Useful Review Articles¶

1. Jordan-Pla, A. and V. Neus (2017). Considerations on Experimental Design and Data Analysis of Chomatin Immunoprecitation Experiments. https://link.springer.com/protocol/10.1007/978-1-4939-7380-4_2
   • Wet bench guidelines and experimental design details. Basics of ChIP-seq analysis.
2. Northrup, D.L. and K. Zhao (2011). Application of ChIP-seq and Related Techniques to the Study of Immune Function. https://www.sciencedirect.com/science/article/pii/S1074761311002317
   • Some useful information about the different kinds of histone modifications and their functions, especially in the context of the immune system.
3. Park, P.J. ChIP-seq: advantages and challenges of a maturing technology. https://www.nature.com/articles/nrg2641
   • An old paper that really goes into the molecular biology that is ChIP-seq and connects it to how the bioinformatics needs to be accomplished to account for it
4. Minnow, L. et al. (2021). Chromatin accessibility profiling methods. https://www.nature.com/articles/s43586-020-00008-9.
   • Basic descriptions of a variety of accessibility methods, especially ChIP-seq, ATAC-seq, scATAC-seq. Also mentions CUT & RUN, etc. Article also includes a brief section on bioinformatics analysis tools available at the time of publication and some example applications.
5. Liu, H. et al. (2024): Best practices for the ATAC-seq assay and its data analysis. https://www.sciencedirect.com/science/article/pii/B9780128172186000164
   • Detailed, thorough description of best practices for both the wet bench and the computational aspects of ATAC-seq