We are proud to communicate that RNA Structure Framework has been completely rewritten, and that version 1.0.0alpha is available for download.

New features include: - Full multi-threads support - Added Rouskin et al., 2014 method for data normalization - Added ViennaRNA package 2.2.0 support for soft-constraints

Our article “RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data“ has been published on Bioinformatics.

Check it out: http://goo.gl/TWC7ah

RSF is available at: http://rsf.hugef-research.org

Our editorial “DNA methylation and demethylation dynamics“ has been published on Oncotarget.

Check it out: http://goo.gl/0vTAL9

Our article “TET1 is controlled by pluripotency-associated factors in ESCs and downmodulated by PRC2 in differentiated cells and tissues“ has been published on Nucleic Acids Research.

In the last decade, genome-wide approaches have become key tools toward the comprehension of genome’s structure and gene regulation. With the advent of high-throughput sequencing technologies, the amount of today available genome-wide data is impressive, and constantly growing, but this growth is not efficiently counterbalanced by efficient data analysis.

Given the success of the first edition, Next Generation Intelligence and the Human Genetics Foundation (HuGeF), with the support of the University of Torino and Illumina, are proud to announce the second edition of the EpigeneticSeq Workshop 2015, a beginners practical course on ChIP-Seq and Bisulfite-Seq data analysis, and their integration with RNA-Seq data.

For more informations:

http://epigeneticseq.hugef-research.org

or write an e-mail to:

Our drawing's on the February 10th issue of Cell Reports!

Check it out: http://goo.gl/5c7QxY

Our article "Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics" has been published on Cell Reports.

Check it out: http://goo.gl/5351BC

Our article "TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway" has been published on Oncogene.

Check it out: http://goo.gl/xBndbT

Our article "Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome" has been published on Genome Biology.

Check it out: http://goo.gl/9rq9VF

Our article “High-throughput single nucleotide variants discovery in E14 mouse embryonic stem cells provides a new reference genome assembly" has been published on Genomics.

Check it out: http://goo.gl/v0uGV0

The Greenleaf group at Stanford has "repurposed" the Illumina sequencer to quantitatively measures protein binding to over 10 million RNA targets on the Illumina flow cell surface. This assay gives the ability to perform ultra-high-throughput & quantitative measurement on RNA-protein interactions. The team also developed methods to analyze the images from sequencing reactions to measure equilibrium binding constants and dissociation kinetics.

In the last decade, genome-wide approaches have become key tools toward the comprehension of genome's structure and gene regulation. With the advent of high-throughput sequencing technologies, the amount of today available genome-wide data is impressive, and constantly growing, but this growth is not efficiently counterbalanced by efficient data analysis.

In this perspective, Next Generation Intelligence and the Human Genetics Foundation (HuGeF), with the support of the University of Torino and Illumina, are proud to announce the first edition of the EpigeneticSeq Workshop 2014, a beginners practical course on ChIP-Seq and Bisulfite-Seq data analysis, and their integration with RNA-Seq data.

For more informations:

http://epigeneticseq.hugef-research.org

or write an e-mail to:

Our article “Myc and Max Genome-Wide Binding Sites Analysis Links the Myc Regulatory Network with the Polycomb and the Core Pluripotency Networks in Mouse Embryonic Stem Cells" has been published on PLoS ONE.

Check it out: http://goo.gl/TSqSo1

Yesterday, we participated to an amazing seminar on "Single Molecule Real-Time DNA Sequencing" by Dr. Stephen Turner, Founder and CTO at Pacific Biosciences.

PacBio SMRT technology enables high-throughput sequencing of single molecules with really reduced costs and increased information compared to standard Sanger-based sequencing approaches (~20k long reads on average). It's useless to explain how this method will improve tasks such as:

De novo assembly of genomes

Transcripts/isoforms discovery

Assembly of complex regions (e.g. Major Histocompatibility Complex)

Finding Methylation Patterns and other Genome Modification (e.g. 5mC, 5hmC, m6A, etc.)

Our article "Dnmt3L Antagonizes DNA Methylation at Bivalent Promoters and Favors DNA Methylation at Gene Bodies in ESCs" has been published on Cell.

Check it out: http://t.co/PeRsbnuVEN

Graphical abstract

Our article "Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells" has been published on Genome Biology.

Check it out: http://goo.gl/9d2RPy

Our article "MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets" has been published on Nucleic Acids Research.

Check it out: http://goo.gl/hajNQA