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Predicting gene expression from DNA sequence using deep learning models
Predicting gene expression from DNA sequence using deep learning models
Transcription of genes is regulated by DNA elements such as promoters and enhancers, the activity of which are in turn con...
Cell-type deconvolution methods for spatial transcriptomics
Cell-type deconvolution methods for spatial transcriptomics
Spatial transcriptomics is a powerful method for studying the spatial organization of cells, which is a critical feature i...
Methodological opportunities in genomic data analysis to advance health equity
Methodological opportunities in genomic data analysis to advance health equity
The causes and consequences of inequities in genomic research and medicine are complex and widespread. However, it is wide...
SLAM-RT&Tag: spatiotemporal profiling of RNA within nuclear compartments in situ
SLAM-RT&Tag: spatiotemporal profiling of RNA within nuclear compartments in situ
In this Tools of the Trade article, Nadiya Khyzha describes SLAM-RT&Tag, a method for profiling RNA localization a...
Investigating spatial gene circuits and gene–phenotype mechanisms with Perturb-FISH
Investigating spatial gene circuits and gene–phenotype mechanisms with Perturb-FISH
In this Tools of the Trade article, Loic Binan explains Perturb-FISH, which measures genetic perturbations and gene expres...
Functional synonymous mutations and their evolutionary consequences
Functional synonymous mutations and their evolutionary consequences
Synonymous mutations are coding mutations that do not alter protein sequences. Commonly thought to have little to no funct...
RNA splicing — a central layer of gene regulation
Technological and computational advances in recent years, from cryo-electron microscopy to sequencing technologies and mac...
A crossroads in the timeline of human evolution
A crossroads in the timeline of human evolution
In this Journal Club, Diyendo Massilani recalls two studies by Meyer et al. that reported a mitochondrial genome and nucle...
Causal inference for epigenetic ageing
Causal inference for epigenetic ageing
In this Tools of the Trade article, Kejun Ying describes epigenome-wide Mendelian randomization, which integrates Mendelia...
The phenotypic consequences of enhancer evolution
In this Journal Club, Julie Jung and Thomas King recount a paper by Chan et al. that identified the regulatory changes und...
Slide-tags enables spatial single-nucleus sequencing
Slide-tags enables spatial single-nucleus sequencing
In this Tools of the Trade article, Andrew Russell describes Slide-tags, a method for scalable, spatially resolved single-...
Exploring biodiversity through museomics
Natural history collections are unparalleled resources for studying biodiversity across multiple dimensions. As multi-omic...
Genetic conflict and its resolution between the sexes
Abderrahman Khila highlights an important 2015 paper by Barson et al. that demonstrated how sexual conflict in Atlantic sa...
The design and engineering of synthetic genomes
The design and engineering of synthetic genomes
Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome...
Plant pattern recognition receptors: from evolutionary insight to engineering
Plant pattern recognition receptors: from evolutionary insight to engineering
The plant immune system relies on germline-encoded pattern recognition receptors (PRRs) that sense foreign and plant-deriv...
Biobanking with genetics shapes precision medicine and global health
Biobanking with genetics shapes precision medicine and global health
Precision medicine provides patients with access to personally tailored treatments based on individual-level data. However...
Genetic variation across and within individuals
Genetic variation across and within individuals
Germline variation and somatic mutation are intricately connected and together shape human traits and disease risks. Germl...
Pleiotropy, epistasis and the genetic architecture of quantitative traits
Pleiotropy, epistasis and the genetic architecture of quantitative traits
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions betwe...
Human embryonic genetic mosaicism and its effects on development and disease
Human embryonic genetic mosaicism and its effects on development and disease
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carr...
A developmental exit from totipotency
A developmental exit from totipotency
A paper in Nature Genetics identifies a mechanism involving the transcription factor DUXBL that controls the development o...
SIMPLE-seq to decode DNA methylation dynamics in single cells
SIMPLE-seq to decode DNA methylation dynamics in single cells
In this Tools of the Trade article, Dongsheng Bai and Chenxu Zhu describe SIMPLE-seq, a scalable single-cell sequencing me...
Understanding human uniqueness in the pre-genomic era
In this Journal Club article, Jenny Tung reflects on a 1975 paper from King and Wilson that emphasized the importance of g...
Natural antisense transcripts as versatile regulators of gene expression
Natural antisense transcripts as versatile regulators of gene expression
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developm...
Nuclear mRNA decay: regulatory networks that control gene expression
Nuclear mRNA decay: regulatory networks that control gene expression
Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adapta...
Decoding human genetic variation using a synthetic paradigm
Aashiq Kachroo highlights a recent paper by van Loggerenberg et al. that demonstrates the experimental power of &...
Divergence and conservation of the meiotic recombination machinery
Divergence and conservation of the meiotic recombination machinery
Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during ...
Including diverse populations enhances the discovery of type 2 diabetes loci
Segun Fatumo highlights a paper by Mahajan et al. that uses a multi-ancestry genome-wide association studies approach to u...
Mouse genome rewriting with human DNA for disease modelling
Mouse genome rewriting with human DNA for disease modelling
Zhang et al. describe mSwAP-In, a platform for large-scale, efficient, biallelic and ‘scarless’ genome editing...
Weaponized genomics: potential threats to international and human security
Genetic technologies are revolutionizing human health. In parallel, geopolitical instability has prompted renewed discussi...
Context-specific functions of chromatin remodellers in development and disease
Context-specific functions of chromatin remodellers in development and disease
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human gen...
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