New Book: RNA-seq Data Analysis: A Practical Approach

This Article is Sponsored by CRC Press

A new book has come out on RNA-seq data analysis and it is written by none other than our long time reader Mikael Huss, along with four other authors. You can get the book at the publisher’s website through following link.

RNA-seq Data Analysis: A Practical Approach (By: [...]

Posted on 29 September 2014 | 7:58 am

Nanopore – Truth and Nothing but the Truth

At last we get the analysis of Oxford Nanopore data that we had been looking for since first day. Michael Schatz posted the GI2014 slides of James Gurtowski from his lab in his website.

—————————– Read Length Distribution

Read length goes all the way to ~147Kb, but the longer reads are problematic (see next section).

[...]

Posted on 26 September 2014 | 8:51 am

MEGAHIT: An Ultra-fast Single-node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph

About two years back, we reported about Succinct de Bruijn Graph construction by Alex Bowe and collaborators. Also, earlier this year, HKU group of professor Tak-Wah Lam published their implementation of GPU-Accelerated BWT Construction for Large Collection of Short Reads. Now those two are combined along with ideas from IDBA-UD into a metagenome assembler. The [...]

Posted on 25 September 2014 | 8:03 pm



High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing

Link

RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. However, as ongoing advances are rapidly yielding increasing read lengths, a technical hurdle remains in identifying the degree to which differences in [...]

Posted on 25 September 2014 | 11:01 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



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

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



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



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

Secret Network Connects Harvard Money to Payday Loans

Alex Slusky was under pressure to put the money in his private-equity fund to work. The San Francisco technology financier had raised $1.2 billion in 2007 to buy and turn around struggling software companies. By 2012, investors including Harvard University were upset that about half the money hadn’t been used, according to three people with direct knowledge of the situation. Three Americans on the Caribbean island of St. Croix presented a solution. They had built a network of payday-lending websites, using corporations set up in Belize and the Virgin Islands that obscured their involvement and circumvented U.S. usury laws, according to four former employees of their company, Cane Bay Partners VI LLLP. The sites Cane Bay runs make millions of dollars a month in small loans to desperate people, charging more than 600 percent interest a year, said the ex-employees, who asked not to be identified for fear of retaliation. Slusky’s fund, Vector Capital IV LP, bought into Cane Bay a year and a half ago, according to three people who used to work at Vector and the former Cane Bay employees. One ex-Vector employee said the private-equity firm didn’t tell investors the company is in the payday-lending business, where [...]

Posted on 4 September 2014 | 6:35 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

Hilarious – Road Rage in Russia

Posted on 8 September 2014 | 6:10 pm