Reference Library

Zotero library: Krantz Lab Website References

This group library has similar folder structure to the Docs, so you can easily find references for a specific topic. You can also use the search function to find specific references.

Immunogenomics

1.
Clay SM, Schoettler N, Goldstein AM, et al. Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region. Genome Med. 2022;14(1):55. doi:10.1186/s13073-022-01058-2
2.
Deane CM. Comparative Analysis of the CDR Loops of Antigen Receptors.
3.
, eds.Gore M, Jagtap UB. Computational Drug Discovery and Design. Vol 2714. Springer US; 2024. doi:10.1007/978-1-0716-3441-7
4.
Gumperz JE, Litwin V, Phillips JH, Lanier LL, Parham P. The Bw4 public epitope of HLA-B molecules confers reactivity with natural killer cell clones that express NKB1, a putative HLA receptor. The Journal of Experimental Medicine. 1995;181(3):1133-1144. doi:10.1084/jem.181.3.1133
5.
Hanson AL, International Genetics of Ankylosing Spondylitis Consortium, Vukcevic D, et al. Epistatic interactions between killer immunoglobulin-like receptors and human leukocyte antigen ligands are associated with ankylosing spondylitis, ed.Roopenian DC. PLoS Genet. 2020;16(8):e1008906. doi:10.1371/journal.pgen.1008906
6.
Huisman W, Hageman L, Leboux DAT, et al. Public T-Cell Receptors (TCRs) Revisited by Analysis of the Magnitude of Identical and Highly-Similar TCRs in Virus-Specific T-Cell Repertoires of Healthy Individuals. November 30, 2021. doi:10.1101/2021.11.29.470325
7.
Jia X, Han B, Onengut-Gumuscu S, et al. Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One. 2013;8(6):e64683. doi:10.1371/journal.pone.0064683
8.
Lin Z, Bashirova AA, Viard M, et al. HLA class I signal peptide polymorphism determines the level of CD94/NKG2–HLA-E-mediated regulation of effector cell responses. Nat Immunol. 2023;24(7):1087-1097. doi:10.1038/s41590-023-01523-z
9.
Lin Z, Bashirova AA, Viard M, et al. HLA class I signal peptide polymorphism determines the level of CD94/NKG2–HLA-E-mediated regulation of effector cell responses. Nat Immunol. 2023;24(7):1087-1097. doi:10.1038/s41590-023-01523-z
10.
Liu Y, Yang X, Gan J, Chen S, Xiao ZX, Cao Y. CB-Dock2: Improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Research. 2022;50(W1):W159-W164. doi:10.1093/nar/gkac394
11.
Liu Y, Cao Y. Protein-Ligand Blind Docking Using CB-Dock2. Methods Mol Biol. 2024;2714:113-125. doi:10.1007/978-1-0716-3441-7_6
12.
Lund O, Nielsen M, Kesmir C, et al. Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics. 2004;55(12):797-810. doi:10.1007/s00251-004-0647-4
13.
Maiers M, Louzoun Y, Pymm P, et al. Prediction of KIR3DL1 and human leukocyte antigen binding. Journal of Biological Chemistry. 2025;301(8):110437. doi:10.1016/j.jbc.2025.110437
14.
Migdal M, Ruan DF, Forrest WF, Horowitz A, Hammer C. MiDAS—Meaningful Immunogenetic Data at Scale, ed.Pertea M. PLoS Comput Biol. 2021;17(7):e1009131. doi:10.1371/journal.pcbi.1009131
15.
Pappas DJ, Marin W, Hollenbach JA, Mack SJ. Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An integrated case-control analysis pipeline. Human Immunology. 2016;77(3):283-287. doi:10.1016/j.humimm.2015.12.006
16.
Pavlos R, Deshpande P, Chopra A, et al. New genetic predictors for abacavir tolerance in HLA-B*57:01 positive individuals. Human Immunology. 2020;81(6):300-304. doi:10.1016/j.humimm.2020.02.011
17.
Pavlos R, McKinnon EJ, Ostrov DA, et al. Shared peptide binding of HLA Class I and II alleles associate with cutaneous nevirapine hypersensitivity and identify novel risk alleles. Sci Rep. 2017;7(1):8653. doi:10.1038/s41598-017-08876-0
18.
Petersdorf EW, Gooley TA, Malkki M, et al. HLA-C expression levels define permissible mismatches in hematopoietic cell transplantation. Blood. 2014;124(26):3996-4003. doi:10.1182/blood-2014-09-599969
19.
Pollock NR, Harrison GF, Norman PJ. Immunogenomics of Killer Cell Immunoglobulin-Like Receptor (KIR) and HLA Class I: Coevolution and Consequences for Human Health. The Journal of Allergy and Clinical Immunology: In Practice. 2022;10(7):1763-1775. doi:10.1016/j.jaip.2022.04.036
20.
Reeves E, Edwards CJ, Elliott T, James E. Naturally Occurring ERAP1 Haplotypes Encode Functionally Distinct Alleles with Fine Substrate Specificity. The Journal of Immunology. 2013;191(1):35-43. doi:10.4049/jimmunol.1300598
21.
Schäfer C, Schmidt AH, Sauter J. Hapl-o-Mat: Open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data. BMC Bioinformatics. 2017;18(1):284. doi:10.1186/s12859-017-1692-y
22.
Sidney J, Peters B, Frahm N, Brander C, Sette A. HLA class I supertypes: A revised and updated classification. BMC Immunol. 2008;9(1):1. doi:10.1186/1471-2172-9-1
23.
The Australo-Anglo-American Spondyloarthritis Consortium (TASC), the Wellcome Trust Case Control Consortium 2 (WTCCC2), Spondyloarthritis Research Consortium of Canada (SPARCC), et al. Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet. 2011;43(8):761-767. doi:10.1038/ng.873
24.
Thomsen M, Lundegaard C, Buus S, Lund O, Nielsen M. MHCcluster, a method for functional clustering of MHC molecules. Immunogenetics. 2013;65(9):655-665. doi:10.1007/s00251-013-0714-9
25.
Van Deutekom HWM, Keşmir C. Zooming into the binding groove of HLA molecules: Which positions and which substitutions change peptide binding most? Immunogenetics. 2015;67(8):425-436. doi:10.1007/s00251-015-0849-y
26.
Van Deutekom HWM, Keşmir C. Zooming into the binding groove of HLA molecules: Which positions and which substitutions change peptide binding most? Immunogenetics. 2015;67(8):425-436. doi:10.1007/s00251-015-0849-y
27.
Venturi V, Price DA, Douek DC, Davenport MP. The molecular basis for public T-cell responses? Nat Rev Immunol. 2008;8(3):231-238. doi:10.1038/nri2260
28.
Viard M, O’hUigin C, Yuki Y, et al. Impact of HLA class I functional divergence on HIV control. Science. 2024;383(6680):319-325. doi:10.1126/science.adk0777
29.
Vukcevic D, Traherne JA, Næss S, et al. Imputation of KIR Types from SNP Variation Data. The American Journal of Human Genetics. 2015;97(4):593-607. doi:10.1016/j.ajhg.2015.09.005
30.
Zheng X, Shen J, Cox C, et al. HIBAG–HLA genotype imputation with attribute bagging. Pharmacogenomics J. 2014;14(2):192-200. doi:10.1038/tpj.2013.18