Investigation and Highly Accurate Prediction of Missed Tryptic Cleavages by Deep Learning

DeepDigest: Prediction of Protein Proteolytic Digestion with Deep Learning

(2021) Jinghan Yang et al.   ANALYTICAL CHEMISTRY

PepFormer: End-to-End Transformer-Based Siamese Network to Predict and Enhance Peptide Detectability Based on Sequence Only

(2021) Hao Cheng et al.   ANALYTICAL CHEMISTRY

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

(2020) Yi Yang et al.   Nature Communications

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

(2020) Nikita Prianichnikov et al.   MOLECULAR & CELLULAR PROTEOMICS

Temporal Convolutional Networks for the Advance Prediction of ENSO

(2020) Jining Yan et al.   Scientific Reports

Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets

(2020) Diego Velázquez et al.   Scientific Reports

Lkb1 suppresses amino acid-driven gluconeogenesis in the liver

(2020) Pierre-Alexandre Just et al.   Nature Communications

Stage-specific testes proteomics of Drosophila melanogaster identifies essential proteins for male fertility

(2019) Stefanie M.K. Gärtner et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

(2019) Yansheng Liu et al.   NATURE BIOTECHNOLOGY

AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility

(2019) Zhiqiang Gao et al.   ANALYTICAL CHEMISTRY

CerS6-Derived Sphingolipids Interact with Mff and Promote Mitochondrial Fragmentation in Obesity

(2019) Philipp Hammerschmidt et al.   CELL

Enhanced trypsin on a budget: Stabilization, purification and high-temperature application of inexpensive commercial trypsin for proteomics applications

(2019) Søren Heissel et al.   PLoS One

DeepIso: A Deep Learning Model for Peptide Feature Detection from LC-MS map

(2019) Fatema Tuz Zohora et al.   Scientific Reports

Recent Trends in Deep Learning Based Natural Language Processing [Review Article]

(2018) Tom Young et al.   IEEE Computational Intelligence Magazine

Deep learning for biological image classification

(2017) Carlos Affonso et al.   EXPERT SYSTEMS WITH APPLICATIONS

kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

(2017) Xuebing Wu et al.   NUCLEIC ACIDS RESEARCH

Predicting Tryptic Cleavage from Proteomics Data Using Decision Tree Ensembles

(2013) Thomas Fannes et al.   JOURNAL OF PROTEOME RESEARCH

pLogo: a probabilistic approach to visualizing sequence motifs

(2013) Joseph P O'Shea et al.   NATURE METHODS

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

Prediction of Missed Proteolytic Cleavages for the Selection of Surrogate Peptides for Quantitative Proteomics

(2012) Craig Lawless et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

CONSeQuence: Prediction of Reference Peptides for Absolute Quantitative Proteomics Using Consensus Machine Learning Approaches

(2011) Claire E. Eyers et al.   MOLECULAR & CELLULAR PROTEOMICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY