<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/1970?offset=330 https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics Tue, 17 Mar 2020 06:19:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics <![CDATA[JCVI:Python utility libraries on genome assembly, annotation and comparative genomics]]> Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42713/gggenomes-a-grammar-of-graphics-for-comparative-genomics Mon, 01 Feb 2021 14:47:32 -0600 https://bioinformaticsonline.com/bookmarks/view/42713/gggenomes-a-grammar-of-graphics-for-comparative-genomics <![CDATA[gggenomes: A grammar of graphics for comparative genomics]]> gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization packageggplot2 by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example, quickly zoom in into gene neighborhoods.

Address of the bookmark: https://github.com/thackl/gggenomes

]]> Surabhi Chaudhary https://bioinformaticsonline.com/blog/view/45278/the-day-we-began-reading-the-dna-of-the-world Sat, 05 Sep 2026 01:43:21 -0500 https://bioinformaticsonline.com/blog/view/45278/the-day-we-began-reading-the-dna-of-the-world <![CDATA[The Day We Began Reading the DNA of the World]]> 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
  1. 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.
  2. Vertebrate Genomes Project (VGP) - Focuses on producing high-quality reference genomes for vertebrate species, providing a major foundation for the wider Tree of Life.
  3. Darwin Tree of Life - A UK and Ireland initiative aiming to sequence approximately 70,000 species, creating a detailed genomic map of regional biodiversity.
  4. African BioGenome Project (AfricaBP) - A pan-African initiative focused on sequencing Africa's biodiversity while strengthening genomics and bioinformatics capacity across the continent.
  5. European Reference Genome Atlas (ERGA) - A European effort to generate high-quality reference genomes for Europe's biodiversity and connect national sequencing efforts.
  6. Canada BioGenome Project - Building reference genomes for Canadian biodiversity, supporting conservation, research and the study of ecosystems.
  7. California Conservation Genomics Project - Uses genomics to understand and protect California's biodiversity and help inform conservation decisions.
  8. Bat1K - An ambitious global effort to sequence the genomes of all known bat species, helping scientists study their evolution, longevity, immunity and unique biology.
  9. Bird 10,000 (B10K) - A global project aiming to create genome resources covering the world's bird diversity and reconstruct avian evolutionary history.
  10. Global Invertebrate Genomics Alliance (GIGA) - Builds genomic resources for the enormous and genetically diverse world of invertebrates.
  11. GenomeIndia - India's national human-genome initiative, designed to capture the country's extraordinary population diversity and create a reference resource for Indian genomics.
  12. All of Us Research Program - A US national research program combining genomic information with health and lifestyle data at population scale.
  13. 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.
  14. 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.
  15. Saudi Genome Program - A national genomics initiative focused on genetic diseases, population genomics and precision medicine in Saudi Arabia.
  16. 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.
]]> Jitendra Narayan https://bioinformaticsonline.com/researchlabs/view/44400/pevzner-lab Thu, 02 Nov 2023 05:39:26 -0500 <![CDATA[Pevzner Lab !]]> The laboratory works on genome sequencing, immunoproteogenomics, antibiotics sequencing, and comparative genomics - computational technologies that enabled new applications and allowed scientists to attack biological problems that remained beyond the reach of previous techniques.

https://bioalgorithms.ucsd.edu/research4.html

]]> https://bioinformaticsonline.com/opportunity/view/840/junior-research-fellow-jrf Sat, 13 Jul 2013 11:17:22 -0500 <![CDATA[Junior Research Fellow (JRF)]]> School of Biotechnology
Gautam Buddha University
Greater Noida, UP - 201310

Applications are invited for one position of Junior Research Fellow (JRF) in a Department of Biotechnology (DBT) sponsored research project entitled “Design, synthesis and evaluation of potent aminopeptidase inhibitors for malarial therapy” under the supervision of Dr. Shakti Sahi.

The monthly fellowship of JRF will be Rs 12,000/- plus HRA as per the University rules.

Essential Qualification: Master degree in any discipline of Life Science with NET qualified.

Desirable Qualification: Preference will be given to candidates having research experience in in silico drug designing/Bioinformatics.

Interested candidates may send their resume to undersigned on or before 14th July 2013 by post-mail/e-mail shaktis@gbu.ac.in or shaktisahi@gmail.com. No TA and DA will be paid for appearing for the interview. Dr. Shakti Sahi (Principle Investigator)

Advertisement:
www.gbu.ac.in/Recruitment/JRF_Advt_DBTProject_Shakt

]]> https://bioinformaticsonline.com/opportunity/view/29849/ra-bioinformatics-at-national-institute-of-cancer-prevention-research-icmr Thu, 17 Nov 2016 04:11:09 -0600 <![CDATA[RA Bioinformatics at NATIONAL INSTITUTE OF CANCER PREVENTION & RESEARCH (ICMR)]]> NATIONAL INSTITUTE OF CANCER PREVENTION & RESEARCH (ICMR)

Noida 201301 (U.P)

Applications are invited upto 21.11.2016 from interested candidates as per details available on NICPR website (www.nicpr.res.in)/ ICMR website (www.icmr.nic.in) to fill up following temporary position in the time bound DHR Project entitled “Next generation EGFR inhibitor identification using ligand based QSAR technique” under Dr. Subhash M. Agarwal, Scientist-D, Division of Bioinformatics.

Research Assistant (One)

Rs.27000/- p.m. (Fixed/temporary)

Essential: M.Sc. in Bioinformatics or related field.

Desirable: Experience in QSAR and structure based drug designing.

More Info : www.icmr.nic.in/icmrnews/NICPR_Advertisement%20for%20RA.pdf

]]> https://bioinformaticsonline.com/researchlabs/view/4552/imtech-lab Sun, 15 Sep 2013 09:41:04 -0500 <![CDATA[IMTECH Lab]]> Computer Aided Protein Structure Prediction; Identification of Vaccine
Candidates (T-Epitope prediction); Analysis of Nucleotide/Protein Sequences; Development of Web Server/

Software; Creation of Public Domain Resources in Biology
Present Status::

Developing prediction methods for gene, beta-turn, secondary structure and MHC-binding sites.
Area of Interest ::

Comparison of force field simulations. Analysis of DNA-protein interactions using molecular mechanics methods.Drug Target Identification using in silico biology.

More @ http://www.imtech.res.in/bic/index.php?option=com_content&view=article&id=65

PIs: http://www.imtech.res.in/bic/index.php?option=com_content&view=article&id=69

]]> https://bioinformaticsonline.com/researchlabs/view/4547/bioinformatics-infrastructure-facility Sun, 15 Sep 2013 09:22:25 -0500 <![CDATA[Bioinformatics Infrastructure Facility]]> The Bioinformatics Infrastructure Facility has started working in the year 2007 at Presidency College, Kolkata. It is one of the premier institutes of India and boasts of a rich heritage and great alumni. The Infrastructure Facility has a dedicated team headed by Sayak Ganguli and ably supported by Priayanka Dhar. The coordinator of the facility is Abhijit Datta of the Post Graduate Department of Botany. The lab mainly focusses on the analysis of the RNA Induced Silencing Complex. Recent highlights include the presentation of a paper at the RNAi World Congress.

More @ http://bioinfo-presiuniv.edu.in/index.php

]]> https://bioinformaticsonline.com/researchlabs/view/4546/sowdhamini-lab Sun, 15 Sep 2013 09:19:12 -0500 <![CDATA[SOWDHAMINI Lab]]> Genome sequencing projects have enormous potential for benefiting human endeavors. However, just as acquiring a language's vocabulary does not enable one to speak it, databases that list the amino acid composition of proteins do not directly tell us much about these proteins' higher-level structure and function. The most productive way to indirectly exploit these databases has been to start with the small number of proteins that are fully-characterised and to assume that other "similar" proteins will have a related structure and function. Proteins with very similar amino acid sequence are "no-brainers", but the real test, which our group largely focuses on, is to detect the "essential" similarity in proteins whose non-critical sections have experienced random rearrangements during evolution. In such cases functionally similar proteins may have less than 25% sequence overlap.

More @ http://www.ncbs.res.in/sowdhamini/groups_sowdhamini.htm

]]> https://bioinformaticsonline.com/opportunity/view/4726/advances-in-molecular-dynamics-of-biomolecules-december-3-4-2013-jnu Mon, 23 Sep 2013 10:20:10 -0500 <![CDATA["Advances in Molecular Dynamics of Biomolecules" December 3-4, 2013 @ JNU]]> The extensive growth of computational power and resources over the last two decades has led to a remarkable progress in the large scale simulations at the molecular level. Molecular Dynamics (MD) simulations have been an invaluable tool in elucidating the structural, physico-chemical and dynamic properties of various types of materials both in biology and material science, complementing experimental information. With the state-of -the –art computers, it is currently possible to simulate systems containing several thousands of atoms ranging from hundreds of nanoseconds to microseconds and milliseconds! Since simulation algorithms combine domain knowledge from various disciplines of basic science and computer programming, training manpower in such interdisciplinary fields may be hardly achieved within the boundaries of a prescribed academic curriculum. Thus it is of interest of the academic institutions to conduct regular workshops to advance the existing knowledge in the emerging research areas like Molecular Dynamics of biomolecules.

The objective of this conference is two-fold:

Understanding different algorithms of MD and their relevant applications.
Hands-on practical exercises using NAMD.

More at http://ccbb.jnu.ac.in/advmdbio/

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