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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...characterize these complex regions to gain insight into the impact of genomic diversity on health and disease. Here we resolve the organization of complete major histocompatibility complex (MHC) class II regions in rhesus macaques by using a long-read sequencing strategy (Oxford Nanopore Technologies...
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Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
- Taishan Hu,
- Timothy L. Mosbruger,
- Nikolaos G. Tairis,
- Amalia Dinou,
- Pushkala Jayaraman,
- Mahdi Sarmady,
- Kingham Brewster,
- Yang Li,
- Tristan J. Hayeck,
- Jamie L. Duke,
- and Dimitri S. Monos
Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
..., NY 10029, USA; 9Department of Genomic and Data Sciences, Spark Therapeutics, Philadelphia, PA 19104, USA Corresponding author: monosd@chop.eduAbstractThe human major histocompatibility complex (MHC) is a ∼4 Mb genomic segment on Chromosome 6 that plays a pivotal role in the immune response. Despite...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...et al. 2006). Extensive sequencing of MHC-I transcript and genomic DNA PCR amplicons suggests that this expansion of MHC-B genes is common in both rhesus and cynomolgus macaques (Otting et al. 2005; Doxiadis et al. 2013; Wiseman et al. 2013; Karl et al. 2017; Shortreed et al. 2020). These MHC...
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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...Isoform and pathway-specific regulation of post-1 transcriptional RNA processing in human cells 2 3 Ishwarya Venkata Narayanan1,7, Karan Bedi1,2,3,7, Brian Magnuson1,4, Ariel McShane1.5, 4 Mario Ashaka1, Michelle T. Paulsen1, Thomas E. Wilson3,4 and Mats Ljungman1,3,6 5 6 1 Department of Radiation...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.280534.125 ;gr.280534.125v1 ;gr.280534.125 gr.280534.125 gr.280534.125 Research Abaev-Schneiderman et al. ACTB methylation regulates transcription 1 The Shraga Segal...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...U-seq; Methods) (Cucinotta et al. 2021) we define four classes of genes.View larger version: In this window In a new window Figure 3. Transcriptional output is scant, but homogeneous, in the quiescent population. (A) Representative Genome Browser views of genes classified according to binarized Rpb3-FLAG binding...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
..., and therapeutic perspective. Med Oncol 40: 71. doi:10.1007/s12032-022-01943-1 ↵Calvo-Roitberg E, Daniels RF, Pai AA. 2024. Challenges in identifying mRNA transcript starts and ends from long-read sequencing data. Genome Res 34: 1719–1734. doi:10.1101/gr.279559...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...et al., 2008, 2010), the regulatory basis of the IFN 89 system, and more generally antiviral transcriptional responses, remains poorly understood. 90 To tackle this knowledge gap, we investigated the genomic regulatory mechanisms driving 91 core ISG expression responses in the head kidney of Atlantic...
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Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 ; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome this challenge, we introduce spRefine, a deep learning framework that leverages genomic language models to jointly denoise and impute spatial transcriptomic data. Our results demonstrate that sp...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...-wide landscape of chromatin occupancy for 201 transcriptional regulator mutants. (A) Functional classification of the 201 mutants in our MNase-seq data set. Labels are derived from the Saccharomyces Genome Database. (B) Schematic illustrating chromatin occupancy profiling of 201 yeast mutants via MNase...

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