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.,
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).
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
projects / source.git / commitdiff