From 874d2d6ecd42cf26098502cc686ec87faf9cdd17 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Mon, 15 Jun 2020 16:48:13 +0900 Subject: [PATCH] Bold --- open-source-biologist.mdwn | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn index 86511230..1e386c0d 100644 --- a/open-source-biologist.mdwn +++ b/open-source-biologist.mdwn @@ -1,21 +1,21 @@ Charles Plessy, open-source biologist ------------------------------------- -My training as a researcher started with developmental genetics in -drosophila and zebrafish, where I studied the activity of +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 +**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 +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 +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., @@ -28,10 +28,10 @@ et al., 2016). 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 Genomics Technology, to expand this work on -single cells following a population transcriptomics approach (Plessy +single cells following a **population transcriptomics** approach (Plessy et al., 2013) focused on sampling the largest possible number of -cells. In our ongoing developments, we have reached single-cell and -single molecule resolution through the introduction of transposase +cells. In our ongoing developments, we have reached **single-cell and +single molecule resolution** through the introduction of transposase fragmentation and unique molecular identifiers (Poulain et al., 2017). The protocol exists in two versions, one for FACS-isolated cells, and one for the Fluidigm C1 platform (Kouno et al., 2019). @@ -46,27 +46,27 @@ chimeric transgenes containing a copy of an endogenous promoter, I combined Deep-RACE, CAGE and paired-end sequencing in a technology that we called “Single-Locus CAGE” (Haberle et al., 2014). With my contributions related to CAGE development and analysis, I have been a -member of the FANTOM consortium since FANTOM3. +**member of the FANTOM consortium** since FANTOM3. Together with my colleagues at RIKEN and collaborators in the field of neuroscience, I have applied nanoCAGE to the study of single neuron -cell types, for instance the olfactory neurons (Plessy et al., 2012), +cell types, for instance the **olfactory neurons** (Plessy et al., 2012), or in dopaminergic cells, where we could demonstrate the expression of haemoglobin in the midbrain (Biagioli et al., 2009). We are also -exploring the sub-cellular localisation of RNA in Purkinje neurons +exploring the sub-cellular localisation of RNA in **Purkinje neurons** (Kratz et al., 2014), 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. +repertoire of the **T cell antigen receptors**. -I joined OIST in 2018, to study the genetic structure and population -variations of an animal plankton, Oikopleura dioica, that has a genome +I joined OIST in 2018, to study **the genetic structure and population +variations** of an animal plankton, Oikopleura dioica, that has a genome 50 time more compact than the human one, which empowers us to sequence at chromosomal resolution many individual sampled from all over the World. -I am also a Free Software enthusiast, and contribute to the Debian Med -project, by packaging bioinformatics tools, which are redistributed in +I am also a **Free Software** enthusiast, and contribute to the Debian Med +project, by **packaging bioinformatics tools**, which are redistributed in Debian (Möller et al., 2010) and its derivatives such as Ubuntu and (cloud)Bio-Linux. For digital signature of my contributions and other activities as a RIKEN researcher, I use the GPG key number -- 2.47.3