BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

A new bioinformatics paper from Ruibang Luo​ and others in Tak-Wah Lam’s group.

BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to [...]

Posted on 24 April 2014 | 7:31 pm

Measuring Reproducibility in Computer Systems Research

A research group in Arizona decided to reproduce as many published claims in computer science as possible. They built a website to track each program until they could fully build it and test it, and you can see the results at this link.

Reproducibility is a cornerstone of the scientific process: only if my [...]

Posted on 24 April 2014 | 4:33 pm

Github Book on “Introduction To Applied Bioinformatics”

This seems like a fascinating resource. To browse the book, check here, or grab it from github and enjoy !! (h/t: Nick Loman)

Bioinformatics, as I see it, is the application of the tools of computer science (things like programming languages, algorithms, and databases) to address biological problems (for example, inferring the evolutionary relationship [...]

Posted on 24 April 2014 | 1:35 pm

Ripping Off Young America: The College-Loan Scandal

Matt Taibbi is our favorite investigative journalist. We did not get a chance to mention his late 2013 commentary on student debt, but it is not too late. Be warned, you will be very very angry.

The federal government has made it easier than ever to borrow money for higher education – saddling a generation [...]

Posted on 24 April 2014 | 6:27 pm

American Academy of Arts and Sciences Finds President with Uninflated Resume

Jonathan F. Fanton, the former president of the John D. and Catherine T. MacArthur Foundation and of the New School, will be the new president of the American Academy of Arts and Sciences, academy officials announced on Thursday. Dr. Fanton, 70, is currently the interim director and Franklin D. Roosevelt visiting fellow at the Roosevelt [...]

Posted on 23 April 2014 | 6:13 pm

Harvard Professor Predicts up to Half of US Universities May Fail in 15 Years

Reports zerohedge -

But Harvard Business School professor Clayton Christensen has much more dire warnings of the technological shift…

as many as half of the more than 4,000 universities and colleges in the U.S. may fail in the next 15 years. The growing acceptance of online learning means higher education is ripe for technological upheaval, [...]

Posted on 14 April 2014 | 10:46 pm

Phylogenetic Tree – a More Detailed Description of Programs Out There

In an earlier commentary, we checked for Javascript+HTML5-based programs for drawing phylogenetic trees. Based on Heng Li’s suggestion, we settled on jsPhyloSVG. It is a well-written program built on top of Raphael SVG package.

If one removes the restriction of Javascript+HTML5, here is the entire panorama of programs for solving the same problem.

1. IToL [...]

Posted on 18 April 2014 | 12:03 pm

RSS Feed Parser – What Toolboxes Are Out there?

Previously, we posted about Feedly Source Code and Other Information. Today we are looking at what else is out there to process blog feeds.

1. MWFeedParser -

Looks like the most downloaded code is written in Objective C by mwaterfall. It is written for iOS (MWFeedParser — An RSS and Atom web feed parser for [...]

Posted on 16 April 2014 | 11:45 am

Javascript+HTML5 Applications for Phylogenetic Tree – What Do You Use?

Earlier we posted about Heng Li’s HTML5+Javascript-based code for drawing phylogenetic trees.

We have been poking around github and other places to find what else is out there. We prefer to use Javascript+html. Some other languages are ok, but we are very allergic to any kind of Java applet code.


Before we discuss [...]

Posted on 9 April 2014 | 6:45 am

Goodbye RSEM, Sailfish Paper Published

We wrote about very fast Sailfish algorithm, when it came out in the arxiv (DEseq and Sailfish Papers for RNAseq). Also, one of our readers liked the code and we wrote about it as well -

Good C++ Development Practices in Sailfish Code

Now the readers can find the published paper in Nature Biotech. There [...]

Posted on 21 April 2014 | 9:06 am

Transcriptome in Vivo Analysis (TIVA) of Spatially Defined Single Cells in Live Tissue

One reason for our splitting the RNAseq channel is to be able to write about relevant experimental methods in addition to bioinformatics. Readers will find a recent paper (Jan) in Nature Methods interesting (h/t: gunguez).

Transcriptome profiling of single cells resident in their natural microenvironment depends upon RNA capture methods that are both noninvasive and [...]

Posted on 14 April 2014 | 9:51 am

Flexible Isoform-level Differential Expression Analysis with Ballgown

This new biorxiv paper from Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg, Jeffrey T Leek appears interesting. We have not gone through the details yet and would like to know what our readers found.

We have built a statistical package called Ballgown for estimating differential expression of genes, transcripts, [...]

Posted on 30 March 2014 | 8:05 pm

Sea Anemone is Genetically Half Animal, Half Plant

This press release (Sea anemone is genetically half animal, half plant) got us curious about two interesting papers recently published in Genome Research. The original genome paper of N. vectensis sequenced by JGI came out in Science in 2007 (“Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization”), but the following new [...]

Posted on 26 March 2014 | 9:46 pm

Trichoplax adhaerens at the Root of Multicellular Animal Tree

The following materials are uncritically posted from wiki and are not new discoveries. I have been looking into Trichoplax adhaerens after seeing a lot of analysis in the Hox-TALE paper rely on this animal.

Trichoplax adhaerens is the only extant representative of phylum Placozoa, which is a basal group of multicellular animals (metazoa). Trichoplax [...]

Posted on 25 March 2014 | 5:28 pm

A Good Paper on Hox-TALE Puzzle

Molecular insights into the origin of the Hox-TALE patterning system

Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction [...]

Posted on 25 March 2014 | 5:02 pm

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.


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

Highly Efficient Transformation of Diatom

Diatoms have very strong silicon cell walls. Transformation is not easy.

A number of new papers are coming out claiming that they can do it.

Transformation of diatom Phaeodactylum tricornutum by electroporation and establishment of inducible selection marker

Diatoms are important primary producers in the marine ecosystem. Currently it is difficult to genetically transform [...]

Posted on 27 March 2014 | 11:18 pm

Rainbow Trout Genome Published

Published in Nature Communications -

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome [...]

Posted on 23 April 2014 | 10:53 pm

A Link to Various Fish Genome and Transcriptome Databases




Japanese lamprey in Singapore


Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum)

———————————————————————— Elephant shark




Elephant shark genome provides unique insights into gnathostome evolution

———————————————————————— coelacanth



Posted on 11 April 2014 | 6:25 pm

Your Inner Fish from PBS

Enjoy ! (h/t: @mt_ur_mind)

Posted on 10 April 2014 | 3:47 pm

Adaptive Immune System in Brown Alga?

Highly dynamic exon shuffling in candidate pathogen receptors … what if brown algae were capable of adaptive immunity?

Pathogen recognition is the first step of immune reactions. In animals and plants, direct or indirect pathogen recognition is often mediated by a wealth of fast-evolving receptors, many of which contain ligand-binding and signal transduction domains, such [...]

Posted on 24 April 2014 | 5:49 pm

The Revised Classification of Eukaryotes

Readers may find this 2012 paper interesting. We will come back to the following chart in future discussions.

Posted on 20 April 2014 | 2:03 pm

Regulated Aggregative Multicellularity in a Close Unicellular Relative of Metazoa


The evolution of metazoans from their unicellular ancestors was one of the most important events in the history of life. However, the cellular and genetic changes that ultimately led to the evolution of multicellularity are not known. In this study, we describe an aggregative multicellular stage in the protist Capsaspora owczarzaki, a close unicellular [...]

Posted on 20 April 2014 | 1:36 pm

From Bundy’s Ranch to US Civil War II

Why America Failed is the third and most engaging volume of Morris Berman’s trilogy on the decline of the American empire. In The Twilight of American Culture, Berman examined the internal factors of that decline, showing that they were identical to those of Rome in its late-empire phase.

We finished a wisely written book [...]

Posted on 24 April 2014 | 6:06 pm

First Female Banker Jumps to Her Death

This is an unusual story, because the lady “she questioned her superiors before jumping out the window” !!!

52 Year-Old French Banker Jumps To Her Death In Paris (After Questioning Her Superiors)

There have been 13 senior financial services executives deaths around the world this year, but the most notable thing about the sad suicide [...]

Posted on 24 April 2014 | 5:33 pm

This is an Astonishing Degree of Consensus Thinking

Acting-man points out -

A 100% Consensus

This doesn’t happen very often. Marketwatch reports that Jim Bianco points out in a recent market comment that the 67 economists taking part in a regular Bloomberg survey have a unanimous forecast regarding treasury bond yields: they will be higher 6 months from now. This is a truly [...]

Posted on 23 April 2014 | 10:47 pm