The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.

Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

Homepage: http://www.unice.fr/c3m/EN/Equipe10.html

mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS reliably identified the strains, their numbers and their abundance. Compared with three tools, mixtureS showed better performance in almost all simulated datasets and the vast majority of experimental datasets.

Address of the bookmark: http://www.cs.ucf.edu/~xiaoman/mixtureS/

Address of the bookmark: http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

De Bruijn Graphs for NGS Assembly
Algorithms for PacBio Reads
Software and Hardware Concepts for Bioinformatics
Finding us in Homolog.us (Search Algorithms)
NGS Genome and RNAseq Assembly - a Hands on Primer
Introduction to PERL, Python, R and C/C++ for Bioinformatics

Address of the bookmark: http://www.homolog.us/Tutorials/

1. Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
2. Co-assembly of a large number of metagenomes via merging of individual metagenomes
3. Includes binning and bin checking, for retrieving individual genomes
4. The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
5. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
6. Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

August1-2, 2014

Organised By

Centre of Excellence in Bioinformatics
Bioinformatics Infrastructure Facility
Department of Biochemistry
University of Lucknow
Lucknow-226007

Course Contents

Molecular Modeling
Homology Modeling
Molecular Docking
Post-structural Analyses

Molecular Dynamics (MD)
Simulation
Linux Introduction
Gromacs Installation

MD Simulation of Protein ligand complex
Analyses of MD
Trajectories
Visualization of Dynamic
complexes

Important Dates

Registration Begins June 25, 2014
Registration Closes July 25, 2014

Brochure : www.lkouniv.ac.in/conference/Brochure_August,%202014.pdf

HECIL’s core algorithm by introducing an iterative learning paradigm that enhances the correction policy at each iteration by incorporating knowledge gathered from previous iterations via data-driven confidence metrics assigned to prior corrections.

Address of the bookmark: https://github.com/NDBL/HECIL

Reference

Cuccuru G1, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, Fotia G. (2014) Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics [Epub ahead of print]. [article]

Address of the bookmark: http://orione.crs4.it/

BEAR is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads with read lengths, quality scores, error profiles, and species abundances derived from real user-supplied WGS data.

Address of the bookmark: https://github.com/sej917/BEAR

Most people who have a balanced translocation have the right amount of chromosome material but it has been rearranged in some way. This may happen if two chromosomes swap pieces (a reciprocal translocation). In other cases two whole chromosomes may become stuck together (a Robertsonian translocation). This page describes what happens when someone has a reciprocal translocation.

Reciprocal chromosomal translocations occur following double-strand breaks (DSBs) in DNA when a section of one chromosome is exchanged with that of another, non-homologous chromosome. These exchanges may produce a dysfunctional fusion gene that disrupts cell growth and survival pathways, such as the translocations seen in leukemia and childhood sarcomas.

Chromosomal translocations have been well studied in cancer cell lines which are associated with two types of cancer, acute myeloid leukemia and Ewing's sarcoma, but determining how they contribute to cancer development is complicated by additional mutations and altered gene expression profiles in these cultured cells. Now, Juan Carlos Ramirez, head of the Viral Vector Facility at the Fundacion Centro Nacional de Investigaciones Cardiovasculares (CNIC) and his colleagues Raul Torres at CNIC and Sandra Rodriguez-Peralez at the Spanish National Cancer Center (CNIO) in Madrid, Spain have used a new genome editing tool, CRISPR-Cas9, to induce chromosomal translocations for the first time in a human cell line and in primary cells. The study's authors conclude by stating that the use of this technology will allow for the clarification of how and why chromosomal translocation occurs, which without doubt will allow new anti-cancer therapeutic strategies to be tackled.

Using RNA-Guided Endonuclease (RGEN) technology or CRISPR/Cas9 genome engineering technology, CNIO and CNIC researchers have shown that it is possible to obtain such chromosomal translocations. The CRISPR-Cas9 system is extremely simple to introduce a cut at the desired locus, easier to design, and cheaper than many other systems. Using the CRISPR-Cas9 system, Ramirez and his colleagues reproduced the translocations observed in Ewing’s Sarcoma (ES) and Acute Myeloid Leukemia (AML) patient cell lines in HEK293 cells and also generated the ES translocation in human mesenchymal stem cells and the AML translocation in umbilical cord blood cells.

By focusing on chromosomal translocation without the confounding characteristics of established cell lines, these new cells lines should help answer the fundamental question of what causes a cell to become cancerous. Ramirez and his team now look forward to modeling other chromosome translocations in a variety of cell types.

Reference:

http://en.wikipedia.org/wiki/Chromosomal_translocation

http://www.nature.com/ncomms/2014/140603/ncomms4964/abs/ncomms4964.html