As part of RIKEN's reorganisation that took effect on April 1st, 2018, the Genomics Miniaturisation Technology Unit was dissolved.
On February 17th ,Charles Plessy gave a lecture on reproducible and open science at the 7th Karolinska Institutet - RIKEN Joint International Doctoral Course on bioinformatics analysis of gene regulation in omics data and its applications to medical problems in Yokohama, Japan.
On February 12th, Charles Plessy gave a talk on parallel epigenome and promotome analysis in single cells at the KAUST Research Conference on environmental epigenetics 2017, in King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
Some of the ATAC-seq data presented is already open prior publication.
On December 5th Charles Plessy gave a talk on transcriptomme analysis, from bulk to single cells and single molecules at the Okinawa Institute for Science and Technology (OIST), in Okinawa, Japan.
We are happy to welcome Simon Besson-Girard, a student of the University of Lyon, France, who visits us to analyse our single-cell data.
Today, our single-cell CAGE protocol for the Fluidigm C1 system was released on the maker's ScriptHub page. Of course, we also plan to release this work as a peer-reviewed article later. A pilot analysis of preview data is also available on GitHub.
Our work on pseudo-random primers is completed, and our manuscript is submitted to a peer-reviewed journal. You can already read our preprint on bioRxiv.
At the Single Cell Genomics conference that took place in Utrecht from September 16 to 18, Michael Böttcher and Mickaël Mendez presented our work on Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells and Cell-cycle classification at the single-cell level with Random Forest respectively. Here is a link to the abstract book in PDF format (posters P008 and P058). These works are related to the data that we released in DDBJ, GitHub and Dryad recently.
We released our tool called
This tool converts paired-end data from the BAM to the BED12 format, and is
especially useful to proces CAGEscan data before
displaying it on the Zenbu browser. See
for more details.
In order to classify single-cell transcriptomes by cell cycle phases, we produced a reference data set comprising more than 200 single-cell RNA-seq libraries, together with cell cycle information for each cell. While our analysis is ongoing, we are releasing prior publication some documentation on this data on GitHub. Pull requests are welcome !
We are happy to welcome Iris Bian, a student of the University of Toronto, Canada, who visits us to explore the Nanpore technology with us.
We will be presenting multiple posters on our single-cell research at the The 11th International Workshop on Advanced Genomics on May 21th. See you there !
We are happy to welcome Elo Madissoon, a Ph. D. student of the Karolinska Institute, Stockholm, who visits us to analyse single cells transcriptomes.
On December 16th Charles Plessy gave a talk about single-cell markers of the cell cycle at the 2nd UK / Japan workshop on Neural Epigenetics and Transcription in the University College London.
On December 9th Michael Böttcher, from the Transciptome Technology Team, gave a talk on our joint work on cell cycle profiling at single-cell resolution with Fucci cells at the Cold Spring Harbor Asia conference on single cells, in Suzhou, China.
On November 14th Charles Plessy gave a lecture on single-cell transcriptome analysis at the HPCI seminar 2014 (High Performance Computing Infrastructure) at the CBRC (Computational Biology Research Center), in Ôdaiba, Tôkyô.
We are happy to welcome Marjan Biocanin, from the University of Belgrade, who joins us as intern to study single cells transcriptomics.
Congratulations to the authors of the Zenbu browser, published this night in Nature Biotechnology! Zenbu is the best browser to display CAGE data, and we use it intensively, for instance in the two following illustrations derived from our manuscripts published or under revision.
On February 25th Charles Plessy gave a lecture on non-translated RNAs at the Karolinska Institutet - RIKEN Joint International Doctoral Course 2014 on Employing genome-wide technologies for functional regulation in development and disease, in Stockholm.
We are happy to welcome Lucie Pougnault, who joins us as visiting student to train herself on the transcriptomics of single cells.
We are happy to welcome Ophélie Arnaud, who joins us as post-doctoral researcher to study the transcriptome of single cells.
We are happy to welcome Stéphane Poulain, who joins us as research scientist to study the transcriptome of single cells.
We are happy to welcome Dennis Grishin, a student from the university of Freiburg, who is joining us until February 2014 to work on microfluidics devices for single-cell transcriptomics.
Today Charles Plessy presented at the 2013 conference of the European Chemoreception Organisation (ECRO 2013) the nanoCAGE analysis of the mouse olfactory receptors that was published last year in Genome Research.
We are very honored to reveive a research grant from the Japanese Society for the Promotion of Science to Charles Plessy, for studying the cell cycle and cellular differenciation using population transcriptomics.