BOL: Related items

chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

Jit — Thu, 03 Feb 2022 04:01:55 -0600

chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

USAGE:

-query: sequence A in fasta format
-db: sequence B in fasta format
-out: output matrix
-kmer Integer: k>1 (default 32) Use 32 for chromosomes and genomes and 16 for small bacteria
-diffuse Integer: z>0 (default 4) Use 4 for everything - if using large plant genomes you can try using 1
-dimension Size of the output matrix and plot. Integer: d>0 (default 1000) Use 1000 for everything that is not full genome size, where 2000 is recommended

Address of the bookmark: https://github.com/estebanpw/chromeister

GPS DNA tracking - University of Sheffield

Sat, 10 May 2014 04:33:28 -0500

University of Sheffield geneticist and bioinformatics expert Dr Eran Elhaik demonstrates the power of his new DNA research, which allows people to discover their genetic homeland from 1000 years ago. Find out more about our biological research here http://www.sheffield.ac.uk/aps

Managing and Analyzing Next-Generation Sequence Data

Rahul Agarwal — Sat, 10 May 2014 06:28:06 -0500

Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental technology. Recently faced with an unprecedented flood of data generated by the next generation of DNA sequencers, these groups found it necessary to respond quickly and efficiently to the informatics and infrastructure demands. Centralized Facilities newly facing this challenge need to anticipate time and design considerations of necessary components, including infrastructure upgrades, staffing, and tools for data analyses and management ...

More at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

Address of the bookmark: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

JBrowse 2: a modular genome browser with views of synteny and structural variation

Abhi — Tue, 25 Apr 2023 20:58:52 -0500

igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests)
jb2-web - stock instance of jbrowse-web v1.7.5
jb1 - stock instance of jbrowse 1 v1.16.11
jb2 embedded - a create-react-app with @jbrowse/react-linear-genome-view

Address of the bookmark: https://github.com/GMOD/jb2profile

Visiting Scientist - Computational Genomics (two positions)

Mon, 07 Jul 2014 22:53:41 -0500

Scientific/Managerial & International Recruitment

ICRISAT seeks applications from Indian nationals Visiting Scientist-Computational Genomics (2 positions), to be part of a team of Centre of Excellence in Genomics (CEG), (www.icrisat.org/ceg) to work on legume genomics projects. The positions will be based at ICRISAT’s Headquarters in Patancheru, Hyderabad, India.

ICRISAT is a non-profit, non-political organization that conducts agricultural research for development in Asia and sub-Saharan Africa with a wide array of partners throughout the world. Covering 6.5 million square kilometers of land in 55 countries, the semi-arid tropics is home to over 2 billion people, with 650 million of these are the poorest of the poor. ICRISAT and its partners help empower those living in the semi-arid tropics, especially smallholder farmers, to overcome poverty, hunger, malnutrition and a degraded environment through more efficient and profitable agriculture. ICRISAT is headquartered in Greater Hyderabad, Andhra Pradesh, India and belongs to the Consortium of Centers supported by the Consultative Group on International Agricultural Research (CGIAR).

The Job: Responsibilities for these positions include:

Analyzing and handling large-scale next generation sequencing DNA and RNA data
Data mining and development of pipelines and troubleshooting
Genome diversity analysis such as SNPs, Indels, Structural Variations, population structure
Genome wide association study (GWAS) related analysis- LD analysis, hapmap and trait mapping
Expression analysis based on RNA-Seq data, annotation, gene ontology and metabolic pathway analysis
Epigenome analysis, small RNA identification
Gene family analysis, sequence level protein analysis, orthology/paralogy and molecular modelling
Compiling and analysis of results, writing reports and research papers

The Person: Ph.D. or MSc/MTech/PGDCA with two years research experience in Biotechnology, Computational biology, Agricultural/ Plant Biotechnology, Genetics, Molecular Biology or related discipline. Good knowledge of programming/scripting in at least two of following languages: Perl, C, C++, R, Shell Scripting and Python is plus.

How to apply: Please apply latest by 20 July 2014. The application should include the name of the position applied for, a letter of motivation, a full Curriculum Vita (CV), and the names and contact information of three references that are knowledgeable of the candidate’s professional qualifications and work experience. Technical details and more information about these positions can be obtained from R.K.VARSHNEY@CGIAR.ORG. All applications will be acknowledged, however only short listed candidates will be contacted.

Apply here https://recruit.zoho.com/ats/Portal.na?digest=T642sgLYWZOStExJ77cPrcM*sIMGZETWw4yPxngbmHA-

R programming and Jobs website

Pragati Singh — Sun, 25 May 2014 14:43:57 -0500

Welcome to the R Jobs section of ProgrammingR.com. If your organization has an R employment opportunity that you would like to have posted here, submit it via the contact page. Prospective employees: use the contact information provided in the position listing to apply or contact the hiring organization.

Address of the bookmark: http://www.programmingr.com/category/stype/r-job-listings/

The Day We Began Reading the DNA of the World

Jitendra Narayan — Sat, 05 Sep 2026 01:43:21 -0500

Picture waking up and knowing that in one lab, a scientist is reading the DNA of a whale. In another, a team is sequencing a rare plant. Meanwhile, researchers in India are decoding the genomes of different human populations.

Many organisms. Many countries. All share one remarkable goal: to understand the genetic story of life.

DNA is nature's instruction manual, written with just four letters: A, T, C, and G. For years, scientists could only read small sections of this huge book. Now, new sequencing technology lets us read entire genomes like never before.

One of the most ambitious projects is the Earth BioGenome Project (EBP). Its goal is to create reference genomes for about 1.5 million known eukaryotic species. This project links genome research across continents, species, and scientific fields.

But this story goes beyond just animals and plants.

A New Chapter in Human Genomics

Large human genome projects are changing how we understand our own genetic diversity.

India's GenomeIndia project has sequenced thousands of people from different populations. This work is uncovering genetic variation that global databases have often missed.

Similar population-scale effSimilar large-scale projects are happening worldwide. The All of Us Research Program in the United States, Europe's 1+ Million Genomes initiative, South Korea's national genomic data program, and projects in Saudi Arabia, Australia, and Singapore are all building huge genomic resources.collect DNA.

The real goal is to link genomes with health, disease, and other biological information. This creates a base for more accurate research and, in time, more personalized medicine.

A Race Against Time

There is also an important twist.

We are sequencing Earth's biodiversity even as many species face growing environmental threats.

A genome alone cannot save a species, but it does keep important information about its biology, evolution, and genetic diversity. This knowledge helps scientists understand risks, guide conservation, and find traits that could help agriculture or medicine.

Projects like the Darwin Tree of Life, which studies species in Britain and Ireland, and the African BioGenome Project, which is growing genomics work across Africa, are key parts of this worldwide effort.

Projects to Watch

Earth BioGenome Project (EBP) - A global effort to sequence and annotate roughly 1.5 million known eukaryotic species and create a comprehensive reference library of Earth's biodiversity.
Vertebrate Genomes Project (VGP) - Focuses on producing high-quality reference genomes for vertebrate species, providing a major foundation for the wider Tree of Life.
Darwin Tree of Life - A UK and Ireland initiative aiming to sequence approximately 70,000 species, creating a detailed genomic map of regional biodiversity.
African BioGenome Project (AfricaBP) - A pan-African initiative focused on sequencing Africa's biodiversity while strengthening genomics and bioinformatics capacity across the continent.
European Reference Genome Atlas (ERGA) - A European effort to generate high-quality reference genomes for Europe's biodiversity and connect national sequencing efforts.
Canada BioGenome Project - Building reference genomes for Canadian biodiversity, supporting conservation, research and the study of ecosystems.
California Conservation Genomics Project - Uses genomics to understand and protect California's biodiversity and help inform conservation decisions.
Bat1K - An ambitious global effort to sequence the genomes of all known bat species, helping scientists study their evolution, longevity, immunity and unique biology.
Bird 10,000 (B10K) - A global project aiming to create genome resources covering the world's bird diversity and reconstruct avian evolutionary history.
Global Invertebrate Genomics Alliance (GIGA) - Builds genomic resources for the enormous and genetically diverse world of invertebrates.
GenomeIndia - India's national human-genome initiative, designed to capture the country's extraordinary population diversity and create a reference resource for Indian genomics.
All of Us Research Program - A US national research program combining genomic information with health and lifestyle data at population scale.
1+ Million Genomes / Genome of Europe - A European effort to enable secure, cross-border use of genomic and health data and develop genome-scale resources involving more than one million people.
Korea National Integrated Bio Big Data Project - South Korea's large-scale national effort combining genomic and health information from a very large population cohort.
Saudi Genome Program - A national genomics initiative focused on genetic diseases, population genomics and precision medicine in Saudi Arabia.
Australian Genomics / Genomics Health Futures Mission - Australia's growing investment in genomic medicine, rare disease research and population-scale health genomics.

The Library of Life

The fuThe future of genomics is not just about sequencing one genome at a time. Now, it is about creating a worldwide network of genomes—human and non-human, individual and species—linked by powerful databases and advanced computational tools.ine a library without shelves.

In this library, the books are genomes. The pages are made of DNA. Scientists and machines are the readers. And this library is still being written. Each genome sequenced today adds a new page to the story of life and helps us better understand our place in it.

Claus-Peter Stelzer Lab

Mon, 15 Mar 2021 15:24:41 -0500

Interested in various topics at the intersection of ecology and evolution. In my research I use rotifers as model organisms for experimental studies at the individual and population level. Rotifers are ideally suited for this, because populations of thousands can be kept in small containers in the lab, while single individuals can still be handled conveniently.

More at https://www.uibk.ac.at/limno/personnel/stelzer/index.html.en#research

Stephen Friend: The hunt for "unexpected genetic heroes"

Sat, 31 May 2014 14:31:47 -0500

What can we learn from people with the genetics to get sick — who don't? With most inherited diseases, only some family members will develop the disease, while others who carry the same genetic risks dodge it. Stephen Friend suggests we start studying those family members who stay healthy. Hear about the Resilience Project, a massive effort to collect genetic materials that may help decode inherited disorders. TEDTalks is a daily video podcast of the best talks and performances from the TED Conference, where the world's leading thinkers and doers give the talk of their lives in 18 minutes (or less). Look for talks on Technology, Entertainment and Design -- plus science, business, global issues, the arts and much more. Find closed captions and translated subtitles in many languages at http://www.ted.com/translate Follow TED news on Twitter: http://www.twitter.com/tednews Like TED on Facebook: https://www.facebook.com/TED Subscribe to our channel: http://www.youtube.com/user/TEDtalksDirector

TEDMED Great Challenges: Genomics and Medicine: Where promise meets clinical practice

Fri, 22 Nov 2013 12:05:32 -0600

November 21, 2013 - NHGRI Director Eric Green, M.D., Ph.D, hosted the TEDMED Google+ Hangout to discuss genomic medicine with an all-star cast that includes Carlos Bustamante, James Evans, Amy McGuire and Sharon Terry. More: http://www.tedmed.com/greatchallenges