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
493 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
261 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
158 2017 DeepPINK: Reproducible feature selection in deep neural networks YY Lu, Y Fan, J Lv, WS Noble
Neural Information Processing Systems (NeurIPS), 8676-8686, 2018
154 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, 93-114, 2018
84 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
69 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
57 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
43 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
18 2017 Ledidi: Designing genomic edits that induce functional activity J Schreiber, YY Lu, WS Noble
ICML Workshop on Computational Biology, 2020
13 2020 DANCE: Enhancing saliency maps using decoys YY Lu, W Guo, X Xing, WS Noble
International Conference on Machine Learning (ICML), 2021
12 2021 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
12 2021 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
11 2018 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
8 2022 Proteome-wide identification of amino acid substitutions deleterious for protein function RA Rodriguez-Mias, KN Hess, BY Ruiz, IR Smith, AS Barente, ...
bioRxiv, 2022
6 2022 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
5 2023 ACE: Explaining cluster from an adversarial perspective YY Lu, T Yu, G Bonora, WS Noble
International Conference on Machine Learning (ICML), 2021
5 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
5 2018 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
4 2023 A wider field of view to predict expression YY Lu, WS Noble
Nature Methods 18, 1155–1156, 2021
4 2021