Searching journal content for articles similar to Crits-Christoph et al. 31 (2): 239.

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Method: BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs
- Dmitry Meleshko,
- Hosein Mohimani,
- Vittorio Tracanna,
- Iman Hajirasouliha,
- Marnix H. Medema,
- Anton Korobeynikov,
- and Pavel A. Pevzner
Genome Res. August 2019 29: 1352-1362; Published in Advance June 3, 2019, doi:10.1101/gr.243477.118
..., Fischbach MA, et al. 2015. IMG-ABC: a knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. MBio 6: e00932-15. doi:10.1128/mBio.00932-15 ↵Huang W, Li L, Myers JR, Marth GT. 2012. ART: a next-generation sequencing read simulator. Bioinformatics 28: 593–594. doi:10...
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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
...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
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Research: Widespread natural selection on metabolite levels in humans
- Yanina Timasheva,
- Kaido Lepik,
- Orsolya Liska,
- Balázs Papp,
- and Zoltán Kutalik
Genome Res. August 2024 34: 1121-1129; Published in Advance August 16, 2024, doi:10.1101/gr.278756.123
...successfully applied to high-level traits, the prevalence and mode of selection acting on molecular traits remain poorly understood. Here, we estimate the action of natural selection on genetic variants associated with metabolite levels, an important layer of molecular traits. By leveraging summary statistics...
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Method: Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
- Jiangyi Shao,
- Shutao Chen,
- Ziwen Wang,
- Zixu Chen,
- and Bin Liu
Genome Res. April 15, 2026 gr.280816.125; Published in Advance April 15, 2026, doi:10.1101/gr.280816.125
...Balancing Gene Ontology annotation specificity in protein function prediction 1 based on the protein sequence large graph 2 Jiangyi Shao1,2, Shutao Chen1, Ziwen Wang 1, Zixu Chen1,2, Bin Liu1,2* 3 1 School of Computer Science and Technology, Beijing Institute of Technology, 4 Beijing 100081, China...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...that the chimeric mitochondrial transcript frequency also increases and correlates strongly with an orthogonal DNA-based mutation assay performed on identical samples. Further, we show that the frequency of chimeric mitochondrial transcripts predicts expression of both nuclear and mitochondrial genes central...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...provides the evidence counts for each gene. (B) Predicted repurposable drug candidates by network proximity and GSEA clustered by ATC first-level class. Left panel shows enriched drug candidates identified by network proximity method, in which gradient colors reflect absolute Z-scores. Right panel shows...
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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
...suboptimally in our ESCC and LUAD_Xing training data sets (AUCPRC 0.028 vs. 0.592 of our gene signature in ESCC and 0.244 vs. 0.513 in LUAD_Xing).Calculation of cancer cell–specific EMT phenotypes using bulk RNA-seq data offers a promising alternative to assess their link with clinical characteristics in cases...
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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. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...downregulated DEGs were enriched in cell adhesion molecules pathways (Supplemental Fig. S5H).To explore the dynamics of gene expression changes with age, we performed clustering analysis of DEGs, identifying distinct groups with varied functions. In oligodendrocytes, for example, we identified four DEG groups...
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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
...or nuclei and bioinformatic platforms that leverage the power of these data to elucidate regulatory processes have only recently been developed (Reyes et al. 2019; Eisenstein 2020; Chen et al. 2023; Lee et al. 2023; Zhang et al. 2024). Gene expression dynamics, which mediate the biosynthetic tissue...
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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
...for predicting gene expression (ScPGE) from discrete candidate CREs (cCREs). ScPGE assembles DNA sequences, transcription factor (TF) binding scores, and epigenomic tracks from discrete cCREs into three-dimensional tensors, and then models the relationships between cCREs and genes by combining convolutional...
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