Artificial intelligence in molecular medicine
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Combining machine learning and computational chemistry for predictive insights into chemical systems
Machine learning models are poised to make a transformative impact on chemical sciences
by dramatically accelerating computational algorithms and amplifying insights available from …
by dramatically accelerating computational algorithms and amplifying insights available from …
Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …
AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics
Abstract Machine learning and in particular deep learning (DL) are increasingly important in
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …
Artificial intelligence for proteomics and biomarker discovery
There is an avalanche of biomedical data generation and a parallel expansion in
computational capabilities to analyze and make sense of these data. Starting with genome …
computational capabilities to analyze and make sense of these data. Starting with genome …
Data‐independent acquisition mass spectrometry‐based proteomics and software tools: a glimpse in 2020
F Zhang, W Ge, G Ruan, X Cai, T Guo - Proteomics, 2020 - Wiley Online Library
This review provides a brief overview of the development of data‐independent acquisition
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …
Prediction of peptide mass spectral libraries with machine learning
J Cox - Nature Biotechnology, 2023 - nature.com
The recent development of machine learning methods to identify peptides in complex mass
spectrometric data constitutes a major breakthrough in proteomics. Longstanding methods …
spectrometric data constitutes a major breakthrough in proteomics. Longstanding methods …
Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
In mass-spectrometry-based proteomics, the identification and quantification of peptides and
proteins heavily rely on sequence database searching or spectral library matching. The lack …
proteins heavily rely on sequence database searching or spectral library matching. The lack …
[HTML][HTML] Acquisition and analysis of DIA-based proteomic data: A comprehensive survey in 2023
R Lou, W Shui - Molecular & Cellular Proteomics, 2024 - Elsevier
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful
technology for high-throughput, accurate, and reproducible quantitative proteomics. This …
technology for high-throughput, accurate, and reproducible quantitative proteomics. This …
Machine learning meets omics: applications and perspectives
The innovation of biotechnologies has allowed the accumulation of omics data at an
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …