Benchmarking splice variant prediction algorithms using massively parallel splicing assays
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Volume 24, issue 1, December 2023
294 articles in this issue
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ENGEP: advancing spatial transcriptomics with accurate unmeasured gene expression prediction
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scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles
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Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data
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Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root
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Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
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A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation
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SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
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DNA methylation modulated genetic variant effect on gene transcriptional regulation
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Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies
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Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers
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Cotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding
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GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins
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Meiosis in an asymmetric dikaryotic genome of Tremella fuciformis Tr01 facilitates new chromosome formation
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Dengue and Zika RNA-RNA interactomes reveal pro- and anti-viral RNA in human cells
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Integration of datasets for individual prediction of DNA methylation-based biomarkers
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Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
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Comparing methods for constructing and representing human pangenome graphs
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STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer
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ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
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Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
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Cooperation of MLL1 and Jun in controlling H3K4me3 on enhancers in colorectal cancer
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Acute expression of human APOBEC3B in mice results in RNA editing and lethality
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CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
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Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate
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Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation
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N-of-one differential gene expression without control samples using a deep generative model
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Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
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Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis
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Statistical learning quantifies transposable element-mediated cis-regulation
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A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry
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Phytochromes transmit photoperiod information via the evening complex in Brachypodium
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Author Correction: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
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Quantification of evolved DNA-editing enzymes at scale with DEQSeq
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The chromatin landscape of the euryarchaeon Haloferax volcanii
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In-organoid single-cell CRISPR screening reveals determinants of hepatocyte differentiation and maturation
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Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses
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CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
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Landscape of enhancer disruption and functional screen in melanoma cells
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MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing
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Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates
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The Quartet Data Portal: integration of community-wide resources for multiomics quality control
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