job: bioinformatician for NGS analysis of SARS-CoV-2

RESEARCH CONTRACT: SARS-COV-2 BIOINFORMATICS

  • Workplace: Phylogenomics Lab, CINBIO, Universidade de Vigo, Spain
  • Duration: 12 months starting Sept-Oct
  • Gross remuneration: 16,000-25,000 euros per year depending on qualifications

 
TASKS TO BE PERFORMED

  • Bioinformatic analysis of SARS-CoV-2 genomes

 
ESSENTIAL REQUIREMENTS

  • Experience in the analysis of next-generation sequencing data
  • University degree of master or doctorate
  • Medium-high English level

 
MERITS TO VALUE

  • Bioinformatics knowledge
  • Background in viral evolution
  • Script programming
  • Supercomputing capabilities

 
APPLICATION

  • Until August 7
  • to David Posada (dposada@uvigo.es), with “bioinfo epicovigal” in the subject of the email.
  • Send:
    • CV (1-3 pages)
    • motivation letter (1 page)
    • contact details of two references 
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CellCoal: NGS simulation of single-cell somatic evolution

Check my new simulator CellCoal for the coalescent simulation of single-cell sequencing genotypes. CellCoal simulates the history of single-cell samples obtained from somatic cell populations with different demographic histories and produces single-nucleotide variants under a variety of mutation models, sequencing read counts, and genotype likelihoods, considering allelic imbalance, allelic dropout, amplification, and sequencing errors, typical of this type of data.

Publication: https://academic.oup.com/mbe/article/37/5/1535/5728646

Code: https://github.com/dapogon/cellcoal

Manual: https://dapogon.github.io/cellcoal/cellcoal.manual.v1.1.html

 

Effect of sequencing coverage heterogeneity on single-cell genotypes. (A) Probability that the maximum likelihood genotype is wrong. (B) Proportion of genotypes called. (C) Total number of single-nucleotide variants (SNVs) called. GATK and true (GATK+ADO) are the likelihood models used for calling genotypes. Coverage dispersion corresponds to the negative binomial dispersion parameter. The smaller this parameter is, the more heterogeneity there is. At the top, 1×, 5×, and 25× are different overall sequencing depths. In the boxplots, the central line indicates the median, whereas the box limits correspond to the Q1 and Q3 quartiles and the asterisk to the mean.

 

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A next-generation version of modeltest

The Stamatakis lab as taken over the Modeltest series! check Modeltest-NG. ModelTest-NG is much faster than jModelTest and ProtTest but equally accurate and introduces new features, such as ascertainment bias correction, mixture, and free-rate models, or the automatic processing of single partitions.

https://academic.oup.com/mbe/article/37/1/291/5552155

https://github.com/ddarriba/modeltest

 

Model selection accuracy comparison between ModelTest-NG, jModelTest/ProtTest, and ModelFinder for simulated data (top) and LOESS curved fitted to a scatter plot of ModelTest-NG run times versus ModelFinder for empirical data (bottom), for DNA (left) and protein (right) MSAs. The dashed line represents equal run times.

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paper in Nature Communications on cancer biogeography

We have published a new paper in Nature Communications where we show how statistical phylogenetics can help to understand tumoral dynamics over time and space:
https://www.nature.com/articles/s41467-019-12926-8
 
Fig. 3

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Excellence grant from the Galician government!

We have been awarded an excellence 3-year structural grant for research groups from the Galician government.
So now our GXB group has been stamped as Competitive Reference Group.
We want to thank Xunta de Galicia for this support

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New PhD thesis in the lab!

Congratulations to Nuria for passing with honors her Ph.D. viva!IMG_0028

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New paper on germline evolution of human cancer genes by Alberto Vicens

https://www.mdpi.com/2073-4425/9/12/582

Screenshot 2018-11-30 at 10.14.40

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Comparing single-cell whole-genome amplification strategies

We finally put it together:

https://www.biorxiv.org/content/early/2018/10/16/443754

Fig2

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Welcome to Monica and Fabian!

Monica Valecha (India) and Fabián Crespo (Cuba/Ecuador) just arrived to start as PhD students in the CONTRA Marie Curie Innovative Training Network on Computational Oncology.  They are going to work on different aspects of cancer evolution.

Fabian_MonicaV

Welcome to the lab!.

Now we have people from three continents!

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Merly got her PhD

Congratulations to Merly for her PhD awarded today on NGS phylogenomics! You’ve been a GREAT student. Good luck for your postdoc at UC Santa Cruz. We’ll miss you…

 

merly.thesis.040518

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