Publications by Ray Marcel Marin Florez

Genome Sequence of the Drosophila melanogaster Male-Killing Spiroplasma Strain MSRO Endosymbiont

Bruno Lemaitre, Ray Marcel Marin Florez, Jeremy Keith Herren, Juan Camilo Paredes Escobar

Spiroplasmas are helical and motile members of a cell wall-less eubacterial group called Mollicutes. Although all spiroplasmas are associated with arthropods, they exhibit great diversity with respect to both their modes of transmission and their effects o ...

American Society for Microbiology2015

Control of mitophagie by microRNAs - A key step of erythropoiesis

Didier Trono, Isabelle Barde, Sonia Verp, Andrea Corsinotti, Jiri Vanicek, Sandra Eloise Kjeldsen, Adamantia Kapopoulou, Ray Marcel Marin Florez, Benjamin Rauwel

Edp Sciences S A2014

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

Didier Trono, Isabelle Barde, Sonia Verp, Andrea Corsinotti, Jiri Vanicek, Sandra Eloise Kjeldsen, Adamantia Kapopoulou, Ray Marcel Marin Florez, Benjamin Rauwel

During hematopoiesis, lineage- and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. Here, we explored the role of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofa ...

American Association for the Advancement of Science2013

Searching the coding region for microRNA targets

Jiri Vanicek, Ray Marcel Marin Florez, Miroslav Sulc

Finding microRNA targets in the coding region is difficult due to the overwhelming signal encoding the amino acid sequence. Here, we introduce an algorithm (called PACCMIT-CDS) that finds potential microRNA targets within coding sequences by searching for ...

2013

Optimal use of conservation and accessibility filters in microRNA target prediction

Jiri Vanicek, Ray Marcel Marin Florez

It is generally accepted that filtering microRNA (miRNA) target predictions by conservation or by accessibility can reduce the false discovery rate. However, these two strategies are usually not exploited in a combined and flexible manner. Here, we introdu ...

Public Library of Science2012

Highly Specific Methods for the Prediction of Genes Regulated by MicroRNAs

Ray Marcel Marin Florez

MicroRNAs (miRNAs) comprise a large set of short noncoding RNAs that bind to messenger RNAs (mRNAs) to reduce their translation into functional proteins. Computational prediction of miRNA targets is the first stage in the discovery and validation of new re ...

EPFL2012

Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3'-end of the seed match

Franziska Voellmy, Thibaud Edouard Alistair von Erlach, Jiri Vanicek, Ray Marcel Marin Florez

To find out whether the AGO-miRNA complex is more sensitive to the accessibility of a particular region inside the seed match, we analyze in detail the accessibility of a wide set of miRNA binding sites validated by PAR-CLIP and HITS-CLIP experiments. Our ...

Cold Spring Harbor Lab Press, Publications Dept2012

Efficient use of accessibility in microRNA target prediction

Jiri Vanicek, Ray Marcel Marin Florez

Considering accessibility of the 3'UTR is believed to increase the precision of microRNA target predictions. We show that, contrary to common belief, ranking by the hybridization energy or by the sum of the opening and hybridization energies, used in curre ...

Oxford University Press2011