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A survey of mapping algorithms in the long-reads era
A survey of mapping algorithms in the long-reads era
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctiv...
Pervasive tandem duplications and convergent evolution shape coral genomes
Pervasive tandem duplications and convergent evolution shape coral genomes
Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organis...
mutscan—a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data
mutscan—a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data
Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by sel...
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries
We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (H...
Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Genetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (ca...
Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis
Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis
Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, ...
Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer
Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer
Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferat...
Profiling the immune epigenome across global cattle breeds
Profiling the immune epigenome across global cattle breeds
Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential...
SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors
SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. C...
In silico methods for predicting functional synonymous variants
In silico methods for predicting functional synonymous variants
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be &...
Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on v...
SPUMONI 2: improved classification using a pangenome index of minimizer digests
SPUMONI 2: improved classification using a pangenome index of minimizer digests
Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an effici...
Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans
Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans
The variation in the rate at which humans age may be rooted in early events acting through the genomic regions that are in...
RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches
RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches
We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our...
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but ...
Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
Spatial transcriptomics maps gene expression across tissues, posing the challenge of determining the spatial arrangement o...
Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications
Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications
Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice si...
The VGNC: expanding standardized vertebrate gene nomenclature
The VGNC: expanding standardized vertebrate gene nomenclature
The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HUGO Gene Nomenclatur...
Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, whic...
Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton
Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton
Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known ...
Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
Group heteroscedasticity is commonly observed in pseudo-bulk single-cell RNA-seq datasets and its presence can hamper the ...
DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis
DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis
Plants memorize previous pathogen attacks and are “primed” to produce a faster and stronger defense response, ...
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations
Deep neural networks (DNNs) hold promise for functional genomics prediction, but their generalization capability may be li...
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize
Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic dive...
Author Correction: DNA methylation entropy as a measure of stem cell replication and aging
Author Correction: DNA methylation entropy as a measure of stem cell replication and aging
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, whic...
Boosting genome editing efficiency in human cells and plants with novel LbCas12a variants
Boosting genome editing efficiency in human cells and plants with novel LbCas12a variants
Cas12a (formerly known as Cpf1), the class II type V CRISPR nuclease, has been widely used for genome editing in mammalian...
m6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis
m6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis
RNA N6-methyladenosine (m6A) modification is critical for plant growth and crop yield. m6A reader proteins can recognize m...
SNV-FEAST: microbial source tracking with single nucleotide variants
SNV-FEAST: microbial source tracking with single nucleotide variants
Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of ...
DREAMS: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection
DREAMS: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection
Circulating tumor DNA detection using next-generation sequencing (NGS) data of plasma DNA is promising for cancer identifi...
Identifying yield-related genes in maize based on ear trait plasticity
Identifying yield-related genes in maize based on ear trait plasticity
Phenotypic plasticity is defined as the phenotypic variation of a trait when an organism is exposed to different environme...
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