Sequence clustering in bioinformatics: an empirical study

Q Zou, G Lin, X Jiang, X Liu, X Zeng - Briefings in bioinformatics, 2020 - academic.oup.com
Sequence clustering is a basic bioinformatics task that is attracting renewed attention with
the development of metagenomics and microbiomics. The latest sequencing techniques …

Impacts of bioinformatics to medicinal chemistry

KC Chou - Medicinal chemistry, 2015 - ingentaconnect.com
Facing the explosive growth of biological sequence data, such as those of protein/peptide
and DNA/RNA, generated in the post-genomic age, many bioinformatical and mathematical …

SBSM-Pro: support bio-sequence machine for proteins

Y Wang, Y Zhai, Y Ding, Q Zou - Science China Information Sciences, 2024 - Springer
Proteins play a pivotal role in biological systems. The use of machine learning algorithms for
protein classification can assist and even guide biological experiments, offering crucial …

BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models

HL Li, YH Pang, B Liu - Nucleic acids research, 2021 - academic.oup.com
In order to uncover the meanings of 'book of life', 155 different biological language models
(BLMs) for DNA, RNA and protein sequence analysis are discussed in this study, which are …

BioSeq-Analysis2. 0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning …

B Liu, X Gao, H Zhang - Nucleic acids research, 2019 - academic.oup.com
As the first web server to analyze various biological sequences at sequence level based on
machine learning approaches, many powerful predictors in the field of computational …

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

B Liu, F Liu, X Wang, J Chen, L Fang… - Nucleic acids …, 2015 - academic.oup.com
With the avalanche of biological sequences generated in the post-genomic age, one of the
most challenging problems in computational biology is how to effectively formulate the …

BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches

B Liu - Briefings in bioinformatics, 2019 - academic.oup.com
With the avalanche of biological sequences generated in the post-genomic age, one of the
most challenging problems is how to computationally analyze their structures and functions …

iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC

B Liu, F Yang, DS Huang, KC Chou - Bioinformatics, 2018 - academic.oup.com
Motivation Being responsible for initiating transaction of a particular gene in genome,
promoter is a short region of DNA. Promoters have various types with different functions …

iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition

B Liu, L Fang, R Long, X Lan, KC Chou - Bioinformatics, 2016 - academic.oup.com
Motivation: Enhancers are of short regulatory DNA elements. They can be bound with
proteins (activators) to activate transcription of a gene, and hence play a critical role in …

iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition

W Chen, P Feng, H Ding, H Lin, KC Chou - Analytical biochemistry, 2015 - Elsevier
Occurring at adenine (A) with the consensus motif GAC, N 6-methyladenosine (m 6 A) is one
of the most abundant modifications in RNA, which plays very important roles in many …