Broke UK Government Taxing Soldiers’ Medal for Bravery to Fund #100KGP GWAS Madness

If you check the twitter page of UK company Genomics England, a happy picture emerges of an ambitious company building the latest medical knowledge base. Dig a bit deeper and you find that Genomics England is just an arm of UK government (“Genomics England was established in July 2013 as a company 100% owned [...]

Posted on 26 August 2014 | 6:54 am

Our New PNAS Paper Debunks the Genomics of Positivity

Readers may recall our blog post from last year -

Tragedy of the Day: PNAS Got Duped by Positivity Lady !!

Whiskey Tango Foxtrot – Arianna Huffington Embraces PNAS-published Junk Science of Positivity !!!

UC Berkeley, Lior Pachter’s University, Offers MOOC Course on ‘Science’ of Positivity

That blog post led to a formal paper that [...]

Posted on 25 August 2014 | 2:00 pm

Gene expression study shows those enjoying subtle humor are healthier than those who do not

Here is a riddle for our readers. Let us say you open the newspaper and read about the latest and greatest new study.

“Gene expression Study shows those enjoying subtle humor are healthier than those who do not”

“Gene expression Study shows Republican-type people are smarter than Democrat-type people”

“Gene expression study in mice [...]

Posted on 25 August 2014 | 9:26 am



Influence of RNA Extraction Methods and Library Selection Schemes on RNA-seq Data

We came across this BMC Genomics paper in twitter, but did not get time to read yet. Hopefully, the readers will find it useful.

Background Gene expression analysis by RNA sequencing is now widely used in a number of applications surveying the whole transcriptomes of cells and tissues. The recent introduction of ribosomal RNA [...]

Posted on 12 August 2014 | 9:49 am

Benchmark Analysis of RNA-Seq is an Excellent Confirmation of ‘Short Read’ Noise

In the past, we talked about ‘short read noise’, which is the noise introduced by clean short reads due to being short. Readers may take at these two of our earlier commentaries for details.

End of Short-Read Era? – (Part I)

End of Short-Read Era? – (Part II)

An excellent biorxiv paper analyzing RNA-seq assemblies [...]

Posted on 16 July 2014 | 3:14 am

‘Transcriptome Assembly is Hard’, but Not Any More with Richard Smith’s Transrate

Richard Smith-Una, whose work was covered in our blog, releases a new quality assessment program (transrate) that we surely like to check out.

Transcriptome assembly is hard. The algorithms are complex, the data are messy, and it’s often not clear how to determine whether an assembly is suitable for answering a biological question.

Transrate [...]

Posted on 8 July 2014 | 7:53 am



A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria

New paper from Nick Lane and colleagues in PLOS Biology (h/t: ‏@ErichMSchwarz ) - Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria—the deepest branches in the tree of life—are fundamentally different. This deep divergence in membrane...

Posted on 26 August 2014 | 12:02 pm

Shadow Enhancers Enable Hunchback Bifunctionality in the Drosophila Embryo

The following new paper is posted in arxiv. When bifunctional transcription factors activate and repress target genes within the same cell, these opposing activities must be encoded in regulatory DNA. Here, we use cellular resolution gene expression data and computational...

Posted on 13 August 2014 | 7:06 am

Evolution of my Little Pet Dinosaur

Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and...

Posted on 2 August 2014 | 9:43 am



BioXSD: the common data-exchange format for everyday bioinformatics web services

A paper on common standards came out in 2010 in Bioinformatics. It is being discussed in #socbin14 conference. Isn’t JSON more appropriate? Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and

Posted on 12 June 2014 | 3:43 am

d3.js – Tutorials, Books, Examples

d3.js is a SVG-based framework. 1. mbostock/d3 github gallery This is the best source for hands on learning and comes from the author of d3.js. There are many examples to choose from and study their codes. We have been going

Posted on 6 May 2014 | 11:28 am

We Plan to Be Early Adopters of Meteorchart

Earlier we talked about HTML5 and SVG, as well as kinetic.js, raphael and d3.js. Eric Rowell, the author of kinetic.js, developed a new program called Meteorchart, which seems interesting. We plan to use it for our bioinformatics applications. The program

Posted on 3 May 2014 | 7:21 am



Non-random DNA fragmentation in next-generation sequencing

link

Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed “reads” are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA [...]

Posted on 10 June 2014 | 6:08 am

PacBio P4-C2, P5-C3, etc. – What Do They Mean?

We had been pondering about those cryptic terms and found by asking some people around that the P stands for polymerase and C stands for chemistry. Therefore, P4-C2 means polymerase of fourth generation and chemistry of second generation.

Polymerase

That got us curious about what the actual DNA polymerase sequences are for 2nd, 3rd or [...]

Posted on 4 April 2014 | 4:58 am

Three Amazing Applications of CRISPR/cas9

Changing genome in plants used to be incredibly difficult, but not any more. Here is an excellent review -

Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system

Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) [...]

Posted on 31 March 2014 | 9:58 pm



Lorenz Attractor Spreading into Chaos

h/t: @infoecho

Posted on 28 July 2014 | 11:47 pm

Branches of Mathematics and Fermat’s Last Theorem

In the next few months, we like to go over Andrew Wiles’ proof of Fermat’s last theorem. For the time being, let us consider the evolution of various branches of mathematics and a very short intro of the proof. History...

Posted on 7 July 2014 | 1:23 pm

For Your Summer Reading – A Few Well-written Math Books

1. Visual Complex Analysis – Tristan Needham 2. Learning Modern Algebra – Couco and Rotman 3. Naive Lie Theory – John Stillwell 4. Nonlinear Dynamics and Chaos – Steven Strogatz 5. Concrete Mathematics: A Foundation for Computer Science – Ronald...

Posted on 7 July 2014 | 1:13 pm



Early Evolution of Fish – A Primitive Fish from the Cambrian of North America

New Nature paper - Knowledge of the early evolution of fish largely depends on soft-bodied material from the Lower (Series 2) Cambrian period of South China1, 2. Owing to the rarity of some of these forms and a general lack...

Posted on 12 June 2014 | 3:48 am

The Fishiest Story Ever – (ii)

This is a follow up of previous commentary – The Fishiest Story Ever – (i). All orders of fish are shown below based on the following phylogeny (courtesy: Professor James Albert). Please note that we (humans, tetrapods) are also a...

Posted on 7 May 2014 | 7:48 pm

Rare Megamouth Shark Caught in Japan

Source Megamouth shark was first seen in 1976 and is so rare that - According to WPTV, it was only the 58th megamouth to have been captured or sighted by man. The Florida Museum of Natural History states that the...

Posted on 7 May 2014 | 7:38 pm



With 72x Genome Duplication, Why Isn’t Rapeseed Smarter than Us?

Seems like we need another ENCODE project here. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling,...

Posted on 21 August 2014 | 5:21 pm

Genomic-scale Exchange of mRNA Between a Parasitic Plant and its Hosts

A new paper published in Science shines light on horizontal gene (mRNA) transfer between parasitic plant strangleweed and its host (h/t: Keith Robison). Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is...

Posted on 16 August 2014 | 6:34 pm

Immune System in Plants – A Good Review from 2011

We earlier posted on the possibility of LRR-type immune system of Ectocarpus. Readers may find the following review useful in that context. Arabidopsis and the Plant Immune System Notes. 1. The first challenge was to dispel the notion that Arabidopsis...

Posted on 8 July 2014 | 10:55 am



The Evolving Zionist Funding Disaster at the Univ of Illinois

The following report from Inside Higher Ed shows how much the academic principles have fallen in US universities. On Friday, officials of the University of Illinois offered their first public explanations of the decision to block the hiring of Steven Salaita. They denied that his criticism of Israel was the reason, and said that they were committed to promoting an atmosphere in which people and ideas are not demeaned. “What we cannot and will not tolerate at the University of Illinois are personal and disrespectful words or actions that demean and abuse either viewpoints themselves or those who express them. We have a particular duty to our students to ensure that they live in a community of scholarship that challenges their assumptions about the world but that also respects their rights as individuals,” said an email from Phyllis M. Wise (below right), chancellor of the Urbana-Champaign campus where the American Indian studies program offered Salaita a tenured position that he and the department believe he accepted. [snip] While many of the emails are fairly similar, some stand out. For instance, there is an email from Travis Smith, senior director of development for the University of Illinois Foundation, to Wise, with [...]

Posted on 26 August 2014 | 8:54 am

What Academic Wasteland Will Turn into, When Welfare Money Dries Out

Retraction Watch covered an interesting story from Portugal. For those who do not know, Portugal is in an advanced stage of collapse that most other Western countries are heading into. (h/t: Neuroskeptic) “I am not a monster and I am not unreasonable:” Student attacks professor with axe after grant is cut A physics graduate student at the University of Coimbra in Portugal attacked a professor with an axe earlier this month after losing a grant. The student, Colin Paul Gloster, attacked physics lecturer Maria Filomena Santos, who according to the Irish Mirror will “require reconstructive surgery as the axe cut very close to the tendons.” More from Irish Mirror - In one of his online postings, Colin claims that he applied for a first grant that year but he failed to obtain it. He said that he paid over €3,000 in fees and was left penniless until a lawyer helped him get another, second scholarship from the Fundation for Science and Technology. However, the physicist claims he was forced to drop out of his Phd in 2013 when this grant was cut and he could no longer afford to remain a student. Mr Gloster wrote that the payments stopped the [...]

Posted on 26 August 2014 | 8:39 am

Subprime Loans Are Just the Start of the Massive Student Debt Scam

Wall Street Examiner covers this analysis - This is amazing. If you thought there was only one component to the gargantuan student debt scam, think again. Because here’s the thing: If you’re about to become a college student, if you’re already a college student, or if you’re simply in debt and need more credit and plan on becoming a student again, you’re in luck. Financial services giants Discover Financial Services Inc.(NYSE: DFS), Capital One Financial Corp. (NYSE: COF), Bank of America Corp. (NYSE: BAC), Citigroup Inc. (NYSE: C), and U.S. Bancorp (NYSE: USB), to name a few players in the student credit game, are bending over backward for you. The folks at Discover want you to “Get the card for college and beyond.” They’ve named and registered it as “Discover It Chrome for Students” because, after all, they’re “Looking out for you.” But they aren’t the only do-gooders looking out for you. You can also apply for the Capital One Journey Student Rewards Credit Card, the Bank of Americard for Students, the U.S. Bank College Visa Card, or the Citi Dividend Platinum Select Visa Card for College Students. Heck, why not apply for all of them? But wait. Before switching [...]

Posted on 11 August 2014 | 5:15 pm



Gaza Child Pulled out of the Rubble after Zionist Air Strikes

h/t: Gilad Atzmon

Posted on 26 August 2014 | 10:11 am

Scottish Independence Debate – Alex Salmond Wins 2-1 Over Alistair Darling

A turning point for Britain coming?

Posted on 26 August 2014 | 7:37 am

Interview: Dimtry Orlov

We previously covered the work of Dimitry Orlov, who wrote the interesting book The Five Stages of Collapse. Orlov immigrated to USA from USSR in the 70s and visited collapsing USSR from time to time in the 90s. In 2006, he wrote a thoughtful essay highlighting the similarities between Soviet Union and USA and the book is an extension of his essay. Here is his latest interview.

Posted on 25 August 2014 | 7:44 pm