In collaboration with Bruno Lemaitre's Lab at the EPFL, we published our study examining the impact of genetic variation on gut immunocompetence in Drosophila, revealing that small genetic and molecular differences can result into overt physiological and organismal variation. This paper was covered in distinct press outlets (on-line, Swiss Radio, EPFL). Thanks to the entire team for letting this ambitious study come to live.
A warm welcome to three new postdoctoral associates who have recently joined our lab: Drs. Daniel Alpern (from IGBMC, Strasbourg, France), Wanze Chen (from Xiamen University, China), and Vincent Gardeux (from University of Arizona, USA). Also a big congrats to Michael and Roel for passing their respective one-year PhD exam.
In collaboration with the labs of Konrad Basler (UZürich) and Erik van Nimwegen (UBasel), we report in Genome Research the generation of about 600 UAS-transcription factor transgenic fly lines and report an intriguing link between bivalent chromatin and misexpression phenotypes in the wing.
We are very happy to welcome Riccardo Dainese, a new PhD student, as well as Julie Russeil, our new lab technician. But we also have to wave goodbye to our recently graduated student Irina Krier and our technician, Jean-Daniel Feuz, who was there from the start. We wish them both all the best in their next endeavors.
Building on our work published last year in Nature Methods, we report our efforts in building a transcription factor-specific proteotypic peptide database in Proteomics.
We congratulate Antonio (Meireles) and Rachana (Pradhan) for being awarded respectively a Marie-Curie Intra-European Fellowship and a Carigest Doctoral Scholarship.
Our comprehensive characterization of Drosophila Genetic Reference Panel genomic variation is published in Genome Research as part of a collaboration with the Mackay Lab (NCSU). All the data and analysis tools are available on the DGRP website.
Roel Bevers and Michael Frochaux are accepted to the EPFL-IBI Doctoral Program and will join our lab as PhD students, studying the impact of genomic variation on gut immunocompetence and aging. Big welcome to both!
Petra Schwalie was just informed that she received an HFSP Postdoctoral Fellowship, aiming to expand our venture in single cell gene expression analyses. Congrats Petra!
Our study, in collaboration with the labs of Profs. Manolis Dermitzakis (UGeneva), Alex Reymond and Nouria Hernandez (both UNIL), on the effects of sequence variation on chromatin structure and transcription is published in Science together with an insightful perspective. For a lay-summary, please click here. The paper has also been highlighted by Nature Reviews Genetics. As part of this study, our lab also developed a new computational tool to deal with low-complexity sites when identifiying allele-specific molecular events in ChIP-seq data. This tool was recently accepted in the Journal Bioinformatics and the respective paper is now online. In the meantime, you can find the tool here.
We published a perspective in Developmental Cell on an exciting Nature paper by the Lehner group, reporting a genome-wide map of natural sequence variants that affect the temporal expression dynamics of thousands of genes during development of Caenorhabditis elegans.
Molecular Systems Biology published our work on developing a cross-platform approach involving large-scale yeast one-hybrid and microfluidic assays to experimentally identify and characterize interactions between mouse transcription factors and regulatory elements at unprecedented resolution and throughput.
We wave goodbye to our postdocs Monica Albarca and Sunil Raghav and want to thank them for their great contributions. Monica has joined the sequencing platform at the University of Geneva, while Sunil will establish his own lab as a Ramalingaswami Fellow in Immuno-Genomics and Systems Biology at the Institute of Life Sciences in Orissa (India). Good luck both and thanks again!
After being awarded a FEBS fellowship, Petra learned that she also passed the bar for an EMBO fellowship, big congrats Petra!
Nature Methods has just published our describing our efforts to generate a multiplexed targeted proteomics pipeline to count transcription factors or other lowly abundant proteins during cellular differentiation, specifically adipogenesis. A big thanks to all involved, especially Jovan and Paola from our Lab, our EPFL and SIB collaborators Felix Naef, Benjamin Zoller, and Frédérique Lisacek, as well as all the people from the Proteomics Core Facility, in particular Marc Moniatte and Adrien Schmid. A news clip of the article can be found here and a news article in ProteoMonitor here.
We very much welcome Dr. Petra Schwalie in our Lab as a new postdoc. Petra is originally from Romania but studied in Germany and obtained her PhD at the European Bioinformatics Institute in Cambrdige (UK) supervised by Drs. Paul Flicek and Duncan Odom. She will work on the elucidation of gene regulatory networks underlying fat cell differentiation. Petra also just learned that she was awarded a FEBS long-term post-doctoral fellowship for this project, so big congrats!
Three collaborative projects were recently published: the first involving the Labs of Andy Oates and Sebastian Maerkl used microfluidics and yeast-based screening tools to generate a comprehensive model of the regulatory mechanisms underlying the zebrafish segmentation clock. This work was recently published in PLoS Biology and can be found stemming from our participation in the SystemsX-funded CycliX project and details our efforts to elucidate the dynamic changes of RNA pol II-mediated transcription and local histone modifications during the circadian clock. The third is a collaboration involving the Maerkl Lab focusing on the development of a new gene-centered, microfluidics-inspired protein-DNA interaction detection tool, iSLIM, as published in Nucleic Acids Research.
PLoS Genetics has just published our describing our efforts to map genomic variation in 40 of the Drosophila Genetic Reference Panel lines (DGRP) and to understand how these variants affect gene expression. A big thanks to all involved, especially Andreas and Sebastian from our Lab, as well our collaborators Trudy, Jeff, Eric, Julien, and Manolis.
We unfortunately have to bid farewell to two of the founding members of our Lab: Korneel Hens (postdoc) and Jovan Simicevic (PhD student). But they are off to good places! Korneel is setting up his own Lab at Oxford University and Jovan is starting a new adventure as a postdoc in the group of Peter Scheiffele as well as the Mass Spec Core Facility at the University of Basel. Good luck guys, and thanks for all the fish.
We very much welcome Dr. Paola Gilardoni in our Lab as a new postdoc. Paola is from Argentina but obtained her PhD at the Max Planck Institute in Jena. She will work on the elucidation of transcription factor function using targeted proteomics as part of a joint project with Felix Naef's Lab here at the EPFL. Paola also just learned that she was awarded an EMBO postdoctoral fellowship for this project, so big congrats!
Our article detailing our integrative genomics analyses of the co-repressor Nuclear receptor Co-Repressor 2 (NCoR2 or SMRT) during terminal fat cell differentiation has recently been published in Molecular Cell, congrats to Sunil, Sebastian and the entire lab team for their hard work and persistence! For a lay summary, please see here.
We published a Perspective "Variable Outcome of Mutations" in Science on the article of Ben Lehner's Group reporting that C. elegans worms that are mildly stressed show decreased sensitivity to certain deadly mutations at the cost of decreased fecundity.
Our article reporting the development of an automated yeast and microfluidics-based screening and mapping platform for Drosophila protein-DNA interactions has recently been published in Nature Methods, congrats Korneel! A News and Views Perspective on this Article can be found here.
Our paper describing our gene- and transcript-specific primer database GETPrime has recently been published in the new Journal “Database”, an Oxford Journal of Biological Databases and Curation. Congrats Carine! For a layman summary, please see here.
A book volume on gene regulatory networks that we edited in the Methods in Molecular Biology series together with Dr. Nele Gheldof has recently come on-line. Sunil and Korneel also contributed two chapters describing respectively how to perform bar code-based multiplex Solexa sequencing and large-scale yeast one-hybrid assays.
A warm welcome to our new PhD student Sebastian Waszak, who performed his Master's thesis in Prof. Lancet's group at the Weizmann Institute in collaboration with Prof. Korbel's group at the EMBL, working on a new computational method to detect locus copy-number genotypes in humans. This work has recently been published in PLoS Computational Biology. Congrats Sebastian and welcome again!
Yet another congrats to Korneel, who took away "best poster" award at EMBO 2010 in the "Molecular Systems Biology" category for his work aimed at elucidating the gene regulatory networks underlying insulin-like peptide gene expression. In addition, Carine's poster was among the finalists in the same category, so we're a happy bunch!
Our paper describing our PrInSeS-G algorithm to detect and assemble structural variants in genomes has recently been published in Nature Methods.
Our paper describing the WebPrInSeS platform for automated full-length clone identification and characterization using high-throughput sequencing data has recently been published in Nucleic Acids Research.
Congrats to LSBG member Korneel, who received the "best presentation" award at the 2010 Swiss Fly meeting for his talk "Tools and resources for the systematic study of Drosophila gene regulatory networks".
A warm welcome to Monica Albarca, who is joining us as a post-doctoral fellow. Monica recently obtained her Ph.D. in the Lab of Prof. Winship Herr at the University of Lausanne and will now work on elucidating transcriptional networks underlying wing development in Drosophila.
The EPFL iGEM received a Gold Medal and a Special Prize for the "Best new BioBrick or Device, Engineered". See the iGEM results page for more info.
A warm welcome this time to Irina Krier, who is joining us as a Ph.D. student co-supervised by Prof. Ruth Luthi-Carter. Irina obtained a M.Sc. in Biological Engineering at the School of Life Sciences at the EPFL having performed her Master's thesis in the group of Prof. Jörg Stelling at the ETHZ. As such, she is ideally positioned to use her computation skills to thermodynamically model mammalian gene regulatory networks.
The SNF has announced that it will provide funding for a Sinergia project headed by our lab together with the Basler (UZürich)and van Nimwegen (UBasel) Labs to study the gene regulatory networks underlying post-embronic fly development.
SystemsX.ch has announced that it will provide funding for the Cyclix project. This project will bring together labs from the Centre for Integrative Genomics (CIG), the University of Geneva, the Swiss Institute of Bioinformatics, and the EPFL including our lab and aims to achieve a comprehensive and quantitative understanding of the "core" regulatory network which assures proper integration and coordination among the three mammalian cycling systems: the cell cycle, the circadian cycle, and the nutrient cycle.
A warm welcome this time to Céline Riera and Sunil Raghav, who have recently joined the group as post-doctoral fellows. Céline is an EPFL graduate, who performed her doctoral research at Nestlé, leading to several peer-reviewed first author publications. Sunil performed postdoctoral work at the Biotechnology Centre of Turku, Finland, where he acquired expertise in the application of ChIP-seq technologies.
A warm welcome this time to Carine Gubelmann and Alina Isakova, who have recently joined the group as Ph.D. students. Carine was part of the first group of students who obtained a M.Sc. in Biological Engineering at the School of Life Sciences at the EPFL. As such, she is ideally positioned to study and model mammalian gene regulatory networks underlying cell differentiation. Alina obtained a M.Sc. in Molecular Biophysics at the V.N.Karazin Kharkiv National University in Ukraine. Alina will use her expertise to examine the impact of protein interactions on transcription factor DNA specificity and affinity using structural modeling tools as well as microfluidics-based devices in collaboration with the Dal Peraro and Maerkl Labs at the EPFL.
A warm welcome to Jovan Simicevic,who has recently joined the group as a Ph.D. student. Jovan has a multi-disciplinary background, having obtained a Bachelor's Degree in Economics at the UNIL and Master's Degrees in both Statistics (SDU) and Proteomics and Bioinformatics (UGeneva). Jovan will use his expertise to engineer novel technologies to detect protein-DNA interactions in vivo. In addition, he will explore the emerging field of Genetical Genomics to reverse engineer gene regulatory networks.
A warm welcome to Korneel Hens, who has recently joined the group as a postdoctoral fellow. Korneel will study the gene regulatory networks underlying neuroblast differentiation in Drosophila, a project which will be conducted in collaboration with Prof. Patrick Callaert's group at the Flemish Institute of Biotechnology at the University of Leuven, Belgium.