iPro-WAEL: a comprehensive and robust framework for identifying promoters in multiple species
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 …
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 …
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
Abstract Motivation Three-dimensional (3D) genome organization is of vital importance in
gene regulation and disease mechanisms. Previous studies have shown that CTCF …
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 …
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
Umami ingredients have been identified as important factors in food seasoning and
production. Traditional experimental methods for characterizing peptides exhibiting umami …
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 …
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 …
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
4mC is a type of DNA alteration that has the ability to synchronize multiple biological
movements, for example, DNA replication, gene expressions, and transcriptional …
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 …
transcription factors (TFs). The interactions between enhancers and TFs regulate specific …
Detection of transcription factors binding to methylated DNA by deep recurrent neural network
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 …
is generally accepted in epigenetics that methylated nucleotides could prevent the TFs from …