References which are useful for FACS Measurements and FACS Data Analysis:

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). Cossarizza A et al., Eur. J. Immunol. 2019, 49: 1457–1973. DOI: 10.1002/eji.201970107
The second edition of "Flow Cytometry Guidelines" provides key aspects to consider when performing flow cytometry experiments and data analysis.

Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition). Cossarizza A. et al., Eur. J. Immunol. 2021. 51: 2708–3145. DOI: 10.1002/eji.202170126
The third edition is focusing on biological applications and provides a lot of tips to avoid pitfalls e.g. in sample preparation.

MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Lee JA et al., Cytometry A. 2008 Oct;73(10):926-30. doi: 10.1002/cyto.a.20623.
This publication provides a very useful guide about which information to include when you prepare your own paper containing flow cytometry experiments.

A new "Logicle" display method avoids deceptive effects of logarithmic scaling for low signals and compensated data. Parks DR, Roederer M, Moore AW. Cytometry Part A. 2006, 69(6):541-51. DOI: 10.1002/cyto.a.20258

Interpreting flow cytometry data: a guide for the perplexed. Herzenberg LA et al., Nat Immunol 2006; 7(7):681-685. DOI: 10.1038/ni0706-681.

Compensation in Flow Cytometry. Roederer M, Current Protocols in Cytometry 2002, 1.14.1-1.14.20 DOI: 10.1002/0471142956.cy0114s22

Spectral Compensation for Flow Cytometry: Visualization Artifacts, Limitations, and Caveats. Roederer M, Cytometry 2001, 45:194–205. DOI: 10.1002/1097-0320(20011101)45:3<194::aid-cyto1163>3.0.co;2-c

A gain and dynamic range independent index to quantify spillover spread to aid panel design in flow cytometry. Bhowmick D, van Diepen F, Pfauth A, Tissier R, Ratliff ML, Scientific Reports 2021, 11:20553. DOI: 10.1038/s41598-021-99831-7

Reproducibility of Flow Cytometry Through Standardization: Opportunities and Challenges. Kalina T, Cytometry Part A 2020, 97A: 137–147. DOI: 10.1002/cyto.a.23901

Practical Flow Cytometry. Shapiro HM, 2003 John Wiley & Sons, ISBN:9780471411253, DOI:10.1002/0471722731

Flow Cytometry: An Overview. McKinnon KM, Curr Protoc Immunol. 2018; 120: 5.1.1–5.1.11. DOI:10.1002/cpim.40.

Relevance of Antibody Validation for Flow Cytometry. Kalina T, Lundsten K, Engel P, Cytometry A 2020 Feb;97(2):126-136. DOI: 10.1002/cyto.a.23895.

A Guide to Choosing Fluorescent Protein Combinations for Flow Cytometric Analysis Based on Spectral Overlap. Kleeman B et al, Cytometry A 2018 May;93(5):556-562. DOI: 10.1002/cyto.a.23360

Cell Sorting by Flow Cytometry. Davies D. in: Flow Cytometry Nov 2007 pp.257-276. DOI:10.1007/978-1-59745-451-3_11

Best Practices for Preparing a Single Cell Suspension from Solid Tissues for Flow Cytometry. Reichard A, Asosingh K, Cytometry Part A 2019, 95A: 219–226. DOI: 10.1002/cyto.a.23690

Do more with Less: Improving High Parameter Cytometry Through Overnight Staining. Whyte CE, Tumes DJ, Liston A, Burton OT, Curr Protoc. 2022 Nov;2(11):e589.

What to use to express the variability of data: Standard deviation or standard error of mean? Barde MP, Barde PJ. Perspect Clin Res 2012 Jul;3(3):113-6. doi: 10.4103/2229-3485.100662

Guide to red fluorescent proteins and biosensors for flow cytometry. Piatkevich KD, Verkhusha VV. Methods Cell Biol. 2011;102:431-61. doi: 10.1016/B978-0-12-374912-3.00017-1. PMID: 21704849; PMCID: PMC3987785.

Generalized unmixing model for multispectral flow cytometry utilizing nonsquare compensation matrices. Novo D, Grégori G, Rajwa B. Cytometry A. 2013 May;83(5):508-20. doi: 10.1002/cyto.a.22272. Epub 2013 Mar 22. PMID: 23526804; PMCID: PMC4177998.

Flow cytometry: past and future. Robinson JP. Biotechniques. 2022 Apr;72(4):159-169. doi: 10.2144/btn-2022-0005. Epub 2022 Apr 4. PMID: 35369735.

Development of Spectral Imaging Cytometry. Vorobjev IA, Kussanova A, Barteneva NS. Methods Mol Biol. 2023;2635:3-22. doi: 10.1007/978-1-0716-3020-4_1. PMID: 37074654.

A comparison of spectral unmixing to conventional compensation for the calculation of fluorochrome abundances from flow cytometric data. Novo D. Cytometry A. 2022 Nov;101(11):885-891. doi: 10.1002/cyto.a.24669. Epub 2022 Jul 15. PMID: 35841160.

Panel Design and Optimization for High-Dimensional Immunophenotyping Assays Using Spectral Flow Cytometry. Ferrer-Font L, Pellefigues C, Mayer JU, Small SJ, Jaimes MC, Price KM. Curr Protoc Cytom. 2020 Mar;92(1):e70. doi: 10.1002/cpcy.70. PMID: 32150355.

Panel Optimization for High-Dimensional Immunophenotyping Assays Using Full-Spectrum Flow Cytometry. Ferrer-Font L, Small SJ, Lewer B, Pilkington KR, Johnston LK, Park LM, Lannigan J, Jaimes MC, Price KM. Curr Protoc. 2021 Sep;1(9):e222. doi: 10.1002/cpz1.222. PMID: 34492732.