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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...methylation in the female mouse germline occurs postnatally in growing oocytes arrested at meiotic prophase. This process depends on the de novo methyltransferase DNMT3A and its noncatalytic cofactor DNMT3L (Fig. 2; Bourc'his et al. 2001; Hata et al. 2002; Kaneda et al. 2004). Genome-wide transcriptome...
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Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- Siyuan Chen,
- Jiuming Wang,
- Inkyung Jung,
- Zhaowen Qiu,
- Xin Gao,
- and Yu Li
Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
...classifier for -wide detection. The limitation of the supervised classification framework primarily manifests in its detection speed and relatively small reception fields. Genome-wide detection with a binary classifier can be computationally inefficient as the small window causes scanning to be resource...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...). Recently, using samples from postmortem ASD and control brains, several studies have reported a wide range of dysregulation of gene expression (Voineagu et al. 2011; Guan et al. 2016; Parikshak et al. 2016) in ASD. Moreover, epigenetic factors such as alternatively spliced transcripts (Voineagu et al. 2011...
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Methods: Genome-wide identification of spliced introns using a tiling microarray
- Zhihong Zhang,
- Jay R. Hesselberth,
- and Stanley Fields
Genome Res. April 2007 17: 503-509; Published in Advance March 9, 2007, doi:10.1101/gr.6049107
...-Engele, P. , Kan, Z. , Loerch, P.M. , Armour, C.D. , Santos, R. , Schadt, E.E. , Stoughton, R. , Shoemaker, D.D. ( 2003 ) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays . Science 302 : 2141 – 2144 . ↵ Kampa, D. , Cheng, J. , Kapranov, P. , Yamanaka, M. , Brubaker, S...
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Research: A heterozygous IDH1^R132H/WT mutation induces genome-wide alterations in DNA methylation
- Christopher G. Duncan,
- Benjamin G. Barwick,
- Genglin Jin,
- Carlo Rago,
- Priya Kapoor-Vazirani,
- Doris R. Powell,
- Jen-Tsan Chi,
- Darell D. Bigner,
- Paula M. Vertino,
- and Hai Yan
Genome Res. December 2012 22: 2339-2355; Published in Advance August 16, 2012, doi:10.1101/gr.132738.111
...A heterozygous IDH1 R132H/WT mutation induces genome-wide alterations in DNA methylation Christopher G. Duncan 1 , 6 , Benjamin G. Barwick 2 , 6 , Genglin Jin 1 , Carlo Rago 3 , Priya Kapoor-Vazirani 4 , Doris R. Powell 4...
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Research: DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast
- Joel H. Graber,
- Fathima I. Nazeer,
- Pei-chun Yeh,
- Jason N. Kuehner,
- Sneha Borikar,
- Derick Hoskinson,
- and Claire L. Moore
Genome Res. October 2013 23: 1690-1703; Published in Advance June 20, 2013, doi:10.1101/gr.144964.112
...DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast Joel H. Graber 1 , 4 , Fathima I. Nazeer 2 , Pei-chun Yeh 2 , Jason N. Kuehner 2 , 3 , Sneha Borikar 1 , 2 , Derick Hoskinson 2...
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Research: A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells
- Keren Imberg-Kazdan,
- Susan Ha,
- Alex Greenfield,
- Christopher S. Poultney,
- Richard Bonneau,
- Susan K. Logan,
- and Michael J. Garabedian
Genome Res. April 2013 23: 581-591; Published in Advance February 12, 2013, doi:10.1101/gr.144774.112
...two times. A representative experiment is shown. Genome-wide RNAi screen for AR regulators Genome Research 587 www..org might promote interactions between the head and tail regions (Baidoobonso et al. 2007), with AR associating with MED14, MED15, and/or MED16 (Sharma et al. 2013). MED19 has also been...
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Research: Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
- Claudia Fritsch,
- Alexander Herrmann,
- Michael Nothnagel,
- Karol Szafranski,
- Klaus Huse,
- Frank Schumann,
- Stefan Schreiber,
- Matthias Platzer,
- Michael Krawczak,
- Jochen Hampe,
- and Mario Brosch
Genome Res. November 2012 22: 2208-2218; Published in Advance August 9, 2012, doi:10.1101/gr.139568.112
...Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting Claudia Fritsch 1 , Alexander Herrmann 1 , Michael Nothnagel 2 , Karol Szafranski 3 , Klaus Huse 3 , Frank Schumann 1...
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Method: Differential genome-wide profiling of tandem 3′ UTRs among human breast cancer and normal cells by high-throughput sequencing
- Yonggui Fu,
- Yu Sun,
- Yuxin Li,
- Jie Li,
- Xingqiang Rao,
- Chong Chen,
- and Anlong Xu
Genome Res. May 2011 21: 741-747; Published in Advance April 7, 2011, doi:10.1101/gr.115295.110
...and the dual roles of microRNAs: A hypothesis. Genome Res 19: 734–743. Zaretzki RL, Gilchrist MA, BriggsWM, Armagan A. 2010. Bias correction and Bayesian analysis of aggregate counts in SAGE libraries. BMC Bioinformatics 11: 72. Received September 13, 2010; accepted in revised form March 4, 2011. Genome-wide...
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Research: Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
- Wei Niu,
- Zhi John Lu,
- Mei Zhong,
- Mihail Sarov,
- John I. Murray,
- Cathleen M. Brdlik,
- Judith Janette,
- Chao Chen,
- Pedro Alves,
- Elicia Preston,
- Cindie Slightham,
- Lixia Jiang,
- Anthony A. Hyman,
- Stuart K. Kim,
- Robert H. Waterston,
- Mark Gerstein,
- Michael Snyder,
- and Valerie Reinke
Genome Res. February 2011 21: 245-254; Published in Advance December 22, 2010, doi:10.1101/gr.114587.110
...Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans Wei Niu 1 , Zhi John Lu 2 , 3 , Mei Zhong 4 , Mihail Sarov 5 , John I. Murray 6 , Cathleen M. Brdlik 7 , Judith Janette 1...

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