[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 …

Macrophage clearance of apoptotic cells: a critical assessment

S Gordon, A Plüddemann - Frontiers in immunology, 2018 - frontiersin.org
As the body continues to grow and age, it becomes essential to maintain a balance between
living and dying cells. Macrophages and dendritic cells play a central role in discriminating …

Biosynthesis of medicinal tropane alkaloids in yeast

P Srinivasan, CD Smolke - Nature, 2020 - nature.com
Tropane alkaloids from nightshade plants are neurotransmitter inhibitors that are used for
treating neuromuscular disorders and are classified as essential medicines by the World …

[HTML][HTML] Multi-omic analysis reveals divergent molecular events in scarring and regenerative wound healing

S Mascharak, HE Talbott, M Januszyk, M Griffin… - Cell Stem Cell, 2022 - cell.com
Regeneration is the holy grail of tissue repair, but skin injury typically yields fibrotic, non-
functional scars. Developing pro-regenerative therapies requires rigorous understanding of …

Aquatic and terrestrial cyanobacteria produce methane

M Bižić, T Klintzsch, D Ionescu, MY Hindiyeh… - Science …, 2020 - science.org
Evidence is accumulating to challenge the paradigm that biogenic methanogenesis,
considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that …

The axolotl genome and the evolution of key tissue formation regulators

S Nowoshilow, S Schloissnig, JF Fei, A Dahl… - Nature, 2018 - nature.com
Salamanders serve as important tetrapod models for developmental, regeneration and
evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma …

Evolutionarily divergent mTOR remodels translatome for tissue regeneration

O Zhulyn, HD Rosenblatt, L Shokat, S Dai… - Nature, 2023 - nature.com
An outstanding mystery in biology is why some species, such as the axolotl, can regenerate
tissues whereas mammals cannot. Here, we demonstrate that rapid activation of protein …

[HTML][HTML] Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution

ND Leigh, GS Dunlap, K Johnson, R Mariano… - Nature …, 2018 - nature.com
Regeneration of complex multi-tissue structures, such as limbs, requires the coordinated
effort of multiple cell types. In axolotl limb regeneration, the wound epidermis and blastema …

The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci

S Schloissnig, A Kawaguchi… - Proceedings of the …, 2021 - National Acad Sciences
Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in
genome size. How chromosomal organization scales with genome expansion is unclear …

[HTML][HTML] Annelid functional genomics reveal the origins of bilaterian life cycles

FM Martín-Zamora, Y Liang, K Guynes… - Nature, 2023 - nature.com
Indirect development with an intermediate larva exists in all major animal lineages, which
makes larvae central to most scenarios of animal evolution,,,,,,,,–. Yet how larvae evolved …