BOL: Related items

Computational Genomics: Applied Comparative Genomics

Jit — Wed, 29 Nov 2017 05:11:30 -0600

The primary goal of the course is for students to be grounded in theory and leave the course empowered to conduct independent genomic analyses. We will study the leading computational and quantitative approaches for comparing and analyzing genomes starting from raw sequencing data. The course will focus on human genomics and human medical applications, but the techniques will be broadly applicable across the tree of life. The topics will include genome assembly & comparative genomics, variant identification & analysis, gene expression & regulation, personal genome analysis, and cancer genomics. The grading will be based on assignments, a midterm exam, class presentations, and a significant class project. There are no formal course prerequisites, although the course will require familiarity with UNIX scripting and/or programming to complete the assignments and course project.

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

Atlas of ancient inter-ethnic group !!!

Jit — Fri, 14 Feb 2014 13:16:20 -0600

Now a dayz, almost 3% of the world's population lived outside their country of origin. These migration is increasingly being perceived as a force that can contribute to development, and an integral aspect of the global development process. While migrants make important contributions to the economic prosperity of their host countries, the flow of financial, technological, social and human capital back to their countries of origin also is having a significant impact on poverty reduction and economic development.

However, the ancient invasions and migrations to slavery and trade, history is embroidered with events that led to interactions between previously separate populations. Early humans migrated due to many factors such as changing climate and landscape and inadequate food supply. Historical migration of human populations begins with the movement of Homo erectus out of Africa across Eurasia about a million years ago. Homo sapiens appear to have occupied all of Africa about 150,000 years ago, moved out of Africa 70,000 years ago, and had spread across Australia, Asia and Europe by 40,000 years BC. Indo-Aryan migration from the Indus Valley to the plain of the River Ganges in Northern India is presumed to have taken place in the Middle to Late Bronze Age, contemporary to the Late Harappan phase in India (ca. 1700 to 1300 BC). From 180 BC, a series of invasions from Central Asia followed, including those led by the Indo-Greeks, Indo-Scythians, Indo-Parthians and Kushans in the northwestern Indian subcontinent.

Using the recent advance technologies researchers have created a historical atlas of instances of such mixing. They use a sophisticated statistical method for making inferences about human history and infer populations interbredings ( happen over the past 4,000 years) with an ease.

The study published the findings and presented with an interactive map. http://admixturemap.paintmychromosomes.com/

These sort of genomic study have some limilation. It is hard to precisely define sources of mixing when it occurred between genetically similar groups, and scenarios involving multiple waves of mixing over time or between multiple groups can be difficult to tease apart. But it is believed that larger sample sizes will improve resolution. These high resolution will provide a deeper understanding of human history.

Reference:

http://www.sciencemag.org/content/early/2014/01/28/science.1245938

http://www.ncbi.nlm.nih.gov/pubmed/21390129?dopt=Abstract&holding=npg

http://www.csulb.edu/~kmacd/paper-ethnicity.html

Image: Wikipedia

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

Two postdoc positions to study multiscale genome evolution and cephalopod gene regulation (University of Vienna, Austria)

Thu, 17 Dec 2020 11:45:16 -0600

Vienna Biocenter are seeking two postdoctoral researchers to join our team and work on the ERC funded project "METASCALE: Modes of genome evolution during major metazoan transitions". The task of both positions will be to study co-evolutionary trends within animal genomes and their association with the emergence of new gene regulation. Our group employs methods of comparative and regulatory genomics to study the regulatory impact of transitions in animal genome architecture. More recently, we have identified a major genome reorganization in the "smart" coleoid cephalopod molluscs (squid, octopus, cuttlefish) that, together with other genomic changes, potentially comprises a unique path or mode of genome evolution among animals. We are thus interested in quantifying these modes of genome evolution across all available animal genomes and to test whether their shifts are associated with the emergence of novel regulation (e.g., in cephalopods). One of our main model species is the Hawaiian bobtail squid species Euprymna scolopes. The tasks of the two candidates will be complimentary and highly collaborative with one position focusing on comparative genomics analyses across all metazoans and the other position on regulatory genomics in the squid. A solid background in in bioinformatics and comparative genomics is highly desired for the first position, whereas the second position will benefit from experience in molecular and regulatory genomics methods such as HiC, ATAC-seq, RNA-seq or single cell transcriptomics.

The postdocs will join an international group and network of researchers at the University of Vienna studying a diverse range of species and questions in molecular evolution, development, morphology and genomics. Our group is also part of the large evolVienna network of more than 50 evolutionary biology labs in Vienna, across several universities and research institutes. Our Faculty will be relocating to a new campus at the Vienna Biocenter in summer 2021 (https://biologiezentrum.univie.ac.at/en/). Vienna is a vibrant historic European capital with a high QOL. Information about postdoctoral salaries in Austria can be found on this webpage: https://www.fwf.ac.at/en/research-funding/personnel-costs/

Earliest start date will be after July 2021. Initial term of employment is for two years with the possibility of extension. Remote working, at least initially, is a possibility.

Requirements:
- PhD degree or equivalent by the start date
- Publishing record in peer-reviewed journals or evidence thereof
- At least 2 letters of support

Applications including a letter of motivation should be submitted via the Job Center to the University of Vienna (https://personalwesen.univie.ac.at/en/jobs-recruiting/job-center/,
job reference number 11615).

Application deadline: January 15th 2021.
Application link: https://univis.univie.ac.at/ebewerbung

Suisse Life Science Group

Rahul Agarwal — Sun, 07 Jan 2018 14:42:23 -0600

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Biologically-active treatments (cellular health). No drugs.

Source is Linkedln link :

https://www.linkedin.com/company/5143768/

Address of the bookmark: https://suisselifescience.com/

CBS Comparative Microbial Genomics group - BioTools download page

Neel — Wed, 22 Aug 2018 21:59:41 -0500

he CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures.

Paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060120

Address of the bookmark: http://www.cbs.dtu.dk/biotools/CMGtools/

The Clark Lab

Fri, 07 Feb 2020 13:57:24 -0600

Study the process of Adaptive Evolution, during which species adopt novel traits to overcome challenges. We retrace the evolutionary histories of genomic elements to determine the changes underlying adaptation and to discover previously unknown genetic networks. These discoveries have already led to advances in human health, species conservation, and molecular biology.

More at http://clark.genetics.utah.edu/

Senior Scientist bioinformatics @ Eurofins Genomics India Pvt Ltd, Bengaluru.

Sat, 14 Aug 2021 13:17:36 -0500

Eurofins hiring @ Eurofins Genomics India Pvt Ltd, Bengaluru.

Designation: Senior Scientist bioinformatics
Experience: 8-9 years of experience in bioinformatics analysis of various NGS applications such as WGS, RNASeq, Metagenome, small RNA.

Location: Bangalore

Roles & Responsibilities:
-Develop NGS pipeline for analysis and interpretation of NGS data
-Organizing and managing large scale genomic data
-Should have experience in NGS data analysis, such as WGS, RNASeq, Small RNA, Metagenome (16S, ITS, Whole metagenome)etc.
-Should also have good programming skills in perl or python, PHP,J Query, MySql.
-Manage project timelines and deliverables.
-Implement and execute data processing workflows and automate the pipelines.

If you are interested, please send your profile to me at arpitaghosh@eurofins.com with “Senior Scientist bioinformatics for Genomics” as the subject.

Postdoc in Genomics of Pipefishes and Seahorses at NSF-funded postdoctoral project in Adam Jones' Lab

Thu, 07 Jan 2021 21:22:24 -0600

An NSF-funded postdoctoral position is available in Adam Jones' Lab
at the University of Idaho to study the evolution and development of
the male's brood pouch in syngnathid fishes (seahorses, pipefishes
and seadragons). The project is being conducted in collaboration
with Dr. William Cresko's group at the University of Oregon. The
postdoc will be involved in studies of comparative genomics across
the family Syngnathidae, investigations of brood pouch morphology, and
characterization of the brood pouch microbiome. The position will be
funded for two years, with the possibility of a third year. The postdoc
will be based at the University of Idaho and will interact extensively
with the Cresko Lab at the University of Oregon.

The University of Idaho is in Moscow, a small college town located in
Northern Idaho on the Washington border. Moscow is widely considered to
be a great place to live, and it's known for a pleasant downtown, active
farmer's market, and nearby recreational opportunities. All of Moscow
is within biking or walking distance of the University of Idaho. For
more information about Moscow, see https://visitmoscowid.com/.

The University of Idaho has very strong faculty in evolution and
genomics in multiple departments and interdisciplinary programs. Of
particular note are the Bioinformatics and Computational Biology
Program (BCB: https://www.uidaho.edu/sci/bcb/people/faculty) and
the Institute for Bioinformatics and Evolutionary Studies (IBEST:
https://www.ibest.uidaho.edu/index.php). In addition, the University of
Idaho is only eight miles from Washington State University in Pullman, and
faculty from the two institutions interact and collaborate extensively.

Minimum qualifications include: a Ph.D. in biological sciences,
bioinformatics, or a related discipline; experience conducting research
in genomics or evolutionary biology, as evidenced by publications
in peer-reviewed journals; and evidence of strong written and oral
communication skills. Experience analyzing next-generation sequence
data and familiarity with the genomics of marine fishes are desirable
but not required.

Apply at: https://uidaho.peopleadmin.com/postings/30003

Review of applications will begin January 15, 2021. The start date
is flexible.

The University of Idaho is an equal opportunity/Affirmative Action/equal
access employer.

Informal inquiries are encouraged and can be directed to Adam Jones
(adamjones@uidaho.edu).

"adamjones@uidaho.edu"

Nigerian Bioinformatics and Genomics Network (NBGN)

Tue, 31 Aug 2021 08:29:40 -0500

This is to announce the second official conference of the Nigerian Bioinformatics and Genomics Network (NBGN). October 11-13,2021 at Landmark University, Omu-Aran, Kwara State and Zoom ( conference link to be announced soon

#NBGN21