Searching journal content for articles similar to Ceron-Noriega et al. 33 (1): 112.

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  1. Research: Proteome-wide structural analysis quantifies structural conservation across distant species
    • Shijie Zhang,
    • Teng Zhang,
    • and Yuan Fu
    Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
    ...relies on sequence information to infer evolutionary relationships between genes or proteins. In contrast, protein structural information has long been overlooked, although structures are more conserved and closely linked to the functions than the sequences. To address this gap, we conducted a proteome-wide...
  2. 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
    ...score stability and cross-signature comparability, achieving cell-state annotation accuracy comparable to supervised methods. We demonstrate the practical utility of ANS by developing and validating a gene signature to differentiate cancer-associated fibroblasts from malignant cells undergoing...
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  3. Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
    • Marina Athanasouli,
    • Tobias Loschko,
    • and Christian Rödelsperger
    Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
    ...genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics 21: 708. doi:10.1186/s12864-020-07100-0 ↵Athanasouli M, Akduman N, Röseler W, Theam P, Rödelsperger C. 2023. Thousands of Pristionchus pacificus orphan genes were integrated...
  4. Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
    • Zhitao Huang,
    • Ruiqing Zheng,
    • Pengzhen Jia,
    • Xuhua Yan,
    • Jinmiao Chen,
    • and Min Li
    Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
    ...labels are transferred from well-annotated scRNA-seq data to less-annotated omics data, such as scATAC-seq. This approach leverages the gene expression profiles available in scRNA-seq to help annotate common cell types and even novel cell types for other omics data. However, the heterogeneous features...
  5. 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
    ...microenvironment. The prevalent manual annotation approach groups single cells into several clusters and annotates them based on unique molecular signatures (Clarke et al. 2021). This process needs prior biological knowledge and is time-consuming. However, as scRNA-seq can profile all genes (typically numbering...
  6. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...(causing loss of function), activating, latent (enabling another distinct driver mutation) (Nussinov and Tsai 2015), or, in rare cases, neofunctional, in which the protein function differs from the wild type and benefits the tumor. Many computational tools have been developed to predict cancer driver genes...
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  7. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    ...%) clade mutations that were located along branches of the clonal tree. Because genes affected by ancestral mutations may have a significant impact on early development of tumors, we used ANNOVAR (Wang et al. 2010) to annotate these ancestral mutations and found 48 exonic genes that may potentially...
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  8. Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
    • Marjan Farahbod,
    • Aboud Diab,
    • Paul Sud,
    • Meenakshi S. Kagda,
    • Ian Whaling,
    • Mehdi Foroozandeh,
    • Ishan Goel,
    • Habib Daneshpajouh,
    • Benjamin Hitz,
    • J. Michael Cherry,
    • and Maxwell W. Libbrecht
    Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
    ...of profiled biosamples. Epi mapping facilitates the creation of reference annotations, which enable researchers to understand genomic activity in any of the hundreds of characterized cell and tissue types and thus understand the influence of genomic activity on disease and other phenomena (Stunnenberg et al...
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  9. Method: Robust chromatin state annotation
    • Mehdi Foroozandeh Shahraki,
    • Marjan Farahbod,
    • and Maxwell W. Libbrecht
    Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
    ...across two SAGA models. Thus, we must first detect corresponding states across annotations to enable comparison (Fig. 1C). To establish a correspondence between chromatin states while accounting for varying genomic coverages, we calculate intersection over union (IoU) of overlap, also known as Jaccard...
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  10. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...sRNA-seq and RNA-seq is not due to codetection of housekeeping genesThe association between small RNA and total RNA expression could be partly owing to the codetection of highly expressed housekeeping genes. To rule this out, we functionally annotated the top 10% of the highest expressed genes form...
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