Articles tagged with Genomic Analysis
A genetic analysis of the ancient massacre in Potočani, Croatia, reveals that 70% of the victims were unrelated, suggesting a large and stable local population. The results indicate that large-scale indiscriminate killing occurred in pre-state societies, challenging previous assumptions about the nature of violence in the past.
A genomic analysis of the first wave of COVID-19 in the UK revealed that over 1,000 viral sequences were introduced, with lineages originating from Spain, France, and Italy. The study suggests that earlier travel interventions could have reduced the epidemic's acceleration and intensity.
A genomic analysis of early SARS-CoV-2 outbreaks in Boston found that a small number of importations led to most cases, while superspreading events played a significant role in the spread of the virus. The study tracked the downstream effects of these events and highlights the importance of prevention and mitigation strategies.
The iGenomics app allows iPhone users to create a mobile genetics laboratory, enabling pandemic and ecology workers to study DNA on-the-go. The device can quickly map viral pathogen sequences and identify mutations for diagnosis and treatment.
Researchers sequenced and analyzed coral genomes, discovering genes that may help corals adapt to ocean warming. The study found that Acropora corals diversified when the world's oceans were warmer, suggesting they could handle temperature changes.
A case series of 192 SARS-CoV-2 positive patients in Southern California investigated transmission routes and local community spread within the Los Angeles metropolitan area. The study found that multiple transmission routes existed, including household, healthcare-associated, and travel-related cases.
A new mobile app, Genopo, developed by Garvan Institute of Medical Research, makes genomics more accessible to remote or under-resourced regions and the hospital bedside. The app enables fast, real-time genomic analysis on a smartphone, opening possibilities for point-of-care testing and unlocking information in DNA or RNA.
Researchers found sex differences in gene expression in almost every type of human tissue, with effects observed in genes related to disease and clinical phenotypes. Sex biases were discovered in genes relevant to drug metabolism and placental development.
A unique strain of Shiga-toxin E. coli (STEC) has been identified through genomic analysis, revealing its genetic makeup and potential for severe disease. The study's findings may contribute to the development of vaccines against emerging STEC pathogens.
New research sheds light on penguin evolution, revealing a pivotal role for climate change in their geographic expansion. Genetic analysis indicates that penguins originated along temperate coastlines before expanding into Antarctic regions.
A new ancestral lineage of tuberculosis has been found in East Africa, with genome analyses suggesting a unique origin. The discovery reinforces the hypothesis of an East African origin for the disease and provides insights into its evolution.
A new study analyzing ancient DNA from 93 early Caribbean islanders reveals at least three separate colonization events in the region. The findings provide genetic evidence of distinct population histories and interactions between the earliest settlers and newcomers from South America.
Researchers have developed a new method called redHUMAN to simplify genome-scale metabolic models for analyzing human metabolism. This approach reduces the complexity of human genome-scale models by focusing on specific parts of metabolism while minimizing information loss.
The analysis of ancient genomes has revealed how demographic events such as migrations have spurred major cultural shifts in France. The study found that Magdalenian-associated ancestry survived beyond the Iberian Peninsula, and that Neolithic people who migrated to France descended from Anatolian farmers.
Researchers analyzed genomic data of 20 lion specimens, including extinct cave lions from Siberia and India, finding a shared ancestor 500,000 years ago. The study suggests limited gene flow between modern lions' lineages after their divergence 70,000 years ago.
Researchers analyzed over 2700 C. elegans genomes to understand the causes of mutations. They found that DNA damage and inaccurate repair mechanisms can lead to mutations, which are a root cause of cancer. The study challenges the assumption of a single cause for mutational signatures in cancer genomes.
The evolution of pregnancy in seahorses and pipefishes is linked to modifications of the adaptive immune system. Genomic analysis reveals divergent genomic rearrangements in the MHC II pathway, which may help study immune deficiencies.
Researchers from IDIBELL and ICO conducted a pilot study to analyze intestinal microbiota genome in colon cancer patients. They used two sequencing methods, 16s and Shotgun, and found both techniques consistent, with complete sequencing more sensitive but not contradictory to single-gene sequencing.
Researchers analyzed 6,267 individuals to infer African group contributions to North-, South-American and Caribbean populations, finding enrichment of West-African ancestry in northern latitudes and South/East African ancestry in southern South-America.
The round goby's exceptional adaptability is attributed to its immune system, which features up to 30 times more inflammatory genes than comparable species. This enables the fish to deal with pathogens and extreme environmental conditions, facilitating its successful colonization of diverse waters around the world.
A global surveillance system for antimicrobial resistance can be established through genomic analysis of sewage, providing valuable information about the types of bacteria present in specific areas. This approach has great potential as a tool for monitoring diseases and managing outbreaks globally.
Researchers have identified new genetic drivers of cancer in non-coding regions of the genome, finding that many cancers are driven by mutations in these areas. The study confirmed previously reported drivers and invalidated others, while also identifying novel putative driver rearrangements near genes called AKR1C.
Butler simplifies genomic data analysis by constantly collecting health metrics and automating self-healing modules. This reduces large project execution times from years to months, improving researcher productivity and efficiency.
Researchers used the Pan-Cancer dataset to classify structural variations in cancer genomes and link them to mechanisms of formation. They identified complex processes that can lead to cancer genes becoming active, and developed methods to identify these variations.
KnowEnG, a Knowledge Engine for Genomics, guides researchers through complex genomic datasets by relating genes of interest to existing knowledge. The platform enables seamless analysis and interpretation, removing obstacles faced by biomedical researchers.
A global genetic comparison has discovered ten ancestral lineages in Asia, whereas northern Europe has a single ancestral lineage. The study provides a comprehensive genetic map for Asia, guiding scientists in studying diseases unique to Asians.
Researchers tracked genomic changes in hybrid orangethroat and rainbow darters, finding regions with genetic divergence contributing to reproductive incompatibility. These differences likely disrupt cell division and alter gene expression, driving the evolution of distinct traits.
A recent study reveals that parasitic flukes have a long evolutionary history, with genome comparisons showing significant adaptations to different hosts. The research team found that fasciolid flukes may have originated in ancient African elephants and later expanded into Eurasian herbivores.
Researchers found that decreasing day length alone triggers dramatic weight loss in Siberian hamsters, regardless of food or temperature. The study reveals the cascade of signals that prepare the hamsters for winter, controlled by thyroid hormone and gene expression.
Researchers analyzed 41 ancient sub-Saharan Africans, revealing a multi-stage model for the spread of food production into Kenya and Tanzania. The study found that Stone Age herders across East Africa had closely related genomes, despite cultural differences, and that genes for lactose digestion were rare in first East African herders.
Researchers have discovered powdery mildew on phasey beans in Florida, a species native to tropical Americas. The fungus, Erysiphe fallax, also infects papaya, which could lead to significant financial losses for the industry if left unmanaged.
Michael Snyder received the 2019 George W. Beadle Award for his contributions to systems biology, including the development of widely-used technology for simultaneous gene analysis. His work has enabled the tracking of RNA molecules, proteins, and genes in humans, paving the way for personalized medicine.
Researchers at Garvan Institute of Medical Research have developed a computational method to reduce the amount of memory necessary for genome alignment, allowing for real-time analysis on smartphones. This breakthrough enables remote disease identification and point-of-care microbial infections.
Researchers developed a new technique called GOTI to evaluate genome-editing tool safety, improving detection sensitivity and accuracy. The method detected off-target effects in CRISPR/Cas9 and base editors, raising concerns about emerging technologies' unpredictable risks.
Researchers are studying Bronze Age activity in the Urals to understand demographic processes and settlement structures. They are analyzing palaeogenetic techniques, archaeological excavations, geophysical surveys, material culture, and archaeobotany to find answers about population genetics, cultural transformation, and demography.
A new study uses ancient nuclear genomes to determine the geographic origins of Aboriginal Australian remains, enabling their return to ancestral lands. The analysis shows that for most all of the ancient nuclear genomes, the most closely related contemporary genome was from people living today in the same geographic region.
A genomic analysis of Lassa virus genomes from patients in Nigeria found that the surge in cases in 2018 was not driven by a single dominant virus strain. The study suggests that human-to-human transmission may be rare, with evidence pointing to multiple independent zoonotic transmissions through contact with rodent feces or urine.
The Global Alliance for Genomics and Health (GA4GH) has released three new interoperability standards: Beacon API, refget API, and Workflow Execution Service (WES) API. These standards address variant discovery, patient case discovery, reference sequence harmonization, and cloud computing to enable responsible genomic data sharing.
A study on Asian ladybird beetles reveals a single gene, pannier, that regulates diverse color patterns. The gene's expression affects black and red pigmentation in the forewing, driving morphological evolution.
A team of researchers has successfully sequenced the genomes of 25 ancient individuals from Southeast Asia, revealing six distinct population groups. The findings suggest that prehistoric populations in the region had higher genetic affinities with present-day Japanese and were influenced by language-speaking groups such as Austronesians.
A research group led by Professor Andrei Kozlov has identified a key genetic bottleneck effect that could help design an HIV vaccine. By analyzing blood samples from injecting drug users with early stages of HIV infection, scientists discovered that all viruses share a common ancestor.
Researchers evaluated Stanford University's work on the tiny mummified body, concluding genetic abnormalities could explain perceived abnormalities. However, Otago-led experts found no evidence for these anomalies, revealing normal skeletal development in a fetus.
Professor Stephen Robertson's research team identified the cause of Recessive Spondylocarpotarsal Synostosis Syndrome, a condition resulting in bone fusion. Genome sequencing revealed multiple genes implicated in the disorder, offering diagnostic and therapeutic options.
A recent study published in the journal Genetics found that the fungus Trichophyton rubrum exhibits asexual reproduction as its primary method of reproduction. The research suggests that mating between individuals is rare and requires highly specific conditions, resulting in low genetic variability within the population.
A recent study by researchers at the University of Arizona has found no evidence of domestic dog ancestry in the Mexican wolf population. The analysis of 87 Mexican wolves using genomic technology revealed a low percentage of genetic similarity with domestic dogs, suggesting that the species is genetically pure.
Researchers developed a computational framework to analyze large-scale single-cell gene expression levels, enabling the study of unprecedented cellular heterogeneity in rare cell populations. The BigSCale tool successfully processed 1.3 million individual cells from a mouse brain dataset.
Genomic analyses of fossil remains from 5th and 6th century AD sites in southern Germany uncover evidence of female-biased immigration in Early Medieval Bavaria. Women with artificial cranial deformation (ACD) show predominantly Southeast European ancestry, while one individual exhibits East Asian genetic markers.
A genomic study of ancient and modern horses reveals that the Botai horses, who lived on Central Asian steppes 5,500 years ago, did not contribute to the modern domesticated horse population. However, seven Przewalski's horses, an endangered feral group, show a connection to the original Botai group.
Researchers at Saarland University have created a software tool called WhatsHap that can analyze which gene variants were inherited from each parent, providing a key breakthrough in understanding genetic inheritance. The technology has the potential to become a routine examination in hospitals, similar to blood group identification.
Ancient African genomes show human populations diverged around 350,000-260,000 years ago. The study analyzed 7 ancient genomes, including a Stone Age hunter-gatherer and Iron Age farmers, finding correlations with fossil records.
Scientists analyzed ancient maize genomes to understand its adoption at high elevations. They found that desirable phenotypes were selected for by high-altitude farmers over thousands of years, rather than being introduced from modern-day Mexico.
Researchers at UNIST have sequenced the whole genome of the Myotis rufoniger, a critically endangered bat species, to understand its genetic basis. The study provides valuable insights into the species' demographic history, genomic diversity, and evolutionary origins.
A recent study utilizing genomic big data analyzed the silver birch genome, uncovering population bottlenecks and speciation events that shaped the species' current form. The research also identified genes under natural selection, which have contributed to birch's cold tolerance and rapid growth.
A new study published in Nature Genetics has identified 389 genetic signals linked to the timing of puberty, including associations with an increased risk of breast, ovary, and endometrial cancers in women, and prostate cancer in men. The research also suggests that earlier puberty timing may have negative effects on later health.
Researchers compared the genomes of a 45,000-year-old mainland mammoth with one from Wrangel Island, which had only 300 animals. The analysis revealed an excess of genetic defects, including loss of olfactory receptors and urinary proteins. This study provides insights into the effects of small population sizes on genome deterioration.
The University of Texas Health Science Center at Houston (UTHealth) is part of a $500 million program to bring whole genome sequencing and other
The KAT tool analyzes K-mer datasets to identify error levels, biases, and contamination in sequencing data. It also checks genome assemblies for completeness and accuracy without external reference data.
Researchers have developed Sequins, synthetic DNA sequences that reflect the human genome, allowing for improved analysis and diagnosis of genetic diseases. The technology provides internal standards to assess the accuracy of genomic data generated during sequencing.
CropQuant uses Raspberry Pi computers to control infield cameras capturing crop growth images, then analyzes data on high-performance computers to link environmental data with crop traits. This enables scientists to reduce farming costs and improve crop yields through field-based phenotyping methods.
A new publication by the Association for Molecular Pathology provides cost and value analysis of gene panels, including non-small cell lung cancer and hearing loss. The study demonstrates economic value in optimizing care for patients with hereditary diseases and cancer through targeted gene panels.