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Yang Lu
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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
4802017
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
2582017
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
1572017
DeepPINK: Reproducible feature selection in deep neural networks
YY Lu, Y Fan, J Lv, WS Noble
Neural Information Processing Systems (NeurIPS), 8676-8686, 2018
1502018
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
832018
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
672017
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
562019
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
432019
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
182017
Ledidi: Designing genomic edits that induce functional activity
J Schreiber, YY Lu, WS Noble
ICML Workshop on Computational Biology, 2020
132020
DANCE: Enhancing saliency maps using decoys
YY Lu, W Guo, X Xing, WS Noble
International Conference on Machine Learning (ICML), 2021
122021
DIAmeter: Matching peptides to data-independent acquisition mass spectrometry data
YY Lu, J Bilmes, RA Rodriguez-Mias, J Villén, WS Noble
International Conference on Intelligent Systems for Molecular Biology (ISMB), 2021
122021
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
112018
Reducing peptide sequence bias in quantitative mass spectrometry data with machine learning
AB Dincer, YY Lu, DK Schweppe, S Oh, WS Noble
Journal of Proteome Research 21 (7), 1771-1782, 2022
82022
Proteome-wide identification of amino acid substitutions deleterious for protein function
RA Rodriguez-Mias, KN Hess, BY Ruiz, IR Smith, AS Barente, ...
bioRxiv, 2022
62022
Retrieved Sequence Augmentation for Protein Representation Learning
C Ma, H Zhao, L Zheng, J Xin, Q Li, L Wu, Z Deng, YY Lu, Q Liu, L Kong
bioRxiv, 2023.02. 22.529597, 2023
52023
ACE: Explaining cluster from an adversarial perspective
YY Lu, T Yu, G Bonora, WS Noble
International Conference on Machine Learning (ICML), 2021
52021
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
52018
The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data
A Kertesz-Farkas, FL Nii Adoquaye Acquaye, K Bhimani, JK Eng, ...
Journal of Proteome Research, 2023
42023
A wider field of view to predict expression
YY Lu, WS Noble
Nature Methods 18, 1155–1156, 2021
42021
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