BOL: Related items

Ley Lab !

Fri, 11 Sep 2026 13:21:10 -0500

Research Program aims to elucidate how gut microbial species relate to genotypic differences between human individuals, to identify bacterial and archaeal species that share an evolutionary history with humans, and to determine the molecular basis of long-term host-microbial relationships. We approach these aims through a combination of population-level observations and laboratory-based molecular-level investigations. We link inter-microbial and microbial-host interactions at the molecular scale to patterns at population and evolutionary scales.

More at https://leylab.com/

HumCFS: a database of fragile sites in human chromosomes

Abhimanyu Singh — Sun, 21 Apr 2019 20:17:29 -0500

Fragile sites are specific chromosomal region that exhibit an increased frequency of chromosdomal breakge when cells are exposed to replicative stress. Since from the discovery of chromosomal fragile sites/regions (CFS), several line of evidence suggests their involvement in human pathologies and they have been recognized as a preferential site for integration of exogenous oncogenic DNA viruses and hotspots for chromosomal re-arrangement. There is large gap in our knowledge of human CFS region as knowledge about CFS are unequally distributed in literature, which impose a problem in studying these region. In order to address these issues, we develop this platform HumCFS, which provides comprehensive information about experimentally identified CFS at a single source.

https://link.springer.com/epdf/10.1186/s12864-018-5330-5?author_access_token=ICASEpyMAQaxLlKw--fyCG_BpE1tBhCbnbw3BuzI2RMA57KLmXk5bZabRUiDQzRFHXd6hjm4kWSiLV3mU5XVMitqXUwFMSo4x5vbfty0EDQ9PW1sd1h923_TYXkvJ5niSwAyZ7BklJ0ujFAFhcKtjw%3D%3D

Address of the bookmark: https://webs.iiitd.edu.in/raghava/humcfs/

Does anyone have Nanopore latest updates?

Poonam Mahapatra — Mon, 12 Aug 2013 12:19:29 -0500

There was a lot of buzz about Oxford Nanopore Technologies® is developing the GridION™ system and miniaturised MinION™ device. These are a new generation of electronic molecular analysis system for use in scientific research, personalised medicine, crop science, security/defence and more. The platform technology uses nanopores to analyse single molecules including DNA/RNA and proteins. With a broad patent portfolio, the Oxford Nanopore pipeline includes biological nanopores and solid-state nanopores.

Is this available, or still under trial mode?

https://www.nanoporetech.com/

https://www.nanoporetech.com/technology/the-minion-device-a-miniaturised-sensing-system/the-minion-device-a-miniaturised-sensing-system

The Human Genome Project Video 3D Animation Introduction Low)

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

The genome factory !!!

Madhvan Reddy — Thu, 16 Jan 2014 02:09:31 -0600

Illumina, Inc. announced Tuesday that its new HiSeq X Ten Sequencing System has broken the “sound barrier” of human genomics by enabling the $1,000 genome. “This platform includes dramatic technology breakthroughs that enable researchers to undertake studies of unprecedented scale by providing the throughput to sequence tens of thousands of human whole genomes in a single year in a single lab,” Illumina stated.

Initial customers for the HiSeq X Ten System, which will ship in Q1 2014, include Macrogen, based in Seoul, South Korea and its CLIA laboratory in Rockville, Maryland, the Broad Institute in Cambridge, Massachusetts, and the Garvan Institute of Medical Research in Sydney, Australia.

“For the first time, it looks like it will be possible to deliver the $1,000 genome, which is tremendously exciting,” said Eric Lander, founding director of the Broad Institute and a professor of biology at MIT. “The HiSeq X Ten should give us the ability to analyze complete genomic information from huge sample populations. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine.”

“The HiSeq X Ten is an ideal platform for scientists and institutions focused on the discovery of genotypic variation to enable a deeper understanding of human biology and genetic disease,” Illumina stated. “It can sequence tens of thousands of samples annually with high-quality, high-coverage sequencing, delivering a comprehensive catalog of human variation within and outside coding regions.”

HiSeq X Ten utilizes a number of advanced design features to generate massive throughput. Patterned flow cells, which contain billions of nanowells at fixed locations, combined with a new clustering chemistry deliver a significant increase in data density (6 billion clusters per run). Using state-of-the art optics and faster chemistry, HiSeq X Ten can process sequencing flow cells more quickly than ever before — generating a 10x increase in daily throughput when compared to current HiSeq 2500 performance.

The HiSeq X Ten is sold as a set of 10 or more ultra-high throughput sequencing systems, each generating up to 1.8 terabases (Tb) of sequencing data in less than three days or up to 600 gigabases (Gb) per day, per system, providing the throughput to sequence tens of thousands of high-quality, high-coverage genomes per year. Illumina says the $1,000 includes typical instrument depreciation, DNA extraction, library preparation, and estimated labor.

Next generation sequencing(NGS) books

Abhimanyu Singh — Fri, 30 May 2014 04:48:04 -0500

Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream.

This bookmark is created to provide NGS online books links.

Address of the bookmark: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version

Genomic Medicine - Bruce Korf (2014)

Tue, 24 Jun 2014 07:58:44 -0500

May 21, 2014 - Current Topics in Genome Analysis 2014 A lecture series covering contemporary areas in genomics and bioinformatics. More: http://www.genome.gov/COURSE2014

Roderic Guigó Lab

Mon, 01 Sep 2014 17:13:00 -0500

Research in our group focuses on the investigation of the signals involved in gene specification in genomic sequences (promoter elements, splice sites, translation initiation sites, etc…). We are interested both in the mechanism of their recognition and processing, and in their evolution. In addition, but related to this basic component of our research, our group is also involved in the development of software for gene prediction and annotation in genomic sequences. Our group also actively participates in the analysis of many eukaryotic genomes and it in involved in the NIH-funded ENCODE project. Furthermore we are members of two large cancer-studies consortia (chronic lymphocytic leukemia "CLL" and Breast Cancer -Hospital del Mar/CRG/Roche-).

More at http://big.crg.cat/computational_biology_of_rna_processing

Postdoc position in protein annotation and machine learning - Paris, France

Sat, 04 Oct 2014 08:10:45 -0500

We are interested in finding an excellent postdoc with interests in protein functional annotation, machine learning and computer grids. The position is open for 3.5 years at the Université Pierre et Marie Curie, in the heart of Paris.

Research topic: Protein function annotation, multiple probabilistic models, domain architecture, machine learning, combinatorial optimization, computer grid.

This project is run on the Laboratoire de Biologie Computationnelle et Quantitative UMR7238 CNRS-UPMC – Analytical Genomics team, headed by A.Carbone. It is co-advised with Pierre-Henri Wuillemin, Laboratoire d’Informatique de Paris 6 – Equipe DECISION.

The postdoc will be payed under a contract of Ingénieur de Recherche lasting 3.5 years and it is available from September 1st, 2014.

Group Web Page: http://www.lcqb.upmc.fr/AnalGenom/home.html

Ref. E-Mail: Alessandra Carbone alessandra.carbone@lip6.fr

Sr.Bioinformatics Analyst (NGS) at Ocimum Biosolution

Sat, 15 Nov 2014 04:46:10 -0600

“Ocimum Biosolution” is a comprehensive Integrated Life Science Informatics solutions provider with service offerings that span Sample and Data Management (LIMS, Biologics Data Management), Genomics Data Analysis Services such as Gene Expression, Genotyping, and Next Gen Sequencing, Bioinformatics and Genomics Databases (BioExpress®, ToxExpress®) and Bio-IT consulting services.

Experience Required: 3-5 years of experience

No of Positions : Multiple

Qualifications: Candidates with minimum qualification as M.Sc Bioinformatics with 3-5 years of experience in Life sciences R&D or Pharma Industry.

Ph.D candidates with research experience in Bioinformatics with publications in International journal and minimum 2 years of industry experience in clinical genomics will be preferred for this position.

Requirement:

1. Must have basic understanding of molecular biology and Genomics.

2. Experience in application development or must have expertise in programming using either of Perl/Python.

3. Experience in statistical programming using R/Bioconductor/Matlab.

4. Strong concept in statistical and mathematical modelling.

5. Experience in designing and developing the bioinformatics pipeline.

6. Must have minimum 2+ years of hands on experience in NSG data analysis such as RNA-Seq,Exome-Seq ,Chip-Seq and downstream analysis.

7. Knowledge in WGS ,WES, Targeted re-sequencing,GWAS and population genomics will be preferred.

8. Must have experience working on opensource software/Framework and commercial software for NGS data analysis and reporting.

9. Should be aware of handling big data and guiding team members on multiple projects simultaneously.

10. Should have experience coordinating with different groups of clinical research scientist for various project requirements.

11. Ability to work as team as well as independently with minimal support.

More at http://www.ocimumbio.com/careers1/