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Resource: Organ-level protein networks as a reference for the host effects of the microbiome
- Robert H. Mills,
- Jacob M. Wozniak,
- Alison Vrbanac,
- Anaamika Campeau,
- Benoit Chassaing,
- Andrew Gewirtz,
- Rob Knight,
- and David J. Gonzalez
Genome Res. February 2020 30: 276-286; Published in Advance January 28, 2020, doi:10.1101/gr.256875.119
...In a new window Figure 4. Organism-level protein networks modulated by the microbiome. A multinomial regression controlling for organ and microbial colonization state of the mice was used to assess proteins associated with colonization status. (A) Proteins ranked by regression coefficient; proteins...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...in modeling gene expression changes resulting from sequence variants. Yet, few methods operate at the resolution necessary to capture subtle effects of single-nucleotide changes. Furthermore, it remains unclear which architectural components, such as residual connections, normalization strategies...
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Method: A unified analysis of atlas single-cell data
- Hao Chen,
- Nam D. Nguyen,
- Matthew Ruffalo,
- and Ziv Bar-Joseph
Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
....To further explore the different gene–gene relationships profiled in the HuBMAP (adult human) and human fetal atlases, for each tissue that is common between the two atlases, we identified unique gene modules in the gene-embedding components of each atlas (Supplemental Note 11). Notably, we observed...
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Method: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
- Quanyou Cai,
- Lihui Lin,
- Xin Liu,
- and Jiekai Chen
Genome Res. November 2025 35: 2513-2526; Published in Advance October 22, 2025, doi:10.1101/gr.280532.125
.... 2021). Even though high-resolution spatial transcriptome technologies have been developed, such technologies show significantly lower cell segmentation resolution and the number of detected genes compared with single-cell transcriptome data. Therefore, integrating single-cell and spatial transcriptomic...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...of mouse embryo FFPE sections. Additionally, PCL-seq achieves subcellular resolution, as demonstrated by differential expression profiling between nuclear and cytoplasmic compartments. These characteristics establish PCL-seq as an accessible and versatile workflow for spatial transcriptomic analyses...
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Resource: A single-cell transcriptome atlas of the maturing zebrafish telencephalon
- Shristi Pandey,
- Anna J. Moyer,
- and Summer B. Thyme
Genome Res. April 2023 33: 658-671; Published in Advance April 18, 2023, doi:10.1101/gr.277278.122
..., we delineated nine main neuronal cell types in the pallium and eight in the subpallium and nominated novel marker genes. Comparing zebrafish and mouse neuronal cell types revealed both conserved and absent types and marker genes. Mapping of cell types onto a spatial larval reference atlas created...
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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
...Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease Yunxiao Ren1,2, Ming Hu3,4, Yang E. Li5, Andrew A. Pieper6,7,8,9,10,11, Jeffrey Cummings12 and Feixiong Cheng1,2,4,13 1Cleveland Clinic Genome Center, Cleveland Clinic Research...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost s. We then leverage this atlas to investigate how rediploidization occurred in teleosts at the -wide level. We uncover that some...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...of the molecular basis of species diversification and increased resolution of genomic feature evolution. Our -wide analysis reveals increased positive selection pressure during the diversification of the three honey bee lineages after the divergence of Apis from its most recent common ancestor with Bombus. Our...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...Full-resolution HLA and KIR gene annotations for human assemblies Ying Zhou1, Li Song2 and Heng Li1,3 1Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA; 2Department of Biomedical Data Science, Dartmouth College, Hanover, New Hampshire 03755, USA; 3...

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