From: Charles Plessy Date: Mon, 15 Jun 2020 07:53:33 +0000 (+0900) Subject: Liens X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=5f42abaaf30f0b53a2a9e4fcf5b77f4effccee0e;p=source.git Liens --- diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn index 1e386c0d..80ab04d2 100644 --- a/open-source-biologist.mdwn +++ b/open-source-biologist.mdwn @@ -1,29 +1,30 @@ Charles Plessy, open-source biologist ------------------------------------- -My training as a researcher started with **developmental genetics in -drosophila and zebrafish**, where I studied the activity of -transcription enhancers ([Blader and coll., -2003](https://pubmed.gov/12559493)) and their evolutionary -conservation (Plessy et al., 2005). This gave me a strong interest for -whole-transcriptome analysis and technology. For that purpose, I have -joined RIKEN in 2004, where have worked on high-throughput methods for -**profiling promoters and inferring gene networks**, and in particular on -CAGE (Cap Analysis Gene Expression). +My training as a researcher started with **developmental genetics in drosophila +and zebrafish**, where I studied the activity of transcription enhancers +([Blader and coll., 2003](https://pubmed.gov/12559493)) and their evolutionary +conservation ([Plessy and coll., 2005](https://pubmed.gov/15797614)). This gave +me a strong interest for whole-transcriptome analysis and technology. For that +purpose, I have joined RIKEN in 2004, where have worked on high-throughput +methods for **profiling promoters and inferring gene networks**, and in +particular on CAGE (Cap Analysis Gene Expression). I have developed a miniaturized version of CAGE, termed **nanoCAGE**, to -analyse small samples yielding only nanograms of RNA (Plessy et al., -2010). In the same manuscript, we also introduced its paired-end -variant, **CAGEscan**, which we use to **associate novel promoters with -annotations**. Since then, we have kept improving or expanding these -techniques, by updating the protocol (Salimullah et al., 2011), -reducing the sequence bias introduced by the molecular barcodes (Tang -et al., 2013), combining multiple cap-enrichment steps (Batut et al., -2013), benchmarking the use of locked nucleic acids for template -switching (Harbers et al., 2013), and reducing the number of primer +analyse small samples yielding only nanograms of RNA ([Plessy and coll., +2010](https://pubmed.gov/20543846)). In the same manuscript, we also introduced +its paired-end variant, **CAGEscan**, which we use to **associate novel +promoters with annotations**. Since then, we have kept improving or expanding +these techniques, by updating the protocol ([Salimullah and coll., +2011](https://pubmed.gov/21205859)), reducing the sequence bias introduced by +the molecular barcodes ([Tang and coll., 2013](https://pubmed.gov/23180801)), +combining multiple cap-enrichment steps ([Batut and coll., +2013](https://pubmed.gov/22936248)), benchmarking the use of locked nucleic +acids for template switching ([Harbers and coll., +2013](https://pubmed.gov/24079827)), and reducing the number of primer artefacts and unwanted sequences generated by ribosomal RNAs using -low-complexity “pseudo-random” reverse-transcription primers (Arnaud -et al., 2016). +low-complexity “pseudo-random” reverse-transcription primers ([Arnaud and +coll., 2016](https://pubmed.gov/27071605)). On April 2013, I started a new development cycle as the leader of the Genomics Miniaturization Technology Unit at RIKEN Center for Life