CV en ligne.

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+My training as a researcher started with developmental genetics in
+drosophila and zebrafish, where I studied the activity of
+transcription enhancers (Blader et al., 2003) 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).
+
+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
+artefacts and unwanted sequences generated by ribosomal RNAs using
+low-complexity “pseudo-random” reverse-transcription primers (Arnaud
+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
+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
+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).
+
+I have complemented my work on CAGE with the development of a
+gene-centred technique for detecting promoters, termed Deep-RACE
+(Olivarius et al., 2009, Plessy et al., 2012), which we used to
+validate our discovery of the pervasive expression of retrotransposons
+detected by CAGE (Faulkner et al., 2009). To study transcription start
+activity at nucleotide resolution in zebrafish transfected with
+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.
+
+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),
+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
+(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.
+
+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
+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
+B3443334. My ORCID ID is 0000-0001-7410-6295.