BOL: Related items

"IdeasLab"* workshop !

Wed, 02 Feb 2022 06:13:48 -0600

A new, grant-funded opportunity seeks early career researchers interested
in life's origins: https://templetonideaslab.umbc.edu/

Applications are invited to an all-expenses paid position at a 5-day
"IdeasLab"* workshop to be held near Prague CZ in June 2022. Thirty
successful applicants will be drawn in equal number from the relevant
sectors biological evolution, A-Life anbd theoretical physics. The week's
activities will lead these thirty to form interdisciplinary teams which
each propose how they can advance frontiers of abiogenesis research. Up to
$5 million total funding will be available for developing these ideas
produced by the week's activities. Further details of the event,
including the online application form, are found at the link posted above

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

LEGE — Mon, 06 May 2024 06:21:10 -0500

Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767/

Address of the bookmark: http://synorth.genereg.net/

iTOL: interactive Tree Of Life

Jit — Tue, 31 Jan 2017 05:56:30 -0600

Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized tree (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based.

There are several pre-computed trees available for display, including the main Tree Of Life, described in Ciccarelli, et al., 2006. In addition to the precomputed trees, users can upload and display personal trees and data, using the 'Data upload' page or through a personal user account.

Address of the bookmark: http://itol.embl.de/

alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Jit — Mon, 12 Mar 2018 09:24:40 -0500

Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr

http://www.mdpi.com/2073-4425/8/10/248

Address of the bookmark: http://alienness.sophia.inra.fr/cgi/index.cgi

Senior Bioinformatician (Assembly) Moore Aquatic Symbiosis Project Tree of Life

Sat, 02 Oct 2021 00:28:30 -0500

You will have some previous experience with genome bioinformatics or other large scale scientific data analysis, or a newly qualified graduate student with data science skills interested in DNA sequence data. While desirable, previous experience with DNA sequencing data is not strictly necessary for the position. We have a strong publication record and culture of producing open data resources and open source software development. This role requires an investigative and solution-oriented mindset and excellent communication skills to work effectively within large national and international consortia.

More at https://jobs.sanger.ac.uk/vacancy/senior-bioinformatician-assembly-moore-aquatic-symbiosis-project-tree-of-life-458923.html

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Abhimanyu Singh — Fri, 02 Nov 2018 08:16:27 -0500

Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life.

Address of the bookmark: http://ancestralgenomes.org/

Understanding DUMP files from NCBI Taxonomy database !

Shruti Paniwala — Fri, 15 Jul 2022 04:29:05 -0500

*.dmp files are bcp-like dump from GenBank taxonomy database

General information.

Field terminator is "\t|\t"

Row terminator is "\t|\n"

nodes.dmp file consists of taxonomy nodes. The description for each node includes the following

fields:

tax_id -- node id in GenBank taxonomy database

parent tax_id -- parent node id in GenBank taxonomy database

rank -- rank of this node (superkingdom, kingdom, ...)

embl code -- locus-name prefix; not unique

division id -- see division.dmp file

inherited div flag (1 or 0) -- 1 if node inherits division from parent

genetic code id -- see gencode.dmp file

inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent

mitochondrial genetic code id -- see gencode.dmp file

inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent

GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage

hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet

comments -- free-text comments and citations

Taxonomy names file (names.dmp):

tax_id -- the id of node associated with this name

name_txt -- name itself

unique name -- the unique variant of this name if name not unique

name class -- (synonym, common name, ...)

Divisions file (division.dmp):

division id -- taxonomy database division id

division cde -- GenBank division code (three characters)

division name -- e.g. BCT, PLN, VRT, MAM, PRI...

comments

Genetic codes file (gencode.dmp):

genetic code id -- GenBank genetic code id

abbreviation -- genetic code name abbreviation

name -- genetic code name

cde -- translation table for this genetic code

starts -- start codons for this genetic code

Deleted nodes file (delnodes.dmp):

tax_id -- deleted node id

Merged nodes file (merged.dmp):

old_tax_id -- id of nodes which has been merged

new_tax_id -- id of nodes which is result of merging

Citations file (citations.dmp):

cit_id -- the unique id of citation

cit_key -- citation key

pubmed_id -- unique id in PubMed database (0 if not in PubMed)

medline_id -- unique id in MedLine database (0 if not in MedLine)

url -- URL associated with citation

text -- any text (usually article name and authors).

-- The following characters are escaped in this text by a backslash:

-- newline (appear as "\n"),

-- tab character ("\t"),

-- double quotes ('\"'),

-- backslash character ("\\").

taxid_list -- list of node ids separated by a single space

DNA tale of 3 to 4 years old Serbia boy

Rahul Agarwal — Tue, 26 Nov 2013 17:34:00 -0600

The genome of a young boy found underground at Mal’ta near Lake Baikal of eastern Siberia around 24,000 years ago came out as close relative of Europeans and Native Indians.

Link:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?_r=0

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12736.html

Bionics, Transhumanism, and the end of Evolution (Full Documentary)

Fri, 27 Sep 2013 11:54:17 -0500

Bionics, Transhumanism, and the end of Evolution (Full Documentary) . 2013 This documentary and the rest of the documentaries presented relate to important times and figures in history, historic places and sites, archaeology, science, conspiracy theories, and education. The Topics of these video documentaries are varied and cover ancient history, Rome, Greece, Egypt, science, technology, nature, planet earth, the solar system, the universe, World wars, Battles, education, Biographies, television, archaeology, Illuminati, Area 51, serial killers, paranormal, supernatural, cults, government cover-ups, corruption, martial arts, space, aliens, ufos, conspiracy theories, Annunaki, Nibiru, Nephilim, satanic rituals, religion, strange phenomenon, origins of Mankind

The Cat: evolution, domestication and Genome 10k

Sun, 10 Nov 2013 14:33:56 -0600

A public lecture by Dr Stephen J O'Brien at the UCD Earth Institute, University College Dublin, Ireland. Dr O'Brien is a world leading molecular biologist and dedicated conservationist who uses the tools of molecular biology to help protect endangered species and understand devastating diseases such as cancer and AIDS. He received his PhD in Genetics from Cornell University, USA, in 1971. He then joined the prestigious National Cancer Institute, National Institutes of Health as a post-doc in 1971 and, there, served as Founder and Chief of the Laboratory of Genomic Diversity from 1986-2011. In December 2011, he joined the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia, as Chief Scientific Officer. Convinced of the utility of exploring diverse species to advance our understanding of the human genome, Dr O'Brien and his team have assembled over 62,000 animal and 424,000 human tissue/DNA specimens, facilitating wide-ranging studies of disease gene associations, species adaptation and natural history. His research interests and expertise span human and comparative genomics, genetic epidemiology, HIV/AIDS, retro-virology, bioinformatics biodiversity and species conservation. Dr O'Brien is best known for documenting the remarkable genetic uniformity of African cheetahs, resolving the mammalian tree of life, describing heretofore unrecognized species of Orangutans, African forest elephants, and Bornean clouded leopards. He is credited with the discovery of CCR5 delta 32, the first of 20 human AIDS restriction genes, which imparts natural immunity to HIV. He is the one of the founders of the Genome 10K initiative, has published over 750 leading research papers, written multiple books and is adjunct professor in over 12 international leading universities. The UCD Earth Institute, University College Dublin, is a multidisciplinary research and education centre with a focus on creating and sharing new knowledge. We aim to contribute to sustainable solutions for many of the pressing Earth-related problems affecting societies now and in the near future.