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Mark Ziemann
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How NGS is transforming medicine
Last month, I gave a talk at our departmental meeting, describing in general terms how high throughput sequencing technology was having real impacts in medicine and human health, as well as some emerging trends to watch out for in coming years. Here's the l...

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Introducing the ENCODE Gene Set Hub
TL;DR We curated a bunch of ENCODE data into gene sets that is super useful in pathway analysis (ie GSEA). Link to gene sets and data:  https://sourceforge.net/projects/encodegenesethub/ Poster presentation: DOI:10.13140/RG.2.2.34302.59208 Now for the longe...

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2016 wrap-up
What a rollercoaster. On the good side, we've seen advances in sequencing methods including advances in Nanopore sequencing and single cell methods becoming more common. We also saw 10x genomics come to the party with an emulsion PCR approach that can be ap...

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MSigDB gene sets for mouse
I recently needed to convert MSigDB gene sets to mouse so I thought I would share. GO.v5.2.symbols_mouse.gmt kegg.v5.2.symbols_mouse.gmt msigdb.v5.2.symbols_mouse.gmt reactome.v5.2.symbols_mouse.gmt Below is the code used to do the conversion. It requires a...

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Gene name error scanner webservice
Over the past few weeks, we've had a lot of feedback about our paper describing the sorry state of Excel auto-correct errors in supplemental files in spreadsheets. In our group, we've discussed a number of ways that these errors could be minimised in future...

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My personal thoughts on gene name errors
Well, our paper "Gene name errors are widespread in the scientific literature" in Genome Biology has stirred up some interest. There are a lot of reasons why this article has taken off beyond what I initially envisioned: Most tech-savvy people hate Excel Pe...

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My short paper in Genome Biology shows ~20% of genomics papers with Excel gene lists are affected by auto-correct errors.
http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7
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