I currently mainly work on biological applications of machine learning, but I remain a bio-beginner. Biology is obviously a huge topic. Many references here may be too introductory for your tastes. Note that many biology tools are still very R based (see Bioconductor).
A very biased personal take based on MITx 7.00x:
A great review of biology basics by Eric Lander: MITx 7.00x Introduction to Biology - The Secret of Life
and its textbooks:
Searchable version of Alberts et al Molecular Biology of the Cell, 4th edition
Searchable version of Griffiths et al An Introduction to Genetic Analysis, 7th edition
https://www.ebi.ac.uk/training/online/courses/human-genetic-variation-introduction/
https://proteinstructures.com/
http://eddylab.org/cupbook.html
Intermediate Genetics https://www.ndsu.edu/pubweb/~mcclean/plsc431/431g.htm
https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/primers/primer-medical-and-pop
A guide to machine learning for biologists
https://www.coursera.org/specializations/immunology via a colleague.
Project Rosalind - learn by doing, like Project Euler etc.
Laurent Gatto’s teaching material - very R based.
Machine Learning for Healthcare
Cloud-based Tutorials on Structural Bioinformatics
Modern Statistics for Modern Biology, Susan Holmes Wolfgang Huber, free book.
Introduction to Protein Structure 2nd Edition by Carl Branden (Author), John Tooze (Author)
https://wou.edu/chemistry/courses/online-chemistry-textbooks/ch450-and-ch451-biochemistry-defining-life-at-the-molecular-level/chapter-2-protein-structure/
https://eriqande.github.io/eca-bioinf-handbook/
Church course https://ocw.mit.edu/courses/hst-508-genomics-and-computational-biology-fall-2002/pages/readings/
EMBl-EBI-SIB Trainings
https://www.ebi.ac.uk/training/
https://www.embl.de/training/e-learning/index.html
https://edu.sib.swiss
Immunology References
Deep Learning in Protein Structural Modeling and Design, by Jeff Gray et al. arXiv:2007.08383
A large review article: Opportunities and obstacles for deep learning in biology and medicine
Survey on Representation Learning for Networks in Biology and Medicine by Zitnik et al: https://arxiv.org/abs/2104.04883
Kevin Yang’s excellent github page on ML for proteins: https://github.com/yangkky/Machine-learning-for-proteins