From listmaster animalgenome.org Wed Nov 27 11:20:10 2019
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From: Andreia Fonseca <andreia.fonsecagmail.com>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: PhD position announcement
Date: Wed, 27 Nov 2019 11:20:10 -0600
Dear colleagues,
I am happy to announce that we have one PhD position funded by “La Caixa”
Foundation through the program INPhINIT Fellowships Incoming. Conditions
of eligibility and deadlines are available here: https://tinyurl.com/sqx74nu
Title: Using and developing reproducible computational workflows for the
annotation of the bovine genome.
Lab: Luis Gama Lab
Research centre:
CIISA- Centro de Investigação Interdisciplinar em Sanidade Animal
Location:
Faculty of Veterinarian Medicine, University of Lisbon, Lisbon, Portugal
Further details regarding the position follow bellow.
With kind regards
Andreia
Description: https://www.lacaixafellowships.org/index.aspx
Using and developing reproducible computational workflows for the annotation
of the bovine genome CENTRE
CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal
http://ciisa.fmv.ulisboa.pt/en/about-ciisa
https://cordis.europa.eu/.../223200/factsheet/en
-Research Project / Research Group Description:
Despite the revolution in functional genome analysis a wide gap in
understanding associations between the (epi)genome and complex
phenotypes of interest currently remains and impedes efficient use
of annotated genomes for precision breeding. In the BovReg
consortium (H2020) we aim to provide a comprehensive map of
functionally active genomic features in cattle and how their
(epi)genetic variation in beef and dairy breeds translates into
phenotypes. The BovReg brings together a critical mass of experts
in ruminant research and beyond encompassing bioinformatics, molecular
and quantitative genetics, animal breeding, reproductive physiology,
ethics and social science. BovReg is constituted by 20 partners from
the EU, Canada and Australia forming a global interdisciplinary team,
which builds on previous and running national and EU-funded projects
and many established industry cooperations. In BovReg we will generate
functional genome data based on core assays from representative bovine
tissues and newly established cell lines covering different ontological
stages and phenotypes applying novel bioinformatic pipelines. We will
establish detailed knowledge on traits related to robustness, health
and biological efficiency in cattle, aiming to set up and maintain a
knowledge hub and establish gold standards.
The Faculty of Veterinarian Medicine, namely the Animal Genetic
Resources Laboratory participates as partner in the development of
workflows, analysis pipelines, identification of novel genomic
features of the bovine genome and in the comparative genomic tasks.
These objectives will be achieved in collaboration with the Centre
de Regulation Genómica in Barcelona (CRG), with University of Liège
and with the EMBL-EBI, in the UK. The student will have the
opportunity to develop research, dealing with state-of the art
tools and data, interacting with an International community with
high standards an quality in research.
-Job position description:
The increasing complexity of ‘omics’ data requires complex analysis
and reproducibility of experiments that produce and use ‘big data’.
A solution aiming to provide reproducibility to the analysis process
of ‘omic’ data is Nextflow, a workflow management system that uses
Docker technology for the multi-scale handling of containerized
computation. In silico workflow management systems are an integral
part of large-scale biological analyses. These systems enable the
rapid prototyping and deployment of pipelines that combine
complementary software packages. (Nature Biotechnology, 2017:35).
This proposal aims to contribute to the development of prototyping
and deployment of pipelines that will enable processing of data
generated that will characterize the different layers of genome
architecture, including genetic and epigenetic features. This
proposal will further contribute to the identification of novel
features in the Bovine genome and well as to participate in the
comparative analysis of domestic animal genomes.
The PhD candidate will participate in the following tasks:
1) Develop standardised, validated procedures (raw data quality
control and processing, data retrieval from databases, data analysis
algorithms) integrating existing bioinformatics tools and
experimental data into genomic functional annotation pipelines to
allow interoperability across datasets (RNA-seq, ATAC-seq, ChIP-Seq)
and consortia. The procedures will comply with FAANG and ELIXIR
requirements.
2) Annotate functionally active genomic regions in the bovine genome
based on a comprehensive catalogue of 24 tissues that are highly
relevant for the BovReg target traits, five ontogenetic stages, both
gender and six new cell lines from dairy and beef breeds based on
the analysis of the data generated (see (1)).
3) Conduct comparative genomic analysis across species to reveal
sites evolving in a non-neutral way (positive selection for recent
adaptation, purifying selection for key functional features).
Andreia de Jesus Amaral, PhD
Faculdade de Medicina Veterinária da Universidade de Lisboa
Avenida da Universidade Técnica | 1300-477 Lisboa | Portugal
Tel. (+351) 21 365 28 84 I Fax (+351) 21 365 28 89
Ext. 431376
ORCID: 0000-0003-0958-5570
https://www.researchgate.net/...ofile/Andreia_Amaral
mailto:andreiaamaralfmv.ulisboa.pt
http://www.fmv.ulisboa.pt
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