diff --git a/docs_source/quickstart/overview_of_ligo_parameters.rst b/docs_source/quickstart/overview_of_ligo_parameters.rst index 7d2dd582..ae442151 100644 --- a/docs_source/quickstart/overview_of_ligo_parameters.rst +++ b/docs_source/quickstart/overview_of_ligo_parameters.rst @@ -118,6 +118,10 @@ References - Avnir, Yuval, Corey T. Watson, Jacob Glanville, Eric C. Peterson, Aimee S. Tallarico, Andrew S. Bennett, Kun Qin, et al. 2016. “IGHV1-69 Polymorphism Modulates Anti-Influenza Antibody Repertoires, Correlates with IGHV Utilization Shifts and Varies by Ethnicity.” Scientific Reports 6 (February):20842. +- Chiffelle, Johanna, Raphael Genolet, Marta As Perez, George Coukos, Vincent Zoete, and Alexandre Harari. 2020. “T-Cell Repertoire Analysis and Metrics of Diversity and Clonality.” Current Opinion in Biotechnology 65 (October):284–95. + +- Chronister, William D., Austin Crinklaw, Swapnil Mahajan, Randi Vita, Zeynep Koşaloğlu-Yalçın, Zhen Yan, Jason A. Greenbaum, et al. 2021. “TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors.” Frontiers in Immunology 12 (March):640725. + - Dash, Pradyot, Andrew J. Fiore-Gartland, Tomer Hertz, George C. Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, et al. 2017. “Quantifiable Predictive Features Define Epitope-Specific T Cell Receptor Repertoires.” Nature 547 (7661): 89–93. - Fagiani, Francesca, Michele Catanzaro, and Cristina Lanni. 2020. “Molecular Features of IGHV3-53-Encoded Antibodies Elicited by SARS-CoV-2.” Signal Transduction and Targeted Therapy 5 (1): 170. @@ -126,6 +130,12 @@ References - Glanville, Jacob, Huang Huang, Allison Nau, Olivia Hatton, Lisa E. Wagar, Florian Rubelt, Xuhuai Ji, et al. 2017. “Identifying Specificity Groups in the T Cell Receptor Repertoire.” Nature 547 (June):94–98. +- Glanville, Jacob, Tracy C. Kuo, H-Christian von Büdingen, Lin Guey, Jan Berka, Purnima D. Sundar, Gabriella Huerta, et al. 2011. “Naive Antibody Gene-Segment Frequencies Are Heritable and Unaltered by Chronic Lymphocyte Ablation.” Proceedings of the National Academy of Sciences of the United States of America 108 (50): 20066–71. + +- Goncharov, Mikhail, Dmitry Bagaev, Dmitrii Shcherbinin, Ivan Zvyagin, Dmitry Bolotin, Paul G. Thomas, Anastasia A. Minervina, et al. 2022. “VDJdb in the Pandemic Era: A Compendium of T Cell Receptors Specific for SARS-CoV-2.” Nature Methods 19 (9): 1017–19. + +- Greiff, Victor, Pooja Bhat, Skylar C. Cook, Ulrike Menzel, Wenjing Kang, and Sai T. Reddy. 2015. “A Bioinformatic Framework for Immune Repertoire Diversity Profiling Enables Detection of Immunological Status.” Genome Medicine 7 (1): 49. + - Haakenson, Jeremy K., Ruiqi Huang, and Vaughn V. Smider. 2018. “Diversity in the Cow Ultralong CDR H3 Antibody Repertoire.” Frontiers in Immunology 9 (June):1262. - Imkeller, Katharina, Stephen W. Scally, Alexandre Bosch, Gemma Pidelaserra Martí, Giulia Costa, Gianna Triller, Rajagopal Murugan, et al. 2018. “Antihomotypic Affinity Maturation Improves Human B Cell Responses against a Repetitive Epitope.” Science 360 (6395): 1358–62. @@ -134,8 +144,6 @@ References - Liu, Leyu, and Alexander H. Lucas. 2003. “IGH V3-23*01 and Its Allele V3-23*03 Differ in Their Capacity to Form the Canonical Human Antibody Combining Site Specific for the Capsular Polysaccharide of Haemophilus Influenzae Type B.” Immunogenetics 55 (5): 336–38. -- Marcou, Quentin, Thierry Mora, and Aleksandra M. Walczak. 2018. “High-Throughput Immune Repertoire Analysis with IGoR.” Nature Communications 9 (1): 561. - - Ostmeyer, Jared, Scott Christley, Inimary T. Toby, and Lindsay G. Cowell. 2019. “Biophysicochemical Motifs in T-Cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue.” Cancer Research 79 (7): 1671–80. - Pogorelyy, Mikhail V., Anastasia A. Minervina, Mikhail Shugay, Dmitriy M. Chudakov, Yuri B. Lebedev, Thierry Mora, and Aleksandra M. Walczak. 2019. “Detecting T Cell Receptors Involved in Immune Responses from Single Repertoire Snapshots.” PLoS Biology 17 (6): e3000314. @@ -146,7 +154,9 @@ References - Shrock, Ellen L., Richard T. Timms, Tomasz Kula, Elijah L. Mena, Anthony P. West Jr, Rui Guo, I-Hsiu Lee, et al. 2023. “Germline-Encoded Amino Acid-Binding Motifs Drive Immunodominant Public Antibody Responses.” Science 380 (6640): eadc9498. +- Shugay, Mikhail, Dmitriy V. Bagaev, Ivan V. Zvyagin, Renske M. Vroomans, Jeremy Chase Crawford, Garry Dolton, Ekaterina A. Komech, et al. 2018. “VDJdb: A Curated Database of T-Cell Receptor Sequences with Known Antigen Specificity.” Nucleic Acids Research 46 (D1): D419–27. +- Slabodkin, Andrei, Maria Chernigovskaya, Ivana Mikocziova, Rahmad Akbar, Lonneke Scheffer, Milena Pavlović, Habib Bashour, et al. 2021. “Individualized VDJ Recombination Predisposes the Available Ig Sequence Space.” Genome Research, November. https://doi.org/10.1101/gr.275373.121.