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  1. ...Qinhu Zhang1,2, Siguo Wang1, Zhipeng Li1, Wenzheng Bao3, Wenjian Liu4 and De-Shuang Huang1,5 1Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo 315201, China; 2Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning, 530007, China; 3School...
  2. ...Bioinformatics Division of BNRIST and Department of Automation, MOE Key Lab of Bioinformatics, Tsinghua University, Beijing, 100084, China Corresponding author: sunxq6@mail.sysu.edu.cnAbstractCell-cell communication (CCC) is critical for determining cell fates and functions in multicellular organisms...
  3. ...Benjamin J. Auerbach1, Jian Hu2, Muredach P. Reilly3 and Mingyao Li2 1Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; 2Department of Biostatistics, Epidemiology and Informatics, University...
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  4. ...Town, Cape Town, South Africa 7925; 2Covenant University Bioinformatics Research (CUBRe) and Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria, P.M.B. 1023; 3Centre National de Transfusion Sanguine, Rabat, Morocco 10100; 4Institute Pasteur of Tunis, Tunis...
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  5. ...Vikram S. Shivakumar and Ben Langmead Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding authors: vshivak1@jhu.edu, langmea@cs.jhu.eduAbstractPan collections are growing to hundreds of high-quality s. This necessitates scalable methods...
  6. ...by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (‘‘sequence-based ultrarapid pathogen identification’’), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate...
  7. .... Bioinformatics 38: 3698–3702. doi:10.1093/bioinformatics/btac410 ↵Chandra G, Gibney D, Jain C. 2024. Haplotype-aware sequence alignment to pan graphs. Genome Res 34: 1265–1275. doi:10.1101/gr.279143.124 ↵Computational Pan-Genomics Consortium. 2018. Computational pan-genomics: status, promises and challenges...
  8. ...–5167. doi:10.1093/bioinformatics/btac671 ↵Lv H, Dao FY, Zhang D, Guan ZX, Yang H, Su W, Liu ML, Ding H, Chen W, Lin H. 2020. iDNA-MS: an integrated computational tool for detecting DNA modification sites in multiple s. iScience 23: 100991. doi:10.1016/j.isci.2020.100991 ↵Manavalan B, Basith S, Shin TH, Wei...
  9. ...of sequence data. J Comput Biol 19: 577–590. doi:10.1089/cmb.2012.0084 ↵Bansal V, Bafna V. 2008. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24: i153–i159. doi:10.1093/bioinformatics/btn298 ↵Bengio Y, Louradour J, Collobert R, Weston J. 2009. Curriculum...
  10. ...Kavya Vaddadi1, Mao-Jan Lin1, Sina Majidian1, Taher Mun1, Ben Langmead1 1. Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA Abstract Pan indexes reduce reference bias in sequencing data analysis. However, bias can be reduced...
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