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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...: padamopoulos@biol.uoa.grAbstractEpitranscriptomics, a rapidly evolving field mainly driven by massive parallel sequencing technologies, explores post-transcriptional RNA modifications. N6-methyladenosine (m6A) has emerged as the most prominent and dynamically regulated modification in human mRNAs, being...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...epithelial-to-mesenchymal transition. Overall, ANS provides a robust and reliable gene signature scoring framework, significantly improving the accuracy of score-based annotation of cell types and states in single-cell studies.High-throughput single-cell RNA sequencing (scRNA-seq) is a powerful technology...
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
...base modification information, we developed Methyl-SNP-seq, a technology that takes advantage of the complementarity of the double helix to extract the methylation and original sequence information from a single DNA molecule. More specifically, Methyl-SNP-seq uses bisulfite conversion of one...
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Method: Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9
- Daniel Agudelo,
- Sophie Carter,
- Minja Velimirovic,
- Alexis Duringer,
- Jean-François Rivest,
- Sébastien Levesque,
- Jeremy Loehr,
- Mathilde Mouchiroud,
- Denis Cyr,
- Paula J. Waters,
- Mathieu Laplante,
- Sylvain Moineau,
- Adeline Goulet,
- and Yannick Doyon
Genome Res. January 2020 30: 107-117; Published in Advance January 3, 2020, doi:10.1101/gr.255414.119
...Versatile and robust editing with Streptococcus thermophilus CRISPR1-Cas9 Daniel Agudelo1, Sophie Carter1, Minja Velimirovic1, Alexis Duringer1, Jean-François Rivest1, Sébastien Levesque1, Jeremy Loehr1, Mathilde Mouchiroud2, Denis Cyr3, Paula J. Waters3, Mathieu Laplante2,4, Sylvain Moineau5...
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Research: Cancer-associated rs6983267 SNP and its accompanying long noncoding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations
- Maitri Y. Shah,
- Manuela Ferracin,
- Valentina Pileczki,
- Baoqing Chen,
- Roxana Redis,
- Linda Fabris,
- Xinna Zhang,
- Cristina Ivan,
- Masayoshi Shimizu,
- Cristian Rodriguez-Aguayo,
- Mihnea Dragomir,
- Katrien Van Roosbroeck,
- Maria Ines Almeida,
- Maria Ciccone,
- Daniela Nedelcu,
- Maria Angelica Cortez,
- Taghi Manshouri,
- Steliana Calin,
- Muharrem Muftuoglu,
- Pinaki P. Banerjee,
- Mustafa H. Badiwi,
- Jan Parker-Thornburg,
- Asha Multani,
- James William Welsh,
- Marcos Roberto Estecio,
- Hui Ling,
- Ciprian Tomuleasa,
- Delia Dima,
- Hui Yang,
- Hector Alvarez,
- M. James You,
- Milan Radovich,
- Elizabeth Shpall,
- Muller Fabbri,
- Katy Rezvani,
- Leonard Girnita,
- Ioana Berindan-Neagoe,
- Anirban Maitra,
- Srdan Verstovsek,
- Riccardo Fodde,
- Carlos Bueso-Ramos,
- Mihai Gagea,
- Guillermo Garcia Manero,
- and George A. Calin
Genome Res. April 2018 28: 432-447; Published in Advance March 22, 2018, doi:10.1101/gr.225128.117
..., USA; 23Cell & Gene Therapy, Bioverativ Inc., Waltham, MA 02451 Corresponding author: gcalin@mdanderson.orgAbstractThe cancer-risk-associated rs6983267 single nucleotide polymorphism (SNP) and the accompanying long noncoding RNA CCAT2 in the highly amplified 8q24.21 region have been implicated...
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Method: SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole-genome sequencing of tank milk
- Wouter Coppieters,
- Latifa Karim,
- and Michel Georges
Genome Res. August 2020 30: 1201-1207; Published in Advance June 26, 2020, doi:10.1101/gr.256172.119
...genotype were scored for MAF bins of 0.01 separately for the LD and 50,000 array data. We simulated genotyping-by-sequencing of tank milk as follows. For each of the 8 M SNP positions, we sampled local read depth (r ∈ integers) from a Poisson distribution with mean C, where C is the average -wide coverage...
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Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
- Wilfried M. Guiblet,
- Marzia A. Cremona,
- Monika Cechova,
- Robert S. Harris,
- Iva Kejnovská,
- Eduard Kejnovsky,
- Kristin Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
...Long-read sequencing technology indicates -wide effects of non-B DNA on polymerization speed and error rate Wilfried M. Guiblet1,8, Marzia A. Cremona2,8, Monika Cechova3, Robert S. Harris3, Iva Kejnovská4, Eduard Kejnovsky5, Kristin Eckert6, Francesca Chiaromonte2,7 and Kateryna D. Makova3 1...
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Method: metaSPAdes: a new versatile metagenomic assembler
- Sergey Nurk,
- Dmitry Meleshko,
- Anton Korobeynikov,
- and Pavel A. Pevzner
Genome Res. May 2017 27: 824-834; Published in Advance March 15, 2017, doi:10.1101/gr.213959.116
..., St. Petersburg, Russia 198515; 3Department of Computer Science and Engineering, University of California, San Diego, California 92093-0404, USA While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus...
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Method: 2C-Cas9: a versatile tool for clonal analysis of gene function
- Vincenzo Di Donato,
- Flavia De Santis,
- Thomas O. Auer,
- Noé Testa,
- Héctor Sánchez-Iranzo,
- Nadia Mercader,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. May 2016 26: 681-692; Published in Advance March 8, 2016, doi:10.1101/gr.196170.115
..., this technology has been primarily used to generate genetic knockout animals. Nevertheless, the study of the function of certain loci might require tight spatiotemporal control of gene inactivation. Here, we show that tissue-specific gene disruption can be achieved by driving Cas9 expression with the Gal4/UAS...
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Method: Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease
- Snehit Prabhu and
- Itsik Pe'er
Genome Res. November 2012 22: 2230-2240; Published in Advance July 5, 2012, doi:10.1101/gr.137885.112
...), both for data sets typed on genotyping arrays (;106 SNPs) and sequencing technologies (;107 SNVs). Somemethods address this problem by restricting the analysis to a small subset of candidate markers—those identified through single-locus analysis or those of biological interest (Emily et al. 2009...

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