iPro-WAEL: a comprehensive and robust framework for identifying promoters in multiple species

P Zhang, H Zhang, H Wu - Nucleic Acids Research, 2022 - academic.oup.com
Promoters are consensus DNA sequences located near the transcription start sites and they
play an important role in transcription initiation. Due to their importance in biological …

Deep-STP: a deep learning-based approach to predict snake toxin proteins by using word embeddings

H Zulfiqar, Z Guo, RM Ahmad, Z Ahmed, P Cai… - Frontiers in …, 2024 - frontiersin.org
Snake venom contains many toxic proteins that can destroy the circulatory system or
nervous system of prey. Studies have found that these snake venom proteins have the …

CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types

P Zhang, Y Wu, H Zhou, B Zhou, H Zhang… - Bioinformatics, 2022 - academic.oup.com
Abstract Motivation Three-dimensional (3D) genome organization is of vital importance in
gene regulation and disease mechanisms. Previous studies have shown that CTCF …

Ichrom-deep: an attention-based deep learning model for identifying chromatin interactions

P Zhang, H Wu - IEEE Journal of Biomedical and Health …, 2023 - ieeexplore.ieee.org
Identification of chromatin interactions is crucial for advancing our knowledge of gene
regulation. However, due to the limitations of high-throughput experimental techniques …

UMPred-FRL: A new approach for accurate prediction of umami peptides using feature representation learning

P Charoenkwan, C Nantasenamat, MM Hasan… - International journal of …, 2021 - mdpi.com
Umami ingredients have been identified as important factors in food seasoning and
production. Traditional experimental methods for characterizing peptides exhibiting umami …

[HTML][HTML] Empirical comparison and recent advances of computational prediction of hormone binding proteins using machine learning methods

H Zulfiqar, Z Guo, BK Grace-Mercure, ZY Zhang… - Computational and …, 2023 - Elsevier
Hormone binding proteins (HBPs) belong to the group of soluble carrier proteins. These
proteins selectively and non-covalently interact with hormones and promote growth …

[HTML][HTML] Identification of cyclin protein using gradient boost decision tree algorithm

H Zulfiqar, SS Yuan, QL Huang, ZJ Sun, FY Dao… - Computational and …, 2021 - Elsevier
Cyclin proteins are capable to regulate the cell cycle by forming a complex with cyclin-
dependent kinases to activate cell cycle. Correct recognition of cyclin proteins could provide …

Deep-4mCGP: A Deep Learning Approach to Predict 4mC Sites in Geobacter pickeringii by Using Correlation-Based Feature Selection Technique

H Zulfiqar, QL Huang, H Lv, ZJ Sun, FY Dao… - International Journal of …, 2022 - mdpi.com
4mC is a type of DNA alteration that has the ability to synchronize multiple biological
movements, for example, DNA replication, gene expressions, and transcriptional …

iEnhancer-EBLSTM: identifying enhancers and strengths by ensembles of bidirectional long short-term memory

K Niu, X Luo, S Zhang, Z Teng, T Zhang… - Frontiers in Genetics, 2021 - frontiersin.org
Enhancers are regulatory DNA sequences that could be bound by specific proteins named
transcription factors (TFs). The interactions between enhancers and TFs regulate specific …

Detection of transcription factors binding to methylated DNA by deep recurrent neural network

H Li, Y Gong, Y Liu, H Lin, G Wang - Briefings in bioinformatics, 2022 - academic.oup.com
Transcription factors (TFs) are proteins specifically involved in gene expression regulation. It
is generally accepted in epigenetics that methylated nucleotides could prevent the TFs from …