FPGA-accelerated Bioinformatics at #ASHG – Dragen Aligner from Edico Genome

We thank Max Shen for his generous contribution to support our blog. ———————————————————–

We covered several CPU and GPU-based algorithms in “ASHG/GA4GH Special – A Recap of Interesting NGS Algorithms of the Year”, but no FPGA-accelerated one. Readers interested in FPGAs will find the following ASHG abstract interesting. At the bottom, we discuss the pros [...]

Posted on 20 October 2014 | 11:58 am

Renowned Human Geneticist Michael Hammer Shamed, Joe Pickrell Continues to Support Bad Science

In a world of universal deceit, telling the truth is a revolutionary act – George Orwell

The same spirit applies to the world of population genetics. Needless to say, nobody likes a revolution and the least among which is Joe Pickrell.

We decided to check what the hoopla is about and found a rebuttal [...]

Posted on 20 October 2014 | 9:34 am

Nanopore Updates from David Eccles

Reader David Eccles has been kind enough to keep us regularly posted on his progress with Oxford Nanopore sequencing. To make sure his helpful posts do not get lost in the comment section, we are creating a separate post as a collection of all his comments at different places in our blog. Readers are especially [...]

Posted on 19 October 2014 | 12:28 pm



Chimeras and Fusion Transcripts in RNAseq Assembly

We came across this paper from 2013 that is helpful for those working on RNAseq assembly. (h/t: Richard Smith)

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

Background RNA-seq has shown huge potential for phylogenomic inferences in non-model organisms. However, error, incompleteness, and redundant assembled transcripts for each gene in de novo assembly [...]

Posted on 21 October 2014 | 11:06 pm

RNAseq: Does it Really Matter How You Analyze the Data?

This is certainly an interesting paper that will make the statisticians working on low-level processing of RNAseq data unhappy. Our experience has been in agreement with their final statement –

Our results suggest that RNA-Seq analysis should be extremely biology-aware, and special effort should be devoted to optimizing the last stage of the analysis, [...]

Posted on 21 October 2014 | 7:47 am

SUPPA: a super-fast pipeline for alternative splicing analysis from RNA-Seq

Link

High-throughput RNA sequencing allows genome-wide analyses of pre-mRNA splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of time and storage required for analyses. Here we describe SUPPA, a computational pipeline to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification of a [...]

Posted on 18 October 2014 | 1:23 pm



Alternative meiotic chromatid segregation in the holocentric plant Luzula elegans

Link Holocentric chromosomes occur in a number of independent eukaryotic lineages. They form holokinetic kinetochores along the entire poleward chromatid surfaces, and owing to this alternative chromosome structure, species with holocentric chromosomes cannot use the two-step loss of cohesion during...

Posted on 14 October 2014 | 7:29 pm

T. Ryan Gregory Starts ‘Evolution Consulting Service’ after Reading Gibbon Paper in Nature

T. Ryan Gregory, who had been fighting ENCODE’s junk science since 2007, is fed up with another high-profile paper published in Nature. He wrote in Twitter – The paper in question has over seventy authors, which tends to scare us...

Posted on 10 September 2014 | 8:58 pm

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



Producer-Consumer Queues

How many types of Queues are there? Here is a helpful post. Depending on allowed number of producer and consumer threads: – Multi-producer/multi-consumer queues (MPMC) – Single-producer/multi-consumer queues (SPMC) – Multi-producer/single-consumer queues (MPSC) – Single-producer/single-consumer queues (SPSC) I hope this

Posted on 5 September 2014 | 8:43 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



Lane-by-lane Sequencing Using Illumina’s Genome Analyzer II

We came across this cool paper from 2013.

Next-generation sequencing has become an essential tool in molecular biology that has been successfully applied to a broad variety of experimental approaches. While several platforms for next-generation sequencing exist, the most commonly used approach is sequencing-by-synthesis, implemented on Illumina’s Genome Analyzer II (GAII) and HiSeq2000 systems. A [...]

Posted on 16 September 2014 | 7:14 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



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



UNC Chancellor is Shocked Shocked that ‘Gambling’ is Going on in her Univ

And why not, given that the Universities have now become giant athletic program, which also train students as a side project. UNC probe reveals approximately 1,500 student-athletes took bogus classes Wainstein said many academic and athletic officials knew about the scheme, which began with Deborah Crowder, a longtime manager for the Department of African and Afro-American Studies, and gave student-athletes inflated grades for what Wainstein termed “paper classes.” Paper classes were essentially classes that were independent study, had no professor and just required a paper at the end of the term. According to Wainstein, Crowder never gave students a grade unless they actually submitted a paper, but she awarded “artificially high” grades to the papers submitted regardless of their content. In the end, the disparity was clear. Students enrolled in an Afro-American Studies paper class would finish with a 3.62 GPA versus a 3.28 GPA for students in a regular Afro-American Studies course. For 81 students, the GPA boost from those paper classes gave them a 2.0 GPA that allowed them to graduate from UNC. Chancellor Carol Folt said during the news conference that she was shocked to learn that the academic improprieties were well known around campus and that [...]

Posted on 22 October 2014 | 12:45 pm

E-conmen at Federal Reserve Warn – “College May Not Pay Off for Everyone”

From ‘Liberty Street Economics’ (whatever that means, given that it is a site within NY Fed) - In our recent Current Issues article and blog post on the value of a college degree, we showed that the economic benefits of a bachelor’s degree still far outweigh the costs. However, this does not mean that college is a good investment for everyone. Our work, like the work of many others who come to a similar conclusion, is based in large part on the empirical observation that the average wages of college graduates are significantly higher than the average wages of those with only a high school diploma. However, not all college students come from Lake Wobegon, where “all of the children are above average.” In this post, we show that a good number of college graduates earn wages that are not materially different from those of the typical worker with just a high school diploma. This suggests that, at least from an economic perspective, college may not pay off for a significant number of people. The chart below plots the median annual wage for full-time employed workers with a bachelor’s degree between 1970 and 2013, together with the median annual wage [...]

Posted on 4 September 2014 | 1:50 pm

Imagine That – Finding from Facebook that Your University Closed Doors for Good !!

Morrison University Shuts Down Over Bankruptcy Issues After more than 100 years, Morrison University shut down Friday leaving its students at the crossroads of higher education. Anthem Education, Morrison’s current owner, is embroiled in Chapter 11 Bankruptcy and has listed a number of its schools for sale including Morrison. Students at the college found out about the closure through Facebook or friends as no formal notification was dispatched. Here is the story of the parent company. Anthem Bows Out After years of enrollment losses, Anthem Education, a for-profit chain of colleges and career institutes, filed for bankruptcy Monday. The company has abruptly shut down a number of its campuses, leaving state agencies struggling to funnel displaced students into other institutions. Nine more campuses may close today, Anthem officials said. Anthem had 41 campuses prior to declaring bankruptcy, according to its bankruptcy petition. Before it filed for bankruptcy the company sold 14 campuses to International Education Corporation, said an official involved in the acquisition. Anthem is in the process of selling an additional 14 campuses to IEC, but requires federal approval to do so. Unless the U.S. Department of Education approves the transaction by today, nine of those 14 campuses will [...]

Posted on 4 September 2014 | 6:52 am



USA is Exceptional, but How Exceptional?

A snapshot of ‘trending now’ from yahoo for different countries, all taken between 11:42AM-11:44AM California time. Canada Mexico Brazil Germany UK Arab world and drumbeats USA

Posted on 10 October 2014 | 11:54 am

The Bear and the Dragon

Posted on 15 September 2014 | 6:32 pm

Latest from Scotland

The inky wing of the British Empire does not know what to do. Historians will psychoanalyse the columns of Alan Cochrane in the Telegraph, monitoring their descent from pompous, self-certain swagger to incoherent, panicked meltdown. The Times, the Scotsman, the Mail, the Express, all peer out at Scotland from behind their barbed wire. “We’ve threatened the price of beans, we’ve threatened the cost of mortgages, we’ve told them they won’t have Strictly, we’ve told them they can’t have an NHS. That’s the sum total of their dreams and aspirations. So why won’t these fucking Scots STAY DOWN?” In a room behind a locked door, behind a policeman, behind a gate, behind another policeman, a group of millionaires get together. One, an old Etonian, nominally runs the country. The others, the CEOs of big corporations, actually run the country. They decide on a strategy: terror. We. Will. Take. Your. THINGS. From. You. It’s a fair trade, of sorts – give up your chance of self-determination and in return we will give you the cheap things that you love. This is Britain. In other news, if you look closely, Scotland has just seen the highest proportion of its population in its history [...]

Posted on 15 September 2014 | 6:20 pm