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Resource: Cell type-specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. January 21, 2026 gr.280436.125; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...analysis (GSEA), we then assessed the enrichment of drug-associated 332 16 gene signatures across these temporal categories. The analysis revealed that the nine 333 candidate drugs—galantamine, resveratrol, imatinib, deferoxamine, captopril, 334 staurosporine, quercetin, procaine, and probucol...
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Research: Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation
- Clara Y. Cheong,
- Keefe Chng,
- Shilen Ng,
- Siew Boom Chew,
- Louiza Chan,
- and Anne C. Ferguson-Smith
Genome Res. May 2015 25: 611-623; Published in Advance April 10, 2015, doi:10.1101/gr.183301.114
...- and tissue-specific domains of imprinted expression exist. Using the cynomolgus macaque ( Macaca fascicularis ) to assess primate-specific imprinting, we present a comprehensive view of tissue-specific imprinted expression and DNA methylation at established imprinted gene clusters. For example, like mouse...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
..., Wisconsin 53711, USA Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primate in biomedical research, have the largest natural geographic distribution of any nonhuman primate, and have been the focus of much evolutionary and behavioral investigation. Consequently, rhesus macaques are one...
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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
...in routine clinical practice. Finally, the assessment of HER2 isoform expression in BC cell cultures sensitive or resistant to trastuzumab and ADCs reveals that drug-resistant cells shift their expression toward isoforms lacking antibody-binding domains. Our results broaden the understanding of HER2 isoforms...
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Resource: Inversion variants in human and primate genomes
- Claudia Rita Catacchio,
- Flavia Angela Maria Maggiolini,
- Pietro D'Addabbo,
- Miriana Bitonto,
- Oronzo Capozzi,
- Martina Lepore Signorile,
- Mattia Miroballo,
- Nicoletta Archidiacono,
- Evan E. Eichler,
- Mario Ventura,
- and Francesca Antonacci
Genome Res. May 18, 2018 ; Published in Advance May 18, 2018, doi:10.1101/gr.234831.118
...larger inversions by FISH analysis of cell lines from multiple individuals of chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), orangutan (Pongo pygmaeus), and macaque (Macaca mulatta). When necessary, marmoset (Callithrix jacchus) was used as an outgroup species (Supplemental Tables S3, S4...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...by fluorescence in situ hybridization (FISH) in the same Macaca mulatta individual (MMU1) for which Strand-seq data were generated. To also define if an inversion was polymorphic, 14 inversions were tested on two additional macaque individuals (M. mulatta, MMU2; Macaca fascicularis, MFA63). Owing to technical...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...-beneficial alleles (Rice 1984). In contrast to ancestral sequence, however, few studies have focused on X-Chromosome palindromes, and X palindromes have not been characterized in nonhuman primates. As a result, little is known about the origins of X-Chromosome palindromes or the evolutionary forces that shape them...
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Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
...undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a nonhuman primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254...
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Resource: Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition
- Guillaume Dumas,
- Simon Malesys,
- and Thomas Bourgeron
Genome Res. March 2021 31: 484-496; Published in Advance January 13, 2021, doi:10.1101/gr.262113.120
...on their divergence from those of early hominins, such as Neanderthals, and non-human primates. We confirm that genes encoding brain-related proteins are among the most strongly conserved protein-coding genes in the human . Combining our evolutionary pressure metrics for the protein-coding with recent data sets, we...
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Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
.... Results Data generation, quality assessment, and validation We generated RNA-seq and ChIP-seq data from postmortem livers of three or four individuals per species of mouse lemur (Microcebus murinus), bushbaby (Otolemur garnettii), marmoset (Callithrix jacchus), rhesus macaque (Macaca mulatta), chimpanzee...
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