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Deep Learning in Proteomics

Proteomics (Weinheim), 2020-11, Vol.20 (21-22), p.e1900335-n/a

2020

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A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

Nature communications, 2019-07, Vol.10 (1), p.3404-12, Article 3404

2019

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The structural context of posttranslational modifications at a proteome-wide scale

PLoS biology, 2022-05, Vol.20 (5), p.e3001636-e3001636

2022

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Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3

Nature methods, 2021-12, Vol.18 (12), p.1515

2021

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pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification

Nature communications, 2017-09, Vol.8 (1), p.438-14, Article 438

2017

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A Deep Learning‐Based Tumor Classifier Directly Using MS Raw Data

Proteomics (Weinheim), 2020-11, Vol.20 (21-22), p.e1900344-n/a

2020

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AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics

Nature communications, 2022-11, Vol.13 (1), p.7238-7238, Article 7238

2022

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Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel

Molecular systems biology, 2023-09, Vol.19 (9), p.e11503-e11503

2023

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Bandwidth-Enhanced 5G Mobile Phone Antenna Pair With Tunable Electric Field Null

IEEE transactions on antennas and propagation, 2023-02, Vol.71 (2), p.1960-1964

2023

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IEEE_Xplore

Quantitative multiorgan proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation

EMBO molecular medicine, 2023-09, Vol.15 (9), p.e17459-e17459

2023

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A Series-Fed Slant-Polarized Microstrip Patch Antenna Array

IEEE transactions on antennas and propagation, 2024-06, Vol.72 (6), p.5367-5372

2024

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IEEE_Xplore

Dual-Band Base Station Antenna Array With Cross-Band Scattering and In-Band Coupling Suppression

IEEE transactions on antennas and propagation, 2023-05, Vol.71 (5), p.3983-3991

2023

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IEEE_Xplore

pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level

Nature communications, 2022-12, Vol.13 (1), p.7539-7539, Article 7539

2022

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AlphaPept: a modern and open framework for MS-based proteomics

Nature communications, 2024-03, Vol.15 (1), p.2168-2168, Article 2168

2024

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Eight‐element fifth‐generation multiple‐input multiple‐output antenna designed by modal currents cancelation

International journal of RF and microwave computer-aided engineering, 2022-09, Vol.32 (9), p.n/a

2022

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pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3

Scientific reports, 2016-05, Vol.6 (1), p.25102-25102, Article 25102

2016

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pDeep3: Toward More Accurate Spectrum Prediction with Fast Few-Shot Learning

Analytical chemistry (Washington), 2021-04, Vol.93 (14), p.5815-5822

2021

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Inhibition of Connexin 36 attenuates HMGB1‐mediated depressive‐like behaviors induced by chronic unpredictable mild stress

Brain and behavior, 2022-02, Vol.12 (2), p.e2470-n/a

2022

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pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

Analytical chemistry (Washington), 2017-12, Vol.89 (23), p.12690-12697

2017

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N6-methyladenosine Regulator-Mediated Immune Genes Identify Breast Cancer Immune Subtypes and Predict Immunotherapy Efficacy

Frontiers in genetics, 2021-12, Vol.12, p.790888-790888

2021

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MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning

Analytical chemistry (Washington), 2019-08, Vol.91 (15), p.9724-9731

2019

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IMBAS-MS Discovers Organ-Specific HLA Peptide Patterns in Plasma

Molecular & cellular proteomics, 2024-01, Vol.23 (1), p.100689-100689, Article 100689

2024

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Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

Nature biotechnology, 2018-12, Vol.36 (11), p.1059-1061

2018

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pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

Bioinformatics, 2019-07, Vol.35 (14), p.i183-i190

2019

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Design of Self-Decoupling Dielectric Resonator Antenna With Shared Radiator

IEEE transactions on antennas and propagation, 2023-01, Vol.71 (1), p.1053-1058

2023

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IEEE_Xplore

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Deep Learning in Proteomics

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

The structural context of posttranslational modifications at a proteome-wide scale

Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3

pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification

A Deep Learning‐Based Tumor Classifier Directly Using MS Raw Data

AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics

Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel

Bandwidth-Enhanced 5G Mobile Phone Antenna Pair With Tunable Electric Field Null

Quantitative multiorgan proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation

A Series-Fed Slant-Polarized Microstrip Patch Antenna Array

Dual-Band Base Station Antenna Array With Cross-Band Scattering and In-Band Coupling Suppression

pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level

AlphaPept: a modern and open framework for MS-based proteomics

Eight‐element fifth‐generation multiple‐input multiple‐output antenna designed by modal currents cancelation

pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3

pDeep3: Toward More Accurate Spectrum Prediction with Fast Few-Shot Learning

Inhibition of Connexin 36 attenuates HMGB1‐mediated depressive‐like behaviors induced by chronic unpredictable mild stress

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

N6-methyladenosine Regulator-Mediated Immune Genes Identify Breast Cancer Immune Subtypes and Predict Immunotherapy Efficacy

MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning

IMBAS-MS Discovers Organ-Specific HLA Peptide Patterns in Plasma

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

Design of Self-Decoupling Dielectric Resonator Antenna With Shared Radiator

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