Artificial intelligence for proteomics and biomarker discovery

Urinary proteome profiling for stratifying patients with familial Parkinson’s disease

(2021) Sebastian Virreira Winter et al.   EMBO Molecular Medicine

Ethical Principles, Constraints and Opportunities in Clinical Proteomics

(2021) Sebastian Porsdam Mann et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep learning the collisional cross sections of the peptide universe from a million experimental values

(2021) Florian Meier et al.   Nature Communications

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

(2021) Ching Tarn et al.   ANALYTICAL CHEMISTRY

DeepDigest: Prediction of Protein Proteolytic Digestion with Deep Learning

(2021) Jinghan Yang et al.   ANALYTICAL CHEMISTRY

Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network

(2020) Kaiyuan Liu et al.   ANALYTICAL CHEMISTRY

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics

(2020) Yi Yang et al.   Nature Communications

How Machine Learning Will Transform Biomedicine

(2020) Jeremy Goecks et al.   CELL

Proteomic and interactomic insights into the molecular basis of cell functional diversity

(2020) Isabell Bludau et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Combining lipidomics and machine learning to measure clinical lipids in dried blood spots

(2020) Stuart G. Snowden et al.   Metabolomics

Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease

(2020) Jakob M Bader et al.   Molecular Systems Biology

The proteome landscape of the kingdoms of life

(2020) Johannes B. Müller et al.   NATURE

Responsible, practical genomic data sharing that accelerates research

(2020) James Brian Byrd et al.   NATURE REVIEWS GENETICS

A Comprehensive Evaluation of MS/MS Spectrum Prediction Tools for Shotgun Proteomics

(2020) Rui Xu et al.   PROTEOMICS

Focus on the spectra that matter by clustering of quantification data in shotgun proteomics

(2020) Matthew The et al.   Nature Communications

Adipose tissue morphology, imaging and metabolomics predicting cardiometabolic risk and family history of type 2 diabetes in non-obese men

(2020) Aidin Rawshani et al.   Scientific Reports

Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics

(2020) Mi Yang et al.   Cell Systems

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling

(2020) Tea Dodig-Crnković et al.   EBioMedicine

Deep learning meets metabolomics: a methodological perspective

(2020) Partho Sen et al.   BRIEFINGS IN BIOINFORMATICS

Fragment Mass Spectrum Prediction Facilitates Site Localization of Phosphorylation

(2020) Yi Yang et al.   JOURNAL OF PROTEOME RESEARCH

Deep learning in proteomics

(2020) Bo Wen et al.   PROTEOMICS

DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics

(2020) Kai Li et al.   PROTEOMICS

Integrated proteomics reveals brain-based cerebrospinal fluid biomarkers in asymptomatic and symptomatic Alzheimer’s disease

(2020) Lenora Higginbotham et al.   Science Advances

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

(2019) Siegfried Gessulat et al.   NATURE METHODS

High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis

(2019) Shivani Tiwary et al.   NATURE METHODS

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

(2019) Wen-Feng Zeng et al.   ANALYTICAL CHEMISTRY

scGen predicts single-cell perturbation responses

(2019) Mohammad Lotfollahi et al.   NATURE METHODS

Plasma Proteome Profiling to detect and avoid sample‐related biases in biomarker studies

(2019) Philipp E Geyer et al.   EMBO Molecular Medicine

Data privacy in the age of personal genomics

(2019) Dennis Grishin et al.   NATURE BIOTECHNOLOGY

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

(2019) Vadim Demichev et al.   NATURE METHODS

Proteoforms as the next proteomics currency

(2018) Lloyd M. Smith et al.   SCIENCE

Improved Peptide Retention Time Prediction in Liquid Chromatography through Deep Learning

(2018) Chunwei Ma et al.   ANALYTICAL CHEMISTRY

Assembling the Community-Scale Discoverable Human Proteome

(2018) Mingxun Wang et al.   Cell Systems

High-performance medicine: the convergence of human and artificial intelligence

(2018) Eric J. Topol   NATURE MEDICINE

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery

(2018) Nicolai J. Wewer Albrechtsen et al.   Cell Systems

Revisiting biomarker discovery by plasma proteomics

(2017) Philipp E Geyer et al.   Molecular Systems Biology

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peptide retention time prediction

(2016) Luminita Moruz et al.   MASS SPECTROMETRY REVIEWS

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

(2016) Philipp E Geyer et al.   Molecular Systems Biology

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

MS2PIP: a tool for MS/MS peak intensity prediction

(2013) Sven Degroeve et al.   BIOINFORMATICS

Fast and Accurate Database Searches with MS-GF+Percolator

(2013) Viktor Granholm et al.   JOURNAL OF PROTEOME RESEARCH

MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions

(2012) Shiwei Sun et al.   JOURNAL OF PROTEOME RESEARCH

Text-mining solutions for biomedical research: enabling integrative biology

(2012) Dietrich Rebholz-Schuhmann et al.   NATURE REVIEWS GENETICS

Mining electronic health records: towards better research applications and clinical care

(2012) Peter B. Jensen et al.   NATURE REVIEWS GENETICS

Modeling the Cell Cycle: Why Do Certain Circuits Oscillate?

(2011) James E. Ferrell et al.   CELL

Training, Selection, and Robust Calibration of Retention Time Models for Targeted Proteomics

(2010) Luminita Moruz et al.   JOURNAL OF PROTEOME RESEARCH

Refining Clinical Risk Stratification for Predicting Stroke and Thromboembolism in Atrial Fibrillation Using a Novel Risk Factor-Based Approach

(2009) Gregory Y.H. Lip et al.   CHEST

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

Minimum Reporting Guidelines for Proteomics Released by the Proteomics Standards Initiative

(2008) Andrew R. Jones et al.   MOLECULAR & CELLULAR PROTEOMICS