Machine learning: its challenges and opportunities in plant system biology

M Hesami, M Alizadeh, AMP Jones… - Applied Microbiology and …, 2022 - Springer
Sequencing technologies are evolving at a rapid pace, enabling the generation of massive
amounts of data in multiple dimensions (eg, genomics, epigenomics, transcriptomic …

Data integration and predictive modeling methods for multi-omics datasets

M Kim, I Tagkopoulos - Molecular omics, 2018 - pubs.rsc.org
Translating data to knowledge and actionable insights is the Holy Grail for many scientific
fields, including biology. The unprecedented massive and heterogeneous data have created …

Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

J Zrimec, CS Börlin, F Buric, AS Muhammad… - Nature …, 2020 - nature.com
Understanding the genetic regulatory code governing gene expression is an important
challenge in molecular biology. However, how individual coding and non-coding regions of …

Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks

RK Umarov, VV Solovyev - PloS one, 2017 - journals.plos.org
Accurate computational identification of promoters remains a challenge as these key DNA
regulatory regions have variable structures composed of functional motifs that provide gene …

iProEP: a computational predictor for predicting promoter

HY Lai, ZY Zhang, ZD Su, W Su, H Ding… - … Therapy-Nucleic Acids, 2019 - cell.com
Promoter is a fundamental DNA element located around the transcription start site (TSS) and
could regulate gene transcription. Promoter recognition is of great significance in …

Identification of promoter regions and regulatory sites

VV Solovyev, IA Shahmuradov, AA Salamov - Computational biology of …, 2010 - Springer
Promoter sequences are the main regulatory elements of gene expression. Their recognition
by computer algorithms is fundamental for understanding gene expression patterns, cell …

Machine learning approaches and their current application in plant molecular biology: A systematic review

JCF Silva, RM Teixeira, FF Silva… - Plant Science, 2019 - Elsevier
Abstract Machine learning (ML) is a field of artificial intelligence that has rapidly emerged in
molecular biology, thus allowing the exploitation of Big Data concepts in plant genomics. In …

Artificial miRNAs: A potential tool for genetic improvement of horticultural crops

M Kumar, V Panwar, V Chaudhary, R Kumar - Scientia Horticulturae, 2024 - Elsevier
Gene silencing by artificial microRNAs (amiRNAs) is one of the most crucial methods for the
development of desired horticultural plants. amiRNAs are highly specific, around 21 nt long …

Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction

M Zhang, C Jia, F Li, C Li, Y Zhu, T Akutsu… - Briefings in …, 2022 - academic.oup.com
Promoters are crucial regulatory DNA regions for gene transcriptional activation. Rapid
advances in next-generation sequencing technologies have accelerated the accumulation …

[책][B] Machine learning approaches to bioinformatics

ZR Yang - 2010 - books.google.com
This book covers a wide range of subjects in applying machine learning approaches for
bioinformatics projects. The book succeeds on two key unique features. First, it introduces …