Suchergebnisse - "Bioinformatics (Oxford, England)"

GTDB-Tk v2: memory friendly classification with the genome taxonomy database von Chaumeil, Pierre-Alain, Mussig, Aaron J, Hugenholtz, Philip, Parks, Donovan H

“… The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, …”
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Analysing high-throughput sequencing data in Python with HTSeq 2.0 von Putri, Givanna H, Anders, Simon, Pyl, Paul Theodor, Pimanda, John E, Zanini, Fabio

“… HTSeq 2.0 provides a more extensive application programming interface including a new representation for sparse genomic data, enhancements for htseq-count to …”
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GSEApy: a comprehensive package for performing gene set enrichment analysis in Python von Fang, Zhuoqing, Liu, Xinyuan, Peltz, Gary

“… Abstract Motivation Gene set enrichment analysis (GSEA) is a commonly used algorithm for characterizing gene expression changes. However, the currently …”
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Pharokka: a fast scalable bacteriophage annotation tool von Bouras, George, Nepal, Roshan, Houtak, Ghais, Psaltis, Alkis James, Wormald, Peter-John, Vreugde, Sarah

“… Abstract Summary In recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences …”
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Annotation of biologically relevant ligands in UniProtKB using ChEBI von Coudert, Elisabeth, Gehant, Sebastien, de Castro, Edouard, Pozzato, Monica, Baratin, Delphine, Neto, Teresa, Sigrist, Christian J A, Redaschi, Nicole, Bridge, Alan

“… Abstract Motivation To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB …”
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Protein-to-genome alignment with miniprot von Li, Heng

“… Abstract Motivation Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of …”
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MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval von Jin, Qiao, Kim, Won, Chen, Qingyu, Comeau, Donald C, Yeganova, Lana, Wilbur, W John, Lu, Zhiyong

“… Information retrieval (IR) is essential in biomedical knowledge acquisition and clinical decision support. While recent progress has shown that language model …”
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ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries von Swanson, Kyle, Walther, Parker, Leitz, Jeremy, Mukherjee, Souhrid, Wu, Joseph C, Shivnaraine, Rabindra V, Zou, James

“… The emergence of large chemical repositories and combinatorial chemical spaces, coupled with high-throughput docking and generative AI, have greatly expanded …”
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DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces von Réau, Manon, Renaud, Nicolas, Xue, Li C, Bonvin, Alexandre M J J

“… Abstract Motivation Gaining structural insights into the protein–protein interactome is essential to understand biological phenomena and extract knowledge for …”
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sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure von Yan, Ke, Lv, Hongwu, Guo, Yichen, Peng, Wei, Liu, Bin

“… Abstract Motivation Antimicrobial peptides (AMPs) are essential components of therapeutic peptides for innate immunity. Researchers have developed several …”
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propeller: testing for differences in cell type proportions in single cell data von Phipson, Belinda, Sim, Choon Boon, Porrello, Enzo R, Hewitt, Alex W, Powell, Joseph, Oshlack, Alicia

“… Single cell RNA-Sequencing (scRNA-seq) has rapidly gained popularity over the last few years for profiling the transcriptomes of thousands to millions of …”
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IntelliGenes: a novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles von DeGroat, William, Mendhe, Dinesh, Bhusari, Atharva, Abdelhalim, Habiba, Zeeshan, Saman, Ahmed, Zeeshan

“… Abstract Summary In this article, we present IntelliGenes, a novel machine learning (ML) pipeline for the multi-genomics exploration to discover biomarkers …”
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GeneGPT: augmenting large language models with domain tools for improved access to biomedical information von Jin, Qiao, Yang, Yifan, Chen, Qingyu, Lu, Zhiyong

“… Motivation While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs …”
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plotsr: visualizing structural similarities and rearrangements between multiple genomes von Goel, Manish, Schneeberger, Korbinian

“… Third-generation genome sequencing technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of …”
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The ACPYPE web server for small-molecule MD topology generation von Kagami, Luciano, Wilter, Alan, Diaz, Adrian, Vranken, Wim

“… Abstract Motivation The generation of parameter files for molecular dynamics (MD) simulations of small molecules that are suitable for force fields commonly …”
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RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments von Bittrich, Sebastian, Segura, Joan, Duarte, Jose M, Burley, Stephen K, Rose, Yana

“… Tools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioinformatics, enabling visual …”
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SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization von Yu, Yue, Huang, Kexin, Zhang, Chao, Glass, Lucas M, Sun, Jimeng, Xiao, Cao

“… Thanks to the increasing availability of drug-drug interactions (DDI) datasets and large biomedical knowledge graphs (KGs), accurate detection of adverse DDI …”
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AFsample: improving multimer prediction with AlphaFold using massive sampling von Wallner, Björn

“… Abstract Summary The AlphaFold2 neural network model has revolutionized structural biology with unprecedented performance. We demonstrate that by …”
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PyDESeq2: a python package for bulk RNA-seq differential expression analysis von Muzellec, Boris, Teleńczuk, Maria, Cabeli, Vincent, Andreux, Mathieu

“… Abstract Summary We present PyDESeq2, a python implementation of the DESeq2 workflow for differential expression analysis on bulk RNA-seq data. This …”
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Cytoscape.js 2023 update: a graph theory library for visualization and analysis von Franz, Max, Lopes, Christian T, Fong, Dylan, Kucera, Mike, Cheung, Manfred, Siper, Metin Can, Huck, Gerardo, Dong, Yue, Sumer, Onur, Bader, Gary D

“… Abstract Summary Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be …”
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