From: Charles Date: Mon, 2 Nov 2020 03:50:21 +0000 (+0900) Subject: More papers ! X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=b598684afe86f741cf85fe8fe2a1ed9195bbf74f;p=source%2F.git More papers ! --- diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn index 41a4ad95..a7cabb82 100644 --- a/open-source-biologist.mdwn +++ b/open-source-biologist.mdwn @@ -6,9 +6,9 @@ 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). +purpose, I have worked at RIKEN in 2004–18 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 and coll., @@ -21,13 +21,15 @@ 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 and -coll., 2016](https://pubmed.gov/27071605)). +2013](https://pubmed.gov/24079827)), reducing the number of primer artefacts +and unwanted sequences generated by ribosomal RNAs using low-complexity +“pseudo-random” reverse-transcription primers ([Arnaud and coll., +2016](https://pubmed.gov/27071605)), and screening for optimal parameters of +the template-switching reaction ([Poulain and coll., +2020](https://pubmed.gov/32025730)). -On April 2013, I started a new development cycle as the leader of the Genomics -Miniaturization Technology Unit at RIKEN Center for Life Sciences, Division of +In 2013–8, I lead a new development cycle at the Genomics +Miniaturization Technology Unit in RIKEN's Center for Life Sciences, Division of Genomics Technology, to expand this work on single cells following a **population transcriptomics** approach ([Plessy and coll., 2013](https://pubmed.gov/23281054)) focused on sampling the largest possible @@ -61,8 +63,10 @@ demonstrate the expression of haemoglobin in the midbrain ([Biagioli and coll., localisation of RNA in **Purkinje neurons** ([Kratz and coll., 2014](https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with -this promoter-centric work, I have also explored the huge repertoire of the **T -cell antigen receptors**. +this promoter-centric work, I have also explored the huge repertoire of the T +cell antigen receptors. I also applied the nanoCAGE technology to patient +samples infected with the human papillomavirus (HPV) ([Taguchi and coll., +2020](https://pubmed.gov/33093512)). I joined OIST in 2018, to study **the genetic structure and population variations** of an animal plankton, _Oikopleura dioica_, that has a genome