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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
...2016; Norton et al. 2018; Chang et al. 2020). Taken together, precise and robust identification of TADs, hierarchical TADs, and partially overlapping TADs using Hi-C data are essential for a deeper understanding of 3D-folding mechanisms and their epigenetic and gene regulatory functions.In recent years...
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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
...the genomic position on the chromosomes (1 Mb bins), and the y-axis indicates copy numbers. (C) Correlation of CNA-derived TF between NanoRCS and NovaSeq. (D) NanoRCS copy number of genes often amplified (red) and deleted (blue) according to literature. The boxplots show the observed copy number distribution...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...mice were used in this study, we examined the gender distribution 496 within each cell subclass. To do this, we utilized the aforementioned midbrain single-cell RNA 497 seq dataset from ABC Atlas, which contains the gender information, to train a model for gender 498 prediction. Six genes, including...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...PCR primers designed against nonregulatory regions of the gene when enrichment is not expected, and ensuring DNA shearing with fragments that are not too long in order to prevent nonspecific GOI identification. ChIP has had a revolutionary impact on our understanding of biology and has spearheaded clinical...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...genomic loci.Human quasi-primes are associated with brain development and cognitive functionWe analyzed the expression of quasi-prime-containing genes across human tissues. In total, we examined the consensus normalized expression from RNA-seq experiments across 50 tissues (Pontén et al. 2008). We observe...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...assembly.Repeat annotation and gene predictionDe novo identification of repeats was performed by the RepeatModeler (Flynn et al. 2020) under default parameters. We also recovered 107 satellite DNA sequences belonging to 62 families in L. migratoria (Ruiz-Ruano et al. 2016). Using the ab initio repeat...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...examples like histone genes (Maxson et al. 1983), rDNA arrays (Hall et al. 2022), and immunoglobulin genes (Watson and Breden 2012). Tandem repeats are prone to rapid copy number changes mediated through mechanisms such as unequal crossing over, replication slippage, gene conversion, and intrachromatid...
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Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
- Lin Li,
- Xianbin Su,
- and Ze-Guang Han
Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
...biases in the identification of gene programs. Moreover, neither method adequately incorporates location information into the characterization of gene programs, resulting in a lack of tailoring for the unique features of ST data. On the other hand, although current methods specifically developed for ST...
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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
...for reads that map to multiple genomic loci. Reads identified as candidate chimeric reads are further assessed as fusion evidence by modeling fusion contigs containing the candidate fusion genes in their proper order and orientation followed by realignment of candidate chimeric reads to the fusion contigs...
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