Results 41 to 50 of about 261,045 (224)

Calpain small subunit homodimerization is robust and calcium‐independent

FEBS Letters, EarlyView.
Calpains dimerize via penta‐EF‐hand (PEF) domains. Using single‐molecule force spectroscopy, we measured the strength and kinetics of PEF–PEF homodimer binding. The interaction is robust, shows a transient conformational step before dissociation, and remains largely insensitive to Ca2+.
Nesha May O. Andoy, Trina Dykstra‐MacPherson, Mathias A. Bell, Peter L. Davies, Ruby May A. Sullan   +4 more
wiley   +1 more source

Improvements in viral gene annotation using large language models and soft alignments

BMC Bioinformatics
Background The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known proteins when using alignment, k-mer, or ...
William L. Harrigan, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber, Mahdi Belcaid   +5 more
doaj   +1 more source

GOPET: A tool for automated predictions of Gene Ontology terms

BMC Bioinformatics, 2006
Background Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task.
Glatting Karl-Heinz, Eils Roland, Schubert Falk, del Val Coral, Vinayagam Arunachalam, Suhai Sándor, König Rainer   +6 more
doaj   +1 more source

Diversity and complexity in neural organoids

FEBS Letters, EarlyView.
Neural organoid research aims to expand genetic diversity on one side and increase tissue complexity on the other. Chimeroids integrate multiple donor genomes within single organoids. Self‐organising multi‐identity organoids, exogenous cell seeding, or enforced assembly of region‐specific organoids contribute to tissue complexity.
Ilaria Chiaradia, Madeline A. Lancaster
wiley   +1 more source

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

BMC Genomics, 2020
Background The process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry.
Michal Levin, Marion Scheibe, Falk Butter   +2 more
doaj   +1 more source

Linking neurogenesis, oligodendrogenesis, and myelination defects to neurodevelopmental disruption in primary mitochondrial disorders

FEBS Letters, EarlyView.
Mitochondrial remodeling shapes neural and glial lineage progression by matching metabolic supply with demand. Elevated OXPHOS supports differentiation and myelin formation, while myelin compaction lowers mitochondrial dependence, revealing mitochondria as key drivers of developmental energy adaptation.
Sahitya Ranjan Biswas, Porter L. Tomsick, Alicia M. Pickrell, Paul D. Morton   +3 more
wiley   +1 more source

Draft genome sequence of Venturia carpophila, the causal agent of peach scab

Standards in Genomic Sciences, 2017
Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V.
Chunxian Chen, Clive H. Bock, Bruce W. Wood   +2 more
doaj   +1 more source

Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. [PDF]

PLoS ONE, 2010
High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome.
Eric Venner, Andreas Martin Lisewski, Serkan Erdin, R Matthew Ward, Shivas R Amin, Olivier Lichtarge   +5 more
doaj   +1 more source

Epigenetic blind spots – the role of DNA methylation dynamics in stem cell‐based models of embryogenesis

FEBS Letters, EarlyView.
Embryo‐like structures (stembryos) are an innovative tool, but they are hindered by experimental variability and limited developmental potential. DNA methylation is crucial for mammalian development, but its status in stembryo models is poorly characterized.
Sara Canil, Anna Corrà, Annalisa Scapolatiello, Chengxiang Qiu, Gianluca Amadei   +4 more
wiley   +1 more source

An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation

Nature Communications
Genome annotation currently requires performing dozens of molecular assays in hundreds of cell and tissue samples, an expensive endeavor which is impractical to replicate across all species and conditions of interest.
Zhaoxi Zhang, Xiaoya Fan, Jiaxin Zhong, Lijuan Jia, Yuanyuan Han, Chenyi Yang, Zengyou He, Xiaoyan Li, Shing-Tung Yau, Rongling Wu, Charles G. Danko, Zhong Wang   +11 more
doaj   +1 more source