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Method: Gene prediction in the immunoglobulin loci
- Vikram Sirupurapu,
- Yana Safonova,
- and Pavel A. Pevzner
Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
...tasks (Das et al. 2012; Pettinello and Dooley 2014).Mammalian s have three IG loci—heavy chain (IGH), kappa light chain (IGK), and lambda light chain (IGL)—as well as four T-cell antigen receptor (TCR) loci (TRA, TRB, TRG, and TRD). In this work, we mainly focus on the IGH locus. The V, D, and J genes...
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ARTICLE: One-megabase sequence analysis of the human immunoglobulin lambda gene locus.
- K Kawasaki,
- S Minoshima,
- E Nakato,
- K Shibuya,
- A Shintani,
- J L Schmeits,
- J Wang,
- and N Shimizu
Genome Res. March 1997 7: 250-261; doi:10.1101/gr.7.3.250
...,025,415 bases of nucleotide sequence, including the entire human immunoglobulin lambda gene locus has been determined. This is the largest contiguous human DNA sequence ever published. The sequence data revealed the organization of 36 potentially active V lambda gene segments, 33 pseudogene segments, and seven...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
..., Smith ML, Watson CT. 2024. Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry. Genes Immun 25: 297–306. doi:10.1038/s41435-024-00279-2 ↵Ford M, Haghshenas E, Watson CT, Sahinalp SC. 2020. Genotyping and copy...
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Research: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
- Christelle Cayrou,
- Philippe Coulombe,
- Alice Vigneron,
- Slavica Stanojcic,
- Olivier Ganier,
- Isabelle Peiffer,
- Eric Rivals,
- Aurore Puy,
- Sabine Laurent-Chabalier,
- Romain Desprat,
- and Marcel Méchali
Genome Res. September 2011 21: 1438-1449; Published in Advance July 12, 2011, doi:10.1101/gr.121830.111
...in Supplementary Information). We further validated the Ori maps by quantitative PCR (qPCR) analysis of known Oris in the mouse Myc gene and Hoxb domain (Supplemental Fig. 1F,G) and Drosophila Histone gene locus (Supplemental Fig. 2A), as well as of randomly chosen putative Oris validated in this study...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...the IG kappa (IGK) locus on Chromosome 2 or the IG lambda (IGL) locus on Chromosome 22. The IG loci have complex genomic organization, high sequence diversity and undergo extensive rearrangement in B cells during antigen-mediated activation and maturation. Consequently, assembly of these loci benefits...
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RESEARCH: The Organization of the γ-Glutamyl Transferase Genes and Other Low Copy Repeats in Human Chromosome 22q11
- John E. Collins,
- Andrew J. Mungall,
- Karen L. Badcock,
- Joanne M. Fay,
- and Ian Dunham
Genome Res. May 1, 1997 7: 522-531; doi:10.1101/gr.7.5.522
.... (1994) isolated seven genomic clones that could encode the GGT mRNA. They concluded that a single GGT locus encoded a ubiquitously expressed gene and proposed that a further four genes were expressed in a tissue-specific manner. At least four immunoglobulin λ (IGL)-like loci have been mapped...
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LETTER: Changes in Gene Expression Profiles in Developing B Cells of Murine Bone Marrow
- Reinhard Hoffmann,
- Thomas Seidl,
- Martin Neeb,
- Antonius Rolink,
- and Fritz Melchers
Genome Res. January 1, 2002 12: 98-111; doi:10.1101/gr.201501
...by changing status of their immunoglobulin gene rearrangements ( Tonegawa 1983 ; ten Boekel et al. 1995 ). Cell cycle status and the differential surface expression of c-kit, CD25, IgM, and IgD on B220+ cells distinguish five consecutive stages of development ( Rolink et al. 1994 ). Therefore, fluorescence...
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RESOURCE: A Large Database of Chicken Bursal ESTs as a Resource for the Analysis of Vertebrate Gene Function
- Igor Abdrakhmanov,
- Dmitry Lodygin,
- Paul Geroth,
- Hiroshi Arakawa,
- Andy Law,
- Jiri Plachy,
- Berndt Korn,
- and Jean-Marie Buerstedde
Genome Res. December 1, 2000 10: 2062-2069; doi:10.1101/gr.1137900
...the database reflects the gene expression profile of bursal lymphocytes, it provides valuable hints as to which genes might be involved in B-cell–specific processes related to immunoglobulin repertoire formation, signal transduction, transcription, and apoptosis. This large collection of chicken ESTs will also...
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ARTICLE: A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13.
- M A Ansari-Lari,
- D M Muzny,
- J Lu,
- F Lu,
- C E Lilley,
- S Spanos,
- T Malley,
- and R A Gibbs
Genome Res. April 1996 6: 314-326; doi:10.1101/gr.6.4.314
...-subunit polypeptide. Proc. Natl. Acad. Sci. 87 : 2329 – 2333 . Littman, D.R. , Gettner. S.N. Littman, D.R. and Gettner. S.N. 1987 . Unusual intron in the immunoglobulin domain of the newly isolated murine CD4 (L3T4) gene. Nature 325 : 453 – 455 . Maddon, P.J., , Littman, D.R. , Godfrey, M. , Maddon, D.E. , Chess, L...
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Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
- Charles Cole,
- Ashley Byrne,
- Matthew Adams,
- Roger Volden,
- and Christopher Vollmers
Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
...as well as B cell and T cell receptors (BCR and TCR). Determining which alleles an individual possesses for each HLA gene (high-resolution HLA typing) is essential to establish donor–recipient compatibility in organ and bone marrow transplantations. In turn, the repertoires of millions of unique BCR...

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