Posts Tagged genomics

Blogimmuniqué: titles and series (and Not Just DNA #0) Grant Jacobs Sep 12

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Blogimmuniqués are my irregular commmuniqués about Code for life.

Over the next few weeks you’ll notice a few changes in the titles of posts, identifying the intended audience of different articles.


  • Articles ending in (Not Just DNA #1), with an appropriate post number in place of ‘1’, are part of an irregular series of sorts on how our genomes that make our genomes work. The first post will be Is a genome enough (Not Just DNA #1). This isn’t a series in the true sense, but rather a theme – posts for it are likely to be irregular and the topic is taken in it’s broadest sense. Most articles in it will aimed at non-specialists – that is, everyone. More thoughts on this series in Not Just DNA #0, below.
  • Articles intended for bioinformatics scientists will start with Bioinformatics: just as my previous post did: Bioinformatics: WikiProject computational biology competition 2013.
  • Articles with neither a specialist focus nor a particular topical focus will have titles without appellations.

I may introduce other themes later.

Why not separate blogs?

Most people set up separate blogs for separate themes or focuses and I’d agree it usually is the best idea. Part of the reason I’m not opting for this, aside from avoiding managing several blogs, is that I like the idea of showing more than a narrow focus on one thing.[1]

I suspect most of what non-scientists see of scientists on-line are them talking about their speciality or things close to it. It must look incredibly narrow-minded.

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Epigenetic dynamics – free Grant Jacobs Mar 15

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Those with interests in epigenetics and genome structure may want to check out Nature Structural and Molecular Biology’s focus on epigenetic dynamics. (This gives me an opportunity to briefly sound off on a favourite topic…)

One fascinating development over the past few years has been explorations of the three-dimensional nature of genomes, how they are arranged within the nucleus of our cells, how the spatial organisation of genomes might affect how genes are used, interactions between parts of our genomes and far, far too many other questions…

I guess you could say you know an interesting area of science by the questions it raises.

Yeast genome model. From Duan et al, Nature, 2010.

Yeast genome model. From Duan et al, Nature, 2010.

As a student, I studied proteins that bind DNA and the protein-DNA interactions they make. I’m still interested in that—old interests don’t die that easily in science—but these things now fall within a wide range of aspects.

Although a relatively short list of reviews, the focus on epigenetic dynamics covers an interesting range of topics that illustrate how studying gene regulation have moved from simple beginnings of the immediate promoter and protein binding sites in DNA of the 1980s (or so) to the rich complexity of DNA and histone modifications, nucleosome (re-)positioning, protein complexes, chromatin loops, chromosomal domains, regulatory RNAs and more.*

Particularly appealing is that all of the articles are free for anyone to read.**

(Original from Luger lab, sourced from Biomedical Beat.)

(Original from Luger lab, sourced from Biomedical Beat.)

Speaking for myself, it’s great to see a more ‘spatial’ thinking about genomes emerge in molecular biology over the past few years. One of the appealing things about 3-D genome structure work (to me) is that it shifts whole genomes into computational structural biology rather than the more ‘linear’ approach typical of the current genome projects.***

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Whole genome sequencing for serious vaccine complaints? Grant Jacobs Nov 30

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While I work on longer pieces, a stray thought: how far away are we from genome screening for (court) inquiries about ‘vaccine damage’ so that those with genetic causes might be resolved promptly?

A number of countries maintain databases of reports of possible adverse reactions to medications. For possible vaccine reactions, in New Zealand we have the CARM database[1]; in the USA there is VAERS.

In the USA claims for ‘vaccine damage’ can be filed to the National Vaccine Injury Compensation Program.

I imagine these proceedings can take considerable time and cost. What fraction of the alleged cases of ‘vaccine damage’ are in fact rare genetic defects? How many of these case are in effect a cohort of sorts of rare disorders like mitochondrial defect conditions, heart disorders, seizure disorders (e.g. Dravet syndrome) – with genetic causes? Will it be pragmatic soon to routinely screen these cases for genetic conditions?

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Sea stars and mosaics Grant Jacobs Nov 29

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At first you wonder if this sea star is real. It looks more like a kid’s geometric doodle from a distracted afternoon at school than an animal.[1]

Click on image for source; Creative Commons Attribution-Noncommercial-Share Alike 3.0 license

The World Asteriodea Database indicates Iconaster longimanus was first described in 1859. (The photo above was taken by Dieter in the Philippines in February 2007.)

(Source: Wikimeda, pubic domain.)

Among the later descriptions in the Asteriodea Database entries are ones from the famous HMS Challenger voyage.

To most today the name Challenger recalls the space shuttle that horrifically broke up little over a minute into it’s flight and brought a temporary halt to the shuttle program. The shuttle Challenger was named after the HMS Challenger, whose voyage was a grand British scientific survey of it’s day.[2]

Unlike the short life of the ill-fated space-farer, HMS Challenger’s voyage spanned over several years, 1872-1876 and travelled the world.

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All together now: high-throughput sequence mapping tool compendium Grant Jacobs Oct 16

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Biologists and bioinformatics people interested in high-throughput (HTS) mapping may find this this one-page summary of all currently-available HTS mapping tools useful. The comparison table of the different features of each mapping tools will certainly beat having to dig this information out of the papers or on-line documentation. There’s also a timeline of when the methods first appeared. DNA, RNA, miRNA and bisulphite mappers are listed.

Features noted in the comparison table include: Read the rest of this entry »

Download your copy of the ENCODE poster Grant Jacobs Sep 08

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While you’re waiting for me to write something about the ENOCDE project, you can download a copy of the ENCODE project poster (large PDF file; 21.4 Mb. Reduced image shown below).

Other articles on Code for life:

George Church on genomics and personalised medicine

In the near future: genome sequencing for the masses

Epigenetics and 3-D gene structure

Teaching bioinformatics at high school

Bioinformatics – QC, reproducible, statistical and sequence-oriented

Online lecture series on genomics and bioinformatics

Epigenetics overview (video) Grant Jacobs Apr 11

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Below Jessica Tyler, from the University of Texas MD Anderson Cancer Center, introduces epigenetics, a topic I’ve touched on a few times and would like to elaborate further on. Her introduction is fairly gentle; hopefully some of the essence of the thing will come across to non-specialists!

You may need to wait until the video is buffered before it starts displaying. Feel free to ask questions in the comments below.

(Excuse the back-to-back videos and no articles – I’m very busy until at least Friday!)

Other articles on Code for life:

Epigenetics, growing old and identical twins becoming unique

Doggie ERVs

Transcribing a gene, free poster

Autism — looking for parent-of-origin effects

Coiling bacterial DNA

Epigenetics and 3-D gene structure

George Church on genomics and personalised medicine Grant Jacobs Apr 06

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Weekend video – for general readers.

This TEDxCambridge lecture by Professor George Church* offers an informal look at progress in genomics and personalised medicine. While very informal compared to some TED lectures, but it does give glimpses of where genomics and personalised medicine might be headed in a series of quick snapshots.**

In the middle of his talk you’ll hear about some kids sequencing genes for their own interest or school projects. For some like me who has been doing computational biology from before the genome projects*** it’s a measure of how far things have come.

There are some examples of new possible treatments being explored.

YouTube Preview Image

His talk assumes a bit of background in places – he’s giving a high-flying overview. Feel free to ask anything in comments below.

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The world in DNA sequencers Grant Jacobs Mar 22


Powerful DNA sequencing technology gets a lot of attention and the amount of DNA sequence data pouring out these days is impressive (and is set to rise further).

So where are these devices? There’s an interactive map of where they all are on


Click on each blue location marker for details about the centre. Clicking on circles will produce an enlarged map of that region. Along the top you can limit those shown to particular types of sequencers (not shown in the image above). Read the rest of this entry »

Talking points: endless genomes and microbes, natural products industry, drunk animals, earthquake waves Grant Jacobs Mar 05


For a little light relief, a short collection of talking points that I wrote some time ago but for some reason never published. (I’ve no idea why.)

More genomes than you can shake a stick at

This summary of a news report from Science headlines how BGI aims to dominate the world of genome sequencing, including setting up centres outside of China and plans to sequence a million human genomes. Not to mention a million plant and animal genomes and a million microbial genomes. (The full report is subscription-only.)

More microbes that you might think

Food for thought via twitter:

Sandra Porter @digitalbio

Uncultured microbe session #AAASmtg There are more [oceanic] microbes than stars in known universe.

When animals binge.[1a] Not something you see everyday: an elk stuck up a tree. Admittedly not very far up a tree. It’s not so much that this elk has climbed the tree, so much as drunkenly tangled itself up in it. Some of the comments are entertaining too: Read the rest of this entry »

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