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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...trypanosomatid evolution either as a greater than diploid chromosome or as a syntenic duplication in two chromosomes in African trypanosomes, resulting in higher nucleotide diversity, unusual gene organization, gene expression regulation, and evolution. This is the most comprehensive evaluation of aneuploidies...
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Resource: A comparison of gene expression and DNA methylation patterns across tissues and species
- Lauren E. Blake,
- Julien Roux,
- Irene Hernando-Herraez,
- Nicholas E. Banovich,
- Raquel Garcia Perez,
- Chiaowen Joyce Hsiao,
- Ittai Eres,
- Claudia Cuevas,
- Tomas Marques-Bonet,
- and Yoav Gilad
Genome Res. February 2020 30: 250-262; Published in Advance January 17, 2020, doi:10.1101/gr.254904.119
...believe that this catalog can be useful for many future applications and can serve as a new benchmark for regulatory divergence in primates.ResultsStudy design and data collectionTo comparatively study gene expression levels and DNA methylation patterns in primates, we collected primary heart, kidney...
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ARTICLE: Regional Patterns of Gene Expression in Human and Chimpanzee Brains
- Philipp Khaitovich,
- Bjoern Muetzel,
- Xinwei She,
- Michael Lachmann,
- Ines Hellmann,
- Janko Dietzsch,
- Stephan Steigele,
- Hong-Hai Do,
- Gunter Weiss,
- Wolfgang Enard,
- Florian Heissig,
- Thomas Arendt,
- Kay Nieselt-Struwe,
- Evan E. Eichler,
- and Svante Pääbo
Genome Res. August 2004 14: 1462-1473; doi:10.1101/gr.2538704
...Regional Patterns of Gene Expression in Human and Chimpanzee Brains Philipp Khaitovich 1 , 7 , Bjoern Muetzel 1 , Xinwei She 2 , Michael Lachmann 1 , Ines Hellmann 1 , Janko Dietzsch 3 , Stephan Steigele 3 , Hong...
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RESOURCE: eVOC: A Controlled Vocabulary for Unifying Gene Expression Data
- Janet Kelso,
- Johann Visagie,
- Gregory Theiler,
- Alan Christoffels,
- Soraya Bardien,
- Damian Smedley,
- Darren Otgaar,
- Gary Greyling,
- C. Victor Jongeneel,
- Mark I. McCarthy,
- Tania Hide,
- and Winston Hide
Genome Res. June 2003 13: 1222-1230; doi:10.1101/gr.985203
...Gene Expression Data Janet Kelso 1 , Johann Visagie 2 , Gregory Theiler 3 , Alan Christoffels 1 , 6 , Soraya Bardien 1 , Damian Smedley 4 , Darren Otgaar 2 , Gary Greyling 2 , C. Victor Jongeneel 3 , Mark I. McCarthy 4 , 5 , Tania Hide 2 , and Winston Hide 1 , 7 1 South African National Bioinformatics...
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LETTER: Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
- Yoav Gilad,
- Scott A. Rifkin,
- Paul Bertone,
- Mark Gerstein,
- and Kevin P. White
Genome Res. May 2005 15: 674-680; doi:10.1101/gr.3335705
...and African great ape cultured fibroblasts. Genome Res. 13 : 1619 –1630. ↵ Kent, W.J. 2002 . BLAT–the BLAST-like alignment tool. Genome Res. 12 : 656 –664. ↵ Kerr, M.K., Afshari, C.A., Bennett, L., Bushel, P., Martinez, J., Walker, N.J., and Churchill, G.A. 2002 . Statistical analysis of a gene expression...
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Research: Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
...to glucocorticoids in activated PBMCs from 96 African American youths with asthma and the genetic basis of variation in gene expression mean and variability across individuals.ResultsIdentification of major cell types and gene expression patternsTo systematically characterize genetic determinants of transcriptional...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...-encoded OXPHOS gene expression, led to mouse embryonic lethality (Chan et al. 1998). Third, knockout of another regulator of OXPHOS genes expression, Nfe2l2 (also known as Nrf2), led to a reduction in the levels of NADPH and the NADPH/NADP+ ratio in embryonic mouse fibroblasts (Singh et al. 2013), and ATP levels...
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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
....56, Z-score = −5.54, P-adjusted = 0.06) (Supplemental Fig. S10).View larger version: In this window In a new window Figure 3. Inversion affecting Chromosome 9 (BH16643-1). (A) Pedigree displaying inheritance pattern for inversion 9. (B) G-banded chromosome analysis showed a paracentric inversion...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...reported between leukocytes of apes and African and Asian monkeys (Hawash et al. 2021). These changes have also been seen when comparing human, chimpanzee, and rhesus macaque primary monocytes (Barreiro et al. 2010) across multiple time points after stimulation. Considering the functional specialization...
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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
...in the African great apes ancestor, although three of these show the direct orientation in chimpanzee (which means that either the region in chimpanzee flipped back to the direct orientation or it represents a case of incomplete lineage sorting); eight (10.3%) occurred in the great ape ancestor; and 25 (32...

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