BOL: Related items

postdoctoral fellow for a large-scale microbial comparative genomics !

Thu, 29 Apr 2021 08:44:53 -0500

Asaf Levy hiring a postdoctoral fellow for a large-scale microbial comparative genomics project at the Hebrew University of Jerusalem (Israel).
The project is a continuation of Levy Asaf et al. Nature Genetics 2018 paper.
Requirements:
1.Experience with programming in at least one programming language, preferably Python.
2.A PhD in bioinformatics/computational biology
3.At least one first authorship publication in a good journal, preferably more.
4.Good communication skills in English
5.Ability to enter and study in Israel (not applicable for Pakistani people, for example).
6.Ability to work in a team.
Please send CV to alevy@mail.huji.ac.il

LoVis4u: Locus Visualisation tool for comparative genomics

LEGE — Tue, 17 Sep 2024 02:30:57 -0500

Description

LoVis4u is a bioinformatics tool for Loci Visualisation.

LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.

https://art-egorov.github.io/lovis4u/

Address of the bookmark: https://github.com/art-egorov/lovis4u

PLANT COMPUTATIONAL GENOMICS LAB – JILL WEGRZYN

Thu, 20 Aug 2020 19:49:12 -0500

Our research focuses on the computational analysis of genomic and transcriptomic sequences from non-model plant species. We do this by developing approaches to examine gene finding, gene expression, transcriptome assembly, and conserved element identification, through machine learning and computational statistics. We use these novel methods to address questions related to genome biology and population genomics.

We also develop web-based applications that integrate data across domains to facilitate the forest geneticist or ecologist’s ability to analyze, share, and visualize their data. Such integration requires the implementation of semantic technologies and ontologies to connect genotype, phenotype, and environmental data.

http://plantcompgenomics.com/

Nicolas Corradi Lab

Tue, 26 May 2015 16:19:02 -0500

The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance.
To achieve this goal, our team combines the power of next generation DNA sequencing and bioinformatics with molecular biology and experimental procedures.

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

Comparative genomics educational material and papers bookmarks

Jit — Wed, 09 Nov 2016 16:23:30 -0600

Alignment of the porcine genome against seven other mammalian genomes (Supplementary Information) identified homologous synteny blocks (HSBs). Using porcine HSBs and stringent filtering criteria, 192 pig-specific evolutionary breakpoint regions (EBRs) were located. The number of porcine EBRs is comparable to the number of bovine-lineage-specific EBRs (100) reported earlier using a slightly lower resolution (500 kilobases (kb)), indicating that both lineages evolved with an average rate of ~2.1 large-scale rearrangements per million years after the divergence from a common cetartiodactyl ancestor ~60 Myr ago². This rate compares to ~1.9 rearrangements per million years within the primate lineage (Supplementary Table 11). A total of 20 and 18 cetartiodactyl EBRs (shared by pigs and cattle) were detected using the pig and human genomes as a reference, respectively.

Address of the bookmark: http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html

Postdoctoral Research Assistant at RVC

Mon, 09 Jul 2018 00:47:38 -0500

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

Rennison Lab !

Sat, 26 Oct 2024 15:10:32 -0500

Welcome to the Rennison lab in the School of Biological Sciences at the University of California San Diego. We are a group interested in the evolution and maintenance of biodiversity. We study the processes related to biodiversity using methods from the fields of evolution, ecology, population genomics, and theory.

More at https://rennisonlab.com/

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

BioStar — Fri, 21 Sep 2018 10:19:52 -0500

Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:

sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config

On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:

sudo fink install bzip2-dev pkgconfig

Address of the bookmark: https://github.com/neufeld/pandaseq

ComparativeGenomics Exercise2

Neel — Wed, 22 Aug 2018 22:10:56 -0500

COMPARATIVE MICROBIAL GENOMICS ANALYSIS WORKSHOP @ cbs.dtu.dk

Free Bioinformatics workbench https://www.mn.uio.no/ifi/english/research/networks/clsi/earlier_seminars/2012/tammivesth_osloseminarfinal.pdf

Comparative genomics visualisation tools !

Neel — Thu, 17 Feb 2022 05:37:55 -0600

Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative