Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

S Bryce-Smith, D Burri, MR Gazzara, CJ Herrmann… - RNA, 2023 - rnajournal.cshlp.org
The tremendous rate with which data is generated and analysis methods emerge makes it
increasingly difficult to keep track of their domain of applicability, assumptions, limitations …

Regional patterning and regulation of melanin pigmentation in insects

A Popadić, D Tsitlakidou - Current Opinion in Genetics & Development, 2021 - Elsevier
Insects display an immense diversity in melanin pigmentation, which is generated by the
interplay between the regulatory genes (that provide general patterning information) and …

The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes

SS Ryazansky, C Chen, M Potters, AN Naumenko… - BMC biology, 2024 - Springer
Background Understanding genome organization and evolution is important for species
involved in transmission of human diseases, such as mosquitoes. Anophelinae and …

Screens in fly and beetle reveal vastly divergent gene sets required for developmental processes

MS Hakeemi, S Ansari, M Teuscher, M Weißkopf… - BMC biology, 2022 - Springer
Background Most of the known genes required for developmental processes have been
identified by genetic screens in a few well-studied model organisms, which have been …

Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network

IV Soluri, LM Zumerling, OA Payan Parra, EG Clark… - Elife, 2020 - elifesciences.org
Because chromatin determines whether information encoded in DNA is accessible to
transcription factors, dynamic chromatin states in development may constrain how gene …

Temporal control of RNAi reveals both robust and labile feedback loops in the segmentation clock of the red flour beetle

F Kaufholz, J Ulrich, MS Hakeemi… - Proceedings of the …, 2024 - National Acad Sciences
Animals from all major clades have evolved a segmented trunk, reflected in the human spine
or the insect segments. These units emerge during embryogenesis from a posterior segment …

Juxtapose: a gene-embedding approach for comparing co-expression networks

K Ovens, F Maleki, BF Eames, I McQuillan - BMC bioinformatics, 2021 - Springer
Background Gene co-expression networks (GCNs) are not easily comparable due to their
complex structure. In this paper, we propose a tool, Juxtapose, together with similarity …

Neofunctionalization driven by positive selection led to the retention of the loqs2 gene encoding an Aedes specific dsRNA binding protein

CF Estevez-Castro, MF Rodrigues, A Babarit… - BMC biology, 2024 - Springer
Background Mosquito borne viruses, such as dengue, Zika, yellow fever and Chikungunya,
cause millions of infections every year. These viruses are mostly transmitted by two urban …

[PDF][PDF] Identification of antennal alternative splicing by combining genome and full-length transcriptome analysis in Bactrocera dorsalis

Q Wang, J Zhang, C Liu, C Ru, Q Qian… - Frontiers in …, 2024 - researchgate.net
Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism and
enables the generation of structurally variable transcripts from a single gene (Verta and …

Improved methodology for fixation and preparation of Aedes aegypti embryos

W Reid, G Sterling-Lentsch, MS Halfon - Plos one, 2024 - journals.plos.org
The yellow fever mosquito Aedes aegypti is a major disease vector and an increasingly
popular emerging model research organism. We present here an improved protocol for the …