Offer
We offer a full-time contract for two years. The contract starts between October 2021
and December 2021. The position involves no or extremely light teaching load, if the
candidate is interested. Salaries are competitive at the European level. The recruited
person will benefit from the Belgian social insurance scheme (health care, etc.) without
additional expenses.

Profile
Applicants are expected to show outstanding commitment to research and must have
obtained a PhD by the start of the position. A strong expertise in genomics is required.
More specifically, solid competences in bioinformatics (e.g. scripting pipelines) and in
genome evolution are needed. Knowledge or interest regarding recombination,
metazoan evolution, phylogenomics and population genomics is an added-value.

Application
Applications should be submitted via email to karine.van.doninck@ulb.be. The
application package should contain the following documents:
- A curriculum vitae with the complete list of publications
- A cover letter mentioning why the candidate is interested in the position
- Minimum 2 recommendation letters
Interviews: Interviews will be conducted with the selected candidates. Selected
candidates could also be invited to give a seminar to MBE ULB.
For any additional information, please contact karine.van.doninck@ulb.be

Our research centres on the use of genetics/genomics and phenotypic studies to address complex questions in the ecology, epidemiology and evolution of microbes. Our most recent interest focuses upon comparative genome analysis to describe the core and flexible genome of pathogenic bacteria (Campylobacter, Acinetobacter, Escherichia coli, Helicobacter, Staphylococcus and Streptococcus suis) and how this is related to population genetic structuring, the maintenance of species, and the evolution of host/niche adaptation and virulence.

More at https://sheppardlab.com/research/

In this post, we’ll explore the core methods used in comparative genomics, the questions they help answer, and how they’re shaping our understanding of life.

1. Whole-Genome Alignment
Whole-genome alignment involves mapping the entire genome of one species to another. Tools like MUMmer, MAUVE, and LASTZ perform large-scale sequence alignments to detect conserved regions, rearrangements, insertions, and deletions.

Use Case:
Comparing human and chimpanzee genomes to identify evolutionary conserved sequences (ECS) and regions of divergence.

Key Challenges:
Handling repetitive sequences and genome rearrangements.

Computational complexity in large genomes.

2. Synteny and Collinearity Analysis
Synteny refers to conserved blocks of gene order across species. Tools like MCScanX, SynMap, or CHITRA (for visualizing synteny interactively) detect these blocks to understand chromosomal evolution.

Use Case:
Studying ancient genome duplications in plants.

Investigating chromosomal rearrangements in cancer genomes.

3. Ortholog and Paralog Detection
Orthologs are genes in different species that evolved from a common ancestor, while paralogs are genes duplicated within a genome. Identifying them is crucial for functional annotation and evolutionary studies.

Popular Tools:
OrthoFinder, Orthologous MAtrix (OMA), InParanoid, and EggNOG.

Use Case:
Functional prediction of uncharacterized genes based on orthologs in model organisms.

Tracing gene family evolution.

4. Phylogenomic Analysis
Phylogenomic methods combine phylogenetics and genomics to infer evolutionary trees based on genome-wide data. These methods can handle dozens to hundreds of genomes, using concatenated alignments or gene trees.

Tools:
RAxML, IQ-TREE, ASTRAL, Phylip, BEAST.

Use Case:
Resolving the evolutionary relationships between microbial species.

Studying speciation events.

5. Pan-Genome Analysis
The pan-genome consists of the core genome (shared by all strains) and the accessory genome (strain-specific genes). This is especially popular in microbial genomics.

Tools:
Roary, Panaroo, BPGA, PGAP.

Use Case:
Understanding virulence factor diversity in E. coli.

Designing broad-spectrum vaccines.

6. Comparative Transcriptomics
Comparing transcriptomes across species or conditions reveals conserved and unique expression patterns. RNA-seq data can be mapped to reference genomes to identify orthologous expression profiles.

Use Case:
Comparing stress response in extremophiles and model species.

Studying conserved regulatory networks.

7. Functional Element Comparison
Beyond genes, comparative genomics also targets non-coding regions—enhancers, promoters, miRNAs. Conservation across species often implies functional importance.

Tools:
PhastCons, GERP, phyloP (based on multiple alignments).

Use Case:
Detecting conserved non-coding elements in vertebrates.

Studying regulatory divergence in human evolution.

8. Horizontal Gene Transfer (HGT) Detection
In microbes, genes often jump across species boundaries. Comparative genomics can detect HGT by identifying genes that defy the expected phylogenetic pattern.

Tools:
HGTector, DarkHorse, AlienHunter, SIGI-HMM.

Use Case:
Tracing antibiotic resistance genes.

Exploring microbial adaptability in extreme environments.

Final Thoughts
Comparative genomics is a powerful lens to observe the diversity and unity of life. With a broad toolkit—from aligners to orthology pipelines, phylogenetic engines to visualization tools—it allows scientists to ask big questions: How did genomes evolve? What makes species unique? Where do new genes come from?

Whether you're studying extremophiles, building better crops, or exploring human ancestry, comparative genomics offers the methods to connect the dots across the tree of life.

Address of the bookmark: https://github.com/schatzlab/appliedgenomics

Date : June 10-13

Organizers: The Society for Bioinformatics in Northern European countries (SocBiN) and the Norwegian Bioinformatics Platform / ELIXIR.NO

Venue: Department of Informatics, University of Oslo, Norway

Topics:
Tools and technologies for integrative bioinformatics
Metagenomics
Comparative genomics and phylogeny
Post-ENCODE bioinformatics
Gene regulation
Cancer genomes
Marine genomics

More at https://www.sydney.edu.au/science/about/our-people/academic-staff/kathy-belov.html

More at https://www.mariottigenomicslab.com/

Annotation

https://bigd.big.ac.cn/ncov/variation/annotation

Genome wharehouse 

https://bigd.big.ac.cn/gwh/browse/index

Released Genome

https://bigd.big.ac.cn/ncov/release_genome

Download data 

ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/

Raw data

https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae

Address of the bookmark: https://bigd.big.ac.cn/ncov/about

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms. 
Application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.
The effect on traditional scientific classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered. Proponents even claim that taxonomy was previously based on morphology alone, which of course is utter fable.

For additional information on phylogenetics, see list of Phylogenetics Resources on the Internet.

Phylogeny and Reconstructing Phylogenetic Trees: http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html
the CBRG and Department of Statistics Phylogeny tutorial: http://www.compbio.ox.ac.uk/tutorials/phylogeny/
TUTORIAL: PHYLOGENETIC ANALYSIS USING PARSIMONY:http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html

PHYLIP: http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html
An Introduction to Molecular Phylogeny: http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf

How to make a phylogenetic tree: http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Treetutorial.html
Phylogenetic Trees: http://cnx.org/content/m11052/latest/
Phylogeny by Ron Shamir: http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf
Introduction to Phylogeny: http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm
Lecturer notes on Phylogeny: http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf
Principles and Practice of Phylogenetic Systematics:http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm

Inferring phylogenetic trees: http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf

Lecture Notes

Chapter 1 - The Diversity, Classification, and Evolution of Vertebrates:http://academic.emporia.edu/mooredwi/nathist/chap1.htm

Algorithms for Phylogenetic Reconstructions:http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf

Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. For more detail : http://www.phylogeny.fr/version2_cgi/index.cgi

A Brief Tutorial on Phylogenetics
http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf

A Brief Tutorial on Phylogenetics Human Rabbit Chicken
http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf

Phylogenetic Tree Computation Tutorial Overview
http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf

MrBayes: A program for the Bayesian inference of phylogeny
http://golab.unl.edu/teaching/SBseminar/manual.pdf

Web sites providing software for the construction of phylogenetic trees

• BioEdit

• Coelocanth-Fish Out of Time

• Computational Biochemistry Research Group

• Digital Taxonomy

• Hennig 86

• Hyperclean from Bioinformatics Solutions, Inc.

• Memorial University of Newfoundland

• Mr. Bayes

• NONA

• Oxford University Evolutionary Biology Group

• Paleobiology Database

• PAUP

• Phylip Homepage

• Poy

• Sinauer Associates

• TNT-Tree Analysis Using New Technology

• Tree Base

• Treefinder

• Tree-Puzzle

• Tree View-Taxonomy and Systematics Group at Glasgow

• Washington University-List of Phylogeny Software