I will try to put updates on my Polonez fellowship here, together with some materials, links and other useful information. Major updates on Remus development should also find its way on the timeline down here.
Some basic information about the project's scope and aims can be found here and on hosting departments' pages.
Remus has been published in Frontiers in Genetics as part of the research topic Non-Coding Variants: From Interpretation to Personalized Medicine. The manuscript is freely available online here.
Remus has been accepted for publication in Frontiers in Genetics. Stay tuned for the updates!
New relase of Remus is out -> v0.5
Towards the end of last year I started writing a series of articles on bioinformatics and analysis of whole-genome sequencing data. The articles were targetted to a broad audience and written in Polsih. The first two of them are out in the first issue of an online genetics magazine genetyka.bio, together with a bunch of other very good articles. If you read Polish - enjoy the reading!
Our manuscript "A cross-sectional study of patients referred for HNF1B-MODY genetic testing due to cystic kidneys and diabetesis" is available online.
The project officially ends, but the work on Remus, the manuscripts and the data is not complete yet. I will post the most important updates here.
Great news from Pediatric Diabetes - out manuscript on HNF1B-MODY has been accepted for publication. I will post a link a soon as the online version of the article is ready.
We had a nice turnout at the workshop on whole-exome sequencing data analysis and variant interpretation. Thanks to all the participants!
Last week Arek presented our work on HNF1B-MODY at the [45th ISPAD conference](https://2019.ispad.org/ in Boston. Here is the poster.
Last weekend I attended my second Polonez training. This one's topic was "Working with others", and one of the main themes was communication. Did you know that one of the main reasons why projects fail is poor communication?
Trying to become even more effective after the "Personal Effectiveness" training organized by National Science Centre and Vitae this weekend. Starting today, I will (among other things) stop checking email as the first thing in the morning. Hope that this will prevent distraction and allow me to use the morning hours on important tasks. Let's see how it goes.
Last week, together with Arek, we were presenting our work on European Human Genetics Conference (ESHG19) in Gothenburg, Sweden. Here you can view the posters for Remus and HNF1b study
After a longer break, a new release of Remus is out - v0.4. Starting from this version, hg19 and hg38 ENCODE data are lifted over to hg38 and hg19 (respectively), joined, and used for querying enhancer and available chromatin regions. Similarly, hg19-based FANTOM5 promoter and enhancer data is lifted over to GRCh38. Support for both genome build to full extent.
Yesterday I came back from a very inspiring study visit at MNM.bio. Look forward to cutting-edge whole-genome analystics in rare-disease and cancer diagnostics!
I have spent some time recently tuning a custom pipeline that will be used here at BTM to process NGS data from microRNA profiling experiments. Tested out three different mappers, several approaches and settled on one that is implemented as a default path this one. In short, UMI-extraction, followed by bowtie2 local mapping to forward strand of miRBase mature miRs, and separate counting of unique and multimapping reads. Plus some QC stats generation. All stitched together with Ruffus. Help yourselves, if you fancy.
Remus has gotten its permanent URL: http://remus.btm.umed.pl. Currently it points to a test/development version of the tool, but I hope to be ready to provide a production release soon.
We will be going to Gothenburg to present Remus and our study on HNF1B-MODY at ESHG 2019. Looking forward to many great talks and meeting some colleagues from abroad.
And here is an example of igv-screenshooter-html in action on some trio data: igv-screenshooter-trio.html
Let me introduce Dawid, student of final year of Applied Computer Science at Lodz University of Technology. I will be co-supervising Dawid's MSc thesis where he develops a system for sharing genetic variant frequency data. Check out projects's repo here.
BTM team participated in Gliwice Scientific Meetings conference, where Remus was presented on a poster.
I have a pleasure to announce that Remus supports hg38 now. The master branch contains liftover code for both ENCODE and FANTOM5 data, which are lifted over both ways, i.e. hg19->hg38 and hg38->hg19. In the last minor revision few performance improvements were also added.
I was invited to give a talk at excellent PhD School in Molecular Medicine organized by prof. Bożena Kamińska. Had a great time in Krakow presenting my view on shift from WES to WGS in medical diagnostics of rare disorders, and an update on Remus development. The slides are here.
Had a great time at Intelliseq and some good fun implementing IGV-screenshooter.
Check it out! 
I am starting a study visit at Intelliseq today. Looking forward to great discussions, exchange of experience, and some practical work done.
This year's Polish Bioinformatics Society Symposium (PTBi2018) is taking place in Wrocław. I have a pleasue to present a flash talk on improving detection accuracy of duplications.
Damian has passed his MSc exam yesterday. As part of his thesis under my co-supervision Damian developed Remus. I will be continuing this work and keep extending the software in this fork repo. Stay tuned!
I am at excellent bioinformatics conference in Toruń - BIT18, presenting Remus.
Today I visited fellow bioinformaticians from Biostatistics Group at Wroclaw University of Enviromental and Life Sciences. I was invited for a presentation for students of BSc and MSc programmes to talk about my work. I took this opportunity to also presented them a list of volountary summer projects where they could get some programming practice and hands-on experience with NGS data analysis. Maybe our group will source some bioinformatitians from this crowd...
Continuing the search for patients for the project: this time at the XIX Congress of the Polish Diabetological Association in Katowice (PTD 2018). Here are slides of a short presentation (in Polish).
Let me introduce Damian who has been working with me on Remus, a web application that will facilitate analysis of regulatory variats in WGS data. The project is the practical part of Damian's MSc thesis at the Department of Genetics of Wroclaw University of Enviromenal and LIfe Sciences. PS Remus is for REgulatory MUtation Search.
Today I am at meeting of Pediatric Section of the Polish Diabetological Association meeting people and spreading news about the project. Slides for my presentation are here.
This project is funded by NCN Polonez grant no 2016/23/P/NZ2/04251. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665778.
