Rui Qiao

12 papers in the catalog · Canada

Rui Qiao: 12 papers in the catalog · Canada · Bioinformatics Solutions Inc., University of Waterloo · Works on DIAVariant, DeepNovo Peptidome, DeepNovo V2

Affiliations

Bioinformatics Solutions Inc.
University of Waterloo · Department of Statistics and Actuarial Science

Elsewhere

ORCID 0000-0001-5811-0550 · OpenAlex

Papers

De Novo sequencing-assisted homology search for DIA data analysis enables low abundance peptide variants discovery (2025, bioRxiv)
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing (2024, Molecular & Cellular Proteomics)
NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing (2024, bioRxiv)
A complete mass spectrometry-based immunopeptidomics pipeline for neoantigen identification and validation (2023, Research Square)
Discovering and Validating Neoantigens by Mass Spectrometry-based Immunopeptidomics and Deep Learning (2022, bioRxiv)
A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics (2022, Nature Communications)
Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices (2021, Nature Machine Intelligence)
Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2020, Nature Machine Intelligence)
Peptide Sequencing with Deep Learning (2020)
Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2019, bioRxiv)
DeepNovoV2: Better de novo peptide sequencing with deep learning (2019, arXiv)
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry (2018, Nature Methods)

Thesis supervisor

Ali Ghodsi, for Peptide Sequencing with Deep Learning

Methods and tools

DIAVariant, DeepNovo Peptidome, DeepNovo V2, DeepNovo-DIA, DeepNovoAA, NovoBoard, PEAKS, PointNovo

Patents (3)

US11694769B2 Systems and methods for de novo peptide sequencing from data-independent acquisition using deep learning ↗ (Bioinformatics Solutions Inc., priority 2017-07-17, active)
US20200243164A1 Systems and methods for patient-specific identification of neoantigens by de novo peptide sequencing for personalized immunotherapy ↗ (Bioinformatics Solutions Inc., priority 2019-01-30, abandoned)
US11644470B2 Systems and methods for de novo peptide sequencing using deep learning and spectrum pairs ↗ (Bioinformatics Solutions Inc., priority 2019-04-15, active)

Patent families naming this author as an inventor. The link is made only where the same person is evident: they wrote a paper describing the patented method, or worked at the assignee.

Co-authors (28)

Ranked by Newman fractional collaboration strength, so a pair on a two-author paper counts for more than a pair on a 50-author consortium paper.

Baozhen Shan strength 1.61, 11 shared
Lei Xin strength 1.61, 11 shared
Ming Li strength 1.36, 10 shared
Ngoc Hieu Tran strength 1.36, 10 shared
Xin Chen (Waterloo) strength 0.79, 5 shared
Ali Ghodsi strength 0.49, 3 shared
Qing Zhang strength 0.37, 4 shared
Wenting Li strength 0.37, 4 shared
Haibo Bian strength 0.35, 2 shared
Shengying Pan strength 0.35, 3 shared
Hechen Li strength 0.25, 1 shared
Zeping Mao strength 0.25, 2 shared
Chuyi Liu strength 0.12, 1 shared
Xianglilan Zhang strength 0.12, 1 shared
Chao Peng strength 0.12, 2 shared
Chungong Yu strength 0.12, 2 shared
Dongbo Bu strength 0.12, 2 shared
Haicang Zhang strength 0.12, 2 shared
Haiming Qin strength 0.12, 2 shared
Haofei Miao strength 0.12, 2 shared
Jingxiang Lang strength 0.12, 2 shared
Ping Wu strength 0.12, 2 shared
Qingyang Lei strength 0.12, 2 shared
Xiaolong Liu strength 0.12, 2 shared
Yi Zhang strength 0.12, 2 shared
Brenton Morse strength 0.10, 1 shared
Sahar Rabinoviz strength 0.10, 1 shared
Xianliang He strength 0.10, 1 shared

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