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MutScape: an analytical toolkit for probing the mutational landscape in cancer genomics JOURNAL ARTICLE published 4 October 2021 in NAR Genomics and Bioinformatics Research funded by Industrial Technology Research Institute (110HT654005) | YongLin Healthcare Foundation (FB002-7) | National Taiwan University (GTZ300; 109L104704-2) |
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Correction to ‘Spike-in normalization for single-cell RNA-seq reveals dynamic global transcriptional activity mediating anticancer drug response’ JOURNAL ARTICLE published 29 March 2023 in NAR Genomics and Bioinformatics |
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Correction to ‘Optocoder: computational decoding of spatially indexed bead arrays’ JOURNAL ARTICLE published 29 March 2023 in NAR Genomics and Bioinformatics |
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Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol JOURNAL ARTICLE published 9 April 2021 in NAR Genomics and Bioinformatics |
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UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network JOURNAL ARTICLE published 1 March 2020 in NAR Genomics and Bioinformatics |
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NG-Circos: next-generation Circos for data visualization and interpretation JOURNAL ARTICLE published 1 September 2020 in NAR Genomics and Bioinformatics |
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STAMP: a multiplex sequencing method for simultaneous evaluation of mitochondrial DNA heteroplasmies and content JOURNAL ARTICLE published 19 October 2020 in NAR Genomics and Bioinformatics Research funded by NIH (R01AI085286) |
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Systematic evaluation of parameters in RNA bisulfite sequencing data generation and analysis JOURNAL ARTICLE published 31 March 2022 in NAR Genomics and Bioinformatics Research funded by National Institute of Neurological Disorders and Stroke (NS094574) | National Institute of Mental Health (MH120498) | National Institute of Environmental Health Sciences (ES031521) | National Science Foundation (1922428) |
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Combined statistical modeling enables accurate mining of circadian transcription JOURNAL ARTICLE published 9 April 2021 in NAR Genomics and Bioinformatics Research funded by Ministerio de Ciencia e Innovación (BES-2016-076635,RTI2018-095497-B-I00,RTI2018-102084-B-I00) | European Commission Fellowship (MSCA-IF-EF-748381) |
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gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms JOURNAL ARTICLE published 1 September 2020 in NAR Genomics and Bioinformatics Research funded by Ministerio de Ciencia, Innovación y Universidades (PGC2018-099344-B-I0,FPU15/01203) | Generalitat Valenciana (PROMETEO/2018/133) | Research Foundation Flanders (1S90918N) | Deutsche Forschungsgemeinschaft (RE 3474/2-2) |
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GRACE: a comprehensive web-based platform for integrative single-cell transcriptome analysis JOURNAL ARTICLE published 29 March 2023 in NAR Genomics and Bioinformatics Research funded by National Key R&D Program of China (2022YFA1103300,2022YFA1103303,2022YFA1103304) | National Natural Science Foundation of China (82020108004) | Natural Science Foundation of Chongqing (cstc2019jcyj-msxmX0421) | Translational Research Grant of NCRCH (2020ZKZC02) | Army Medical University (2022YQB014) |
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Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli JOURNAL ARTICLE published 10 January 2023 in NAR Genomics and Bioinformatics Research funded by MSIT (2021M3A9I4024840,2022M3A9I5018934) | National Institute of General Medical Sciences (5R01GM057089-19,GM102098) |
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PolyQ length co-evolution in neural proteins JOURNAL ARTICLE published 9 April 2021 in NAR Genomics and Bioinformatics Research funded by Ministero dell’Istruzione, dell’Università e della Ricerca (FFABR-2017) |
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Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2.0 JOURNAL ARTICLE published 29 March 2023 in NAR Genomics and Bioinformatics Research funded by New Zealand–China Non Communicable Diseases Research (UOOX1601) |
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Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads JOURNAL ARTICLE published 29 March 2023 in NAR Genomics and Bioinformatics |
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Faster SARS-CoV-2 sequence validation and annotation for GenBank using VADR JOURNAL ARTICLE published 10 January 2023 in NAR Genomics and Bioinformatics |
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Identification and characterization of histones inPhysarum polycephalumevidence a phylogenetic vicinity of Mycetozoans to the animal kingdom JOURNAL ARTICLE published 4 October 2021 in NAR Genomics and Bioinformatics Research funded by National Institutes of Health (R35GM128661,R01GM052426) |
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Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation JOURNAL ARTICLE published 5 January 2024 in NAR Genomics and Bioinformatics Research funded by National Natural Science Foundation of China (32370717) |
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ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways JOURNAL ARTICLE published 4 October 2021 in NAR Genomics and Bioinformatics |
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Deep learning identifies erroneous microarray-based, gene-level conclusions in literature JOURNAL ARTICLE published 4 October 2021 in NAR Genomics and Bioinformatics Research funded by National Institutes of Health (R35GM133346) |