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 | 487 | 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 | 260 | 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 | 157 | 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 | 153 | 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 | 68 | 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 | 56 | 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 |