ProtSyntax is a protein language model that improves PTM site prediction and functional inference by integrating contextual and structural information.

DOI 10.64898/2026.07.18.739331

protein sequencedeep learning

BioinformaticsbioRxivPreprintMay 2, 2022

GraphPred: An approach to predict multiple DNA motifs from ATAC-seq data using graph neural network and coexisting probability

Shuangquan Zhang, Lili Yang, Xiaotian Wu…·Yan Wang

GraphPred predicts multiple DNA motifs from ATAC-seq data using a graph neural network and coexisting probability, outperforming existing methods on 88 datasets.

DOI 10.1101/2022.05.02.490240

ATAC-seqgraph neural network

BioinformaticsBriefings in BioinformaticsPeer-reviewedSep 8, 2021

Assessing deep learning algorithms in cis-regulatory motif finding based on genomic sequencing data

Yan Wang, Shuangquan Zhang, Anjun Ma…·Qin Ma

This study evaluates 20 deep learning models for cis-regulatory motif finding using genomic data, finding that model choice depends on data type and size.

25 citations

ChIP-seqdeep learning

BioinformaticsNucleic Acids ResearchPeer-reviewedJul 24, 2019

Systematic Prediction of Regulatory Motifs from Human ChIP-Sequencing Data Based on a Deep Learning Framework

Jinyu Yang, Anjun Ma, Adam D. Hoppe…·Qin Ma

The paper introduces DESSO, a deep learning framework for predicting regulatory motifs from ChIP-Seq data, showing improved accuracy over existing tools.

67 citations

humanChIP-seq