Bioinformatics project ideas
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- Опубліковано 4 лип 2024
- How to find bioinformatics projects for early career scientists and students.
Here is the Twitter thread: / 1301039878923190273
Some ideas
* Reproduce the results of a paper -- look for one with a detailed methods section and data available.
* Reproduce a paper’s analysis on a different dataset -- this is easier for slightly older papers where new datasets have come out after publication.
* Reproduce an older paper’s analysis on a newer reference genome and compare to their original results. Do they hold up?
* Benchmark similar tools against each other.
* Improve, dockerize, or document bioinformatics software tools. - Наука та технологія
Heey, thanks for this great video!!! UA-cam recommended this video to me, and I remembered that I have been subscribed to your channel for two or more years due to the bash script video. Sadly, I have not been able to work in this area since then, however this video has been a great inspiration to come back to work in bioinformatics! Thank you very much for all the ideas and advice given here, this video is a must see for those that want to start working in bioinformatics.
Great! Thanks for making this video. I really like the idea on taking somewhat old, not maintained, but still useful projet and make a wraper/docker for it.
Wow. It's been a while. Very welcome addition!
Now that was a really informative video. Thank you.
Currently dockerizing ArchR! Excited to deploy it so you all can try it!
Very detailed! thank you very much for this video
Thank you so much for making this video
Great advice Maria!
thank you Maria, good tips and ideas.
Wow amazing video! I started a masters in this field and honestly i really didnt see a direction to what to do besides taking random class.
Thank you so much for this
I think it's always good to start with learning existing tools. Once you are conformable with using tools, then pick up either CS or stats. CS-oriented people may do projects like long-read sequencing. Stats-oriented people may do projects like single-cell RNA seq. It's better to think of a problem like a computer scientist or statistician, rather than a biologist.
Thank you Maria.
Great video, thank you!
Thanks your videos are great ❤❤❤
yep ,trying to do step 3 with grapevine rootstocks. Traditionally their RNA is mapped to grapevine reference genome, and now i sequenced, assembled and annotated their own genome.
very helpful. thanks a lot
Love Love Love that.
Nice video...Informative
I'm going to start with the PCA project.
Thanks Mariia, very informative video. How do you obtaining an access to the population data??
When you are looking at papers, what keywords or topics do you recommend looking up and following?
Hello. Thank you for this great video with lots of interesting ideas. Do you have any suggestions on finding remote projects for a master thesis? i am studying bioinformatics part time and it is not possible to incooperate my thesis into my current job but I would like to keep the job so I am trying to find master thesis projects that would allow me to work on them in my free time. are github collaborations a source for that or is there any network where to find a potential supervisor with a project? kind regards from austria
Thank you mam
Thx right now we are using Mega to create phylogenetic trees and for multiple sequence alignment.
I have MS in Human genetics and cytology, and I'm familiar with python and command line. I'm looking for a PHD in bioinformatics. My question is, would it be better if I enrolled in strict genomics program or in a mixed program of genetics and genomics (dry and wet lab) program?.
Hi.. I am planning on thesis on cnv analysis in WES data for diagnostic yield for rare diseases... Your opinion on that pls?
Very informative video! I find your videos very useful and insightful. Can you suggest some startup ideas in Bioinformatics for a founder having a purely software engineering background or make a video on the same?
Could you do a video on the Genes Mirror Geography project? I am trying to do this but I don't understand how I should convert the data into numbers and can't think of a way to do it such that it would yield anything meaningful. I have so many other questions as well and feel super lost! Thank you for the awesome videos though, as always!! :)
Hmm yea I can try this idea for a video. It could be a good case study for bringing together several practical bioinformatics skills, and it’ll be fun to see how different my implementation is from the original way I did this 8 years ago when it was literally my first time ever using Python. Okay, I’ll try to do this soon!
@@OMGenomics Thank you! I'm trying to do this now but getting a hold of the SNP data is proving to be a huge headache! I have 30 tabs open in my browser trying to get something like a .txt file or anything I can put into excel, no luck :(
I finished the video! ua-cam.com/video/-PCKK_nwFdA/v-deo.html
Thanks for encouraging me to do this one! I hope it helps :)
@@OMGenomics Thank you so much!! I'll watch soon and give it a shot!
Can you make videos on eburst use in mult locus sequence typing
Hi Maria!! I have been watching your videos for quite a time and wanted some advice from you on my current dilemma. A brief background about my current situation, currently I am working in a short term project related to Network Medicine in a lab. It feels good and I
am getting to learn a lot about Coding, Data Analysis and Visualization. Also I am thinking about pursuing PHD in the same field. But also I like doing Bioinformatics work and for the future purpose (like doing a Job or pursuing Post Doc) I would like to stick to Bioinformatics. So my dilemma is should I go on and pursue the PHD in Network Medicine (will the field affect my chances of getting a bioinformatics job in the future?) or should I leave this PHD opportunity and look for a PHD in the field of Bioinformatics?
as long as you get the skills, the tittle doesnt matter... put them on your CV and whenever the job offer states... bioinformatics skills, APPLY and highlight those skills you've gained.
Where was this last year when i was doing my bioinformatics module 🥲🥲🥲
Hi Maria, can you explain the difference between bioinformatics and statistical genetics?
There is probably significant overlap. When I was applying to PhD programs in bioinformatics, I remember some of the programs happened to be called "statistical genetics", but there wasn't much of a real difference in the kind of work they did from those that called it "bioinformatics".
@@OMGenomics Thanks, this was a bit confusing. I'm about to apply for MS, and where I live, we only have statistical genetics concentration within biostatistics programs.
Bioinformatics is a bit more general, and its techniques may include WGS, RNA-seq, CHip-Seq, etc. Statistical genetics is typically GWAS studies (sometimes also include a bit of evolutionary biology), where you see the associations between genotype and phenotype.
I am studying bioinformatics for my bachelors degree and I am wondering if you have ever met bioinformaticians that only had a bachelors or if it is generally required to have a masters degree or above to get into this field?
Yes there are bachelor's called bioinformatics
You can qualify to do projects but you can't really expect the best jobs in bioinformatics without a PhD so consider getting that or atleast a masters degree.
At TUM there is a bachelor and masters that is just bioinformatics not even Cambridge and Oxford offer that
Hey are you wearing aligners if I am not wrong, I am too a bioinformatician currently wearing aligners XD. Anyways good suggestions about the projects. Cheers.
Haha yea we both are, nice catch! They are not entirely invisible up close and with this much laughter 😂
wow
I just saw your channel can you help me in bacterial transcriptome analysis please for further communication pls where I can contact you
I like the background with "genome research" which is written up in "game of thrones" style 🥴
Haha that’s a print of the actual cover when my PhD project paper was published :)
Hi