Výsledky vyhledávání - "Bioinformatics"

YaHS: yet another Hi-C scaffolding tool Autor Zhou, Chenxi, McCarthy, Shane A, Durbin, Richard

“…Abstract Summary We present YaHS, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from Hi-C data. It can be run with a…”
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BioBERT: a pre-trained biomedical language representation model for biomedical text mining Autor 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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ProteinBERT: a universal deep-learning model of protein sequence and function Autor Brandes, Nadav, Ofer, Dan, Peleg, Yam, Rappoport, Nadav, Linial, Michal

“…Abstract Summary Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to…”
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ShinyGO: a graphical gene-set enrichment tool for animals and plants Autor 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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clinker & clustermap.js: automatic generation of gene cluster comparison figures Autor 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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Analysing high-throughput sequencing data in Python with HTSeq 2.0 Autor Putri, Givanna H, Anders, Simon, Pyl, Paul Theodor, Pimanda, John E, Zanini, Fabio

“…Abstract Summary HTSeq 2.0 provides a more extensive application programming interface including a new representation for sparse genomic data, enhancements for…”
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New strategies to improve minimap2 alignment accuracy Autor 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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DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome Autor Ji, Yanrong, Zhou, Zhihan, Liu, Han, Davuluri, Ramana V

“…Abstract Motivation Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex…”
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GraphDTA: predicting drug–target binding affinity with graph neural networks Autor 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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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Autor 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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Identifying and removing haplotypic duplication in primary genome assemblies Autor 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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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference Autor 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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NanoPack2: population-scale evaluation of long-read sequencing data Autor De Coster, Wouter, Rademakers, Rosa

“…Abstract Summary Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of…”
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KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold Autor 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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PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations Autor 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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TISIDB: an integrated repository portal for tumor–immune system interactions Autor 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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Liftoff: accurate mapping of gene annotations Autor Shumate, Alaina, Salzberg, Steven L

“…Abstract Motivation Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality…”
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Cooler: scalable storage for Hi-C data and other genomically labeled arrays Autor Abdennur, Nezar, Mirny, Leonid A

“…Abstract Motivation Most existing coverage-based (epi)genomic datasets are one-dimensional, but newer technologies probing interactions (physical, genetic,…”
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igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) Autor Robinson, James T, Thorvaldsdottir, Helga, Turner, Douglass, Mesirov, Jill P

“…Abstract Summary igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a…”
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ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2 Autor Gustavsson, Emil K, Zhang, David, Reynolds, Regina H, Garcia-Ruiz, Sonia, Ryten, Mina

“…Abstract Motivation The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However,…”
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