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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
...and to enable large-scale joint analyses of atlas-level data, we developed a new method, gene-based data integration and analysis technique (GIANT), that focuses on genes rather than on cells. Genes provide a level of granularity, which, on the one hand, can serve as anchor points common to all modalities but...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...consists of epithelial cells of 182 the pharyngeal endoderm and intestinal rod, as well as the developing pancreas and liver 183 primordia. As expected, we found strong enrichment for anatomical terms consistent with 184 epithelial structures, gut, liver and pancreas, for DARs more accessible in both 185...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...-seq data across the liver, spleen, ovary, and oviduct shell gland, key tissues representing metabolism, immunity, and reproduction, to generate a comprehensive regulatory variants atlas in ducks. Leveraging this resource, we dissect the genetic regulatory mechanisms underlying duck reproductive performance...
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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
...and identify therapeutic opportunities. Here, we develop a cell type–specific regulatory atlas of the human middle temporal gyrus via leveraging single-nucleus RNA-seq (1,197,032 nuclei) and ATAC-seq (740,875 nuclei) data sets from 84 donors across four stages of AD neuropathological change (ADNC). We observe...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...genes involved in drug response (Supplemental Table 17). Using the Human Protein Atlas (Uhlén et al. 2015), we identified 469 target genes whose expression was enriched in liver tissue (Fig. 3E; Supplemental Table 17), including HMGCL and CDO1 (Fig. 3B,C). Relative to genes not linked to caPeaks, ca...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...Generation and analysis of a mouse multitissue annotation atlas Matthew Adams1 and Christopher Vollmers2 1Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA; 2Department of Biomolecular Engineering, University...
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Research: Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states
- Oliver J. Ziff,
- Benjamin E. Clarke,
- Doaa M. Taha,
- Hamish Crerar,
- Nicholas M. Luscombe,
- and Rickie Patani
Genome Res. January 2022 32: 71-84; Published in Advance December 28, 2021, doi:10.1101/gr.275939.121
...://shiny.crick.ac.uk/ALS_reactive_astrocytes_meta/).View larger version: In this window In a new window Figure 5. Working model. Multi-omic signatures of healthy astrocytes (left, blue) and ALS astrocytes (right, red).We identified overlapping signatures between inflammatory reactive astrocytes and ALS mutant astrocytes, characterized by common up...
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Research: Diploid genome architecture revealed by multi-omic data of hybrid mice
- Zhijun Han,
- Kairong Cui,
- Katarzyna Placek,
- Ni Hong,
- Chengqi Lin,
- Wei Chen,
- Keji Zhao,
- and Wenfei Jin
Genome Res. August 2020 30: 1097-1106; Published in Advance August 5, 2020, doi:10.1101/gr.257568.119
...Diploid architecture revealed by multi-omic data of hybrid mice Zhijun Han1,2, Kairong Cui3, Katarzyna Placek3, Ni Hong1, Chengqi Lin2, Wei Chen1, Keji Zhao3 and Wenfei Jin1 1Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; 2Institute of Life...
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Resource: The time-resolved transcriptome of C. elegans
- Max E. Boeck,
- Chau Huynh,
- Lou Gevirtzman,
- Owen A. Thompson,
- Guilin Wang,
- Dionna M. Kasper,
- Valerie Reinke,
- LaDeana W. Hillier,
- and Robert H. Waterston
Genome Res. October 2016 26: 1441-1450; Published in Advance August 16, 2016, doi:10.1101/gr.202663.115
...The time-resolved transcriptome of C. elegans Max E. Boeck 1 , 2 , Chau Huynh 1 , Lou Gevirtzman 1 , Owen A. Thompson 1 , Guilin Wang 3 , Dionna M. Kasper 3 , Valerie Reinke 3 , LaDeana W. Hillier 1...
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