9 papers · ranked by Valyu relevance
Olivia W Lang, Benjamin Beer, Dean Zhang, Courtney LeSon + 3 more
The growing diversity of genomic and epigenomic assays has driven a parallel expansion in data formats, analysis workflows, and figure-generation tools. However, tools for analyzing data and assembling publication-quality figures are often specialized to a specific assay, dramatically limiting their interoperability…
Bo Wen, Kai Li, Michael Riffle, Michael J. MacCoss + 2 more
De novo peptide sequencing detects peptides directly from tandem mass spectra without a protein sequence database, and deep learning has substantially advanced its performance. Casanovo, one such widely used model, is distributed as a Python command-line program. Consequently, installation, GPU and dependency…
Roberto Reinosa Fernández
The proliferation of next-generation sequencing (NGS) data has created a computational bottleneck, especially for researchers lacking specialized bioinformatics training. Standard analysis workflows require mastering multiple command-line tools, hindering exploratory data analysis and delaying scientific discovery.…
Abdullah Langgeng, Marie Sigaud, Wendi Prameswari, Nur Purba Priambada + 4 more
Rehabilitation centers are central to the conservation of Javan slow lorises (Nycticebus javanicus) by providing care for individuals confiscated from trade and preparing them for potential release. To evaluate behavioral readiness for reintroduction, we quantified activity budgets and boldness in 10 adult N. javanicus…
Federico Di Petta, Piermichele Rosati, Piero Hierro Canchari, Michela Quadrini + 1 more
Accurate annotation of RNA base-pairing interactions is essential for structural analysis, benchmarking, and data-driven RNA structure prediction. Several tools can extract RNA interactions from three-dimensional coordinates, but their outputs are heterogeneous and may disagree, particularly for non-canonical base…
Areen Arabiat, Hamza Abu Owida, Suhaila Abuowaida, Nawaf Alshdaifat + 2 more
This study emphasizes the potential of computational techniques in cancer risk assessment, highlighting opportunities for specific and data-driven healthcare solutions. It examines the use of artificial intelligence (AI), machine learning (ML), and deep learning (DL) approaches to improve cancer risk assessment using a…
Gusti Ayu Prani Pradani, Almira Alifia, Alia Putri Syahbaniati, Alamanda Larasmanah + 9 more
As drug-resistant tuberculosis (DR-TB) cases rise, resistance detection in a timely manner is essential to lead effective treatment and limit transmission. Targeted next-generation sequencing (tNGS) offers quick results with multiple important drugs covered, but assessments regarding its performance for DR-TB…
Arion Dey, Jared A. Weis, Victoria G. Weis
Histological analysis is crucial for understanding gastrointestinal (GI) tract homeostasis and disease pathophysiology. Various histological stains are commonly used in research settings for assessing development, disease pathogenesis, and therapeutic impacts. Specifically in the ordered architecture of the GI…
Joshua S. Bamford, Amanda R. Bamford
Drumming—rhythmic, percussive sound production using body parts or external objects—is rare among non-human animals, with confirmed tool-assisted cases previously limited to primates and Palm Cockatoos. Here, we report the first documented instance of spontaneous, tool-assisted drumming in a Galah (Eolophus…