Clustering and classification methods for single-cell RNA-sequencing data

R Qi, A Ma, Q Ma, Q Zou - Briefings in bioinformatics, 2020 - academic.oup.com
Appropriate ways to measure the similarity between single-cell RNA-sequencing (scRNA-
seq) data are ubiquitous in bioinformatics, but using single clustering or classification …

Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting

C Solís-Lemus, C Ané - PLoS genetics, 2016 - journals.plos.org
Phylogenetic networks are necessary to represent the tree of life expanded by edges to
represent events such as horizontal gene transfers, hybridizations or gene flow. Not all …

A random forest sub-Golgi protein classifier optimized via dipeptide and amino acid composition features

Z Lv, S Jin, H Ding, Q Zou - Frontiers in bioengineering and …, 2019 - frontiersin.org
To gain insight into the malfunction of the Golgi apparatus and its relationship to various
genetic and neurodegenerative diseases, the identification of sub-Golgi proteins, both cis …

Inconsistency of species tree methods under gene flow

C Solís-Lemus, M Yang, C Ané - Systematic biology, 2016 - academic.oup.com
Coalescent-based methods are now broadly used to infer evolutionary relationships
between groups of organisms under the assumption that incomplete lineage sorting (ILS) is …

A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data

R Qi, J Wu, F Guo, L Xu, Q Zou - Briefings in Bioinformatics, 2021 - academic.oup.com
Single-cell RNA-sequencing (scRNA-seq) data widely exist in bioinformatics. It is crucial to
devise a distance metric for scRNA-seq data. Almost all existing clustering methods based …

Evaluation of the MGISEQ-2000 sequencing platform for Illumina target capture sequencing libraries

J Lang, R Zhu, X Sun, S Zhu, T Li, X Shi, Y Sun… - Frontiers in …, 2021 - frontiersin.org
Illumina is the leading sequencing platform in the next-generation sequencing (NGS) market
globally. In recent years, MGI Tech has presented a series of new sequencers, including …

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

E Gross, L van Iersel, R Janssen, M Jones… - Journal of Mathematical …, 2021 - Springer
Phylogenetic networks can represent evolutionary events that cannot be described by
phylogenetic trees. These networks are able to incorporate reticulate evolutionary events …

Statistical learning with phylogenetic network invariants

T Barton, E Gross, C Long, J Rusinko - arXiv preprint arXiv:2211.11919, 2022 - arxiv.org
Phylogenetic networks provide a means of describing the evolutionary history of sets of
species believed to have undergone hybridization or gene flow during their evolution. The …

Genetic Polymorphism Study on Aedes albopictus of Different Geographical Regions Based on DNA Barcoding

Y Fang, J Zhang, R Wu, B Xue… - BioMed Research …, 2018 - Wiley Online Library
Aedes albopictus is a very important vector for pathogens of many infectious diseases
including dengue fever. In this study, we explored the genetic polymorphism of Aedes …

Pathogenicity and Whole Genome Sequence Analysis of a Pseudorabies Virus Strain FJ‐2012 Isolated from Fujian, Southern China

X Wu, Q Chen, R Chen, Y Che, L Wang… - Canadian Journal of …, 2017 - Wiley Online Library
The outbreaks of pseudorabies have been frequently reported in Bartha‐K61‐vaccinated
farms in China since 2011. To study the pathogenicity and evolution of the circulating …