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.

Walk in interview for Research Associate, Studentship and Traineeship at BIF

Applications are invited for the Post of Research Associate, Traineeship and Studentship in the DBT sponsored Bioinformatics Infrastructure Facility (BIF) at the Bioinformatics Centre, Department of RDAP, North-Eastern Hil University, Tura Campus, Tura-79402, Meghalaya. The Posts are purely temporary and terminable at any time without prior notice or assigning any reason thereof. The person engaged, shall not be entailed for any claim implicit or explicit for permanent absorption in the University.

Research Associate- 01

Essential Qualification: M.Sc. in Bioinformatics/Biotechnology from a recognized University/ institute.

Desirable: PhD or Pursuing PhD in the relevant subject(s) or equivalent published work in reputed peer reviewed journals or Advance PG diploma in Bioinformatics courses.

Duties: Creation of database, web designing, maintenance of internet, training of students in Bioinformatics, handling and knowledge of Bioinformatics software tools and technique, conducting Bioinformatics based research and other day to day laboratory work, writing report and scientific papers.

Pay:Rs. 2,00/- + Admissible 10% HRA per month

Age: Below 35 years

Traineeship- 02

Students who have completed Masters Degree in Bioinformatics/Biotechnology or any branch of Life Sciences/Agricultural Sciences/Computer Science to cary out a project work in Bioinformatics.

Desirable: Prior Knowledge of programming languages such as C, JAVA, MySQL is preferable.

Stipend: Rs. 800/- p.m. fixed. Purely temporary for a period of six months.

Studentship: 02

Students pursuing postgraduate degree in Bioinformatics/biotechnology/Agricultural Sciences or any branch of Life Science

Desirable: Prior knowledge of bioinformatics/ programming language is preferable.

Stipend: 800/- p.m. fixed. Purely temporary for a period of six months.

Candidates must send the detailed Biodata via mail/post and bring al the relevant documents in original and one set of attested photocopies of the same at the time of interview. No TA/DA will be paid for attending the interview and candidates have to make their own arrangements.

Last date for receiving application by mail or by post: 16.02.2014

Contact Information:
Dr.B.K. Mishra
Cordinator BIF,
RDAP Department, NEHU, Tura Campus
Phone: 91-03651-23107
Fax: 91-03651-23953
E-mail: drbkm1972@yaho.co.in, birendramishra14@gmail.com

Advertisement: http://www.nehu.ac.in/Advertisements/BIF_TuraAdtvPV_171214.pdf

You might learn a lot about that house—the rooms, the doors, the furniture—but you would miss the bigger story: the streets, the neighborhoods, and all the ways the city changes from one place to another.

Something similar happens when scientists study bacterial genomes one at a time.

Over the past decade, researchers have collected thousands of bacterial genomes. These genomes contain an enormous amount of information about how bacteria survive, adapt, and evolve. But comparing thousands of individual genomes can quickly become a computational maze.

That is where PANORAMA enters the story.

Developed by Jérôme Arnoux and colleagues, PANORAMA is a computational tool designed to explore bacterial pangenomes—the complete collection of genetic possibilities found across a species or group of related organisms. Instead of looking at every genome as an isolated object, the approach represents their shared and variable genetic features as a graph.

Think of this graph as a giant subway map.

Some stations appear on almost every route. These represent genes that are highly conserved. Other stations appear only on certain routes, representing genes that some bacteria possess while others do not. By looking at the entire network, scientists can begin to see not just *what genes exist*, but how they are organized and how biological systems are distributed across populations.

The researchers put PANORAMA to the test using 941 genomes of Pseudomonas aeruginosa, a bacterium important in human health. They used the tool to investigate biological systems, including bacterial defense mechanisms against viruses known as bacteriophages. They then expanded the analysis to more than 6,000 genomes from four Enterobacteriaceae species.

The result is more than a faster way to process data.

PANORAMA allows researchers to ask a bigger question: What can an entire microbial species do, genetically speaking?

By comparing pangenomes, the researchers could identify systems shared between species as well as distinctive features. They could also find recurring genomic locations where genetic material is inserted—clues that may reveal common evolutionary processes.

And this is perhaps the most exciting part of the story.

Every bacterial genome is like a page in a huge evolutionary book. Until recently, reading thousands of those pages together was difficult. PANORAMA provides a way to turn those pages into a map, allowing scientists to see patterns that might disappear when each genome is studied separately.

The study, published in PLOS Computational Biology in July 2026, presents PANORAMA as a foundation for large-scale comparative pangenomics. The software and accompanying analysis resources are openly available, giving other researchers the opportunity to explore microbial diversity themselves.

So the story is not really about one bacterium or one genome.

It is about changing the way we look at life.

Instead of asking, “What is inside this genome?”, scientists can increasingly ask, “What is the full genetic landscape of this species—and how did it become this way?”

And sometimes, when you stop looking at one house and finally see the whole city, the most interesting discoveries are hiding in the streets between them.

Read more at https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013856

Ref. No. GU/Estt/T/308(VI)/2014/6451-61

Applications are invited from the Indian citizens for five (5) teaching posts of Assistant Professor (Contractual) under various departments of Gauhati University. Details of the advertisement, other terms and conditions and the application forms are available in the University website www.gauhati.ac.in

Asstt. Professor (Contractual)

2. M.Sc. Microbiology Course in Botany

3 1.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biochemistry (1 post). (Preference will be given to candidates having experience in Biochemistry).

2.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Bioinformatics).

3.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Microbial Genetics).

As per UGC norms

Pay Band & Academic Grade Pay : (Consolidated pay) : Rs. 21,600/- per month

Application Form : Prescribe application form may download from the G.U. website www.gauhati.ac.in

Last date of receipt of filled-in application is 08.01.2015.

Advertisement: www.gauhati.ac.in/openfile.php?file=Notice1258.pdf

A recent study by Webster and Chapman introduces Buscogeny (https://github.com/Jwebster89/Buscogeny), an open-source bioinformatics pipeline designed to make this process easier. The tool uses BUSCO (Benchmarking Universal Single-Copy Orthologs), which identifies conserved genes that are expected to occur as single copies in particular groups of organisms. These genes act like evolutionary landmarks, allowing researchers to compare genomes and investigate their relationships.

Buscogeny brings several steps of phylogenomic analysis into one workflow. It identifies BUSCO genes, extracts and aligns their sequences, removes unreliable regions, combines information from multiple genes, and uses the resulting data to construct a phylogenetic tree. It also provides quality-control information, helping researchers identify genomes that may be too incomplete for reliable analysis.

The authors demonstrate the usefulness of Buscogeny with bacterial and fungal genomes, including Alternaria. This is particularly valuable because fungal genomes can vary greatly in quality and annotation. Ultimately, Buscogeny helps transform massive amounts of genomic data into an understandable evolutionary story. Each DNA sequence becomes a clue, each conserved gene becomes a landmark, and together these clues reveal a picture of how life is connected.

More at https://link.springer.com/article/10.1007/s10123-025-00752-6?

Study Subject(s): PhD position is award in the field of Bioinformatics/Computer Science.
Course Level: Position is available for pursuing PhD degree level at the University of Macau.
Scholarship Provider: University of Macau
Scholarship can be taken at: China

Eligibility: The ideal candidate would be a master degree holder in Bioinformatics or related disciplines with knowledge in Medical sciences or Life sciences (with GPA of at least 3.0 on a 4-point scale or equivalent) . Knowledge in programming (C and C++) and Linux scripting are necessary; experience in molecular docking, molecular dynamics simulations or molecular modeling is an advantage. The candidate should be fluent in spoken and written English; preference will be given to applicants with good publication records in relevant areas.

Scholarship Open for International Students: Researchers from China can apply for this PhD position.

Scholarship Description:

The Computational Biology and Bioinformatics Group at the University of Macau is looking for a motivated PhD student in Bioinformatics or Computer Science to work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems.

Number of award(s): There is only one PhD position available.

Duration of award(s): The duration of this PhD position is 2-3 years.

What does it cover? Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month).

Selection Criteria: Not Known

Notification: Not Known

How to Apply: Send your current CV, your academic transcripts, a letter of motivation and research interests, two letters of recommendations from academic faculty to Dr. Shirley Siu at shirleysiu[at]umac.mo before March 2015.

Scholarship Application Deadline: The applications should be submitted before March 2015.

You can also add your favourite NGS educational material, or workshop tutorial by commenting on this bookmarks for user benefit. 

Understanding the basics of genome sequencing:

Tutorial by Luke Jostins.

http://www.genetic-inference.co.uk/blog/2009/04/basics-sequencing-dna-part-1/

http://www.genetic-inference.co.uk/blog/2009/08/basics-sequencing-dna-part-2/

A window into third-generation sequencing

http://hmg.oxfordjournals.org/content/19/R2/R227.full.pdf

==============================================

NGS data analysis pipelines

• Detecting and annotating genetic variations using the HugeSeq pipeline  DOI: 10.1038/nbt.2134
• NARWHAL, a primary analysis pipeline for NGS data http://bioinformatics.oxfordjournals.org/cgi/content/abstract/28/2/284?etoc
• RseqFlow: Workflows for RNA-Seq data analysis  DOI: 10.1093/bioinformatics/btr441
• ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence  10.1186/1471-2164-12-285
• A framework for variation discovery and genotyping using next-generation DNA sequencing data  PubMed: 21478889
• SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects  DOI: 10.1186/1471-2105-12-134 Abstract: http://www.biomedcentral.com/1471-2105/12/134/abstract
• WEP: a high-performance analysis pipeline for whole-exome data http://www.biomedcentral.com/1471-2105/14/S7/S11
• DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. http://www.ncbi.nlm.nih.gov/pubmed/23657089
• GATK: a Toolkit for Genome Analysis http://www.broadinstitute.org/gatk/
• Metagenomics:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsmetagenomics/
• RNASeq:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsrnaseq/
• Bioinformatics and Seq courses: http://www.isb-sib.ch/training/training-activities-schedule/archive-2013.html
• Variant Detection (Model organism) Advanced tutorial https://docs.google.com/document/pub?id=1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM
• Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI
• Microbial de novo Assembly for Illumina Data Introductory tutorial https://docs.google.com/document/pub?id=1N3AB9ptISUu4zULqe1kXpVF0BDyGb5f5yzxWSJd_WNM
• RNAseq Differential Gene Expression Introductory tutorial https://docs.google.com/document/pub?id=1KbTiBHtvHLfPRZ39AY3uriazrINA8TJzgjjwn1zPP7Y

" Please add your favourite NGS link below in comment section for the benefit of bioinformatics community ". 

Address of the bookmark: http://chagall.med.cornell.edu/NGScourse/

Recruitment for Project

Applications were invited from the citizens of India for filling up the following temporary position for the CSIR sponsored Fellowship in the School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067. This position is temporary for a period of two and half years or tenable only for the duration of the project. The requisite qualifications & experience are given below.

Project Title : "Understanding Complex dynamics and Information processing in Brain Networks"
Funding Agency : CSIR

Principal Investigator : Dr. R.K. Brojen Singh

Position : Junior Research Fellow(One post)

Salary : As per CSIR rules and guidelines for JRF.

Qualifications & Experience : M.Sc. in Physics/Mathematics/Biology/B.Tech. In Eng. Physics/Comp. Sc. and desirable CSIR-UGC NET Qualified. Candidates should also have at least one years research experience after M. Sc./B.Tech. in works related to Neuroscience/Mathematical modeling.

Candidates possessing requisite qualifications may apply either on plain paper stating the project title along with CV and send to the following address or send as email attachment (pdf or word format) so as to reach on or before 8 January, 2014.

Dr. R.K. Brojen Singh
School of Computational and Integrative Sciences
Jawharlal Nehru University
New Delhi 110067
Email: brojen@jnu.ac.in, brojen@mail.jnu.ac.in

Address of the bookmark: http://www.nature.com/srep/2015/150707/srep11996/full/srep11996.html

Address of the bookmark: https://github.com/vice87/gam-ngs