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Research: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes
- Gilad Barshad,
- Amit Blumberg,
- Tal Cohen,
- and Dan Mishmar
Genome Res. July 2018 28: 952-967; Published in Advance June 14, 2018, doi:10.1101/gr.226324.117
...vertebrate evolution (MacLean 1990; Emery and Clayton 2005; Mashour and Alkire 2013) (hereby termed “primitive” brain), we found striking negative correlation between nDNA- and mtDNA-encoded OXPHOS genes expression. Such anti-correlation between mtDNA- and nDNA-encoded OXPHOS genes expression within...
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Corrigendum: Corrigendum: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. February 2026 36: 432; doi:10.1101/gr.281294.125
...Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.281294.125 ;36/2/432 ;gr.281294.125 432 gr.281294.125 Corrigendum Corrigendum Corrigenda Corrigendum Corrigendum Razavi-Mohseni Milad Huang Weitai Guo Yu A. Shigaki Dustin Ho Shamaine Wei Ting Tan Patrick Skanderup Anders J...
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Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
- Khang Ma and
- Rinki Ratnapriya
Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
...correlation) to red (high correlation). Column labels correspond to retina cell types, and row labels represent brain cell types. (B) XY plot depicting the log2-transformed gene expression profiles of microglia from the retina (y-axis) and brain (x-axis). The correlation coefficient, displayed at the top...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
..., with significantly improved raw read accuracy (Q20+), offers a potential solution to this problem. The aim of this study is to evaluate the performance of ONT's latest chemistry for bacterial genomic typing against the gold-standard Illumina technology, focusing on three respiratory pathogens of public health...
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Corrigendum: Corrigendum: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
- Wenli Xu,
- Chang Liu,
- Bing Deng,
- Penghui Lin,
- Zhenghua Sun,
- Anrui Liu,
- Jiajia Xuan,
- Yuying Li,
- Keren Zhou,
- Xiaoqin Zhang,
- Qiaojuan Huang,
- Hui Zhou,
- Qingyu He,
- Bin Li,
- Lianghu Qu,
- and Jianhua Yang
Genome Res. April 2026 36: 885; doi:10.1101/gr.282041.126
....126 Published by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.282041.126 ;36/4/885 ;gr.282041.126 885 gr.282041.126 Corrigendum Corrigendum Corrigenda Corrigendum Corrigendum Xu Wenli Liu...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...hypoxia (oxygen deprivation), given the brain's high metabolic demand and susceptibility to oxidative damage (Cobley et al. 2018). Hypoxia is a well-known neurological risk factor throughout life, arising from conditions such as sleep apnea, high altitude, respiratory infections, and premature birth...
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Method: Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data
- Alicia Petrany,
- Ruoyu Chen,
- Shaoqiang Zhang,
- and Yong Chen
Genome Res. October 2024 34: 1636-1650; Published in Advance October 15, 2024, doi:10.1101/gr.278843.123
...on testing the statistical significance for the difference of two negative binomial distributions (DOTNB). Although negative binomial distributions are well studied, the theoretical results for DOTNB remain largely unexplored. Here, we derive basic analytical results for DOTNB and examine its asymptotic...
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Corrigendum: Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. June 2025 35: 1472-1; doi:10.1101/gr.280860.125
...and apologize for any confusion this may have caused.doi: 10.1101/gr.280860.125 Published by Cold Spring Harbor Laboratory Press Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana Jonathan Cahn , James P.B. Lloyd , Ino D. Karemaker , Pascal W.T.C. Jansen , Jahnvi Pflueger...
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Corrigendum: Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. October 2025 35: 2375; doi:10.1101/gr.281340.125
...Corrigendum: A sheep pan reveals the spectrum of structural variations and their effects on tail phenotypes Ran Li, Mian Gong, Xinmiao Zhang, Fei Wang, Zhenyu Liu, Lei Zhang, Qimeng Yang, Yuan Xu, Mengsi Xu, Huanhuan Zhang, Yunfeng Zhang, Xuelei Dai, Yuanpeng Gao, Zhuangbiao Zhang, Wenwen Fang...
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Corrigendum: Corrigendum: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere
- Lee H. Wong,
- Kate H. Brettingham-Moore,
- Lyn Chan,
- Julie M. Quach,
- Melissa A. Anderson,
- Emma L. Northrop,
- Ross Hannan,
- Richard Saffery,
- Margaret L. Shaw,
- Evan Williams,
- and K.H. Andy Choo
Genome Res. June 2024 34: 979-980; doi:10.1101/gr.279693.124
.... Published by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.279693.124 ;34/6/979 ;gr.279693.124 979 gr.279693.124 Corrigendum Corrigendum Corrigenda Wong Lee H. Brettingham-Moore Kate H...
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