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written 4 days ago by Omics! Omics! by Keith Robinson
London Calling has been over for nearly three weeks. I originally wanted to write up at least something after the first night, but fatigue overcame me and I didn't get anything useful put together. And then travel and more fatigue set in. But beyond that and the usual temptation to procrastinate, there is the challenge of forming a coherent narrative from all the different threads at the meeting. There's all the Oxford Nanopore official announcements and then various user presentation tidbits. After several failed mental attempts to compose a big picture take on everything, I've decided to try to write a series (number yet indeterminate) of posts that will focus of various axes of the meeting. Hopefully they won't be to redundant -- or self-contradictory -- and that by following one particular thread I can actually condense some coherent thoughts. This first such thread starts with Flongle.Read more »
written 9 days ago by Living in an Ivory Basement by Titus Brown
How long does it take to produce scientific software?
written 11 days ago by Ensembl Blog
From Ensembl 93 onwards, we plan to recommend newer versions of Perl (5.14- 5.26) and BioPerl (1.6.924) when using the Ensembl Perl API. This may affect pipelines which employ the Ensembl Perl API, since we will no longer actively support older versions of Perl and BioPerl. At Ensembl, we’ve been using Perl since the project […]
written 11 days ago by miRBase blog
You might have noticed some additional information on the mature miRNA pages in the last few weeks. See for example: http://mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000123 http://mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069 The new section “QuickGO function” contains a set of high quality manual annotations of Gene Ontology terms for mature miRNAs, the vast majority of which come from the work of Rachel Huntley et [...]
written 13 days ago by Ensembl Blog
As of Ensembl release 93, which is due at the end of the month, the Gene Variant Image view will be retired for human. We have elected to retire this page because we feel that the density of known genetic variation is too great for this view to be informative in its current form. The […]
written 13 days ago by Opinionomics by Mick Watson
Yes, I still blog! A quick history. As many of you will be aware, Jain et al published a fantastic paper where they produced the first de novo genome assembly of a human genome using the MinION, a portable DNA sequencer that uses nanopores to detect the sequence of single molecules. After fixing errors with Illumina, […]
written 14 days ago by Bits of DNA by Lior Pachter
Here are two IQ test questions for you: Fill in the blank in the sequence 1, 4, 9, 16, 25, __ , 49, 64, 81. What number comes next in the sequence 1, 1, 2, 3, 5, 8, 13, .. ? Please stop and think about these questions before proceeding. Spoiler alert: the blog post […]
written 14 days ago by Bioinformatics I/O
This figure is an update of Figure 1 in “A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.” published by Zhang et al (2011). The figure was produced in SVG so you should be able to click on the name of the assembler which should take you straight to the […]
written 16 days ago by Living in an Ivory Basement by Titus Brown
Using sourmash to find candidate contaminants
written 17 days ago by Ensembl Blog
We’re excited to announce that we have received a grant from the Wellcome Trust to deliver Ensembl training in low-middle income countries at no charge. We know that there’s a real need for training in low-middle income countries. A quick glance at data available in the GWAS catalog and gnomAD show that non-European ethnicities are under-represented […]
written 19 days ago by Ensembl Blog
We’re looking for a bioinformatician to work on integrating, analysing and testing data for the Ensembl Plants database. We’re looking for experience delivering a service in bioinformatics, with knowledge of relational databases and programming. Closes 8th July 2018. Location: EMBL-EBI Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years Grading: 5 (monthly […]
written 19 days ago by Ensembl Blog
Both Ensembl release 93 and Ensembl Genomes release 40 are scheduled for late June and early July 2018, respectively. Included are a number of new genomes and genebuilds for vertebrates and plants (including leopard, Amur tiger, hagfish, pigeon pea, carrot and adzuki bean) and significant updates to the mouse GENCODE annotation and regulatory build. This […]
written 19 days ago by Bits of DNA by Lior Pachter
Earlier this month I posted a new paper on the bioRxiv: Jase Gehring, Jeff Park, Sisi Chen, Matt Thomson, and Lior Pachter, Highly Multiplexed Single-Cell RNA-seq for Defining Cell Population and Transciptional Spaces, bioRxiv, 2018. The paper offers some insights into the benefits of multiplex single-cell RNA-Seq, a molecular implementation of information multiplexing. The paper also […]
written 19 days ago by Living in an Ivory Basement by Titus Brown
It's hard enough to keep people inside informed...
written 20 days ago by Ensembl Blog
Some Variant Effect Predictor (VEP) jobs are small, just ten or fewer variants, and that’s easy. Some VEP jobs are big, if you do variant calling on one whole human genome, that’s five million variants! The more variants you have, the more computing power the VEP needs to process them, which can make it slow. […]
written 21 days ago by Living in an Ivory Basement by Titus Brown
Keeping the Data Commons community coordinated and engaged
written 26 days ago by What You're Doing Is Rather Desperate by Neil Saunders
A brief message for anyone who uses my PubMed retractions report. It’s no longer available at RPubs; instead, you will find it here at Github. Github pages hosting is great, once you figure out that docs/ corresponds to your web root :) Now I really must update the code and try to make it more … Continue reading PubMed retractions report has moved
written 26 days ago by Omics! Omics! by Keith Robinson
It's the night before London Calling. I hope to post Thursday, but an after-meeting report won’t be until nest week - I must dash on Friday fir a slightly insane/exhilarating routing to meet my family in Florida for the holiday weekend. Exhilarating as I will have a layover in one of the ancient capitals of Europe, Lisbon, which I’ve never visited. Insane, because it’s a 12 hour overnight layover. Anyway, between the challenge of covering Oxford Nanopore's expanding reach of products and applications and being sleep-addled from taking the redeye flight I'm going to throw out a bunch of thoughts without really trying to fuse them into a coherent narrative.Read more »
written 27 days ago by Omics! Omics! by Keith Robinson
Editorial note: I wrote this in early January, then planned to slot it in after some other items. Then life knocked me upside the head, then AGBT came along and then it was forgotten. Once I remember it, I fretted it had gone stale. But I had put a lot of effort into it and really nothing has changed with regard to iSeq, other than it should be shipping now. Besides, this week is London Calling and so having an Illumina-centric piece could be a bit of useful balance. So, for your consideration:Some of the online discussion around this January's iSeq announcement, springing from my piece or elsewhere, explores how the iSeq fits into the sequencing landscape. In particular, how does it fit in with Illumina's existing MiniSeq and MiSeq and how does it go against Oxford Nanopore's MinION. For example, in Matthew Herper's Forbes piece, genomics maven Elaine Mardis compares iSeq unfavorably to MiSeq in terms of cost-per-basepair. I'm a huge believer in fitting sequencing to ones scientific and practical realities and not the other way 'round: no one platform quite fits all situations nor do even the same metrics fit all situations. So in this piece, I'm going to illustrate what I believe is a plausible scenario in which iSeq would make sense. Now, I have designed this to play to iSeq's characteristics and very realistically have many dials which I could turn to go in another direction. Which I will try to note as I go along.Read ...
written 4 weeks ago by Bits of DNA by Lior Pachter
“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for dragging its feet on supporting the Human Genome Project” “All our social policies are based on the fact that [Africans] intelligence is the same as ours – whereas all […]
written 4 weeks ago by Diving into Genetics and Genomics
written 5 weeks ago by Ensembl Blog
This month we’re meeting Paul Kersey, who is the Ensembl Genomes team leader. What is your job in Ensembl? I’m the leader of the Non-Vertebrate genomics team. That means I’m the “front man” for Ensembl Genomes – our services for bacteria, protists, fungi, plants and invertebrate metazoa – although of course these activities depend on […]
written 5 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders
Today in “blog posts that have spent two years in the draft folder” – “Humans are 50% banana.” “Humans are 50% banana.” Perhaps you have heard this statement, or one like it. It seems to be widely-quoted. As an example it’s hard to go past this article from UK tabloid The Mirror which, in addition … Continue reading 50% bananas
written 5 weeks ago by Inside UniProt
In the March 2018 release, UniProt added the proteins of 10 new primate species to our collection of complete proteomes; the set of proteins believed to be expressed by an organism and typically obtained from the translation of a fully sequenced, annotated genome. As of release 2018_04 the total number of primate complete proteomes in UniProtKB stands at 24, a set which of course includes that of human. So why is this important?Studying non-human primates enables scientists to understand the evolution of genomic change and how this has impacted on protein expression patterns. Comparisons across proteome sets allow us to understand which proteins are shared by all primates, and which are species specific, and how changes in protein expression patterns have affected our evolutionary development. For example, multiple copies of a domain of unknown function, the recently renamed Olduvai domain (IPR010630), are found in neuroblastoma breakpoint family (NBPF) proteins. The copy number is highest in humans, lower in African great apes and further reduced in Orangutan and Old World monkeys. It has been speculated that this may be directly related to the size of the primate’s brain, more specifically to the volume of the neocortex, and links between domain copy number and both cognitive function and the severity of autism have been identified. Another study looked at why gene duplication has led to a marked expansion of HLA proteins in macaque monkeys in comparison to other primates. The HLA cell-surface proteins are responsible for the regulation of the immune system, ...
written 6 weeks ago by KidsGenomics
Access to samples is one of the main challenges of studying rare inherited conditions, particularly those whose molecular basis is unknown. Every individual harbors 3-5 million genetic variants compared to the human reference sequence. Even if we winnow these down to only rare variants likely to disrupt a protein-coding gene, hundreds still remain. The Power […] The post Rare Disease Research Collaboration: RLIM in X-linked Intellectual Disability appeared first on KidsGenomics.
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
241 posts, last updated 4 days ago
bioinformatics education, metagenomics assembly, python programming
233 posts, last updated 9 days ago
News about the Ensembl Project and its genome browser
165 posts, last updated 11 days ago
miRBase news and views
15 posts, last updated 11 days ago
bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"
45 posts, last updated 13 days ago
Reviews and commentary on computational biology
87 posts, last updated 14 days ago
Tips && tricks from a cluster of bioinformaticians
16 posts, last updated 14 days ago
Notes from the life of a computational biologist
100 posts, last updated 26 days ago
A wet lab biologist' bioinformatic notes. Mostly is about Linux, R, python, reproducible research, open science and NGS. I am into data science! I am working on glioblastoma (a terrible brain cancer) genomics at MD Anderson cancer center. Disclaimer: For posts that I copied from other places, credits go to the original authors.
51 posts, last updated 4 weeks ago
News and commentary from the UniProt developers
34 posts, last updated 5 weeks ago
KidsGenomics focuses on genetic diseases that affect children, including rare inherited disorders and pediatric cancers.
5 posts, last updated 6 weeks ago
Making Sense of Next-Gen Sequencing Data
88 posts, last updated 7 weeks ago
Weblog on Bioinformatics, Genome Science and Next Generation Sequencing
69 posts, last updated 3 months ago
Medical genomics in the post-genome era
71 posts, last updated 3 months ago
My name is Guillaume Filion. I am a scientist who loves biology and mathematics. As of late I also got into computers and the Internet. I intend my blog to be recreational, and not academic nor educational. I wish you will find some of the posts inspiring for your own reflection.
28 posts, last updated 4 months ago
Assistant professor of computer science at University of Iceland.
9 posts, last updated 4 months ago
Biology, sequencing, bioinformatics and more
32 posts, last updated 5 months ago
A news portal with postings about genomics resources, genomics news and research, science and more.
391 posts, last updated 8 months ago
This blog is written by Giovanni M. Dall’Olio, a research associate at the Cancer Evolutionary Genomics‘s group of Francesca Ciccarelli at the King’s College of London. My primary interests are in the system biology of cancer and in identifying new potential drug targets for this disease.
13 posts, last updated 11 months ago
My worklog on bioinformatics, science and research. Small tasks and cute tricks included :)
34 posts, last updated 13 months ago
Getting Things Done in Genetics & Bioinformatics Research
60 posts, last updated 16 months ago
virology, bioinformatics, genetics, science, java
65 posts, last updated 17 months ago
Thoughts and opinions from the associate director of the EMBL-European Bioinformatics Institute
57 posts, last updated 18 months ago
Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann from Melbourne, Australia.
25 posts, last updated 21 months ago
Bioinformatics tips, tricks, tools and commentary - all with a microbiological NGS bent. Authored by Dr Torsten Seemann from Melbourne, Australia.
29 posts, last updated 21 months ago
Frontier in Bioinformatics
185 posts, last updated 2.1 years ago
bioinformatics, biopython, genomic analysis
38 posts, last updated 2.2 years ago
bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"
78 posts, last updated 2.4 years ago
21 posts, last updated 3.5 years ago
A group blog providing expert, independent commentary on the personal genomics industry.
34 posts, last updated 3.6 years ago
The Knight Lab at Yale University » BlogThe Knight Lab at Yale University » Bioinformatics and Genetics
Bioinformatics and Genetics
3 posts, last updated 3.8 years ago
25 posts, last updated 4.5 years ago
Mostly bioinformatics, NGS, and cat litter box reviews
25 posts, last updated 4.7 years ago
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