I just posted a preprint that results from a little project that I took on. I used two challenging datasets, a developmental time course and combined data from different source labs, to evaluate RNA-seq normalization methods. It turned out that these tasks were indeed so tricky to normalise for that most, if not all, normalization methods did not perform particularly well. The paper is formatted as a short report, so it is a quick read. Here is the preprint on bioRxiv: Evaluation of RNA-seq normalization methods using challenging datasets.
In my latest paper, my colleagues and I take a next step in analysing allele-specific gene expression. We present RPASE, a method that detects allele-specific expression with nothing more but aligned RNA-seq reads and a list of SNPs from your favourite organism. No genome sequence needed, an assembled transcriptome sequence is sufficient to create this input data. Try it out and let us know what you think! Here's a link to the GitHub repository: wangmi811/RPASE. And here's the paper, published in Molecular Ecology Resources: RPASE: Individual‐based allele‐specific expression detection without prior knowledge of haplotype phase.
The bioRxiv preprint we posted last year has now been published in Development! My colleague Richard Sarro deleted the single most important limb enhancer for the Pitx1 gene and found no compensatory effects in the changed regulatory topology of the locus. No other enhancers increased their activity, no shadow enhancers found! Development was normal nonetheless! The paper is now available in online early version: Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development. Here is the link to the bioRxiv preprint.
When I was a Master's student in Uppsala, I started writing a literature summary for the Target Rat (Stochomys longicaudatus), a murid rodent living in Central African rainforests, named for its long guard hairs sticking out of the fur. I finally managed to collect all the literature I needed to finish the project; it has now been accepted for publication in Mammalian Species. Thanks to everyone who helped me on the way!
My last PhD thesis chapter has now been published in Genome Biology and Evolution! Mi Wang, Hans Ellegren, and I take a look at genes that are allele-specifically expressed in natural flycatcher populations. Link: Bayesian inference of allele-specific gene expression indicates abundant cis-regulatory variation in natural flycatcher populations. #OA
Starting this month, my postdoctoral research is supported by a Research Fellowship from the German Research Council (DFG). This will allow me to study functional enhancer mutations in primate brain development in the Noonan lab for the coming two years. I am excitedly looking forward to this opportunity and thank the DFG for their support!
The Wink lab invited me to give a talk on my PhD thesis. I had a great time meeting various people from the lab. Visiting my alma mater I also took the chance to sit in a basic biology lecture which I found had not changed much since I was a student in Heidelberg back in 2005.
My work on gene expression diversity and divergence in collared and pied flycatchers has now been published in Molecular Ecology. Thanks to all my colleagues who have contributed to this work! Link: Divergence in gene expression within and between two closely related flycatcher species.
I presented my PhD thesis work in a talk hosted by the Hoekstra lab at Harvard University. It was my first time in Cambridge/Boston and a neat experience. Many thanks for invitation and hospitality to Felix Baier.
Today I am starting my new postdoc position in Jim Noonan's lab at Yale University. I am looking forward to a some exciting years to come!
My PhD thesis has arrived fresh from the press. Many thanks to everyone who helped me getting this done! Want a digital copy? Just drop me a message!
I was featured by Alex Cagan as I was giving my talk at the SMBE meeting. Check out his other sketches, his works are super cool!
UPDATE: Alex does not only do cool work, he is also a cool dude and allowed me to use his sketch for the cover of my PhD thesis. Big thanks!