Results 121 to 130 of about 551,388 (334)

Navigating Eukaryotic Genome Annotation Pipelines: A Route Map to BRAKER, Galba, and TSEBRA [PDF]

arXiv
Annotating the structure of protein-coding genes represents a major challenge in the analysis of eukaryotic genomes. This task sets the groundwork for subsequent genomic studies aimed at understanding the functions of individual genes. BRAKER and Galba are two fully automated and containerized pipelines designed to perform accurate genome annotation ...
arxiv  

Relation between Insertion Sequences and Genome Rearrangements in Pseudomonas aeruginosa [PDF]

arXiv, 2017
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some elements that play an important role in genome rearrangements are called insertion sequences (ISs), they are the ...
arxiv  

Response to neoadjuvant chemotherapy in early breast cancers is associated with epithelial–mesenchymal transition and tumor‐infiltrating lymphocytes

Molecular Oncology, EarlyView.
Epithelial–mesenchymal transition (EMT) and tumor‐infiltrating lymphocytes (TILs) are associated with early breast cancer response to neoadjuvant chemotherapy (NAC). This study evaluated EMT and TIL shifts, with immunofluorescence and RNA sequencing, at diagnosis and in residual tumors as potential biomarkers associated with treatment response.
Françoise Derouane, Jérôme Ambroise, Cédric van Marcke, Mieke Van Bockstal, Martine Berlière, Christine Galant, Hélène Dano, Médina Lougué, Elena Benidovskaya, Guy Jerusalem, Vincent Bours, Claire Josse, Jérôme Thiry, Aurélie Daumerie, Caroline Bouzin, Cyril Corbet, François P. Duhoux   +16 more
wiley   +1 more source

Vascular endothelial‐cadherin as a marker of endothelial injury in preclinical Alzheimer disease

Annals of Clinical and Translational Neurology, Volume 9, Issue 12, Page 1926-1940, December 2022., 2022
Abstract Objective Endothelial dysfunction is an early and prevalent pathology in Alzheimer disease (AD). We here investigate the value of vascular endothelial‐cadherin (VEC) as a cerebrospinal fluid (CSF) marker of endothelial injury in preclinical AD.
Rawan Tarawneh, Rachel S. Kasper, Jessie Sanford, Chia‐Ling Phuah, Jason Hassenstab, Carlos Cruchaga   +5 more
wiley   +1 more source

Genomic predictions under different genetic architectures are impacted by mating designs

Veterinary and Animal Science
Mating in animal communities must be managed in a way that assures the performance increase in the progenies without increasing the rate of inbreeding. It has currently become possible to identify millions of single nucleotide polymorphisms (SNPs), and ...
Sahar Ansari, Navid Ghavi Hossein-Zadeh, Abdol Ahad Shadparvar   +2 more
doaj  

OmniGenBench: Automating Large-scale in-silico Benchmarking for Genomic Foundation Models [PDF]

arXiv
The advancements in artificial intelligence in recent years, such as Large Language Models (LLMs), have fueled expectations for breakthroughs in genomic foundation models (GFMs). The code of nature, hidden in diverse genomes since the very beginning of life's evolution, holds immense potential for impacting humans and ecosystems through genome modeling.
arxiv  

Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer

Molecular Oncology, EarlyView.
We used whole exome and RNA‐sequencing to profile divergent genomic and transcriptomic landscapes of microsatellite stable (MSS) and microsatellite instable (MSI) colorectal cancer. Alterations were classified using a computational score for integrative cancer variant annotation and prioritization.
Efstathios‐Iason Vlachavas, Konstantinos Voutetakis, Vivian Kosmidou, Spyridon Tsikalakis, Spyridon Roditis, Konstantinos Pateas, Ryangguk Kim, Kymberleigh Pagel, Stephan Wolf, Gregor Warsow, Antonia Dimitrakopoulou‐Strauss, Georgios N. Zografos, Alexander Pintzas, Johannes Betge, Olga Papadodima, Stefan Wiemann   +15 more
wiley   +1 more source

The clinical spectrum of SMA‐PME and in vitro normalization of its cellular ceramide profile

Annals of Clinical and Translational Neurology, Volume 9, Issue 12, Page 1941-1952, December 2022., 2022
Abstract Objective The objectives of this study were to define the clinical and biochemical spectrum of spinal muscular atrophy with progressive myoclonic epilepsy (SMA‐PME) and to determine if aberrant cellular ceramide accumulation could be normalized by enzyme replacement.
Michelle M. Lee, Graeme S. V. McDowell, Darryl C. De Vivo, Daniel Friedman, Samuel F. Berkovic, Maria Spanou, Argirios Dinopoulos, Katheryn Grand, Pedro A. Sanchez‐Lara, Michelle Allen‐Sharpley, Jodi Warman‐Chardon, Alexander Solyom, Thierry Levade, Edward H. Schuchman, Steffany A. L. Bennett, David A. Dyment, Toni S. Pearson   +16 more
wiley   +1 more source

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower

G3: Genes, Genomes, Genetics, 2018
Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS) and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic ...
Patrick Thorwarth, Eltohamy A. A. Yousef, Karl J. Schmid   +2 more
doaj   +1 more source

Integrating genomic homology into gene structure prediction [PDF]

, 2001
Ian Korf, Paul Flicek, Daniel Duan, Michael R. Brent   +3 more
openalex   +1 more source