Bioinformatics

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Bioinformatics

Biology Wed Jun 13 2018 15:14:00 GMT+0000 (UTC)
WHERE THE PARTY'S AT -- The last two posts — one concerning the histone code and cerebral embryogenesis https://luysii.wordpress.com/2018/06/07/omar-khayyam-and-the-embryology-of-the-cerebral-cortex/and the other concerning PVT1 enhancers promoters and cancer http
A brief message for anyone who uses my PubMed retractions report. It’s no longer available at RPubs; instead, you will find it here at Github. Github pages hosting is great, once you figure out that docs/ corresponds to your web root :) Now
Some papers are in the review pipeline for longer than they ought to be and the travel-part of conference attendance is a good opportunity to read books. So, instead of writing more about research, heres a blogpost with a book review instead, being S
First off, let me say that what follows is a lot of arm waving to try and obscure how little I understand what I'm talking about. I'm going to sketch out what I think is a "radical" idea for a GBIF Challenge entry. TL;DR GBIF should issue it's own cr
This blog post is part of a yearly series and marks the end of the 5th year as a group leader at EBI. In March we had an external evaluation of all research groups at EMBL-EBI. It was an interesting experience and overall it was judged a great succes
“The moving finger writes; and, having writ, moves on”. Did Omar Khayyam realize he was talking about the embryology of the human cerebral cortex? Although apparently far removed from chemistry, embryology most certainly is not. T
"Our findings support the need for a multidisciplinary approach to management of children with CP [cerebral palsy] to adequately identify and address all facets of presentation, including ASD [autism spectrum disorder]."So
Today in “blog posts that have spent two years in the draft folder” – “Humans are 50% banana.” “Humans are 50% banana.” Perhaps you have heard this statement, or one like it. It se
Marshall McLuhan famously said the mediumisthe message. Who knew he was talking about molecular biology? But he was, if you think of the process of transcription of DNA into various forms of RNA as themediumand the products of transcription as themes
David Shorthouse (@dpsspiders) makes some very cool things, and his latest project World Taxonomists & Systematists is a great example of using automation to assemble a list of the world's taxonomists and systematists. The project uses ORCID. As
There are several local and regional conferences in (Sub-Saharan) Africa with a focus on Africa in one way or another, be it for, say, computer science and information systems in (mainly) South Africa, computer networks in Africa, or for (computer) e
If you still follow my Twitter feed – I pity you, as it’s been rather boring of late. Consisting largely of Github commit messages, many including the words “knit to github document”. Here’s why. RPub
The latest instalment of this blog post series is by Omar Wagih (@omarwagih, Gscholar) who has just last month successfully defended his PhD. Along with Marco, Omar has been part of the group working on studying how DNA variants relate to ph
Adenotonsillectomy refers to the surgical removal of the tonsils and adenoids and is typically indicated for a variety of reasons, not least in cases of obstructive sleep apnoea (OSA) (where breathing is interrupted during sleep). I
Neurologists and drug chemists pretty much view amyloid as a bad thing. It is the major component of the senile plaque of Alzheimer’s disease, and when deposited in nerve causes amyloidotic polyneuropathy. A recent paper and editorial casts
Last year I finished my four-year stint as Chair of the GBIF Science Committee. During that time, partly as a result of my urging, GBIF launched an annual "GBIF Ebbe Nielsen Challenge", and I'm please that this year GBIF is continuing to run the chal
Here’s some advertisement to submit a paper to an great scientific event that has a constructive and stimulating atmosphere. How can one say these positive aspects upfront, one might wonder. I happened to have participated in previous editi
PubMed Commons, the NCBI’s experiment in comments for PubMed articles, has been discontinued. Thoroughly too, with all traces of it expunged from the NCBI website. Last time I wrote about the service, I concluded “all it needs now
SpaceX just launched and landed another two rockets over the weekend. I dont get tired of watching those images of re-entry and landing. The precision is mesmerizing and extremely inspiring. Leading a research group in academia I often look at resear
by Piter Kehoma Boll Three weeks ago our Friday Fellow was a moss, being the third non-vascular plant to be introduced. And before going back to vascular plants, let’s take a look at another non-vascular fellow from the only non-vascular &a
“To get Hawking radiation we have to give up on the idea that spacetime always had 3 space dimensions and one time dimension to get a quantum theory of the big bang.” I’ve been studying relativity for some years now in t
It's been a little quiet on this blog as I've been teaching, and spending a lot of time data wrangling and trying to get my head around "data lakes" and "triple stores". So there are a few things to catch up on, and a few side projects to report on.
South Africa has 11 official languages with English as the language of business, as decided during the post-Apartheid negotiations. In practice, that decision has resulted in the other 10 being sidelined, which holds even more so for the nine indigen
You know the drill by now. Grab the tweets. Generate the report using RMarkdown. Push to Github. Publish to RPubs. This time it’s the Australian Bioinformatics & Computational Biology Society Conference 2017, including the COMBINE s
Why do some mutations cause cancer in some tissues and not others ? What happens to the cell signalling pathways during differentiation ? Why are some genes essential in some cell types and not others or why are some drugs more effective at killing s
Of the many themes that seem to quite consistently surface on this blog looking at the peer-reviewed science in relation to various behavioural/psychiatric labels, the idea that various pharmacological interventions might do quite a bit more than 'wh
Tom Wolfe has passed on. It’s worth republishing an appreciation of him and how he changed writing in America. It contains links to a 3 part review of what was probably his last book “The Kingdom of Speech” Tom Wolfe ana
The following is a guest post by Bob Mesibov. Nico Franz and Becekett Sterner created a stir last year with a preprint in bioRxiv about expert validation (or the lack of it) in the "backbone" classifications used by aggregators. The final version of
Last week I participated in the Workshop on Logic, Algebra, and Category theory (LAC2018) (and their applications in computer science), which was held 12-16 February at La Trobe University in Melbourne, Australia. Its not fully in my research area, s
The R language provides many different tools for creating maps and adding data to them. I’ve been using the leaflet package at work recently, so I thought I’d provide a short example here. Whilst searching for some data that might
I know that 17 years is not a very round number. It is also fairly arbitrary as I am assuming systems biology started around 2000 (see below). I was last week in Portugal, where every year for the past 8 years I have been teaching a week long course
So: "These results support the potential of creating a quick, accurate and widely accessible method for differentiating risks between ASD [autism spectrum disorder] and ADHD [attention-deficit hyperactivity disorder]."That
IfDeng Xiaoping can have Socialism with Chinese Characteristics, I can have a Chinese saying with neuroscientific characteristics — “The axon and the dendrite are long and the nucleus is far away” mimicking “Th
David Attenboroughs latest homage to biodiversity, Blue Planet II is, as always, visually magnificent. Much of its impact derives from the new views of life afforded by technological advances in cameras, drones, diving gear, and submersibles. One mig
Noting that February is the month of language activism in South Africa and that 21 February is the International Mother Language Day (a United Nations event since 2000), let me add my proverbial two cents to that. Since the launch of the isiZulu spel
Sometime in 2009, I began listening to a science podcast titled This Week in Virology, or TWiV for short. I thought it was pretty good and listened regularly up until sometime in 2016, when it seemed that most episodes were approaching two hours in d
Cancer datasets as a resource to study cell biologyThe amazing resources that have been developed in the context of cancer biology can serve as tools to study "normal" cell biology. The genetic perturbations that happen in cancer can be viewed almost
For bumblebees, big cities are a bummer. Layers ofasphalt, concrete, brick and metal add up tofewer places for the insects to nest. But one big cityDetroitreverses that trend. That means shrinking cities might be a growing opportunity for at-risk pol
Yes, a touching mothers day story for you all. It was 51 years ago (yes over half a century ago ! ! ), and I was an intern at a big city hospital on rotation in their emergency room in a rough neighborhood. The ER entrance was half a block from an in
A post by on the Plaza blog Expanded access to images in the Biodiversity Literature Repository has prompted me to write up a little toy I created earlier this week. The Biodiversity Literature Repository (BLR) is a repository of taxonomic papers hos
In 2016 when I was a PC chair of the International School for Applied Ontology (ISAO 2016), the idea of organising a contest for the participants turned into a pub quiz somehow. The lecturers provided one or more questions on the topics theyd be teac
A reminder that when idle queries pop into your head, the answer can often be found using R + online data. And a brief excursion into accessing the Weather Underground. One interesting aspect of Australian life, even in coastal urban areas like Sydne
It has been 4 years since I started as a group leader at the EMBL-EBI (see past yearly reports 1, 2 and 3). This year the group composition has been mostly stable, with the exception of interns that have rotated through the group. We had Bruno Ariano
"Black women from East Africa had more than 3.5 times the odds of autism spectrum disorder with intellectual disability in their children than Caucasian nonimmigrant women."So said the study results reported by Jenny Fairthorn and colleagues [1] (ope
Very sad —Nature vol. 557 p. 144 ’18 (