Tài liệu miễn phí Sinh học
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Characterizing the interplay between gene nucleotide composition bias and splicing
Nucleotide composition bias plays an important role in the 1D and 3D organization of the human genome. Here, we investigate the potential interplay between nucleotide composition bias and the regulation of exon recognition during splicing.
4/6/2023 9:10:56 AM +00:00
MIA-Sig: Multiplex chromatin interaction analysis by signal processing and statistical algorithms
The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chromatin organization, yet introduce new computational challenges.
4/6/2023 9:10:43 AM +00:00
Correlation of homologous recombination deficiency induced mutational signatures with sensitivity to PARP inhibitors and cytotoxic agents
Homologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations. In this genetic study, we ask whether inactivating mutations in further genes of the HR pathway or the DNA damage checkpoint also give rise to somatic mutation patterns that can be used for treatment prediction.
4/6/2023 9:10:36 AM +00:00
Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
Multiplexed single-cell RNA-seq analysis of multiple samples using pooling is a promising experimental design, offering increased throughput while allowing to overcome batch variation. To reconstruct the sample identify of each cell, genetic variants that segregate between the samples in the pool have been proposed as natural barcode for cell demultiplexing.
4/6/2023 9:10:29 AM +00:00
Systematic comparative analysis of singlenucleotide variant detection methods from single-cell RNA sequencing data
While SNV detection from abundant single-cell RNA sequencing (scRNA-seq) data is applicable and cost-effective in identifying expressed variants, inferring sub-clones, and deciphering genotype-phenotype linkages, there is a lack of computational methods specifically developed for SNV calling in scRNA-seq.
4/6/2023 9:10:21 AM +00:00
CRUP: A comprehensive framework to predict condition-specific regulatory units
We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data.
4/6/2023 9:10:13 AM +00:00
Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize
DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping diversity of both gene expression and phenotypes are hotly debated. Here, we investigate the genetic basis and biological functions of DNA methylation at a population scale in maize.
4/6/2023 9:10:06 AM +00:00
Evaluating nanopore sequencing data processing pipelines for structural variation identification
Structural variations (SVs) account for about 1% of the differences among human genomes and play a significant role in phenotypic variation and disease susceptibility. The emerging nanopore sequencing technology can generate long sequence reads and can potentially provide accurate SV identification.
4/6/2023 9:09:59 AM +00:00
NanoSatellite: Accurate characterization of expanded tandem repeat length and sequence through whole genome longread sequencing on PromethION
Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer’s disease-associated ABCA7 VNTR.
4/6/2023 9:09:52 AM +00:00
Common DNA sequence variation influences 3-dimensional conformation of the human genome
The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer.
4/6/2023 9:09:40 AM +00:00
Assessment of computational methods for the analysis of single-cell ATAC-seq data
Recent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells. scATAC-seq data analysis presents unique methodological challenges.
4/6/2023 9:09:33 AM +00:00
EpiMethylTag: Simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation
Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately.
4/6/2023 9:09:21 AM +00:00
Genotype-free demultiplexing of pooled single-cell RNA-seq
A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling.
4/6/2023 9:09:14 AM +00:00
Differential co-expression-based detection of conditional relationships in transcriptional data: Comparative analysis and application to breast cancer
Elucidation of regulatory networks, including identification of regulatory mechanisms specific to a given biological context, is a key aim in systems biology. This has motivated the move from co-expression to differential co-expression analysis and numerous methods have been developed subsequently to address this task; however, evaluation of methods and interpretation of the resulting networks has been hindered by the lack of known context-specific regulatory interactions.
4/6/2023 9:09:01 AM +00:00
Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis
Patient-derived xenograft and cell line models are popular models for clinical cancer research. However, the inevitable inclusion of a mouse genome in a patient-derived model is a remaining concern in the analysis.
4/6/2023 9:08:54 AM +00:00
Pharmacogenomic analysis of patientderived tumor cells in gynecologic cancers
Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, progression, and metastasis of gynecologic tumors.
4/6/2023 9:08:48 AM +00:00
RegSNPs-intron: A computational framework for predicting pathogenic impact of intronic single nucleotide variants
Single nucleotide variants (SNVs) in intronic regions have yet to be systematically investigated for their diseasecausing potential. Using known pathogenic and neutral intronic SNVs (iSNVs) as training data, we develop the RegSNPs-intron algorithm based on a random forest classifier that integrates RNA splicing, protein structure, and evolutionary conservation features.
4/6/2023 9:08:40 AM +00:00
MaveDB: An open-source platform to distribute and interpret data from multiplexed assays of variant effect
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution.
4/6/2023 9:08:34 AM +00:00
HOPS: A quantitative score reveals pervasive horizontal pleiotropy in human genetic variation is driven by extreme polygenicity of human traits and diseases
Horizontal pleiotropy, where one variant has independent effects on multiple traits, is important for our understanding of the genetic architecture of human phenotypes. We develop a method to quantify horizontal pleiotropy using genome-wide association summary statistics and apply it to 372 heritable phenotypes measured in 361,194 UK Biobank individuals. Horizontal pleiotropy is pervasive throughout the human genome, prominent among highly polygenic phenotypes, and enriched in active regulatory regions.
4/6/2023 9:08:27 AM +00:00
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods
Accurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA-seq, based on either read mapping or de novo fusion transcript assembly.
4/6/2023 9:08:20 AM +00:00
Mash Screen: High-throughput sequence containment estimation for genome discovery
The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here, we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets.
4/6/2023 9:08:14 AM +00:00
Genetic regulation of gene expression and splicing during a 10-year period of human aging
Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age.
4/6/2023 9:08:05 AM +00:00
Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs
A variety of base editors have been developed to achieve C-to-T editing in different genomic contexts. Here, we compare a panel of five base editors on their C-to-T editing efficiencies and product purity at commonly editable sites, including some human pathogenic C-to-T mutations.
4/6/2023 9:07:57 AM +00:00
PGG.SNV: Understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations
Despite the tremendous growth of the DNA sequencing data in the last decade, our understanding of the human genome is still in its infancy. To understand the implications of genetic variants in the light of population genetics and molecular evolution.
4/6/2023 9:07:50 AM +00:00
DeepImpute: An accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data
Single-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. We present DeepImpute, a deep neural network-based imputation algorithm that uses dropout layers and loss functions to learn patterns in the data, allowing for accurate imputation.
4/6/2023 9:07:42 AM +00:00
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed.
4/6/2023 9:07:33 AM +00:00
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing.
4/6/2023 9:07:24 AM +00:00
Endogenous retroviral insertions drive noncanonical imprinting in extra-embryonic tissues
Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on the parent of origin and is typically regulated by differential DNA methylation inherited from gametes.
4/6/2023 9:07:17 AM +00:00
OrthoFinder: Phylogenetic orthology inference for comparative genomics
Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics.
4/6/2023 9:07:07 AM +00:00
Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenaseassociated stress responses
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex biological systems, such as tumor heterogeneity and tissue microenvironments. However, the sources of technical and biological variation in primary solid tumor tissues and patient-derived mouse xenografts for scRNA-seq are not well understood.
4/6/2023 9:07:00 AM +00:00