BOL: Related items

Memories Can Be Passed Down Through DNA

Sat, 10 May 2014 21:24:10 -0500

The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how this process works, and if it might apply to humans as well. Read More: Parental olfactory experience influences behavior and neural structure in subsequent generations http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3594.html "Using olfactory molecular specificity, we examined the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood." What Is Epigenetics? http://www.sciencemag.org/content/330/6004/611 "The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)-genetics." Epigenetics http://en.wikipedia.org/wiki/Epigenetics Watch More: How to Change Your Genes https://www.youtube.com/watch?v=B5DU9lgbsSE TestTube Wild Card http://testtube.com/dnews/dnews-231-how-too-many-screens-affect-our-brain?utm_source=YT&utm_medium=DNews&utm_campaign=DNWC Is Sexiness Hereditary? https://www.youtube.com/watch?v=z6STRCncvM8 ____________________ DNews is dedicated to satisfying your curiosity and to bringing you mind-bending stories & perspectives you won't find anywhere else! New videos twice daily. Watch More DNews on TestTube http://testtube.com/dnews Subscribe now! http://www.youtube.com/subscription_center?add_user=dnewschannel DNews on Twitter http://twitter.com/dnews Anthony Carboni on Twitter http://twitter.com/acarboni Laci Green on Twitter http://twitter.com/gogreen18 Trace Dominguez on Twitter http://twitter.com/trace501 DNews on Facebook http://facebook.com/dnews DNews on Google+ http://gplus.to/dnews Discovery News http://discoverynews.com

Alignment of closely related whole genomes/scaffolds

Rahul Nayak — Fri, 29 Jan 2016 10:37:27 -0600

With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length, to aid in the study of populations, pan-genomes, and genome evolution.This bookmaks have been created to report new tools for whole genome alignments.

Please report new whole genome alignment tools under comment sections.

Address of the bookmark: http://www.cs.utoronto.ca/~brudno/721.full.pdf

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.

The Gene Detectives: How a New Computational Tool Is Helping Us Read the History Written in Our Genes

BioStar — Thu, 10 Sep 2026 21:23:42 -0500

Imagine opening an ancient family album with no names, dates, or captions. Some photographs are missing, others have been copied, and a few show people who look almost identical. Your challenge is to discover who is related to whom and reconstruct the family story. In evolutionary biology, scientists face a similar mystery when they study genes. Every genome contains clues about its past, but genes can be duplicated, lost, and changed over millions of years, making their history difficult to trace.

A recent study published in PLOS Computational Biology introduces REvolutionH-tl 2.0 (https://pypi.org/project/revolutionhtl/), a computational tool designed to help solve this mystery. The software analyzes protein sequences and identifies evolutionary relationships between genes. It can help researchers detect important events such as gene duplication, gene loss, and speciation, allowing them to reconstruct how genes evolved across different organisms.

What makes the tool especially interesting is its focus on both speed and interpretation. The researchers compared REvolutionH-tl 2.0 with several existing computational tools and reported that it achieved competitive accuracy while requiring less computational time in their tests. The tool also includes visualization features, helping researchers turn complicated genetic data into evolutionary stories that are easier to explore.

Genes are more than simple sequences of DNA; they are records of life’s long history. Each surviving gene carries traces of the changes that shaped it. By bringing together computational analysis and visualization, REvolutionH-tl 2.0 acts like a detective, helping scientists uncover these hidden stories. Ultimately, tools like this can improve our understanding of how genomes evolved and how genes acquired the roles they perform today.

More at https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013017

Center for Molecular Dynamics Nepal (CMDN), Nepal

Wed, 23 Jul 2014 13:54:51 -0500

Center for Molecular Dynamics Nepal (CMDN), established 2007 prides itself as a research driven nongovernmental organization. Unlike other civil society organizations, CMDN is dedicated entirely to promoting research in the country. With its team of energetic and highly motivated experts, CMDN is now recognized as the leading public health and wildlife research organization of the country.

More at http://www.cmdn.org.np/main/index.php

Porechop: tool for finding and removing adapters from Oxford Nanopore reads

Rahul Nayak — Tue, 29 May 2018 07:33:44 -0500

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Address of the bookmark: https://github.com/rrwick/Porechop

JRF in Bioinformatics @ Bioinformatics Centre, North-Eastern Hill University

Thu, 06 Nov 2014 10:24:05 -0600

Applications with complete bio-data are invited for JRF (3) and Project Assistant (1) in a DBT project "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" sanctioned for a period of 3 years.

Details are available at www.nehu.ac.in and www.bicnehu.ac.in.

Applications must reach the undersigned within 15 days from the date of publication of this advertisement.

Prof. Pramod Tandon. PI/Mr. Devendra Kumar Biswal (Co-PI)

Nanopolis: polish a genome assembly

Rahul Nayak — Thu, 26 Jul 2018 04:51:28 -0500

Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

Quickstart

http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

Algorithms

http://simpsonlab.github.io/2017/06/30/nanopolish-v0.7.0/

Address of the bookmark: https://github.com/jts/nanopolish

Long read assembly workshop !

Rahul Nayak — Thu, 04 Oct 2018 17:23:18 -0500

This is a tutorial for a workshop on long-read (PacBio) genome assembly.

It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data.

Please comment if you know any other long read addembly tutorial.

Address of the bookmark: http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/

ICGEB Bioinformatics RA/SRF/JRF Vacancies

Thu, 13 Nov 2014 13:39:30 -0600

Research Associate/JRF/SRF position, DBT Sponsored Bioinformatics Infrastructure Facility

Applicants should hold a PhD or a first class MSc/MTech degree in Bioinformatics of Biotechnology/Life Sciences; experience in using bioinformatics tools, working in Linux and knowledge of computer network administration.

Submit CV and letter of interest by email to: Dr. Dinesh Gupta atdinesh@icgeb.res.in