postdoc computational systems biology Luxemburg

Postdoctoral Fellow in Computational Systems Biology at the Luxembourg Centre for Systems Biomedicine in collaboration with the Black Family Stem Cell Institute of the Mount Sinai School of Medicine

http://www.nature.com/naturejobs/science/jobs/425291-postdoctoral-fellow-in-systems-biology

The Computational Biology Group seeks a highly skilled and motivated Postdotoral Fellow to work on an exciting project on the application of network biology approaches to study the role of gene expression stochasticity in cell fate commitment. In particular, the selected candidate shall develop a computational model that integrates transcriptomics and epigenomics data to describe heterogeneity in embryonic stem cells and its implication in differentiation. Single cell and cell perturbation experiments will be performed in order to validate the predictions generated by the model. This project will be carried out in collaboration with Profs. Ihor Lemischka and Kateri Moore at the Black Family Stem Cell Institute of the Mount Sinai School of Medicine. The selected applicant will have the opportunity to visit the experimental labs of our collaborators at the Mount Sinai School of Medicine.

Requirements of the ideal candidate:

• Ph.D. in Bioinformatics, Computer Science, Biology or a related discipline
• Strong computational skills
• Prior experience in mathematical modelling of biological networks, especially in network inference and analysis
• A strong first-author publication record in the fields of Bioinformatics and Computational Biology
• Excellent working knowledge in English.

We offer:

• Opportunity to do applied research to medical problems within a highly dynamic research institution (LCSB) and in collaboration with internationally recognized partners
• An exciting international environment
• A very competitive salary

For further information, please contact:

Prof. Dr. Antonio del Sol, Luxembourg Centre for Systems Biomedicine
E-mail: antonio.delsol@uni.lu

posdoc bioinformática/proteómica (Oxford)

Location:	Oxford, UK
Salary:	£29,837 to £36,661 discretionary range to £40,046 p.a.
Hours:	Full Time
Contract:	Contract / Temporary

Placed on:	20th May 2014
Closes:	13th June 2014
Job Ref:	113376

Sir William Dunn School of Pathology, South Parks Road, Oxford

The Central Proteomics Facility at the Sir William Dunn School of Pathology, University of Oxford is looking for an enthusiastic team member experienced in computational and statistical methods to provide bioinformatics support to researchers using proteomics (http://www.proteomics.ox.ac.uk).

The successful candidate will work collaboratively with existing bioinformaticians, facility staff and academic researchers. The position will cover two main roles. The first is to advise research scientists on statistically rigorous experimental design and data analysis procedures. The second is to maintain and expand the range of computational and statistical tools the facility uses for the analysis of proteomics data. 

You will have a degree in statistics, computing, bioinformatics or equivalent with considerable demonstrable practical experience. You should have strong communication and organisational skills, experience with analysing high dimensional datasets, statistical programming and experience with at least one scripting language. While it is desirable to have previous experience with proteomics and mass spectrometry data this is not essential as training will be provided.

The post is available as a fixed-term contract for 2 years in the first instance. If you are interested in this role, please apply online. You will be required to upload a CV and supporting statement as part of your online application. 

Interviews will be held during the week commencing 23 June 2014.

http://www.jobs.ac.uk/job/AIU252/postdoctoral-bioinformatician-biostatistician

Cuando Blastn no es Blastn

BLAST cambió hace ya algún tiempo a mejor con su versión BLAST+ pero por el camino se olvidó de algún detalle que puede confundir a más de uno.

El antiguo BLAST se ejecutaba con el comando 'blastall':

Blastall
--------

Blastall may be used to perform all five flavors of blast comparison. One
may obtain the blastall options by executing 'blastall -' (note the dash). A
typical use of blastall would be to perform a blastn search (nucl. vs. nucl.) 
of a file called QUERY would be:

blastall -p blastn -d nr -i QUERY -o out.QUERY

The output is placed into the output file out.QUERY and the search is performed
against the 'nr' database.  If a protein vs. protein search is desired,
then 'blastn' should be replaced with 'blastp' etc.

De esta forma un alineamiento de proteínas comenzaría como 'blastall -p blastp' y uno de ácidos nucleicos como 'blastall -p blastn' y si queremos usar MEGABLAST tenemos el comando diferente 'megablast'.

Sin embargo en la 'nueva' versión BLAST+, se separaron el alineamiento de proteínas y el de ácidos nucleicos en dos comandos: 'blastp' y 'blastn' (ver manual). Hasta aquí todo parece lógico y normal, lo que no todo el mundo sabe es que LA OPCIÓN POR DEFECTO DE BLASTN ES MEGABLAST, si ejecutamos 'blastn -help' encontraremos lo siguiente:

 *** General search options
 -task                 'megablast' 'rmblastn' >
   Task to execute
   Default = `megablast'

Y es que no todo el mundo está interesado en la velocidad de búsqueda de alineamientos, muchos de los que todavía usamos Blastn es porque apreciamos su gran sensibilidad para detectar alineamientos. En la actualidad usamos Blast para alinear miles de secuencias en tiempos muy razonables de minutos e incluso segundos. Para ganar velocidad en alineamientos de millones de secuencias existen otras mejores alternativas como Bowtie2.

La CONCLUSIÓN de todo esto, si usamos Blastn y nos interesa la sensibilidad deberemos ejecutarlo como:

 blastn -task blastn

Si lo hacemos sin añadir esta opción estaremos ejecutando MEGABLAST y correremos el peligro de perder una gran sensibilidad y no encontrar los alineamientos que deseamos. Por ejemplo, busquemos homología entre la 2'beta microglobulina humana (NM_004048.2) y la de ratón (NM_009735.3) usando la herramienta online de Blastn con las opciones por defecto ('Highly similar sequences (megablast)'):

Sin embargo si cambiamos la opción de búsqueda a 'Somewhat similar sequences (blastn)':

La diferencia es considerable, ¿no creéis? pasamos de no encontrar similaritud a un alineamiento con E-valor de 1.5E-56!!!!

2nd CNB Course on Introduction to Research

Hola,
pego un anuncio de un curso para estudiantes interesados en investigar que se realizará en Madrid del  30 de Junio al 25 de Julio en el Centro Nacional de Biotecnología-CSIC, que me parece puede ser una excelente oportunidad para algunos de los seguidores del blog. Los alumnos elegidos tendrán la oportunidad de interaccionar con investigadores de todas las áreas del centro, y en concreto en el departamento de Biología de Sistemas hay varios grupos con tradición en la formación en biología computacional.

Toda la información en http://tinyurl.com/lnqtmgp.
 
Un saludo,
Bruno

XII Jornadas de Bioinformática / XII Symposium on Bioinformatics

Hola,

hoy damos difusión a las pŕoximas Jornadas de Bioinformática, el mayor evento científico sobre biología computacional en España. Esta es la información que tengo de momento:

The XII Symposium on Bioinformatics (XII Jornadas de Bioinformática) will take place on 21-24 September in Sevilla, Spain, at cicCartuja (CSIC-US). 

The 21st will be the student symposium, and the main conference will start on Monday the 22nd. The URL for the meeting is: 

http://www.bioinformaticsconference2014.org/

(programme/committees are still preliminar, but will be updated periodically)

With the aim of encouraging the participation of younger bioinformaticians this year’s symposium main theme is “Bioinformatics: The New Breed”.Abstracts topics include but are not limited to:

• Integrative Biology (NGS, -omics technologies...)
• Structural Bioinformatics and function prediction
• Algorithms, method, and tools development
• Metagenomics
• Medical Informatics 
  
  Abstract submission closes Thursday, July 31, 2014 

PD 25 de Agosto: nuestro laboratorio presentará dos charlas seleccionadas en las secciones de Metagenómica y Estructura y Función. Además Álvaro Sebastián, colaborador habitual del blog presentará un libro de texto sobre Bioinformática en español, en la sección The Unworkshop format.