Search Results - "Bioinformatics"

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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Minimap2: pairwise alignment for nucleotide sequences by Li, Heng

“…Abstract Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high…”
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KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold by Aramaki, Takuya, Blanc-Mathieu, Romain, Endo, Hisashi, Ohkubo, Koichi, Kanehisa, Minoru, Goto, Susumu, Ogata, Hiroyuki

“…Abstract Summary KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov…”
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clinker & clustermap.js: automatic generation of gene cluster comparison figures by Gilchrist, Cameron L M, Chooi, Yit-Heng

“…Abstract Summary Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their…”
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Nextstrain: real-time tracking of pathogen evolution by Hadfield, James, Megill, Colin, Bell, Sidney M, Huddleston, John, Potter, Barney, Callender, Charlton, Sagulenko, Pavel, Bedford, Trevor, Neher, Richard A

“…Abstract Summary Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of…”
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VarSome: the human genomic variant search engine by Kopanos, Christos, Tsiolkas, Vasilis, Kouris, Alexandros, Chapple, Charles E, Albarca Aguilera, Monica, Meyer, Richard, Massouras, Andreas

“…VarSome.com is a search engine, aggregator and impact analysis tool for human genetic variation and a community-driven project aiming at sharing global…”
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New strategies to improve minimap2 alignment accuracy by Li, Heng

“…Abstract Summary We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more…”
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Analysing high-throughput sequencing data in Python with HTSeq 2.0 by 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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Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences by Zhu, Anqi, Ibrahim, Joseph G, Love, Michael I

“…In RNA-seq differential expression analysis, investigators aim to detect those genes with changes in expression level across conditions, despite technical and…”
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GraphDTA: predicting drug–target binding affinity with graph neural networks by Nguyen, Thin, Le, Hang, Quinn, Thomas P, Nguyen, Tri, Le, Thuc Duy, Venkatesh, Svetha

“…Abstract Summary The development of new drugs is costly, time consuming and often accompanied with safety issues. Drug repurposing can avoid the expensive and…”
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NanoPack: visualizing and processing long-read sequencing data by De Coster, Wouter, D'Hert, Svenn, Schultz, Darrin T, Cruts, Marc, Van Broeckhoven, Christine

“…Abstract Summary Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore…”
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