Yang Lu
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
J Ren, NA Ahlgren, YY Lu, JA Fuhrman, F Sun
Microbiome 5 (1), 1-20, 2017
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
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
DeepPINK: reproducible feature selection in deep neural networks
YY Lu, Y Fan, J Lv, WS Noble
Proceedings of the 32nd International Conference on Neural Information …, 2018
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, 2018
CAFE: aCcelerated Alignment-FrEe sequence analysis
YY Lu, K Tang, J Ren, JA Fuhrman, MS Waterman, F Sun
Nucleic Acids Research 45 (W1), W554-W559, 2017
SolidBin: improving metagenome binning with semi-supervised normalized cut
Z Wang, Z Wang, YY Lu, F Sun, S Zhu
Bioinformatics 35 (21), 4229-4238, 2019
Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features
DF Read, K Cook, YY Lu, KGL Roch, WS Noble
PLoS Computational Biology 15 (9), e1007329, 2019
Improving contig binning of metagenomic data using oligonucleotide frequency dissimilarity
Y Wang, K Wang, YY Lu, F Sun
BMC Bioinformatics 18 (1), 1-14, 2017
Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer
K Tang, YY Lu, F Sun
Frontiers in microbiology 9, 711, 2018
Ledidi: Designing genomic edits that induce functional activity
J Schreiber, YY Lu, WS Noble
ICML Workshop on Computational Biology, 2020
DANCE: Enhancing saliency maps using decoys
YY Lu, W Guo, X Xing, WS Noble
Proceedings of the 38th International Conference on Machine Learning (ICML), 2021
Joint precursor elution profile inference via regression for peptide detection in data-independent acquisition mass spectra
A Hu, YY Lu, J Bilmes, WS Noble
Journal of Proteome Research 18 (1), 86-94, 2018
DIAmeter: Matching peptides to data-independent acquisition mass spectrometry data
YY Lu, J Bilmes, RA Rodriguez-Mias, J Villén, WS Noble
Proceedings of the 29th International Conference on Intelligent Systems for …, 2021
CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase
YY Lu, JX Bai, Y Wang, Y Wang, F Sun
Bioinformatics 37 (2), 155-161, 2020
Proteome-wide identification of amino acid substitutions deleterious for protein function
RA Rodriguez-Mias, KN Hess, BY Ruiz, IR Smith, AS Barente, ...
bioRxiv, 2022
A wider field of view to predict expression
YY Lu, WS Noble
Nature Methods 18, 1155–1156, 2021
ACE: Explaining cluster from an adversarial perspective
YY Lu, T Yu, G Bonora, WS Noble
Proceedings of the 38th International Conference on Machine Learning (ICML), 2021
Towards enhanced and interpretable clustering/classification in integrative genomics
YY Lu, J Lv, JA Fuhrman, F Sun
Nucleic Acids Research 45 (20), e169, 2017
Metric learning for comparing genomic data with triplet network
Z Ma, YY Lu, Y Wang, R Lin, Z Yang, F Zhang, Y Wang
Briefings in bioinformatics, bbac345, 2022
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