Topics in biology that are not researched as much as they should be. Initial offering is made by the participants of Russian-speaking Biology-related telegram chat Лапкочат GANG.
RNN instead of HMMs - there are a lot of application of HMMs in Bioinformatics (classic example is multiple sequence alignment) but RNNs have pretty much the same properties while being way stronger as sequence modellers. Don't see much of RNN application in lieu of HMMs in Bioinf though. Maybe Transformers would be helpful as well?
Proper visualization of long DNA sequences - it would be nice to have an understandable visualization of long DNA sequences. Some good attempts are available in this library.
Prediction of response to psychopharma - there is some research but pretty recent and not much.
Functions of genes - from about 20k of known human genes we somewhat know a function of about 5k (update: 10k). Imagine the situation for other species.
Metagenomics of clouds - metagenomics is fast growing approach in modern biology.Investigation of microbial community of atmosphere (for example clouds) is very interesting and not fully understood field of microbiology.
Oxygen-resistant nitrogenases anyone? There could be a very promising application in industry since the current way of nitrogen fixation is quite compicated. There was a paper twenty years ago with claims of finding such nitrogenase but current results contradict it.
Light detection in bacteria - how does it work?
Larvamima - ant parasytes that mimic the larvae. After the discovery about 30 years ago only twelve mentions in reviews.
Mimicry in plants - quite self-explanatory. There are a number of examples (rice and Echinochloa crus-galli, fallen leaves and Monotropsis oderata) but it still remains pretty unclear.
Myrmecophilidae - live almost everywhere where ants do, no assembled genomes, no research on their ecology and molecular biology.
Archaeal virii - morphology differences from bacteriophages and eukaryote virii. Are there any archaeal virii with hybrid RNA-DNA genome?
Fungal virii - Why they are so often non-pathogenic for their hosts?
Streptococcus mutans vaccine - how to evict the stuff that eats your teeth. There is some research but no known solution yet.
Original list - includes many fields (Math, Physics etc).
Open questions: CRISPR biology - review of open questions in CRISPR by Eugene Koonin
Wiki list of unsolved problems in biology - note that unsolved doesn't imply under-investigated.