Functional Genomics
Articles tagged with Functional Genomics
DEGU debuts with better AI predictions and explanations
Researchers have developed DEGU, a tool that improves the accuracy and efficiency of deep neural networks in predicting genomic experiment results. DEGU reduces the size of models while maintaining predictive capabilities, making it easier to understand uncertainty and drive reliable discoveries.
Machine-learned biomarker identifies those at high risk for liver cancer
A study by RIKEN researchers identifies a MYCN-driven biomarker that predicts the risk of liver cancer. The biomarker, known as the MYCN niche score, uses machine learning to analyze gene expression patterns and indicates whether a tumor-free liver is at high risk for developing tumors.
Does the motion of our DNA influence its activity?
False alarm in newborn screening: how zebrafish can prevent unnecessary SMA therapies
A zebrafish model was used to test the functional significance of rare SMN1 variants in children with false positive SMA diagnoses. The research found that both variants were functional and did not cause the disease. This breakthrough could prevent unnecessary SMA therapies and provide families with security.
Upcycling genes: New platform breathes life into underperforming genetic parts
A research team has developed a 'SUPER' platform that utilizes synthetic small RNAs as add-on controllers for genetic switches. This technology enhances the performance and stability of gene regulatory devices by addressing the issue of 'leakage', where genes continue to express at low levels even in the 'OFF' state.
The “broker” family helps tidy up the cell
A research team at Goethe University Frankfurt has compiled a catalog of human E3 ligases and mapped their relationships, revealing family-specific functions. The study identifies 40 additional E3 ligases suitable for PROTAC development, expanding the range of tissues and diseases targeted by degradation therapies.
Children’s Hospital of Philadelphia researchers develop novel approach for guiding immunotherapies toward treating “cold” tumor cells
Children's Hospital of Philadelphia researchers have developed a method to help cancer immunotherapies reach 'invisible' tumors. HLA-Shuttle is an engineered protein complex that restores antigen presentation in immunologically 'cold' neuroblastoma cells, identifying previously unknown targets across 30 genes linked to neuroblastoma.
Scientists identify first non-coding gene that controls cell size
Researchers at The Hospital for Sick Children have identified a non-coding gene called CISTR-ACT that regulates cell size. By exploring its molecular mechanism, the team found that CISTR-ACT guides a protein called FOSL2 to bind to other genes, controlling cell growth and development.
Smarter tools for peering into the microscopic world
Researchers at Arizona State University introduce powerful tools to analyze microbial family trees and biological data, strengthening microbiome research, disease tracking and environmental monitoring. The new software library scikit-bio provides a foundation for analyzing large biological datasets.
Genomic maps untangle the complex roots of disease
Researchers develop comprehensive method to connect diseases with underlying genetic machinery, revealing intricate gene networks that influence complex traits. The new technique provides actionable insights into how specific genes affect cell functions, shedding light on biological mechanisms and potential therapeutic targets.
New statistical tools sharpen the search for causal DNA changes in livestock
Researchers developed a new suite of statistical methods to pinpoint DNA changes responsible for important traits in livestock. The work addresses challenges in fine-mapping, especially in populations with closely related animals, and introduces tools that incorporate 'relatedness-adjusted' genomic correlations.
Human gene maps are biased towards European ancestries
A recent study found thousands of missing transcripts in people from non-European populations, potentially leading to new insights into disease risk and genetic variations. The study highlights a lack of global representation in current gene maps, built largely from European DNA sequences.
Inflammation may be responsible for driving earliest stages of lung cancer
Researchers at University of Texas M. D. Anderson Cancer Center discover that inflammation is responsible for driving the earliest stages of lung cancer, identifying potential targets for early intervention and suggesting a promising approach to intercepting lung cancer development.
How plants rot: New method decodes hidden decomposers of wood and leaves
A new bioinformatics-based method, fDOG, has been developed to search for genes with certain functions, including those involved in plant cell wall degradation. The study reveals a detailed global map of enzymes capable of degrading plant cell walls, with surprising discoveries among fungi and animals.
Charting the evolution of life through the ancient chaetognath
Researchers have finally pinned down the genomic, epigenomic, and cellular landscape of the enigmatic arrow worm, connecting its unique genetic markup to specialized cell-types. The study reveals an unprecedented rate of gene genesis and duplication, as well as a unique method of chromosomal organization.
ORC2 regulation of human gene expression shows unexpected breadth and scale
A recent study reveals that ORC2 subunit regulates epigenetics and gene expression by compacting chromatin and attracting repressive histone marks at some sites, but activating gene expression at others. This regulation also prevents CTCF binding at certain sites, leading to changes in chromatin structure and gene expression.
ISGlobal develops a bioinformaticstool to boost omics data analysis in precision medicine
HTGAnalyzer is an automated tool simplifying complex transcriptomic workflows, enabling clinicians without bioinformatics expertise to perform essential analyses in precision medicine. The tool has been validated using multiple datasets and identified differentially expressed genes linked to cancer diagnosis, treatment, and prognosis.
Finding human brain genes in duplicated DNA
Researchers identify two human brain genes that contribute to brain size and synapse signaling in zebrafish, providing a roadmap for discovering more genes. The study's findings have significant implications for understanding language disorders and autism.
New study reveals hidden regulatory roles of “junk” DNA
Researchers discovered that MER11 sequences, once thought as genetic junk, play powerful roles in regulating gene expression. The team used a new method to classify these elements and found they can activate gene expression in human stem cells and early-stage neural cells.
Developing software for easy estimation of 3D gene expression distribution
Researchers developed tomoseqr, a user-friendly software to estimate 3D spatial gene expression distribution. The software successfully reproduced known gene expression patterns and mapped the 3D spatial distribution of genes in zebrafish and planarians.
Aligning Science Across Parkinson’s (ASAP) launches a new funding opportunity to join the Collaborative Research Network
The Aligning Science Across Parkinson’s initiative is launching a new funding opportunity to support collaborative research teams focused on understanding Parkinson’s disease heterogeneity across six focus areas. The grants will provide up to $3 million per year over three years.
Mapping the sex life of Malaria parasites at single cell resolution, reveals the genetics underlying Malaria transmission
Scientists have mapped the global repertoire of genes that determine the male or female sexual fates in Plasmodium falciparum malaria parasites. This study reveals key regulators of gene expression during development and identifies novel candidate 'driver' genes, shedding light on the complex biology of malaria transmission.
The first spatial map of malaria infection in the liver opens new possibilities for more effective malaria treatments
Researchers have created the first spatial map of malaria infection in the mouse liver using Spatial Transcriptomics and single-cell RNA-sequencing. This discovery sheds light on the parasite's lifecycle, revealing changes in host cell gene expression near infected areas.
ERC Advanced Grant for Helle Ulrich for research on DNA repair and genome stability
Professor Helle Ulrich will investigate how a small regulatory protein called ubiquitin contributes to DNA replication and repair, and decipher how cells direct different pathways. The ERC Advanced Grant aims to gain a deeper mechanistic understanding of ubiquitin's function in preventing mutations that can cause ageing and cancer.
Using next-gen CRISPR tool, Gladstone scientists create unprecedented molecular map of human immune response
Gladstone scientists have created an intricate map of how the immune system functions, examining the detailed molecular structures governing human T cells. This study will accelerate the development of new and better therapies for cancer and autoimmune diseases.
New data representation of nucleotide sequences transcription factors bind to
The study reveals that approximately half of examined transcription factors possess distinct binding sequences for specific cell types. MOCCS profiles also predict the effect of single nucleotide polymorphisms on DNA binding of transcription factors.
Powerful gene editing approach boosts rotifers in pantheon of laboratory animals
Researchers at the Marine Biological Laboratory have devised a method to precisely alter rotifer genomes using CRISPR-Cas9, enabling the study of fundamental biology and evolution. The new approach will allow scientists to investigate various aspects of biology, including aging, DNA repair mechanisms, and mitochondrial function.
Prof. Fabio Coppedè joins Current Genomics as Editor-in-Chief
Professor Coppedè's appointment aims to enhance the journal's focus on cutting-edge genomics research, covering topics like genome sequencing and functional genomics. He will lead Current Genomics to greater success by staying at the forefront of genomics discoveries and advancements.
The digital dark matter clouding AI
Scientists using popular computational tools to interpret AI predictions are picking up too much 'noise' when analyzing DNA. Researchers have found a way to fix this by applying a new line of code, leading to more reliable explanations and potentially unlocking the next breakthrough in health and medicine.
Analyzing diverse data types can accelerate drug discovery, study says
A new study in Cell Systems explores the benefits of using multiple data types in drug discovery. Gene expression and cell morphology provide complementary information for drug prioritization, advancing drug discovery, functional genomics, and precision medicine.
Redefining human diseases through the lens of your DNA
Researchers at Osaka University analyzed data from over 200 health-related traits and diseases in an Asian population to identify specific genomic loci related to medical indications. The study found 14,000 genomic loci of phenotypic significance, including 5,000 novel discoveries.
Yale team finds way to protect genetic privacy in research
Researchers at Yale University have developed a way to safeguard individual genetic information while maintaining the advantages of open data exchange. The approach enables scientists to preserve most genetic data for analysis while restricting access to identifiable information.
Researchers simulate privacy leaks in functional genomics studies
A study demonstrates that it's possible to de-identify raw data in functional genomics studies to ensure patient privacy, but also shows how this can be breached through simple means like DNA from a discarded coffee cup
New file type improves genomic data sharing while maintaining participant privacy
Researchers have developed a new file format for functional genomics data that enables data sharing while protecting personal information of research participants. The format reduces leakage and promotes collaboration in the field.
Mechanism by which metformin inhibits food intake
The study found that metformin significantly reduced food intake and body weight gain by inhibiting neuropeptide Y expression in the hypothalamus. Metformin also improved lipid metabolism by reducing plasma low-density lipoprotein levels.
International consortium to get to heart of coronary artery disease
An international consortium, led by Professor Dominique Gauguier, aims to understand the complex causes of coronary artery disease (CAD) and develop effective treatments. The project will use advanced genomics techniques to identify biomarkers for predicting CAD risk factors, offering insights into disease diagnosis and prevention.
NYU biologists identify gene that coordinates two cellular processes
A team of NYU biologists has identified a gene, mel-28, that plays a crucial role in coordinating two cellular processes: chromosome segregation and nuclear envelope function. The study, published in Current Biology, used functional genomic tools to reveal the dual role of mel-28 in these processes.
No single gene for ageing
The study highlights the complex interplay between genetic and environmental factors in determining human aging. While there is no single gene responsible for aging, genetics account for approximately 25% of how a person ages, with stress, environment, nutrition, lifestyle, and immunity also playing significant roles.
NYU biologists map out early stages of embryo formation
Researchers at NYU's Center for Comparative Functional Genomics have developed a diagram for the early stages of embryo formation in C. elegans, suggesting a core set of less than 1,000 genes are required for coordination. This finding may provide new insights into human embryogenesis and cancer research.
NIAID takes next genome step
The NIAID's new center will support research on three to 10 important pathogens over the next three years. It will develop new technologies for analyzing gene function, train researchers, and provide resources for the scientific community. The center aims to better understand individual genes and proteins to develop targeted treatments.