Functional Genomics
No mentions found
This entity hasn't been tracked yet, or Iris is still building its knowledge base.
Related Articles from SNS
Scalable in vivo cardiac functional genomics with compressed AAV-Perturb-seq reveals a common mitochondrial response to perturbation
Efficient identification of new targets to treat human disease requires a scalable way to link genotype to phenotype directly in the target organ. Pooled CRISPR screening with single-cell RNA sequencing as a readout (Perturb-seq) has emerged as a method for functional genomics but is typically applied in vitro and is limited in scale. Here, we combine in vivo Perturb-seq via adeno-associated virus (AAV)-mediated delivery with a statistical framework allowing for signal deconvolution after...
A functional genomics screen identifies novel drivers of FR900359 resistance in uveal melanoma cells
Uveal melanoma (UM) is the most common form of intraocular cancer in adults and has a median survival rate of ~1 year after metastasis occurs. Metastatic UM is largely refractory to treatment and there are no effective pharmacological therapies, resulting in poor overall survival. Activating mutations in GNAQ and GNA11 proteins (GNAQ/11) are the oncogenic initiators in >90% UM cases.
Convergent Evolution in Tumor Genomes Targets Functional Domains
Tumor evolution is shaped by selective pressures that repeatedly favor similar functional outcomes across genetically distinct cancers. While convergent evolution in cancer has been studied at the gene level, this work investigates selection on smaller functional units, namely protein domains. Using >9,500 primary tumor exomes from The Cancer Genome Atlas, we quantified selection strengths acting on missense and truncating mutations aggregated by protein domain.
Ultra-Fast Implementation of Multivariate GWAS in Genomic SEM Using Flexible Analytic Estimation
Many medical, physiological, and psychiatric traits and disorders are highly polygenic and exhibit complex patterns of genetic sharing and differentiation. In 2018, we introduced Genomic Structural Equation Modelling (Genomic SEM) as a formal framework and free, open source, R-based software for modelling the multivariate genetic architecture of both continuous and binary Genome-Wide Association Study (GWAS) phenotypes, interrogating their joint and distinct functional genomic pathways, and...
KBase Research Agent: Automated Multi-Agent Workflow Construction for Reproducible Genome Analysis
Constructing multi-step bioinformatics workflows, from read quality control through genome assembly to functional annotation, requires expertise in both biology and computational tool selection, creating a bottleneck for scalable and reproducible analysis. We present the KBase Research Agent, a multi-agent system for automating such workflows within the DOE Systems Biology Knowledgebase (KBase). Given a set of sequencing reads and a research objective, the agent constructs an analysis plan...
Integrative genomics reveals shared and stress-specific adaptive pathways underlying acidic soil-associated metal toxicity in rice
Soil acidity-associated toxicities of aluminum (Al), cadmium (Cd), and manganese (Mn) severely constrain rice productivity in upland ecosystems. To investigate the genomic basis of adaptation to acidic soil-related metal stress, we conducted an integrated meta-QTL (M-QTL) and functional genomics analysis in rice. Meta-analysis of 681 QTLs and MTAs from 53 QTL mapping and GWAS studies identified 79 robust M-QTLs, including ten overlapping regions associated with Al-, Cd-, and Mn-responsive...
DNMT mRNA stability and YB-1 cooperatively regulate ABCB1 to drive cisplatin chemoresistance in cholangiocarcinoma
Background and Aims: Intrahepatic cholangiocarcinoma (iCCA) is a tumor type with a high lethality due to late diagnosis and profound resistance to conventional chemotherapy. To date the molecular mechanisms underlying multidrug resistance remain poorly defined. Here, we integrate single-cell transcriptomics, clinicopathological analysis, and functional genomics to elucidate the molecular basis of cisplatin resistance in iCCA.
Why does the Y chromosome retain UTY?
Why does the Y chromosome retain UTY? Sadie Harley Scientific Editor Andrew Zinin Lead Editor A study, published in the journal Development, is the first to precisely map endogenous UTY occupancy across the human genome and demonstrate that UTY remains functionally involved in transcriptional regulation during early human development.
TgmRHel drives unified RNA processing of coxI mRNA generated from a complex mitochondrial genomic context
The mitochondrial genome of Toxoplasma gondii is highly fragmented and recombination-prone, creating a structurally dynamic genetic landscape. How such a genome is used efficiently to produce functional mRNAs remains unclear: it is unknown whether transcription draws from many alternative genomic configurations or a restricted subset, and how any resulting precursor RNAs are processed into mature transcripts. More broadly, mitochondrial RNA processing mechanisms in this system are poorly...
GENEB: Why Genomic Models Are Hard to Compare
arXiv:2606.04525v2 Announce Type: replace Abstract: Progress in genomic foundation models is difficult to assess due to fragmented benchmarks, incompatible evaluation protocols, and task-specific reporting. As a result, claims of superiority or generality across models are often not directly comparable. We introduce GENEB, a large-scale diagnostic benchmark that evaluates frozen representations from 40 genomic foundation models across 100 tasks spanning 13 functional categories under a...