[PDF][PDF] A simple guide to de novo transcriptome assembly and annotation

V Raghavan, L Kraft, F Mesny… - Briefings in …, 2022 - academic.oup.com
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …

[HTML][HTML] Linking pollution and cancer in aquatic environments: A review

C Baines, A Lerebours, F Thomas, J Fort… - Environment …, 2021 - Elsevier
Due to the interconnectedness of aquatic ecosystems through the highly effective marine
and atmospheric transport routes, all aquatic ecosystems are potentially vulnerable to …

[HTML][HTML] Exploring pan-genomes: an overview of resources and tools for unraveling structure, function, and evolution of crop genes and genomes

S Naithani, CH Deng, SK Sahu, P Jaiswal - Biomolecules, 2023 - mdpi.com
The availability of multiple sequenced genomes from a single species made it possible to
explore intra-and inter-specific genomic comparisons at higher resolution and build clade …

Ten years of collaborative progress in the quest for orthologs

B Linard, I Ebersberger, SE McGlynn… - Molecular biology …, 2021 - academic.oup.com
Accurate determination of the evolutionary relationships between genes is a foundational
challenge in biology. Homology—evolutionary relatedness—is in many cases readily …

Why should we compare morphological and molecular disparity?

C Van Den Ende, MN Puttick… - Methods in Ecology …, 2023 - Wiley Online Library
Indices of morphological disparity seek to summarise the highly multivariate morphological
variation across groups of species within clades, time bins or other groups. Morphological …

The role of homology and orthology in the phylogenomic analysis of metazoan gene content

W Pett, M Adamski, M Adamska… - Molecular biology …, 2019 - academic.oup.com
Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin
of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan …

PlacentaCellEnrich: A tool to characterize gene sets using placenta cell-specific gene enrichment analysis

A Jain, G Tuteja - Placenta, 2021 - Elsevier
Abstract Single-cell RNA-Sequencing (scRNA-Seq) has improved our understanding of
individual cell types in the human placenta. However, placental scRNA-Seq data is not …

Assembling animals: trees, genomes, cells, and contrast to plants

J Paps, ME Rossi, AMC Bowles… - Frontiers in Ecology and …, 2023 - frontiersin.org
The Animal Kingdom is an astonishingly diverse group. Together with plants and fungi is
one of the three major lineages of multicellular eukaryotes. Due to anthropocentrism and/or …

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

VA Lyubetsky, LI Rubanov, MB Tereshina, AS Ivanova… - Biology Direct, 2023 - Springer
Background It is generally accepted that most evolutionary transformations at the phenotype
level are associated either with rearrangements of genomic regulatory elements, which …

[HTML][HTML] Ancestral sequence reconstruction-An underused approach to understand the evolution of gene function in plants?

F Scossa, AR Fernie - Computational and Structural Biotechnology Journal, 2021 - Elsevier
Whilst substantial research effort has been placed on understanding the interactions of plant
proteins with their molecular partners, relatively few studies in plants-by contrast to work in …