9 papers · ranked by Valyu relevance
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…
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…
Sivasubramani Selvanayagam, Jesus Quiroz-Chavez, Ricardo H. Ramirez-Gonzalez, Cristobal Uauy + 2 more
In the era of multiple genome references, researchers often align sequencing reads against distinct assemblies or even multiple references simultaneously. This enables applications such as the detection of introgressed segments or highly variable genomic regions, which are especially prevalent in large-genome crop…
Demian Kong, Shaoqi Bei, Yueyue Wu, Bixia Tang + 1 more
AI-driven data search and integration represent an emerging research direction. Although several LLM-based backend frameworks and agentic frameworks have emerged, significant gap remains in developing a one-stop, configurable agent framework that supports various data sources and provides a web interface for efficient…
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.…
Zehua Zeng, Xuehai Wang, Zhi Luo, Yawen Zheng + 3 more
Advances in bulk, single-cell and spatial omics have transformed biological discovery, yet analysis remains fragmented across packages with incompatible interfaces, heterogeneous dependencies and limited workflow reproducibility. Here, we present OmicClaw, an executable natural-language framework for multi-omics…
Raul C. Sîmpetru, Ricardo G. Molinari, Devon R. Rohlf, Rebeka L. Batichotti + 3 more
Understanding human motor control requires integrating cortical and spinal cord activity, muscle mechanics, and electrophysiology, levels that are often studied separately. We present MyoGen, an open-source framework that unifies spinal circuitry, proprioceptive feedback, musculotendon dynamics, cortical activity, and…
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…