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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
...manipulation of this modification in mRNAs. Here, we present Dem6A-Vec, an “all-in-one” plasmid vector designed for site-specific m6A demethylation in human mRNAs. Dem6A-Vec integrates the expression of a catalytically inactive RfxCas13d fused to the m6A demethylase ALKBH5 and a U6-driven customizable guide...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...-nucleotide variations (SNVs) are, however, much harder to identify with low sequencing depth due to sequencing errors. Here, we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA and consensus calling based on -wide long-read nanopore sequencing to enable...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
..., and technical batch, consistent with the findings of Parsana et al. (2019) (Supplemental Figs. S5I–L, S6C). Thus, regressing PCs computed by accounting for tissue and cross-study heterogeneity from expression is integral to excluding technical effects and unwanted biological signals.We examined the effect of PC...
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Method: STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
- Congcong Hu,
- Nana Wei,
- Jiyuan Yang,
- Hua-Jun Wu,
- and Xiaoqi Zheng
Genome Res. June 2025 35: 1415-1428; Published in Advance May 12, 2025, doi:10.1101/gr.280031.124
...in the integration of vast data sets, wNMF-based underscores the enhancement in performance through consensus weighting. When it comes to the selection of consensus algorithms, we recommend (1) thoroughly exploring parameters of single baseline algorithm that could impact clustering results to attain the optimal...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...normalization methods on the performance of BINDER but also validate the effectiveness of integrating the community discovery method with the neural network model (Supplemental Table S10). These results highlight the robustness of the consensus boundary strategy of BINDER across various feature combinations...
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Research: The predicted RNA-binding protein regulome of axonal mRNAs
- Raphaëlle Luisier,
- Catia Andreassi,
- Lisa Fournier,
- and Antonella Riccio
Genome Res. September 2023 33: 1497-1512; Published in Advance August 15, 2023, doi:10.1101/gr.277804.123
...programsTo identify mRNAs localized in cell bodies and axons of sympathetic neurons in response to neurotrophins, we integrated previously published 3′ UTR sequencing data obtained from compartmentalized cultures of sympathetic neurons exposed to NGF (Andreassi et al. 2021), with data simultaneously...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...in detecting distant cCREs, whereas ScPGE-KL excels at identifying proximal cCREs.ScPGE captures important TF motifsTo capture cell type–specific TF motifs, we first selected all true positives from the test set, and then ran the MEME-ChIP program (Machanick and Bailey 2011), which integrates multiple tools...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...Zaslavsky1, Todd Trappe4, Scott Trappe4,9 and Stuart C. Sealfon1,9 1Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York 10029, USA; 2Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; 3Center for Computational...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
...A classification score for all examples in the validation set. The classification score ranks the validation examples, and precision is computed at every score threshold. At the end of this phase, we select a score threshold to achieve the target precision. In this work, we use a target precision...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...of soil samples in which soil depth and biogeochemical conditions select for different strain variant populations. By examining read mappings across multiple samples from the same environment, we established a larger repertoire of MGEs than could be found from the analysis of any single meta. Integrated...
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