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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...techniques. Our 324 framework also accepts multi-omics inputs to better support downstream target phenotype 325 prediction—an approach shown to outperform single-dimensional predictions (Sammut et al. 326 16 2022; Kaplow et al. 2023; Wang et al. 2024), , making the toolkit versatile for diverse 327...
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Method: Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
- Joseph B. Hiatt,
- Colin C. Pritchard,
- Stephen J. Salipante,
- Brian J. O'Roak,
- and Jay Shendure
Genome Res. May 2013 23: 843-854; Published in Advance February 4, 2013, doi:10.1101/gr.147686.112
...-neoplastic cell admixture or tumor heterogeneity (Navin et al. 2011; Carter et al. 2012; Gerlinger et al. 2012; Nik-Zainal et al. 2012). Furthermore, recent pioneering studies have explained the rapid emergence of resistance to targeted therapy in colon cancer by showing that drug-resistance mutations may...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
..., complicating bulk-tissue analyses. Here, using 71 patient-derived PAAD organoids, we show that TE activities may potentially promote tumorigenesis and provide a source of novel immunotherapeutic targets. We identify 16 new TE-derived transcripts fused with 15 known oncogenes, exhibiting potential oncogenic...
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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
...Methods, Sec. S10). The results in Supplemental Figure S2 show that ScisTree2 is robust to a certain level of noise.Simulation for targeted sequencingCurrent single-cell targeted DNA sequencing usually generates data with a large number of cells but relatively small number of SNVs. To evaluate...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...unclear. Finally, the structural stability of the in these lineages is not known.Gars (Lepisosteidae) are a clade of seven living species that have emerged as a model system for studying evolution in ancient lineages characterized by slow evolutionary rates (Braasch et al. 2016; Thompson et al. 2021...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...antiandrogens the cornerstone of treatment for patients (Bolis et al. 2021; Paakinaho and Palvimo 2021). Although AR remains the principal therapeutic target in PCa, other TFs, notably GR and FOXA1, play critical roles in disease progression and the emergence of antiandrogen resistance (Sahu et al. 2011; Bolis...
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Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
...improving the efficacy of lentiviral gene therapies, a sizeable proportion of produced vector contains an incomplete and thus potentially nonfunctional RNA . This can undermine gene delivery by the lentivirus as well as increase manufacturing costs and must be improved to facilitate the widespread clinical...
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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
...responses generated by mutant KRAS and BRAF in T cells are also prime targets for antitumor immune therapy (Wilmott et al. 2012; Tran et al. 2016). The partial regulatory actions of these genes demonstrate heterogeneity across diverse cell types, facilitating the understanding of cell functions within...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
.... These findings emphasize the importance of considering both repeat length and motif organization in TR genotyping.With new sequencing technologies emerging that combine longer read length and higher accuracy, it is now possible to deeply characterize TRs. As such, multiple methods have been developed to genotype...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...tracing in cancer cell origin, metastasis, and drug resistanceThe presence of heterogeneous cell populations within tumors, each characterized by distinct genetic and molecular profiles, poses a significant challenge in the development of targeted therapies. This inherent diversity contributes...
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