Online Bioinformatics Contest from Stepik/Rosalind

Dear Readers, Happy New Year ! Here is a great way to bring some fun and challenges to your new year. We got a note from Nikolay Vyahhi, who helped build Rosalind and Stepik, that their organization is hosting a bioinformatics competition. The details are posted below -

Roche Dumps Pacbio

Yesterday, Pacbio received its Christmas present for 2016. Roche decided to abruptly terminate its three year-long alliance with the company. During this collaboration, Roche paid Pacbio to develop the Sequel instrument and reserved the exclusive right to sell it in the human clinical market.

Business analysis - Oxford Nanopore

Investor warning: The following post is for entertainment purpose only, and should not be considered as financial advice of any sort. Please consult your favorite government-certified investment adviser or central banker regarding decisions on investing your life savings.

GRASS for Rapid Reannotation of RNAseq Data

Many exciting papers/preprints on RNAseq came out over the last few months. Among them, a recently posted preprint solves an important problem - improving annotations based on new RNAseq data. There were other papers on quantification, compression and search, and we like to cover them in the next few posts.

Using Multidimensional Bloom filters to Search RNAseq Libraries - (i)

A number of recent papers are proposing to use multidimensional Bloom filters to identify genes from a large collection of RNAseq libraries. This post provides general perspective on these papers. In a later post, we will go in depth and explain the algorithm of the recent preprint by carrying out an example.

Postdoctoral Scholar Position in Comparative Plant Genomics and Bioinformatics

Job Title: Postdoctoral Scholar Position in Comparative Plant Genomics and Bioinformatics
The Computational Plant Genomics Lab invites applications for a Postdoctoral position in the Department of Ecology and Evolutionary Biology at the University of Connecticut. We focus on developing computational approaches that integrate next generation sequence data to address questions in non-model plants, particularly forest trees. The lab has the following ongoing projects: 1) Understanding the evolution of alternative translation initiation using RNA-seq data 2) Integrating new and existing approaches to gene prediction to improve the annotation of complex genomes 3) Analysis of gene family evolution and related comparative genomics questions 4) Detecting variation in populations from GBS and related sequence data.

Zipper plot for visualizing transcriptional activity of genomic regions

Abstract: Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. The Zipper plot is an application that enables users to interrogate putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity. These features are obtained from publicly available datasets including CAGE-sequencing (CAGE-seq), ChIP-sequencing (ChIP-seq) for histone marks and DNase-sequencing (DNase-seq). The Zipper plot application requires three input fields (chromosome, genomic coordinate (hg19) of the TSS and strand) and generates a report that includes a detailed summary table, a Zipper plot and several statistics derived from this plot.

SuperTranscript - a reference for analysis and visualization of the transcriptome

Abstract: Transcriptomes are tremendously diverse and highly dynamic; visualizing and analysing this complexity is a major challenge. Here we present superTranscript, a single linear representation for each gene. SuperTranscripts contain all unique exonic sequence, built from any combination of transcripts, including reference assemblies, de novo assemblies and long-read sequencing. Our approach enables visualization of transcript structure and provides increased power to detect differential isoform usage.

Designing Molecular LEGOs in Lisp Language

This is a fascinating talk that our readers from both computational and life sciences sides will enjoy. The author realized shortcomings of common programming languages in solving his domain-specific task and developed Clasp starting from common Lisp.

Upgrade to the blog

We are back after making extensive changes to the blog software being used here. Most important among the changes, we got rid of Wordpress and made a commitment to never use Wordpress again. Wordpress is easy to install, but nightmare to maintain with its entire panoply of buggy plugins. Moreover, it sucks up time by failing at the most unfortunate times.

Lior Pachter's Zika Paper

Lynn Yi, Harlod Pimentel and Lior Pachter published a new RNAseq paper that our readers will definitely find interesting. In this paper, the authors showcase the new RNAseq technologies Pachterlab has been developing over the last few years. We covered those components (e.g Kallisto, Sleuth) in earlier posts, but here you can see a biological application to get new insights from already published data.

Ongoing Pacbio bioinformatics meeting (#SMRTBFX)

Readers may keep an eye on #SMRTBFX hashtag on twitter to follow an ongoing conference. This is the best place to know about the latest bioinformatics algorithms on long reads. Gene Myers is again the star of the show. He has been distributing a lot of goodies through his Dazzlerblog, such as -

Qudaich - a Smart Sequence Aligner

Suicide Epidemic: Since NIH-funded Clowns Do Not Want to Discuss It, We Will

A large number of NIH-funded parasites waste taxpayers’ money with the excuse that they are working toward improving the health of Americans. Francis Collins, the head of NIH, uses every opportunity to tell everyone how research funded by NIH helps in improving the life expectancy of Americans (a flat out lie). Yet, when research by Deaton and Case uncovered that the life expectancy of Americans of prime age (45-54) was falling, primarily due to rising suicides, Collins and his minions went completely silent.

Population Genetics of Ancient Jewish Population in India

‘Ancient’ Bene Israel Jews and late-arrived Baghdadi Jews in India started the Bollywood movie industry. Many famous early Indian actresses also came from these communities. This is not common knowledge in India, because those actresses took Muslim (Firoza Begum) or Hindu (Sulochana, Pramila) screen names.

Was Google Really Censoring Elhaik's Khazar Research in 2013?

In 2013, Dr. Elhaik complained about his home page at John Hopkins University mysteriously disappearing from google searches right after his first Jewish genomics paper started to gain attention. We reproduced his complaint here, and then his page came back on top again after a few days.

Transistors, Translation and tRNAs

Organoids and the Coming Medical Revolution - (ii)

Transfer RNAs and Neurodegenerative Disorders

Among all biomolecules within the cell, tRNAs got the least respect. Their supposed importance ended right after the ‘adaptors’ related to entries in the genetic code table were identified (mid-60s). Since then, the attention shifted to more complex RNAs like the rRNAs.

Organoids and the Coming Medical Revolution - (i)

Among various biotechnology inventions of the last few years with potential to revolutionize medicine, nothing excites us more than growing of three- dimensional human organoids on matrigel. Therefore, we plan to devote a number of posts on this topic to keep our readers aware of the practices, potentials and challenges.

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