Improved Prediction Model of Protein Lysine Crotonylation Sites Using Bidirectional Recurrent Neural Networks

Histone crotonylation-centric gene regulation

(2021) Kun Li et al.   Epigenetics & Chromatin

nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning

(2021) Yong-Zi Chen et al.   BRIEFINGS IN BIOINFORMATICS

Prediction of DNA binding proteins using local features and long-term dependencies with primary sequences based on deep learning

(2021) Guobin Li et al.   PeerJ

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

(2021) Bo Sun et al.   JOURNAL OF PROTEOME RESEARCH

BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models

(2021) Yanhua Qiao et al.   BIOINFORMATICS

Global crotonylome reveals CDYL-regulated RPA1 crotonylation in homologous recombination–mediated DNA repair

(2020) Huajing Yu et al.   Science Advances

Deep-Kcr: accurate detection of lysine crotonylation sites using deep learning method

(2020) Hao Lv et al.   BRIEFINGS IN BIOINFORMATICS

Deep learning in proteomics

(2020) Bo Wen et al.   PROTEOMICS

ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representation

(2020) Lijun Cai et al.   BRIEFINGS IN BIOINFORMATICS

DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins

(2019) Hongli Fu et al.   BMC BIOINFORMATICS

Lysine crotonylation is involved in hepatocellular carcinoma progression

(2019) Junhu Wan et al.   BIOMEDICINE & PHARMACOTHERAPY

Fertility-GRU: Identifying fertility-related proteins by incorporating deep gated recurrent units and original PSSM profiles

(2019) Nguyen Quoc Khanh Le   JOURNAL OF PROTEOME RESEARCH

Functions and mechanisms of lysine crotonylation

(2019) Junhu Wan et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

A novel molecular representation with BiGRU neural networks for learning atom

(2019) Xuan Lin et al.   BRIEFINGS IN BIOINFORMATICS

Predicting protein phosphorylation sites based on deep learning

(2019) Haixia Long et al.   Current Bioinformatics

iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou’s 5-step rule

(2019) Sharaf Jameel Malebary et al.   PLoS One

HIV latency is reversed by ACSS2-driven histone crotonylation

(2018) Guochun Jiang et al.   JOURNAL OF CLINICAL INVESTIGATION

Machine-Learning-Based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency with Improved Accuracy

(2018) Balachandran Manavalan et al.   JOURNAL OF PROTEOME RESEARCH

Dynamics of Telomere Rejuvenation during Chemical Induction to Pluripotent Stem Cells

(2018) Haifeng Fu et al.   Stem Cell Reports

Chromodomain Y-like Protein–Mediated Histone Crotonylation Regulates Stress-Induced Depressive Behaviors

(2018) Yongqing Liu et al.   BIOLOGICAL PSYCHIATRY

iKcr-PseEns: Identify lysine crotonylation sites in histone proteins with pseudo components and ensemble classifier

(2017) Wang-Ren Qiu et al.   GENOMICS

Prediction of lysine crotonylation sites by incorporating the composition of k -spaced amino acid pairs into Chou’s general PseAAC

(2017) Zhe Ju et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Chromodomain Protein CDYL Acts as a Crotonyl-CoA Hydratase to Regulate Histone Crotonylation and Spermatogenesis

(2017) Shumeng Liu et al.   MOLECULAR CELL

MOF as an evolutionarily conserved histone crotonyltransferase and transcriptional activation by histone acetyltransferase-deficient and crotonyltransferase-competent CBP/p300

(2017) Xiaoguang Liu et al.   Cell Discovery

Diverse Activities of Histone Acylations Connect Metabolism to Chromatin Function

(2016) Arnob Dutta et al.   MOLECULAR CELL

Metabolic regulation of gene expression through histone acylations

(2016) Benjamin R. Sabari et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Intracellular Crotonyl-CoA Stimulates Transcription through p300-Catalyzed Histone Crotonylation

(2015) Benjamin R. Sabari et al.   MOLECULAR CELL

Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark

(2014) Lunzhi Dai et al.   Nature Chemical Biology

50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond

(2014) Eric Verdin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mechanisms of Epithelial Repair and Regeneration After Acute Kidney Injury

(2014) Katja Berger et al.   SEMINARS IN NEPHROLOGY

Identification of ‘erasers’ for lysine crotonylated histone marks using a chemical proteomics approach

(2014) Xiucong Bao et al.   eLife

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL