Search Results - "Bioinformatics (Oxford, England)"

Annotation of biologically relevant ligands in UniProtKB using ChEBI by 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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DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces by 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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FlashPCA2: principal component analysis of Biobank-scale genotype datasets by Abraham, Gad, Qiu, Yixuan, Inouye, Michael

“…Principal component analysis (PCA) is a crucial step in quality control of genomic data and a common approach for understanding population genetic structure…”
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BERN2: an advanced neural biomedical named entity recognition and normalization tool by Sung, Mujeen, Jeong, Minbyul, Choi, Yonghwa, Kim, Donghyeon, Lee, Jinhyuk, Kang, Jaewoo

“…Abstract   In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the…”
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propeller: testing for differences in cell type proportions in single cell data by Phipson, Belinda, Sim, Choon Boon, Porrello, Enzo R, Hewitt, Alex W, Powell, Joseph, Oshlack, Alicia

“…Abstract Motivation Single cell RNA-Sequencing (scRNA-seq) has rapidly gained popularity over the last few years for profiling the transcriptomes of thousands…”
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plotsr: visualizing structural similarities and rearrangements between multiple genomes by 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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SoluProt: prediction of soluble protein expression in Escherichia coli by Hon, Jiri, Marusiak, Martin, Martinek, Tomas, Kunka, Antonin, Zendulka, Jaroslav, Bednar, David, Damborsky, Jiri

“…Abstract Motivation Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase…”
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Interfacing Seurat with the R tidy universe by Mangiola, Stefano, Doyle, Maria A, Papenfuss, Anthony T

“…Abstract Motivation Seurat is one of the most popular software suites for the analysis of single-cell RNA sequencing data. Considering the popularity of the…”
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Impact of protein conformational diversity on AlphaFold predictions by Saldaño, Tadeo, Escobedo, Nahuel, Marchetti, Julia, Zea, Diego Javier, Mac Donagh, Juan, Velez Rueda, Ana Julia, Gonik, Eduardo, García Melani, Agustina, Novomisky Nechcoff, Julieta, Salas, Martín N, Peters, Tomás, Demitroff, Nicolás, Fernandez Alberti, Sebastian, Palopoli, Nicolas, Fornasari, Maria Silvina, Parisi, Gustavo

“…After the outstanding breakthrough of AlphaFold in predicting protein 3D models, new questions appeared and remain unanswered. The ensemble nature of proteins,…”
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Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes by Zhu, Wensi, Shenoy, Aditi, Kundrotas, Petras, Elofsson, Arne

“…Abstract Motivation Despite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods…”
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BioBERT: a pre-trained biomedical language representation model for biomedical text mining by Lee, Jinhyuk, Yoon, Wonjin, Kim, Sungdong, Kim, Donghyeon, Kim, Sunkyu, So, Chan Ho, Kang, Jaewoo

“…Abstract Motivation Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural…”
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ShinyGO: a graphical gene-set enrichment tool for animals and plants by Ge, Steven Xijin, Jung, Dongmin, Yao, Runan

“…Abstract Motivation Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene lists with underlying molecular…”
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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database by Chaumeil, Pierre-Alain, Mussig, Aaron J, Hugenholtz, Philip, Parks, Donovan H

“…Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB…”
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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference by Kozlov, Alexey M, Darriba, Diego, Flouri, Tomáš, Morel, Benoit, Stamatakis, Alexandros

“…Abstract Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and…”
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PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations by Kamat, Mihir A, Blackshaw, James A, Young, Robin, Surendran, Praveen, Burgess, Stephen, Danesh, John, Butterworth, Adam S, Staley, James R

“…Abstract Summary PhenoScanner is a curated database of publicly available results from large-scale genetic association studies in humans. This online tool…”
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fastp: an ultra-fast all-in-one FASTQ preprocessor by Chen, Shifu, Zhou, Yanqing, Chen, Yaru, Gu, Jia

“…Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different…”
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Identifying and removing haplotypic duplication in primary genome assemblies by Guan, Dengfeng, McCarthy, Shane A, Wood, Jonathan, Howe, Kerstin, Wang, Yadong, Durbin, Richard

“…Abstract Motivation Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for…”
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GTDB-Tk v2: memory friendly classification with the genome taxonomy database by 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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TISIDB: an integrated repository portal for tumor–immune system interactions by Ru, Beibei, Wong, Ching Ngar, Tong, Yin, Zhong, Jia Yi, Zhong, Sophia Shek Wa, Wu, Wai Chung, Chu, Ka Chi, Wong, Choi Yiu, Lau, Chit Ying, Chen, Ian, Chan, Nam Wai, Zhang, Jiangwen

“…Abstract Summary The interaction between tumor and immune system plays a crucial role in both cancer development and treatment response. To facilitate…”
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ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R by Paradis, Emmanuel, Schliep, Klaus

“…Abstract Summary After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of…”
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