[HTML][HTML] Computational biology helps understand how polyploid giant cancer cells drive tumor success

MC Casotti, DD Meira, ASS Zetum, BC Araújo… - Genes, 2023 - mdpi.com
Precision and organization govern the cell cycle, ensuring normal proliferation. However,
some cells may undergo abnormal cell divisions (neosis) or variations of mitotic cycles …

Genome sequence assembly algorithms and misassembly identification methods

Y Meng, Y Lei, J Gao, Y Liu, E Ma, Y Ding, Y Bian… - Molecular biology …, 2022 - Springer
The sequence assembly algorithms have rapidly evolved with the vigorous growth of
genome sequencing technology over the past two decades. Assembly mainly uses the …

[HTML][HTML] Comparing de novo transcriptome assembly tools in di-and autotetraploid non-model plant species

S Madritsch, A Burg, EM Sehr - BMC bioinformatics, 2021 - Springer
Background Polyploidy is very common in plants and can be seen as one of the key drivers
in the domestication of crops and the establishment of important agronomic traits. It can be …

Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of …

L Zhang, J He, H He, J Wu, M Li - Horticulture research, 2021 - academic.oup.com
Raphanobrassica (R r R r C r C r, 2n= 4x= 36), which is generated by distant hybridization
between the maternal parent Raphanus sativus (R s R s, 2n= 2x= 18) and the paternal …

[HTML][HTML] Design, execution, and interpretation of plant RNA-seq analyses

RN Upton, FH Correr, J Lile, GL Reynolds… - Frontiers in Plant …, 2023 - frontiersin.org
Genomics has transformed our understanding of the genetic architecture of traits and the
genetic variation present in plants. Here, we present a review of how RNA-seq can be …

Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids

G Hu, CE Grover, MA Arick, M Liu… - Briefings in …, 2021 - academic.oup.com
Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of
duplicated genomes, polyploids offer unique challenges for estimating gene expression …

De novo assembly and annotation of the transcriptome of the endangered seagrass Zostera capensis: Insights from differential gene expression under thermal stress

A Ndhlovu, S von der Heyden - Marine Genomics, 2022 - Elsevier
Seagrasses are important marine ecosystem engineers but anthropogenic impacts and
climate change have led to numerous population declines globally. In South Africa, Zostera …

[PDF][PDF] Plant transcriptome assembly: review and benchmarking

S Behera, A Voshall - Bioinformatics, 2022 - par.nsf.gov
Transcriptome assembly using next-generation sequencing data is an important step in a
wide range of biological studies at the molecular level. The quality of computationally …

Elevated temperatures reduce population‐specific transcriptional plasticity in developing lake sturgeon (Acipenser fulvescens)

WS Bugg, MJ Thorstensen, KE Marshall… - Molecular …, 2023 - Wiley Online Library
Rising mean and variance in temperatures elevates threats to endangered freshwater
species such as lake sturgeon, Acipenser fulvescens. Previous research demonstrated that …

Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish

MJ Thorstensen, AM Weinrauch, WS Bugg… - Database, 2023 - academic.oup.com
The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with
conservation challenges across its range in North America, but a lack of genomic resources …