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Statistical Methods for Pairwise Comparison of Metagenomic Samples
K Song, F Sun
Statistical Analysis of Microbiome Data; Subharup Guha and Somnath Datta …, 2021
Mandate: National Natural Science Foundation of China
Disponibile undeva: 110
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
LCX Weiss, Sophie, Will Van Treuren, Catherine Lozupone, Karoline Faust ...
The ISME Journal. 10, 1669–1681, 2016
Mandate: US National Science Foundation, US National Institutes of Health, Howard …
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.
J Ren, NA Ahlgren, YY Lu, JA Fuhrman, FZ Sun
Microbiome 5 (1), 69, 2017
Mandate: US National Science Foundation, US National Institutes of Health
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
L Peña-Castillo, M Tasan, CL Myers, H Lee, T Joshi, C Zhang, Y Guan, ...
Genome Biol 9 (Suppl 1), S2, 2008
Mandate: US National Institutes of Health, Canadian Institutes of Health Research …
Alignment-free oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
NA Ahlgren, J Ren, YY Lu, JA Fuhrman, F Sun
Nucleic Acids Research 45 (1), 39-53, 2017
Mandate: US National Science Foundation, US National Institutes of Health
CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA
S Kang, Q Li, Q Chen, Y Zhou, S Park, G Lee, B Grimes, K Krysan, M Yu, ...
Genome Biology 18 (1), 53, 2017
Mandate: US National Institutes of Health
Critical Assessment of Metagenome Interpretation: the second round of challenges
F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ...
Nature Methods 19, 429–440, 2022
Mandate: US National Science Foundation, US Department of Energy, Swiss National …
Alignment-free sequence comparison (I): statistics and power
G Reinert, D Chew, F Sun, MS Waterman
Journal of Computational Biology 16 (12), 1615-1634, 2009
Mandate: US National Institutes of Health
Benchmarking of alignment-free sequence comparison methods
A Zielezinski, HZ Girgis, G Bernard, CA Leimeister, K Tang, T Dencker, ...
Genome Biology 20, 144, 2019
Mandate: US National Science Foundation, US Department of Energy, US National …
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing
K Song, J Ren, G Reinert, M Deng, MS Waterman, F Sun
Briefings in Bioinformatics 15 (3), 343-353, 2013
Mandate: US National Institutes of Health, UK Engineering and Physical Sciences …
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank
R You, Z Zhang, Y Xiong, F Sun, H Mamitsuka, S Zhu
Bioinformatics 34 (14), 2465–2473, 2018
Mandate: National Natural Science Foundation of China, Academy of Finland, Finnish …
Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny
Q Chang, Y Luan, F Sun
BMC bioinformatics 12 (1), 118, 2011
Mandate: John D. and Catherine T. MacArthur Foundation
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge
YY Lu, T Chen, JA Fuhrman, F Sun
Bioinformatics 33 (6), 791-798, 2017
Mandate: US National Science Foundation
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
LC Xia, D Ai, J Cram, JA Fuhrman, F Sun
Bioinformatics 29 (2), 230-237, 2013
Mandate: US National Institutes of Health
NetGO: improving large-scale protein function prediction with massive network information
R You, S Yao, Y Xiong, X Huang, F Sun, H Mamitsuka, S Zhu
Nucleic acids research 47 (W1), W379-W387, 2019
Mandate: National Natural Science Foundation of China, Academy of Finland, Finnish …
Alignment-free sequence comparison (II): theoretical power of comparison statistics
L Wan, G Reinert, F Sun, MS Waterman
Journal of Computational Biology 17 (11), 1467-1490, 2010
Mandate: US National Institutes of Health
Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders
J Li, W Zhang, H Yang, DP Howrigan, B Wilkinson, T Souaiaia, ...
Nature Neuroscience 20, 1150–1161, 2017
Mandate: US Department of Defense, US National Institutes of Health
A network-based integrated framework for predicting virus–prokaryote interactions
W Wang, J Ren, K Tang, E Dart, JC Ignacio-Espinoza, JA Fuhrman, ...
NAR Genomics and Bioinformatics 2 (2), lqaa044, 2020
Mandate: US National Science Foundation, US National Institutes of Health, Gordon and …
DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections
CC Liu, YT Tseng, W Li, CY Wu, I Mayzus, A Rzhetsky, F Sun, ...
Nucleic acids research 42 (W1), W137-W146, 2014
Mandate: US National Institutes of Health
Alignment-Free Sequence Analysis and Applications
J Ren, X Bai, YY Lu, K Tang, Y Wang, G Reinert, F Sun
Annual Review of Biomedical Data Science 1, 93-114, 2018
Mandate: US National Science Foundation, US National Institutes of Health, National …
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