Blog posts collected by the Biostar aggregator. To follow subscribe to the planet feed
<prev • 2,352 results • page 2 of 95 • next >

My approach to community building and coordination

written 9 weeks ago by Living in an Ivory Basement by Titus Brown

How do you grow community? Slowly and carefully.

With great power comes great responsibility

written 9 weeks ago by Opinionomics by Mick Watson

Recently I published a blog post about a fairly simple test to find out whether you have “short” protein predictions in your bacterial genomes, and predicted that some of these short peptides may be the result of unresolved errors in long-read, single molecule assemblies. Perhaps not surprisingly, there was a reaction from the PacBio community […]

Farewell then, PubMed Commons

written 9 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

PubMed Commons, the NCBI’s experiment in comments for PubMed articles, has been discontinued. Thoroughly too, with all traces of it expunged from the NCBI website. Last time I wrote about the service, I concluded “all it needs now is more active users, more comments per user and a real API.” None of those things happened. … Continue reading Farewell then, PubMed Commons

Getting to know us: Jon from HAVANA

written 10 weeks ago by Ensembl Blog

This month we are meeting Jonathan Mudge who is the Annotation Project Leader in the HAVANA group. What is your job in Ensembl? I’m a Team Leader in the HAVANA group. We focus on manual gene annotation of the human and mouse genomes, which forms the core of the genesets produced for these species […]

The genomic landscape of pediatric cancers

written 10 weeks ago by KidsGenomics

Although pediatric cancer is rare, it’s the leading cause of disease-related death among children who survive past infancy (in the Western world). Around 1 in 500 children will be diagnosed with cancer by age 15. Like most rare diseases, childhood cancer is difficult to study because so few patients are available. Even for the most […] The post The genomic landscape of pediatric cancers appeared first on KidsGenomics.

A simple test for uncorrected insertions and deletions (indels) in bacterial genomes

written 10 weeks ago by Opinionomics by Mick Watson

A friend and a colleague of mine once said about me “he’s a details man”, and it was after we had discussed the fact some of my papers consist solely in pointing out the errors other people ignore – in RNA-Seq for example, or in genome assemblies (I have another under review!). By now, those […]

A Morning Visit to SeqLL

written 11 weeks ago by Omics! Omics! by Keith Robinson

I've written in the past about SeqLL, the company which purchased all of the hard assets from Helicos after the latter's demise. At the end of last year, CEO Elizabeth Reczek invited me to stop by for a visit and so I spent a morning having a frank discussion with Dr. Reczek and Director of Sales Lee Dalton and also was treated to a tour of their facilities.Read more »

Would you like to annotate function with UniProt's annotation systems?

written 11 weeks ago by Inside UniProt

Register your interest here: https://goo.gl/forms/IFo28dAOa5HEwfSk1One of the core activities at UniProt is to develop computational methods for the functional annotation of protein sequences. UniProt has developed two prediction systems, UniRule and the Statistical Automatic Annotation System (SAAS) to automatically annotate the unreviewed records in UniProtKB/TrEMBL with high coverage and a high degree of accuracy.These prediction systems can annotate protein properties such as protein names, function, catalytic activity, pathway membership, and subcellular location, along with sequence-specific information, such as the positions of post-translational modifications and active sites.As a result of discussions with researchers and genome sequencing centres interested in functional annotation, we plan to make our annotation rules publicly available for download. We would like to engage with users in the development of a standardised format for sharing these annotation rules, to help you use the rules for functional annotation of your own data.Apply the UniProt rules on your own proteinsWe also plan to provide a standalone tool to execute the UniProt annotation rules and enrich your own data with high-quality annotations. We invite user feedback towards the provision of such a tool for functional annotation of coding sequences.By providing input data such as the protein sequences, taxonomy data and InterProScan signatures, along with the rules, a rule engine will be able to reason on the rules to infer new protein annotations.Get involvedWould you like to try out the UniProt rules to annotate your own data? Would you like an early peek at the systems, formats and functionality we plan to ...

Ensembl sites down

written 11 weeks ago by Ensembl Blog

The main Ensembl site at ensembl.org and the GRCh37 site at grch37.ensembl.org are both down at the moment. The mirror sites at useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org are all available. We are sorry about any inconvenience, and are working on rectifying this.

MassGenomics is Closed, but KidsGenomics is Open

written 11 weeks ago by MassGenomics by Dan Koboldt

Thank you to everyone who sent kind messages after I announced the end of MassGenomics earlier this month. Please rest assured that this website and all of its articles will remain online for the foreseeable future. Also, I have an important announcement. Today is Rare Disease Day, an annual event that aims to raise awareness […]

Why Rare Disease Research Matters

written 11 weeks ago by KidsGenomics

February 28th is International Rare Disease Day, an event that aims to raise awareness of rare diseases and the pressing need for more research. Rare Diseases By The Numbers Rare diseases might be rare, but the patients and families affected by them are numerous. Here are some statistics courtesy of the National Organization for Rare […] The post Why Rare Disease Research Matters appeared first on KidsGenomics.

Patients with Multiple Rare Diseases

written 12 weeks ago by KidsGenomics

We often think of rare diseases in simplistic terms — a single gene in which mutations cause a recognizable disorder. That disorder might affect multiple cells, tissues, and organs, and the severity can vary significantly among patients. When a diagnosis is obtained from genetic testing, it’s tempting to consider all aspects of the patient’s condition […] The post Patients with Multiple Rare Diseases appeared first on KidsGenomics.

PromethION: Straining at the Starting Gate

written 12 weeks ago by Omics! Omics! by Keith Robinson

Due to the usual time conflicts, I've only watched bits-and-pieces of the Winter Olympics from South Korea. Which is unfortunate, as I do enjoy observing many of these events as so many combine grace, power and finesse. In the various timed events, the competitors can be seen tightly wound, ready to spring out at the crack of the start. Increasingly, that is how Oxford Nanopore's PromethION looks: a superb performer ready to bolt away.Read more »

Assessment report for ANGUS 2017

written 12 weeks ago by Living in an Ivory Basement by Titus Brown

An assessment report on ANGUS 2017.

Exploring the 1000 genome dataset with Hail on Amazon EMR and Amazon Athena

written 12 weeks ago by Kevin's GATTACA World

Blog post from Roy Hasson https://aws.amazon.com/blogs/big-data/genomic-analysis-with-hail-on-amazon-emr-and-amazon-athena/?nc1=b_rpGenomics analysis has taken off in recent years as organizations continue to adopt the cloud for its elasticity, durability, and cost. With the AWS Cloud, customers have a number of performant options to choose from. These options include AWS Batch in conjunction with AWS Lambda and AWS Step Functions; AWS Glue, a serverless extract, transform, and load (ETL) service; and of course, the AWS big data and machine learning workhorse Amazon EMR.For this task, we use Hail, an open source framework for exploring and analyzing genomic data that uses the Apache Spark framework. In this post, we use Amazon EMR to run Hail. We walk through the setup, configuration, and data processing. Finally, we generate an Apache Parquet–formatted variant dataset and explore it using Amazon Athena.

What’s coming in Ensembl 92 and Ensembl Genomes 39

written 3 months ago by Ensembl Blog

Both Ensembl release 92 and Ensembl Genomes release 39 are scheduled for April 2018. Included are new genomes and genebuilds (Goat, Zebrafish, Marmoset, Stalk-eyed fly and Waterflea) and a command line version of our new Linkage Disequilibrium tool. Here are the highlights you can look forward to: Ensembl 92 New assemblies, gene sets and annotations […]

AGBT: It Ain't Over 'til the Tattoo Wears Off

written 3 months ago by Omics! Omics! by Keith Robinson

AGBT officially ended on Thursday night with a space-themed party, but I have a bunch of notes from interviews with company representatives and even a few notes from sessions. So be prepared for a string of further AGBT reports. This dispatch will have some overall thoughts as well as some notes on the possible return of AGBT to Marco Island next year. I also want to mention two good AGBT 2018 summaries, one from Dale Yuzuki and another from Decibio's Stephane Budel.newly appliedRead more »

GDE² = DGE² + DTU² = DTE₁² + DTE₂²

written 3 months ago by Bits of DNA by Lior Pachter

The development of microarray technology two decades ago heralded genome-wide comparative studies of gene expression, but it was the widespread adoption of RNA-Seq that has led to differential expression analysis becoming a staple of molecular biology studies. RNA-Seq provides measurements of transcript abundance, making possible not only gene-level analyses, but also differential analysis of isoforms of […]

Do software and data products advance biology more than papers?

written 3 months ago by Living in an Ivory Basement by Titus Brown

Software and data good.

Waterman’s egg

written 3 months ago by Bits of DNA by Lior Pachter

I recently published a paper on the bioRxiv together with Vasilis Ntranos, Lynn Yi and Páll Melsted on Identification of transcriptional signatures for cell types from single-cell RNA-Seq. The contributions of the paper can be summed up as: The simple technique of logistic regression, by taking advantage of the large number of cells assayed in […]

AGBT: BioNano Launches New Labeling Approach

written 3 months ago by Omics! Omics! by Keith Robinson

AS AGBT opened, optical mapping company BioNano Genomics announced a new scheme for labeling genomic DNA inputs which substantially improves performance. Sven Bocklandt from the company sat down with me yesterday to walk through the new Direct LabelingRead more »

AGBT: Twist Biosciences Launches Sequence Capture Product

written 3 months ago by Omics! Omics! by Keith Robinson

Twist Biosciences today launched a new product into the sequence capture space. CEO Emily Leproust was presenting to the Gold Sponsor workshop as I started writing this, but she also sat down with me yesterday to preview the new offering for targeted sequencing.Read more »

The End of MassGenomics

written 3 months ago by MassGenomics by Dan Koboldt

I started MassGenomics ten years ago, when so-called next-generation sequencing was still in its infancy. I’d joined the Genome Sequencing Center at Washington University, fulfilling a dream I had since high school. At the time, two NGS technologies had begun to emerge: 454 pyrosequencing and Solexa sequencing-by-synthesis. Over the next several years, Solexa was acquired […]

AGBT: 10X Previews Three New Single Cell Applications

written 3 months ago by Omics! Omics! by Keith Robinson

I spent breakfast with 10X Genomic's Michael Schnall-Levin and two of his 10X colleagues gave me a sneak peak at three new single cell products they are rolling out at the workshop I'm typing away at now. These enable measuring protein targets of antibodies, mapping out accessible chromatin regions with ATAC-Seq, and mapping copy number variants (CNVs) at single cell resolution. All use the existing Chromium Controller instrument.Read more »

AGBT 2018: It's Great to Be Back

written 3 months ago by Omics! Omics! by Keith Robinson

All sorts of scheduling snafus have kept me away the past three years. So this time around, I vowed to go and made sure my calendar stayed clear. So clear, I forgot to put a reminder down to actually register for the event. Luckily, there were slots still available when I put my flier in.Read more »
<prev • 2,352 results • page 2 of 95 • next >

Planet Feeds

Bits of DNA by Lior Pachter
Reviews and commentary on computational biology
85 posts, last updated 4 days ago
Diving into Genetics and Genomics
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 6 days ago
Ensembl Blog
News about the Ensembl Project and its genome browser
159 posts, last updated 11 days ago
What You're Doing Is Rather Desperate by Neil Saunders
Notes from the life of a computational biologist
99 posts, last updated 13 days ago
Inside UniProt
News and commentary from the UniProt developers
34 posts, last updated 13 days ago
KidsGenomics
KidsGenomics focuses on genetic diseases that affect children, including rare inherited disorders and pediatric cancers.
5 posts, last updated 15 days ago
Omics! Omics! by Keith Robinson
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
238 posts, last updated 18 days ago
Next Gen Seek
Making Sense of Next-Gen Sequencing Data
88 posts, last updated 24 days ago
Living in an Ivory Basement by Titus Brown
bioinformatics education, metagenomics assembly, python programming
228 posts, last updated 8 weeks ago
Kevin's GATTACA World
Weblog on Bioinformatics, Genome Science and Next Generation Sequencing
69 posts, last updated 9 weeks ago
Opinionomics by Mick Watson
bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"
44 posts, last updated 9 weeks ago
MassGenomics by Dan Koboldt
Medical genomics in the post-genome era
71 posts, last updated 11 weeks ago
The Grand Locus
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 3 months ago
Bits of Bioinformatics by Páll Melsted
Assistant professor of computer science at University of Iceland.
9 posts, last updated 3 months ago
In between lines of code by Lex Nederbragt
Biology, sequencing, bioinformatics and more
32 posts, last updated 5 months ago
Bioinformatics I/O
Tips && tricks from a cluster of bioinformaticians
15 posts, last updated 6 months ago
The OpenHelix Blog
A news portal with postings about genomics resources, genomics news and research, science and more.
391 posts, last updated 8 months ago
BioinfoBlog.it
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 10 months ago
thoughts about ...
My worklog on bioinformatics, science and research. Small tasks and cute tricks included :)
34 posts, last updated 12 months ago
Getting Genetics Done by Stephen Turner
Getting Things Done in Genetics & Bioinformatics Research
60 posts, last updated 15 months ago
YOKOFAKUN by Pierre Lindenbaum
virology, bioinformatics, genetics, science, java
65 posts, last updated 16 months ago
Bioinformatician at large by Ewan Birney
Thoughts and opinions from the associate director of the EMBL-European Bioinformatics Institute
57 posts, last updated 17 months ago
The Genome Factory
Bioinformatics tips, tricks, tools and commentary - all with a microbiological NGS bent. Authored by Dr Torsten Seemann from Melbourne, Australia.
29 posts, last updated 20 months ago
The Genome Factory
Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann from Melbourne, Australia.
25 posts, last updated 20 months ago
Homolog.us - Bioinformatics by Manoj Samanta
Frontier in Bioinformatics
185 posts, last updated 2.1 years ago
Blue Collar Bioinformatics by Brad Chapman
bioinformatics, biopython, genomic analysis
38 posts, last updated 2.1 years ago
opiniomics by Mick Watson
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 2.3 years ago
Bergman Lab
21 posts, last updated 3.4 years ago
Genomes Unzipped
A group blog providing expert, independent commentary on the personal genomics industry.
34 posts, last updated 3.6 years ago
miRBase blog
miRBase news and views
14 posts, last updated 3.8 years ago
Bio and Geo Informatics by Brent Pedersen
Genomics Programming
25 posts, last updated 4.5 years ago
Jermdemo Raised to the Law by Jeremy Leipzig
Mostly bioinformatics, NGS, and cat litter box reviews
25 posts, last updated 4.7 years ago

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1695 users visited in the last hour