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Research: Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum
- Junya Yamagishi,
- Anna Natori,
- Mohammed E.M. Tolba,
- Arthur E. Mongan,
- Chihiro Sugimoto,
- Toshiaki Katayama,
- Shuichi Kawashima,
- Wojciech Makalowski,
- Ryuichiro Maeda,
- Yuki Eshita,
- Josef Tuda,
- and Yutaka Suzuki
Genome Res. September 2014 24: 1433-1444; Published in Advance August 4, 2014, doi:10.1101/gr.158980.113
...in Plasmodium falciparum. Nat Genet 39: 113–119. Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum Junya Yamagishi 1 , 2 , Anna Natori 3 , Mohammed E.M. Tolba 4 , Arthur E. Mongan 5 , Chihiro Sugimoto 6 , Toshiaki Katayama 7 , Shuichi Kawashima 7 , Wojciech Makalowski 8...
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Research: A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...5290002, Israel; 3Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel A-to-I RNA editing, catalyzed by the adenosine deaminase acting on RNA (ADAR) enzymes, is a posttranscriptional process that modifies RNA sequences and diversifies the transcriptome...
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Method: Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum
- Heather J. Painter,
- Manuela Carrasquilla,
- and Manuel Llinás
Genome Res. June 2017 27: 1074-1086; Published in Advance April 17, 2017, doi:10.1101/gr.217356.116
...stage of parasite development, and will allow for future applications to comprehensively measure RNA-protein interactions in the malaria parasite. [Supplemental material is available for this article.] Plasmodium falciparum, the causative agent of malaria, has a complex life cycle that includes...
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Research: Transcriptional variation in the malaria parasite Plasmodium falciparum
- Núria Rovira-Graells,
- Archna P. Gupta,
- Evarist Planet,
- Valerie M. Crowley,
- Sachel Mok,
- Lluís Ribas de Pouplana,
- Peter R. Preiser,
- Zbynek Bozdech,
- and Alfred Cortés
Genome Res. May 2012 22: 925-938; Published in Advance March 13, 2012, doi:10.1101/gr.129692.111
...genetic variation has been extensively characterized, but the level of epigenetic plasticity remains largely unexplored. Here we provide a comprehensive characterization of transcriptional variation in the most lethal malaria parasite, Plasmodium falciparum, based on highly accurate transcriptional...
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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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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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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...-9806, USA; 10Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom Corresponding author: alistair.miles@well.ox.ac.uk Abstract The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity...
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Resource: Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii
- Carlos Vargas-Chavez,
- Neil Michel Longo Pendy,
- Sandrine E. Nsango,
- Laura Aguilera,
- Diego Ayala,
- and Josefa González
Genome Res. January 2022 32: 189-202; Published in Advance December 29, 2021, doi:10.1101/gr.275761.121
...of genes containing insertions -wide (χ2 test P-value = 0.7788). Eleven of the 148 genes containing TE insertions are differentially expressed in response to a Plasmodium invasion (Supplemental Table S12). These 11 genes participate in several pathways of the immune response including the small regulatory...
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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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