Tag Archives: metagenomics

iMicrobe: Fostering Community-Driven Science and Data Discovery. Q&A with Bonnie Hurwitz

- August 2, 2019

In this data-driven era, research is faced with new challenges, from sharing, storing and accessing data, including how to better integrate data to answer big questions in science. With many data repositories available, it is hard to maintain them all – some repositories are forced to close – meaning loss of access to invaluable datasets.  […]

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FUNC in the Fjords: Functional Metagenomics 2019 in Trondheim

- July 27, 2019

The Norwegian city of Trondheim seemed the place to be this June – with hotels in high demand  due to the BarCode Of Life conference, The Big Challenge Science Festival (including a concert by that famous science communicator Sting), and the Functional Metagenomics 2019 conference (#FMG2019) all taking place over the same period (June 16-19th). […]

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Mock the Metagenome. Author Q&A with Nick Loman & Sam Nicholls

- May 15, 2019

mock metagenome

The mock metagenome, MAGs and breaking the first rule of Long Read Club Out today in GigaScience is a new “mock metagenome” Data Note from the Nick Loman lab in Birmingham showcasing the latest long-read sequencing technologies from Oxford Nanopore. Having published the first nanopore E. coli genome with us in 2014 showcasing the then […]

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Meet the GigaScience ICG Prize Winner, Pt. 2: Lisa Johnson Q&A

- December 14, 2018

ICG prize winner

Yesterday we published the winning paper of the second GigaScience prize, with additional detail and coverage in GigaBlog describing why we and the judging panel found it so novel. This was an impressively case study in reproducibility, reassembling & reannotating around 700 microbial eukaryotic transcriptomes to demonstrate this approach can aid in revealing new biologically relevant […]

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Reprocessing the Microbial Genomic Goldmine: Winner of the ICG13 Prize

- December 13, 2018

Microbial goldmine

Out today is the winner of our ICG13 Prize, presenting work that can aid in revealing new biologically relevant findings and missed genes from previously generated transcriptome assemblies. Teaching old data new tricks, and maximising every last nugget of information from previously funded research. Here we present some insight into why the reviewers and judges […]

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Making sense of pangenome networks

- October 15, 2018

Navigating Pangenome’s Labyrinth In the two decades since the first genomes were sequenced, with the exponential growth of new and closely related genomes it has become increasingly difficult to visualise and compare their structure. Particularly with the large diversity and difference in genes within microbial genomes. A new computational pipeline, published in GigaScience, makes it […]

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Of Mice and Men (and Monkey) Microbiomes.

- August 31, 2018

Monkey microbiome

Monkey Microbiome Business Research just out in GigaScience introduces the macaque monkey to the microbial gene catalogue club, joining other important model organisms including the (also recently published in GigaScience) Rat, Mouse, Pig and Cow. To explain more, in this posting we give some insight into what this data shows, and how this growing library […]

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Reproducible Research Resources for Research(ing) Parasites

- June 3, 2016

Two new research papers on scabies and tapeworms published today showcase a new collaboration with protocols.io. This demonstrates a new way to share scientific methods that allows scientists to better repeat and build upon these complicated studies on difficult-to-study parasites. It also highlights a new means of writing all research papers with citable methods that can be updated over time.

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Fermenting a Reproducible Research Revolution

- July 30, 2015

With greater awareness in the difficulties in making scientific research more reproducible, numerous technical fixes are being suggested to move publishing away from static and often un-reproducible papers to more reproducible digital objects that better fit 21st century technology. New research demonstrates one potential approach through publishing open data and code in containerized form using docker, and also allowing scientists to tackle climate change, through better understanding of the production of biofuels.

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New GigaDB Dataset: Ever wondered whats in your gut?

- July 7, 2014

A paper published in Nature Biotechnology today reveals the most comprehensive catalogue of genes in any single microbiome to date. While the roughly 20,000 genes in the human genome have been available for over a decade, the gene catalogue of the microbiome, our much larger “other genome” has to date been much more poorly understood […]

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