Searching journal content for articles similar to Sebestyén et al. 28 (9): 1426.

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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
...analyses in cancer genomics.The ability of ScisTree2 to analyze a large number of cells may be useful in large-scale cancer genomics analyses. One such analysis is identifying rare cancer subclones, which can drive disease recurrence and therapy resistance. For example, relapse of acute myeloid leukemia...
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Research: Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks
- Endre Sebestyén,
- Babita Singh,
- Belén Miñana,
- Amadís Pagès,
- Francesca Mateo,
- Miguel Angel Pujana,
- Juan Valcárcel,
- and Eduardo Eyras
Genome Res. June 2016 26: 732-744; Published in Advance April 13, 2016, doi:10.1101/gr.199935.115
...Large-scale analysis of and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks Endre Sebestyén1,5, Babita Singh1,5, Belén Miñana1,2, Amadís Pagès1, Francesca Mateo3, Miguel Angel Pujana3, Juan Valcárcel1,2,4 and Eduardo Eyras1,4 1Universitat Pompeu Fabra, E...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...(Halo et al. 2021). Eventually, long-read sequencing will become common practice in animal genomics, permanently altering sequencing strategies and analysis techniques while capturing the full spectrum of variation within a single .Large-scale sequencing effortsThe International Dog10K consortium...
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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 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...research focused on understanding the cellular changes in PD-related nigrostriatal pathway. Aging is known to significantly alter transcriptional programs and gene regulatory networks in brain cell types (Mattson and Arumugam 2018; Zhang et al. 2022; Jin et al. 2025). In general, inflammation and cellular...
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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.Microsatellites, also known as short tandem repeats, are genomic sequences composed of tandem repeats of short (1...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...tumors from The Cancer Genome Atlas (TCGA) (Fig. 1B; The Cancer Genome Atlas Network 2012). To have groups of clinically and biologically similar tumors and patients, we initially stratified tumors into six specific subgroups based on their HR status (HR+ or HR−) and HER2 expression levels (HER2-high...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Lê Cao
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...to large-scale single-cell data sets. We demonstrate NNet’s effectiveness through three case studies on transcription factor activity prediction, early hematopoiesis, and tumor microenvironments. Provided as an R package, NNet offers a novel framework for exploring cellular variation in coexpression...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...prediction. We build on these data, implementing further filtering steps to remove families with homology with other species, to identify putative SSOGs in the gut microbiome and to study them systematically. By looking for patterns in large-scale comparisons, we attempt to disentangle the evolutionary...
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Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.Collaborative studies that aim...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...aging. These include changes in DNA methylation, histone modifications, chromatin remodeling, and noncoding RNAs. Collectively, such alterations disrupt gene regulatory networks, leading to transcriptional dysregulation, loss of cellular homeostasis, and increased vulnerability to age-related diseases...
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