Artificial intelligence in molecular medicine

B Gomes, EA Ashley - New England Journal of Medicine, 2023 - Mass Medical Soc
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Combining machine learning and computational chemistry for predictive insights into chemical systems

JA Keith, V Vassilev-Galindo, B Cheng… - Chemical …, 2021 - ACS Publications
Machine learning models are poised to make a transformative impact on chemical sciences
by dramatically accelerating computational algorithms and amplifying insights available from …

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

F Yu, GC Teo, AT Kong, K Fröhlich, GX Li… - Nature …, 2023 - nature.com
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

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

WF Zeng, XX Zhou, S Willems, C Ammar… - Nature …, 2022 - nature.com
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 …

Artificial intelligence for proteomics and biomarker discovery

M Mann, C Kumar, WF Zeng, MT Strauss - Cell systems, 2021 - cell.com
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 …

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 …

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 …

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

S Gessulat, T Schmidt, DP Zolg, P Samaras… - Nature …, 2019 - nature.com
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 …

[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 …

Machine learning meets omics: applications and perspectives

R Li, L Li, Y Xu, J Yang - Briefings in Bioinformatics, 2022 - academic.oup.com
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 …