Author

Alice Cleynen

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Aug 2026

TagGen: High-Performance Barcode Generator and Demultiplexer for High-Throughput and Long-Read Sequencing Applications

Background Long-read sequencing platforms, particularly Oxford Nanopore Technologies (ONT), have transformed transcriptomics through direct RNA sequencing. However, their higher error rates – dominated by insertions and deletions – demand longer, more robust sequence barcodes. Existing barcode generation tools suffer...

F. Chowdhury, Tessa Swain, Roderik Shirokikh et al. · F1000Research · 0 citations

#protein folding Preprint Sep 2026

Pathways of early evolution from the perspectives of a riboreplisome -- the ultimate RNA machine of life

It is proposed that early replication and protein biosynthesis were inseparable functions performed by a single ancient RNA molecule: the riboreplisome, and this hypothesis addresses fundamental challenges facing RNA world, protein world, and RNA-protein co-evolution theories.

Alice Cleynen, Archa H. Fox, Nikolay E. Shirokikh · 0 citations

Open access Jul 2026

Multi-omic dissection of RNA control reveals convergent cis-regulatory programs during glucose starvation in yeast

It is shown that the repressed glycosylation program is distinguished by a convergent stack of independent cis-regulatory signatures: weak Kozak initiation context, high upstream open reading frame burden, excess RNA secondary structure specifically over the start codon, and depletion for the targets of major stabilisi...

O. Rossini, S. Mahmud, Nikolay E. Shirokikh et al. · bioRxiv · 0 citations