BOL: Related items

The Tree That Learned to Read Genomes

BioStar — Fri, 11 Sep 2026 00:51:02 -0500

Imagine trying to reconstruct a family tree when many family photographs are missing, some names are unclear, and different relatives remember the past differently. This is similar to the challenge scientists face when trying to understand how organisms are related. Their family records are genomes, and the family tree is a phylogenetic tree. With modern sequencing technologies, scientists now have access to thousands of genomes, but comparing them can be difficult, especially when genomes are incomplete or poorly annotated.

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?

Centre for Systems Biology & Bioinformatics, Panjab University vacancy of Research Fellow

Wed, 12 Nov 2014 06:18:54 -0600

Applications are invited along with complete bio-data and attested copies of certificates of qualifications, experience etc. for the one post of
Research Fellow and one post of Program Assistant under PURSE Grant of the University in Centre for Systems Biology & Bioinformatics, UIEAST, Panjab University, Chandigarh which is tenable till the period of the project

Essential Qualification
For Research Fellow:-
M.Sc. in Systems Biology and Bioinformatics / Life
Sciences with minimum 55% marks.
Preference will be given to NET/GATE/ICMR qualified candidates without fellowship however, candidates who have cleared the Panjab University Ph.D. entrance test in Systems Biology & Bioinformatics will also be eligible.

Applications should be reach on or before 19-11-2014 in the office of the undersigned. Interview will be held on 21-11-2014 in the office of the Coordinator, Centre for Systems Biology & Bioinformatics, South Campus, Block-3, Sector-25, Panjab University, Chandigarh. No TA/DA will be paid.

more at http://jobs.puchd.ac.in/includes/jobs/2014/20141110143634-Advertisement.pdf

The Human Genome Project Video 3D Animation Introduction Low)

Sat, 24 Aug 2013 19:01:19 -0500

Bioinformatics JRF/RA/SRF position at Institute of Cytology and Preventive Oncology (ICPO)

Wed, 19 Nov 2014 20:16:32 -0600

Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301

Candidates having the below mentioned qualifications may appear for walk in interview at ICPO on 2nd December 2014 between 10.00 AM and 12:00 PM under the below time bound projects under Dr. Subhash M. Agarwal, Scientist C. The post is purely temporary and co-terminus with the project.

Research Assistant (One)
25650/- consolidated
Discovery of EGFR secondary mutant inhibitors using structure based screening approach (ICMR)
Duration: 7 months

Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record.

Desirable: Experience in scripting and molecular docking.

Below 30 years

Junior Research Fellow (One)

16,000 + 30% HRA = Rs. 20800/-

Identification of novel inhibitors targeting EGFR using an integrated ligand and structure based approach (DBT)

Duration: 9 months

Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record. Candidates with CSIR-UGC / ICMR, NET qualification will be preferred

Desirable: Experience in scripting, QSAR and molecular docking.

Below 28 years

Interested eligible candidates may send their applications with Bio-data by email at (smagarwal@gmail.com) or by post addressed to Dr. Subhash M Agarwal, Scientist C, Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301 so as to reach latest by 1st December, 2014. The candidates may appear for interview at ICPO along with 3 copies of CV, photo and relevant certificates of qualifications in original and reprints of publications at the time of interview. It should be noted that No TA/DA will be paid for the walk in Interview.

Advertisement: www.icpo.org.in/advt-walk-in-interview.docx

Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer'

Yeshodari — Wed, 11 Feb 2015 04:59:57 -0600

Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer'

Abstract

Whole exome DNA sequencing (WES) or whole genome DNA sequencing (WGS) allows detection of mutations and polymorphisms in all exonic and genomic regions, respectively, while messenger RNA sequencing (RNA-Seq) enables quantitative analysis of gene expression. Mutations in the genome result in diverse transcriptional aberrations that can be missed in a stand-alone WES/WGS analysis. An integration of DNA variant analysis and RNA-Seq analysis enables one to investigate the consequences of genomic changes in the RNA transcripts including germline and somatic changes, imprinting, RNA editing and allele specific expression (ASE). In this webinar, we will demonstrate this integrated approach using Strand NGS to identify high confidence mutations, RNA editing events and ASE in cancer.

Webinar Details

Sessions	San Francisco Time (PST)	Tokyo Time (GMT+09:00)	Berlin Time (GMT+01:00)	Mumbai Time (GMT+05:30)
Session 1	25 Feb 12:30 AM	25 Feb 5:30 PM	25 Feb 9:30 AM	25 Feb 2:00 PM
Session 2	25 Feb 9:00 AM	26 Feb 2:00 AM	25 Feb 6:00 PM	25 Feb 10:30 PM

Register here: http://www.strand-ngs.com/webinar_registration

About Speaker:

Dr. Veena Hedatale, has a PhD in Plant Genetics from The Radboud University, Netherlands focused on meiosis and recombination. Her prior academic experience at Cornell University was on genetic mapping and gene transformation in Rice. She has worked with Monsanto, and contributed to data mining, database development as well as gene/promoter/pathway discovery for traits related to yield and stress in crop species. At Strand, Veena has worked on Pharmacogenomic analysis of targets and Gene family analysis projects. Currently, she is part of the Strand NGS Application Science team and is involved in the analysis of next generation sequencing data.

Please feel free to contact us 24/5, for availing free online training or if you have any questions.

Email: sales@strandngs.com

Phone (USA): 1-800-752-9122

Phone (ROW): +1-650-353-5060

Genome Origami

Jitendra Narayan — Fri, 12 Dec 2014 22:48:17 -0600

There are several interesting factoid about our genomes, one of them is their folding. If we stretched out the DNA in a single cell, which is only a few millionths of an inch wide, it would span more than six feet. In other word, the size of six feet DNA fold themself to fit in a few millionths of an inch wide space. These DNA folding is a dynamic process that changes over time (!!). Researchers around the world have been trying to understand how DNA folds itself up so efficiently, and a recent post on the NIH Director’s Blog highlights new research illustrating how the human genome folds inside the cell’s nucleus, as well as how DNA folding affects gene regulation. The research team created this delightful video that demonstrates the principles involved using origami art.

http://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome

Researchers have been working to determine how cells regulate gene expression for nearly as long as we’ve known about DNA. How, for example, do nerve cells know to turn off only nerve cell genes and turn off bone cell genes? DNA folding loops are part of the answer. This research team, which published their findings in a paper in Cell http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4 , found that the number of loops is much lower than expected. There are only 10,000 loops instead of the predicted millions, and they form on/off switches in DNA.

More at http://www.eurekalert.org/pub_releases/2014-12/ru-3mr121114.php

Reference http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4

Live Webinar on RNA-Seq Data Analysis on 9 Nov 2016

Strand — Wed, 19 Oct 2016 05:25:27 -0500

Live Webinar on RNA-Seq Data Analysis

Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical approach and Splicing events detection. Strand NGS also supports novel discovery like identification of novel genes, exons and Novel splice junctions, alongside it can also detect gene fusion events. Further downstream analysis such as GO and pathway analysis can be performed on the set of interesting genes. The product has an option to create pipelines for time consuming jobs which automates analysis and leaves more time for end data interpretation. This webinar will give an overview of the features in the RNA-Seq data analysis workflow in Strand NGS and also highlights on parameters within each feature that can be optimized depending on datasets and analysis needs.

Speaker: Mr. Sugandan Sivamani, Senior Application Scientist, Strand Life Sciences

Date: 9th Nov, Session 1 for SAPK/ APFO: 2:30 PM IST Date: 9th Nov, Session 2 for AFO/ EMEA: 9:00 AM PST

WALK – IN – INTERVIEW @ Agricultural Knowledge Management Unit Indian Agricultural Research Institute, New Delhi-110012

Fri, 12 Dec 2014 21:33:02 -0600

Walk-in-interview for the following temporary positions will be conducted on 20th December 2014 (between 10:00 AM to 01:00 PM) at Agricultural Knowledge Management Unit, A0 block (Ground Floor), LBS Building, Indian Agricultural Research Institute, New Delhi-110012:

1 Dr. A.K.Mishra Coordinator & PI (BTISnet)

Traineeship (two) for one year

Rs. 5000/- (consolidated)

M.Sc. (Bioinformatics) with 60 % marks from a recognized University

20-12-2014 (10:00 AM -11:00 AM)

Studentship (four) for one year

Rs. 2500/- (consolidated)

Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University

20-12-2014 (11:00 AM- 1:00 PM)

The positions are purely temporary and co-terminus with the DBT Programme. Eligible candidates are requested to submit the application form in the prescribed format along with original certificates/ documents (Degree, Marks sheets, Work experience, if any) at the time of interview. No TA/DA will be paid. Maximum age limit is 28 years for all positions. Age relaxation of 5 yrs for SC/ST and woman candidates and 3 years for OBC candidates will be given. Canvassing in any form invites disqualification.

Advertisement: http://www.iari.res.in/files/BIC-08122014-20141208-172344.pdf

Quick next generation sequencing (NGS) terms definition

Neel — Fri, 09 Jun 2017 04:52:26 -0500

fragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants, mapping locations of the paired ends span within an interval [δmin,δmax]. Most (>90%) of paired-end reads are sampled from no-SV regions, therefore the fragment size distribution can be learned empirically for each WGS data set separately.

concordant reads: a read pair is called concordant if they can be mapped to the reference genome as “expected”: (a) mapped to opposing strands where the upstream read is mapped to the forward strand and the downstream read is mapped to the reverse strand2, (b) the distance between ends is between the minimum and maximum expected fragment size.

discordant reads: briefly, any non-concordant read pair is considered discordant. Note that, by definition, the discordant read pairs signal potential SVs. The sequence signature produced by these type of reads is known as read-pair signature.

split reads: a read that can only be mapped to the reference genome by breaking into two sub-reads is called a split-read. These types of reads also indicate a potential SV or a short insertion or deletion (indel).

read depth: number of reads that map within a region of the genome. Overall genome-wide read depth is also referred to as depth of coverage. It is expected that the number of reads that “cover” each base-pair to follow a Poisson distribution. Therefore, if the read depth over a certain region deviates significantly from this distribution, it signals for a potential copy number variation (CNV).

MIX: Combining multiple assemblies from NGS data

Rahul Nayak — Tue, 08 May 2018 04:58:05 -0500

Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.

The Mix algorithm, approach and results were published in BMC bioinformatics : http://www.biomedcentral.com/1471-2105/14/S15/S16.

Address of the bookmark: https://github.com/cbib/MIX