Open resources for biology, chemistry, and computation.
├── assets/ # Images and other media.
├── book/ # Draft of comprehensive, open source textbook on biology, chemistry, and computation.
├── flashcards/ # Structure YAML files for things worth memorizing.
├── ideas.md # Ideas for future projects.
├── notes/ # Notes to be converted into book sections, or blog posts.
├── papers/ # Papers to read.
├── README.md # this document
├── reference/ # Reference sheets and other structured data.
├── todo.md # Websites, papers, and other resources to explore.
├── tools.md # A list of tools used in research and education.
└── usnco/ # Resources related to the United States National Chemistry Olympiad.
- Protein folding
- Genome browsers
- Data sources
- Immune system, Human leukocyte antigen (Wikipedia)
- Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. (Rives et al., 2019) (biorxiv)
- Computational methods for single-cell RNA sequencing. (Hie et al., Annual Reviews, 2020) (http, ipfs)
- Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces. (Ding and Regev, 2019) (biorxiv, ipfs, doi)
- DrugBank: a comprehensive resource for in silico drug discovery and exploration. (Wishart et al., Nucelic Acids Res, 2006) (http)
- Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. (Macosko et al., Cell, 2015) (ipfs, doi)
- A cancer cell program promotes T-cell exclusion and resistance to checkpoint blockade. (Jerby-Arnon et al., Cell, 2018) (ipfs, doi)
- Intra- and inter- cellular rewiring of the human colon during ulcerative colitis. (Smillie et al., Cell, 2019) (ipfs, doi)
- Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. (Tirosh et al., Science, 2016) (ipfs, doi)
- Programmable base editing of A/T to G/C in genomic DNA without DNA cleavage. (Gaudelli et al., Nature, 2017) (doi, ipfs)
- Search-and-replace genome editing without double-strand breaks or donor DNA. (Anzalone et al., Nature, 2019) (doi, ipfs)
- Discovering chemistry with an ab initio nanoreactor. (Wang, Titov, McGibbon et al., Nature Chem, 2014) (doi, ipfs)
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. (Kohlhoff, Shukla, Lawrenz, et al., Nature Chem, 2014) (ipfs)
- Exploring chemical space using natural language processing. (Ozturk et al.) (arxiv)
- Small Molecule Targets TMED9 and Promotes Lysosomal Degradation to Reverse Proteinpathy. (Dvela-Levitt et al., Cell, 2019) (ipfs)
- keywords: Human kidney organoids, MUC1
- Potential 2019-nCoV 3C-like protease inhibitors designed using generative deep learning approaches. (Zhavoronkov et al., 2020) (ipfs)
- Integrative Genomics Viewer (IGV). (docs)
- IGV Jupyter widgets. (github)
- Bandage. (docs)
- NCBI Toolbox. (docs)
- Vega Visualization Grammar for Graphing. (docs)
- Linked de Bruijn graphs (LdBG)
- What information do they encode? Why are they useful for bioinformatics?
- Why is the number of distinct de Bruijn sequences B(k, n) equal to (k!)^(k^(n-1)) / (k^n)?
- How can we continue to extend Transformer and related NLP architectures to biological sequences? Are there even more pre-training tasks we can use?
- Topological determinants of protein folding
- What is the right mathematical model to use to develop theory about protein folding?
- Cramer, Essentials of Computational Chemistry: Theories and Models.
- Koch and Holthausen, A Chemist's Guide to Density Functional Theory.
- Protein visualizations and explanations. An educational website that displays many of the commonly encountered proteins in biology, and contains a guided explanation (e.g. waypoints and arrows) of how the protein functions.
- Broad@15 Talk Series: The March Toward Cancer Precision Medicine. (http)
- MIT 20.380: Biological Engineering Design.
- MIT 10.637: Quantum Chemical Simulation. (http)
- Computational genomics course. (youtube)
- Canadian Bioinformatics Workshops. (http)
- Practical cheminformatics. (http)
- Molecular modeling basics. (http