751 citations · 3.2k across the 102 of their papers we have counts for
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Temporal epistasis inference from more than 3,500,000 SARS-CoV-2 Genomic Sequences
Hong-Li Zeng, Yue Liu, Vito Dichio +1
We use Direct Coupling Analysis (DCA) to determine epistatic interactions between loci of variability of the SARS-CoV-2 virus, segmenting genomes by month of sampling. We use full-…
An observation of circular RNAs in bacterial RNA-seq data
Nicolas Innocenti, Hoang-Son Nguyen, Aymeric Fouquier d'hérouël +1
Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea.…
The Bulk and The Tail of Minimal Absent Words in Genome Sequences
Erik Aurell, Nicolas Innocenti, Hai-Jun-Zhou
Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribut…
Whole genome mapping of 5' RNA ends in bacteria by tagged sequencing : A comprehensive view in Enterococcus faecalis
Nicolas Innocenti, Monica Golumbeanu, Aymeric Fouquier d'Hérouël +8
Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first comprehensive view of transcriptional organizations in this bacterium, we used a modified RNA…
SEK: Sparsity exploiting -mer-based estimation of bacterial community composition
Saikat Chatterjee, David Koslicki, Siyuan Dong +8
Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. Since the sample sequence data…
Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends
Nicolas Innocenti, Erik Aurell
High-throughput transcriptomics experiments have reached the stage where the count of the number of reads alignable to a given position can be treated as an almost-continuous signa…