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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
...in the human are highly polymorphic regions that encode the building blocks of the light and heavy chain IG proteins that dimerize to form antibodies. The processes of V(D)J recombination and somatic hypermutation in B cells are responsible for creating an enormous reservoir of highly specific antibodies...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer Gabriela D.A. Guardia1,5, Carlos H. dos Anjos1,5, Aline Rangel-Pozzo2, Filipe F. dos Santos1,3, Alexander Birbrair4, Paula F. Asprino1, Anamaria A. Camargo1 and Pedro A.F. Galante1 1...
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Method: A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls
- Modi Safra,
- Lael Werner,
- Ayelet Peres,
- Pazit Polak,
- Naomi Salamon,
- Michael Schvimer,
- Batia Weiss,
- Iris Barshack,
- Dror S. Shouval,
- and Gur Yaari
Genome Res. January 2023 33: 71-79; Published in Advance December 16, 2022, doi:10.1101/gr.276683.122
...A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls Modi Safra1,2,7, Lael Werner3,4,7, Ayelet Peres1,2, Pazit Polak1,2, Naomi Salamon5, Michael Schvimer6, Batia Weiss4,5, Iris Barshack4,6, Dror S. Shouval3,4,8 and Gur Yaari1,2,8 1The...
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Method: Variations in antibody repertoires correlate with vaccine responses
- Yana Safonova,
- Sung Bong Shin,
- Luke Kramer,
- James Reecy,
- Corey T. Watson,
- Timothy P.L. Smith,
- and Pavel A. Pevzner
Genome Res. April 2022 32: 791-804; Published in Advance March 31, 2022, doi:10.1101/gr.276027.121
...as frequent somatic hypermutations) that affect various features of the antibody repertoire and titers of neutralizing antibodies. In contrast to relatively short human antibodies, cattle have a large fraction of ultralong antibodies that have opened new therapeutic opportunities. Our study reveals...
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Research: A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates
- Alexandra M. Stendahl,
- Rashesh Sanghvi,
- Samuel Peterson,
- Karina Ray,
- Ana C. Lima,
- Raheleh Rahbari,
- and Donald F. Conrad
Genome Res. December 2023 33: 2053-2059; Published in Advance November 20, 2023, doi:10.1101/gr.277977.123
...Center, we identified a rhesus macaque with a rare homozygous frameshift mutation in the gene methyl-CpG binding domain 4, DNA glycosylase (MBD4). MBD4 is responsible for the repair of C > T deamination mutations at CpG dinucleotides and has been linked to somatic hypermutation and cancer predisposition...
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Research: Cellular abundance shapes function in piRNA-guided genome defense
- Pavol Genzor,
- Parthena Konstantinidou,
- Daniel Stoyko,
- Amirhossein Manzourolajdad,
- Celine Marlin Andrews,
- Alexandra R. Elchert,
- Constantinos Stathopoulos,
- and Astrid D. Haase
Genome Res. November 2021 31: 2058-2068; Published in Advance October 19, 2021, doi:10.1101/gr.275478.121
...Cellular abundance shapes function in piRNA-guided defense Pavol Genzor1,4, Parthena Konstantinidou1,2,4, Daniel Stoyko1,4, Amirhossein Manzourolajdad3, Celine Marlin Andrews1, Alexandra R. Elchert1, Constantinos Stathopoulos2 and Astrid D. Haase1 1National Institute of Diabetes and Digestive...
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Research: Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii
- Benjamin Offei,
- Paul Vandecruys,
- Stijn De Graeve,
- María R. Foulquié-Moreno,
- and Johan M. Thevelein
Genome Res. September 2019 29: 1478-1494; Published in Advance August 29, 2019, doi:10.1101/gr.243147.118
...obscure. It is considered conspecific with budding yeast Saccharomyces cerevisiae, which is generally used in classical food applications. They have an almost identical sequence, making the genetic basis of probiotic potency in S. boulardii puzzling. We now show that S. boulardii produces at 37°C...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
...Somatic structural variant formation is guided by and influences architecture Nikos Sidiropoulos1,2,9, Balca R. Mardin3,4,9, F. Germán Rodríguez-González1,2, Ivan D. Bochkov5, Shilpa Garg6, Adrian M. Stütz3, Jan O. Korbel3, Erez Lieberman Aiden5,7 and Joachim Weischenfeldt1,2,8 1Biotech Research...
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Method: Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
- Xiangxiu Wang,
- Wen Wang,
- Yiman Wang,
- Jia Chen,
- Guifen Liu,
- and Yong Zhang
Genome Res. February 2022 32: 378-388; Published in Advance December 29, 2021, doi:10.1101/gr.275837.121
...Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN Xiangxiu Wang1, Wen Wang1, Yiman Wang, Jia Chen, Guifen Liu1 and Yong Zhang Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research...
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Research: Localized hypermutation and associated gene losses in legume chloroplast genomes
- Alan M. Magee,
- Sue Aspinall,
- Danny W. Rice,
- Brian P. Cusack,
- Marie Sémon,
- Antoinette S. Perry,
- Saša Stefanović,
- Dan Milbourne,
- Susanne Barth,
- Jeffrey D. Palmer,
- John C. Gray,
- Tony A. Kavanagh,
- and Kenneth H. Wolfe
Genome Res. December 2010 20: 1700-1710; Published in Advance October 26, 2010, doi:10.1101/gr.111955.110
...Localized hypermutation and associated gene losses in legume chloroplast genomes Alan M. Magee 1 , Sue Aspinall 2 , Danny W. Rice 3 , Brian P. Cusack 1 , Marie Sémon 4 , Antoinette S. Perry 1 , Saša Stefanović 5 , Dan...

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