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
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
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
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
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
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
1. IToL [...]
Posted on 18 April 2014 | 12:03 pm
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
Before we discuss [...]
Posted on 9 April 2014 | 6:45 am
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
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
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
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
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
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
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
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
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
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
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
Posted on 11 April 2014 | 6:25 pm
Enjoy ! (h/t: @mt_ur_mind)
Posted on 10 April 2014 | 3:47 pm
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
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
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
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
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
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