is an important and finely tuned regulatory process during mRNA ma...
Mapping responsive genomic elements to heat stress in a maize diversity panel
Mapping responsive genomic elements to heat stress in a maize diversity panel
Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approa...
Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus
Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus
Regulation of gene expression plays an essential role in controlling the phenotypes of plants. Brassica napus (B. napus) i...
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predictin...
Evolution and function of developmentally dynamic pseudogenes in mammals
Evolution and function of developmentally dynamic pseudogenes in mammals
Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and diseas...
The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites
The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites
Human endogenous retroviruses (HERVs), the remnants of ancient retroviruses, account for 8% of the human genome, but most ...
Folliculin-interacting protein FNIP2 impacts on overweight and obesity through a polymorphism in a conserved 3′ untranslated region
Folliculin-interacting protein FNIP2 impacts on overweight and obesity through a polymorphism in a conserved 3′ untranslated region
Overweight and obesity are defined by an anomalous or excessive fat accumulation that may compromise health. To find singl...
scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We develo...
CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice
CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice
CRISPR tools can generate knockout and knock-in animal models easily, but the models can contain off-target genomic lesion...
INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing
INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing
Comprehensive characterisation of genome engineering technologies is relevant for their development and safe use in human ...
Significant variation in the performance of DNA methylation predictors across data preprocessing and normalization strategies
Significant variation in the performance of DNA methylation predictors across data preprocessing and normalization strategies
DNA methylation (DNAm)-based predictors hold great promise to serve as clinical tools for health interventions and disease...
ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq
ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq
RNA processing, including splicing and alternative polyadenylation, is crucial to gene function and regulation, but method...
Author Correction: Pooled extracellular receptor-ligand interaction screening using CRISPR activation
Author Correction: Pooled extracellular receptor-ligand interaction screening using CRISPR activation
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, whic...
Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses
Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses
A major driver of cancer chromosomal instability is replication stress, the slowing or stalling of DNA replication. How re...
A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1
A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1
We and others have suggested that pioneer activity — a transcription factor’s (TF’s) ability to bind and...
iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations
iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations
In this study, we propose iDNA-ABF, a multi-scale deep biological language learning model that enables the interpretable p...