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BioGPT: generative pre-trained transformer for biomedical text generation and mining
Luo, Renqian, Sun, Liai, Xia, Yingce, Qin, Tao, Zhang, Sheng, Poon, Hoifung, Liu, Tie-Yan
Published in Briefings in bioinformatics (19.11.2022)
Published in Briefings in bioinformatics (19.11.2022)
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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
Uliano-Silva, Marcela, Ferreira, João Gabriel R. N., Krasheninnikova, Ksenia, Blaxter, Mark, Mieszkowska, Nova, Hall, Neil, Holland, Peter, Durbin, Richard, Richards, Thomas, Kersey, Paul, Hollingsworth, Peter, Wilson, Willie, Twyford, Alex, Gaya, Ester, Lawniczak, Mara, Lewis, Owen, Broad, Gavin, Martin, Fergal, Hart, Michelle, Barnes, Ian, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W., Durbin, Richard, Blaxter, Mark, McCarthy, Shane A.
Published in BMC bioinformatics (18.07.2023)
Published in BMC bioinformatics (18.07.2023)
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Analysing high-throughput sequencing data in Python with HTSeq 2.0
Putri, Givanna H, Anders, Simon, Pyl, Paul Theodor, Pimanda, John E, Zanini, Fabio
Published in Bioinformatics (Oxford, England) (13.05.2022)
Published in Bioinformatics (Oxford, England) (13.05.2022)
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MMseqs2 desktop and local web server app for fast, interactive sequence searches
Mirdita, Milot, Steinegger, Martin, Söding, Johannes
Published in Bioinformatics (Oxford, England) (15.08.2019)
Published in Bioinformatics (Oxford, England) (15.08.2019)
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deepDR: a network-based deep learning approach to in silico drug repositioning
Zeng, Xiangxiang, Zhu, Siyi, Liu, Xiangrong, Zhou, Yadi, Nussinov, Ruth, Cheng, Feixiong
Published in Bioinformatics (Oxford, England) (15.12.2019)
Published in Bioinformatics (Oxford, England) (15.12.2019)
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DeepPurpose: a deep learning library for drug–target interaction prediction
Huang, Kexin, Fu, Tianfan, Glass, Lucas M, Zitnik, Marinka, Xiao, Cao, Sun, Jimeng
Published in Bioinformatics (Oxford, England) (01.12.2020)
Published in Bioinformatics (Oxford, England) (01.12.2020)
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CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
Chen, Chaoran, Nadeau, Sarah, Yared, Michael, Voinov, Philippe, Xie, Ning, Roemer, Cornelius, Stadler, Tanja
Published in Bioinformatics (04.03.2022)
Published in Bioinformatics (04.03.2022)
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Graph embedding on biomedical networks: methods, applications and evaluations
Yue, Xiang, Wang, Zhen, Huang, Jingong, Parthasarathy, Srinivasan, Moosavinasab, Soheil, Huang, Yungui, Lin, Simon M, Zhang, Wen, Zhang, Ping, Sun, Huan
Published in Bioinformatics (15.02.2020)
Published in Bioinformatics (15.02.2020)
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GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
Fang, Zhuoqing, Liu, Xinyuan, Peltz, Gary
Published in Bioinformatics (Oxford, England) (01.01.2023)
Published in Bioinformatics (Oxford, England) (01.01.2023)
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Roary: rapid large-scale prokaryote pan genome analysis
Page, Andrew J., Cummins, Carla A., Hunt, Martin, Wong, Vanessa K., Reuter, Sandra, Holden, Matthew T.G., Fookes, Maria, Falush, Daniel, Keane, Jacqueline A., Parkhill, Julian
Published in Bioinformatics (Oxford, England) (15.11.2015)
Published in Bioinformatics (Oxford, England) (15.11.2015)
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LocusZoom.js: interactive and embeddable visualization of genetic association study results
Boughton, Andrew P, Welch, Ryan P, Flickinger, Matthew, VandeHaar, Peter, Taliun, Daniel, Abecasis, Gonçalo R, Boehnke, Michael
Published in Bioinformatics (Oxford, England) (29.09.2021)
Published in Bioinformatics (Oxford, England) (29.09.2021)
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SEDE-GPS: socio-economic data enrichment based on GPS information
Sperlea, Theodor, Füser, Stefan, Boenigk, Jens, Heider, Dominik
Published in BMC bioinformatics (30.11.2018)
Published in BMC bioinformatics (30.11.2018)
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Nebulosa recovers single-cell gene expression signals by kernel density estimation
Alquicira-Hernandez, Jose, Powell, Joseph E
Published in Bioinformatics (Oxford, England) (25.08.2021)
Published in Bioinformatics (Oxford, England) (25.08.2021)
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