<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42798?offset=10 https://bioinformaticsonline.com/opportunity/view/37248/postdoctoral-research-assistant-at-rvc Mon, 09 Jul 2018 00:47:38 -0500 <![CDATA[Postdoctoral Research Assistant at RVC]]> This is a fixed term post for 24 months.

We wish to recruit a highly motivated, postdoctoral scientist to carry out a BBSRC funded project in the laboratory of Dr. Denis Larkin. The project is focused on developing and applying new methods and algorithms to study genome and chromosome evolution in mammals and other animals using whole-genome sequences and existing algorithms (e.g., Damas et al. Genome Res. 2017. 27(5):875-884; Kim et al., Proc Natl Acad Sci USA. 2013. 110 (5)). The post holder will use cutting edge computational and laboratory approaches to generate chromosomal assemblies for sequenced genomes, study chromosomal structures and differences between mammalian and other vertebrate genomes in attempt to identify species- and clade-specific genome signatures.

Applicants must have a Ph.D. and a track record of success, as indicated by first-author publications in international journals. They must possess excellent organisation skills and be capable of individual initiative and of interacting as part of a team. Applicants with extensive practical experience in bioinformatics or computer science, programming, visualization, handling of large data sets, high-performance computing are encouraged to apply. The post will involve collaboration with a wide range of academic partners both within the EU and worldwide.

Experience in programming, bioinformatics and comparative genome analysis is essential. Applicants should have a minimum of a degree and preferably a higher degree in a relevant subject.

The Royal Veterinary College has the largest range of veterinary, para-veterinary and animal science undergraduate and postgraduate courses of any veterinary school in the world and is one of the largest veterinary schools in Europe.

Prospective applicants are encouraged to contact Dr. Denis Larkin, Comparative Biomedical Sciences Department on +442071211906 or email: dlarkin@rvc.ac.uk

We offer a generous reward package.

For further information and to apply on-line please visit our website: www.rvc.ac.uk
Job reference CBS-0084-18

https://jobs.rvc.ac.uk/Vacancy.aspx?ref=CBS-0084-18

]]> https://bioinformaticsonline.com/researchlabs/view/42327/blaxter-lab Thu, 19 Nov 2020 08:05:28 -0600 <![CDATA[Blaxter Lab]]> Using these high quality genomes we explore

the evolutionary history of genes and species, building phylogenetic trees of life
the contrasting roles of horizontal gene transfer and introgression in shaping evolution
the biology of symbioses, especially symbioses between eukaryotes and bacteria, and between parasites and their hosts
the processes that drive the evolution of pattern in the structure of chromosomes
the diversity of meiofauna, particularly tardigrades, nematodes and other Ecdysozoa
the genomics of extremophilia

More at https://www.sanger.ac.uk/group/blaxter-group/

]]> https://bioinformaticsonline.com/opportunity/view/43559/job-offer-for-a-postdoctoral-researcher-in-genomics-bioinformatics-2-years Fri, 22 Oct 2021 04:44:33 -0500 <![CDATA[Job offer for a postdoctoral researcher in genomics / bioinformatics (2 years)]]> Ongoing research in the group of Karine Van Doninck involves topics at the core of
evolutionary biology, including the evolution of sex, genome maintenance,
recombination and extreme stress resistance on different eukaryotic systems,
including rotifers, amoeba and Corbicula clams. We are employing different tools
(including experimental ecology, population genetics, phylogeny, comparative
genomics, transcriptomics, bioinformatics, molecular and cellular biology) to study
evolutionary processes at the level of populations, both experimental and natural, and
genomes.

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

]]> https://bioinformaticsonline.com/researchlabs/view/44639/the-sheppard-lab Fri, 09 Aug 2024 02:48:34 -0500 <![CDATA[The Sheppard Lab]]> Ineos Oxford Institute of Antimicrobial Research – Department of Biology – University of Oxford

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/

]]> https://bioinformaticsonline.com/blog/view/44775/genomic-architecture-surrounding-the-fusion-site-of-human-chromosome-2 Tue, 04 Mar 2025 12:26:29 -0600 https://bioinformaticsonline.com/blog/view/44775/genomic-architecture-surrounding-the-fusion-site-of-human-chromosome-2 <![CDATA[Genomic architecture surrounding the fusion site of human chromosome 2]]> The article "Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13–2q14.1 and Paralogous Regions on Other Human Chromosomes (https://pmc.ncbi.nlm.nih.gov/articles/PMC187548/)" explores the genomic architecture surrounding the fusion site of human chromosome 2. This fusion event is a key evolutionary marker distinguishing humans from other great apes, as humans have 46 chromosomes while chimpanzees, gorillas, and orangutans possess 48. The fusion occurred through an end-to-end joining of two ancestral chromosomes, which remain separate in nonhuman primates.

Key Findings:

  1. Chromosomal Fusion and Its Molecular Signature:

    • The fusion site is located at 2q13–2q14.1 and is characterized by degenerate telomeric sequences appearing interstitially, indicating the historical head-to-head joining of ancestral chromosomes.
    • Despite being a signature of a past fusion event, these telomeric repeats are no longer functional and have undergone sequence degradation over time.

  2. Extensive Duplications in the Surrounding Genomic Region:

    • The study identifies large-scale segmental duplications flanking the fusion site, with several of these regions duplicated and scattered across multiple chromosomes.
    • These duplications are predominantly located in subtelomeric and pericentromeric regions, suggesting their role in genomic instability and chromosomal evolution.

  3. Paralogous Regions and Their Evolutionary Relationships:

    • A 168-kilobase (kb) segment near the fusion site has 98%–99% sequence identity with three regions on chromosome 9 (9pter, 9p11.2, and 9q13).
    • Another 67-kb region distal to the fusion site shows a high degree of homology to sequences in chromosome 22qter.
    • Additionally, a 100-kb segment exhibits 96% sequence identity with a region in chromosome 2q11.2.

  4. Comparative Genomics and Evolutionary Implications:

    • By comparing the duplicated sequences and their arrangement in primates, the researchers traced the order of duplication events leading to their present distribution.
    • The presence of specific repetitive elements within these duplicated segments serves as evolutionary markers that help infer their historical rearrangements.
    • Some of these duplicated regions are associated with chromosomal inversion breakpoints, potentially contributing to evolutionary changes in primates.
    • Recurrent structural rearrangements in these regions have been linked to human chromosomal disorders.

Conclusions and Implications:

  • The findings provide valuable insights into the structural evolution of human chromosome 2, which played a crucial role in human speciation.
  • Understanding these segmental duplications and their evolutionary trajectories sheds light on genomic instability, which may contribute to human genetic diseases.
  • The study highlights how large-scale chromosomal rearrangements, such as fusion and duplication, have influenced the evolutionary divergence of humans from other primates.

This research advances our understanding of human genome evolution and offers a foundation for studying the effects of structural variants in genetic disorders.

]]> LEGE https://bioinformaticsonline.com/researchlabs/view/45224/liberles-research-group Wed, 12 Aug 2026 03:39:53 -0500 <![CDATA[Liberles Research Group]]> The Liberles Research Group works in the areas of computational comparative genomics, and molecular evolution. The central theme in the research group is the detection and characterization of the lineage-specific divergence of protein-encoding genes. Much of the work in the group is done in a phylogenetic context. Ultimately, we want to ask the question, “What makes each species unique at the genomic level?” and “what are the processes driving the functional divergence of genomes?”.

More at https://sites.temple.edu/liberles/

]]> https://bioinformaticsonline.com/researchlabs/view/35752/hejnol-group Thu, 22 Feb 2018 16:02:53 -0600 <![CDATA[Hejnol Group]]> The group studies a broad range of animal taxa using morphological and molecular tools to unravel the evolution and development of animal organ systems.

To understand the evolution of the biodiversity seen on planet earth is one of the major goals in biology. How animals explored new habitats from only being confined to the marine environment and the how the forms diversified is still one of the most tremendous questions to be answered.

http://www.sars.no/research/HejnolGrp.php

]]> https://bioinformaticsonline.com/researchlabs/view/38551/gupta-lab Sat, 29 Dec 2018 13:18:31 -0600 <![CDATA[Gupta Lab]]> Work include (i) understanding the evolutionary relationships among different prokaryotic and eukaryotic organisms; (ii) Understanding the cellular functions of these lineage-specific signature proteins as well as lineage-specific conserved inserts and deletions in important housekeeping proteins by genetic and biochemical studies; (iii) Development of novel diagnostic methods (PCR based and immunological) for identification of different groups of organisms based upon these signature proteins and conserved indels; (iv) The use of these lineage-specific probes with predicitive ability to identify/explore the presence of different groups of organisms in metagenomic sequences from various environments.

https://fhs.mcmaster.ca/gupta-lab/index.html

]]> https://bioinformaticsonline.com/bookmarks/view/42794/tmrca-calculator Wed, 03 Feb 2021 05:07:30 -0600 https://bioinformaticsonline.com/bookmarks/view/42794/tmrca-calculator <![CDATA[TMRCA Calculator]]> This program calculates the probability that two people have a certain number of generations between them, based on the standard infinite alleles formula of Walsh. It calculates both the probability of being at an exact number of generations back to the Most Recent Common Ancestor (MRCA) of a certain pair of people and the cumulative probability that the actual number of generations is less than a certain value. Note that the convention using generations is changed from an earlier version of this calculator which used "transmission events". It can list both result types in a table or graph. In either case the horizontal axis stops at the point where the cumulative probability reaches 95% or 10 generations, whichever is longer, or an absolute max of 50,000. Beyond 90% the calculation becomes inaccurate.

https://clandonaldusa.org/index.php/tmrca-calculator

Address of the bookmark: https://clandonaldusa.org/index.php/tmrca-calculator

]]> BioStar https://bioinformaticsonline.com/blog/view/44219/chromosome-breakpoint-a-breakup-to-remember Tue, 07 Mar 2023 13:31:54 -0600 https://bioinformaticsonline.com/blog/view/44219/chromosome-breakpoint-a-breakup-to-remember <![CDATA[Chromosome breakpoint - a breakup to remember]]>

Chromosome breakpoint refers to the physical location where a chromosome is broken and rearranged. Chromosome breakage can occur spontaneously or be induced by environmental factors such as radiation, chemicals, or viruses. The rearrangement of genetic material resulting from a chromosome breakpoint can have important consequences, including the development of genetic diseases, chromosomal abnormalities, or cancer.

Chromosome breakpoints can occur in two ways: interstitial or terminal. Interstitial breakpoints occur within the chromosome, while terminal breakpoints occur at the end of the chromosome. Terminal breakpoints can lead to the loss of genetic material, whereas interstitial breakpoints can result in the duplication or deletion of genetic material.

Chromosome breakpoints can be detected using a variety of techniques, including cytogenetic analysis, fluorescence in situ hybridization (FISH), and molecular methods such as polymerase chain reaction (PCR) and next-generation sequencing (NGS). These techniques can also help identify the exact location of the breakpoint and the nature of the rearrangement, such as translocations, inversions, deletions, or duplications.

Translocations are one of the most common types of chromosome rearrangements caused by breakpoints. In a translocation, genetic material is exchanged between two different chromosomes, resulting in a balanced or unbalanced distribution of genetic material. Unbalanced translocations can cause genetic diseases or developmental abnormalities, while balanced translocations can be inherited without any apparent phenotypic effects.

Inversions occur when a chromosome segment is inverted, resulting in a change in the order of genetic material. Inversions can be pericentric, involving the centromere, or paracentric, not involving the centromere. Inversions can cause genetic diseases or phenotypic effects if they disrupt the function of essential genes or regulatory elements.

Deletions and duplications are caused by interstitial breakpoints that result in the loss or gain of genetic material. Deletions can cause genetic diseases or developmental abnormalities if they involve essential genes or regulatory elements. Duplications can also have phenotypic effects, depending on the location and size of the duplicated segment.

Chromosome breakpoints can also be involved in the formation of complex chromosomal rearrangements, such as ring chromosomes or dicentric chromosomes. These complex rearrangements can have important clinical implications, as they can cause genetic diseases or cancer.

In conclusion, chromosome breakpoints are important genetic events that can lead to the rearrangement of genetic material and have important clinical implications. The detection and characterization of chromosome breakpoints using cytogenetic, molecular, and genomic methods are essential for the diagnosis, prognosis, and treatment of genetic diseases and cancer. Further research is needed to understand the molecular mechanisms underlying chromosome breakage and to develop new therapies targeting these events.

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