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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...and Nora 2016; Melo et al. 2020; Shrestha et al. 2022). TAD boundaries, which separate adjacent TADs, prove to be well conserved across mammalian species and are more evolutionarily constrained than TADs themselves (McArthur and Capra 2021; Rajderkar et al. 2023). To date, the most comprehensive...
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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
...are reduced by the consensus of multiple (≥3) repeats. NanoRCS offers a precise, multimodal nanopore sequencing-based strategy for cfDNA sequencing through the accurate identification of tumor-informed SNVs along with CNAs and fragmentation length patterns in cfDNA (Fig. 1D).View larger version...
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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
...framework to describe gene-gene relationships and are comprised of nodes that represent genes and edges linking coexpressed genes (Stuart et al. 2003). A comprehensive catalog of gene coexpression relationships has the potential to characterize genes with unknown functions (Schlitt et al. 2003), identify...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...information to comprehensively characterize sSNV biological functions. For splicing dysregulation, SynMall examines whether sSNVs overlap with splice site consensus regions and 2033 exonic splicing regulatory motifs (Supplemental Table S5; Supplemental Methods). SynMall also integrates ESEFinder 3...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...The first affiliated hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China; Corresponding authors: awcarroll@google.com, bpaten@ucsc.edu, shafin@google.comAbstractAccurate assemblies are essential for biological research, but even the highest...
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Research: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
- Gregor Jessberger,
- Csilla Várnai,
- Roman R. Stocsits,
- Wen Tang,
- Georg Stary,
- and Jan-Michael Peters
Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
...with specific consensus sequences located at these boundaries (Nora et al. 2017; Wutz et al. 2017). CTCF is thought to establish TAD boundaries by constraining cohesin-mediated loop extrusion in an orientation-dependent manner, thus limiting the length of chromatin loops that can be formed by cohesin (Rao et al...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...short-read RNA-seq as a modularized software that contains chimeric read extraction, fusion transcripts identification, expression quantification, gene fusion annotation, and interactive visualization. To benchmark existing tools, we collected or generated comprehensive simulation data sets to reflect...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...step in this process is the prediction of a consensus sequence derived from long reads, providing a highly accurate reconstruction of the original template (e.g., circular RNA). This step requires in silico intervention and typically employs widely used tandem repeat detection tools for consensus...
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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
...have been proposed in recent years, their performance varies across data sets and experimental platforms. It is thus an important task to take full advantage of different tools to get a more accurate and stable result through consensus strategy. In this work, we developed STCC, a novel consensus...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
.... To this end, we present a cross–data set cell type annotation methodology with a universal reference data and method selection strategy (CAMUS) to achieve highly accurate and efficient annotations. We demonstrate the advantages of CAMUS by conducting comprehensive analyses on 672 pairs of cross-species sc...

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