Yang Young Lu - Publications, H-index & Citations

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Yang Young Lu

University of Waterloo

11H-index

52Paper Count

1.7KCitation Count

Published Papers 13

Publication Date

Scikit-bio: a fundamental Python library for biological omic data analysis

Nature Methods

IF32.1

2025-12-11

PREAI

Matthew Aton; Daniel McDonald; Jorge Cañardo Alastuey; Raeed Azom; Paarth Batra; Valentyn Bezshapkin; Evan Bolyen; Alexander Cagle; J. Gregory Caporaso; Justine W. Debelius; Kestrel Gorlick; Nirmitha Hamsanipally; Lars Hunger; Aryan Keluskar; Disen Liao; Yang Young Lu; Jose A. Navas-Molina; Anders Pitman; Jai Ram Rideout; Anton Sazonov; Bharath Sathappan; Karen Schwarzberg Lipson; Igor Sfiligoi; Chris Tapo; Yoshiki Vázquez-Baeza; Zijun Wu; Zhenjiang Zech Xu; Mingsong Sam Ye; Jianshu Zhao; Rob Knight; James T. Morton; Qiyun Zhu

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Error-controlled non-additive interaction discovery in machine learning models

Nature Machine Intelligence

IF23.9

2025-09-22

OAAI

Winston Chen; Yifan Jiang; William Stafford Noble; Yang Young Lu

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Modeling microbiome-trait associations with taxonomy-adaptive neural networks

MICROBIOME

IF12.7

2025-03-29

OAAI

Jiang, Yifan; Aton, Matthew; Zhu, Qiyun; Lu, Yang Young

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The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data

JOURNAL OF PROTEOME RESEARCH

IF3.6

2023-01-04

OAAI

Kertesz-Farkas, Attila; Acquaye, Frank Lawrence Nii Adoquaye; Bhimani, Kishankumar; Eng, Jimmy K.; Fondrie, William E.; Grant, Charles; Hoopmann, Michael R.; Lin, Andy; Lu, Yang Y.; Moritz, Robert L.; MacCoss, Michael J.; Noble, William Stafford

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Metric learning for comparing genomic data with triplet network

BRIEFINGS IN BIOINFORMATICS

IF7.7

2022-08-31

PREAI

Ma, Zhi; Lu, Yang Young; Wang, Yiwen; Lin, Renhao; Yang, Zizi; Zhang, Fang; Wang, Ying

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A wider field of view to predict expression

NATURE METHODS

IF32.1

2021-10-04

OAAI

Lu, Yang Young; Noble, William Stafford

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Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra

JOURNAL OF PROTEOME RESEARCH

IF3.6

2018-10-26

OAAI

Hu, Alex; Lu, Yang Young; Bilmes, Jeff; Noble, William Stafford

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Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

FRONTIERS IN MICROBIOLOGY

IF4.5

2018-04-16

OAAI

Tang, Kujin; Lu, Yang Young; Sun, Fengzhu

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Towards enhanced and interpretable clustering/classification in integrative genomics

NUCLEIC ACIDS RESEARCH

IF13.1

2017-08-30

OAAI

Lu, Yang Young; Lv, Jinchi; Fuhrman, Jed A.; Sun, Fengzhu

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VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

MICROBIOME

IF12.7

2017-07-06

412

OAAI

Ren, Jie; Ahlgren, Nathan A.; Lu, Yang Young; Fuhrman, Jed A.; Sun, Fengzhu

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CAFE: aCcelerated Alignment-FrEe sequence analysis

NUCLEIC ACIDS RESEARCH

IF13.1

2017-05-03

OAAI

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A.; Waterman, Michael S.; Sun, Fengzhu

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Alignment-free d2* oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

NUCLEIC ACIDS RESEARCH

IF13.1

2016-11-28

202

OAAI

Ahlgren, Nathan A.; Ren, Jie; Lu, Yang Young; Fuhrman, Jed A.; Sun, Fengzhu

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Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide

Journal of Proteome Research

IF3.6

OAAI

Attila Kertesz-Farkas; Frank Lawrence Nii Adoquaye Acquaye; Vladislav Ostapenko; Rufino Haroldo Locon; Yang Lu; Charles E. Grant; William Stafford Noble

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Research Directions