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Research: Cell-type–specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes
- Tongwu Zhang,
- Jiyeon Choi,
- Michael A. Kovacs,
- Jianxin Shi,
- Mai Xu,
- NISC Comparative Sequencing Program,
- Melanoma Meta-Analysis Consortium,
- Alisa M. Goldstein,
- Adam J. Trower,
- D. Timothy Bishop,
- Mark M. Iles,
- David L. Duffy,
- Stuart MacGregor,
- Laufey T. Amundadottir,
- Matthew H. Law,
- Stacie K. Loftus,
- William J. Pavan,
- and Kevin M. Brown
Genome Res. November 2018 28: 1621-1635; Published in Advance October 17, 2018, doi:10.1101/gr.233304.117
...are co-senior authors and contributed equally to this work. Corresponding authors: bpavan@mail.nih.gov, kevin.brown3@nih.govAbstractMost expression quantitative trait locus (eQTL) studies to date have been performed in heterogeneous tissues as opposed to specific cell types. To better understand the cell-type...
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Research: Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes
- Nathan Lawlor,
- Joshy George,
- Mohan Bolisetty,
- Romy Kursawe,
- Lili Sun,
- V. Sivakamasundari,
- Ina Kycia,
- Paul Robson,
- and Michael L. Stitzel
Genome Res. February 2017 27: 208-222; Published in Advance November 18, 2016, doi:10.1101/gr.212720.116
.... Analyses of ND single-cell transcriptomes identified distinct alpha, beta, delta, and PP/gamma cell-type signatures. Genes linked to rare and common forms of islet dysfunction and diabetes were expressed in the delta and PP/gamma cell types. Moreover, this study revealed that delta cells specifically...
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Research: Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
- Hyunchul Jung,
- Jung Kyoon Choi,
- and Eunjung Alice Lee
Genome Res. August 2018 28: 1136-1146; Published in Advance July 3, 2018, doi:10.1101/gr.231837.117
...diverse immune-stimulatory cell types.Characterization of cancer subgroups with differential immune activityBased on the 49 L1-associated immune pathways in 112 cancer samples, we identified two distinct cancer subgroups with different immune signatures for stomach/esophageal cancer (SE; SE-High and SE...
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Method: Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning
- Zeynep Kalender Atak,
- Ibrahim Ihsan Taskiran,
- Jonas Demeulemeester,
- Christopher Flerin,
- David Mauduit,
- Liesbeth Minnoye,
- Gert Hulselmans,
- Valerie Christiaens,
- Ghanem-Elias Ghanem,
- Jasper Wouters,
- and Stein Aerts
Genome Res. June 2021 31: 1082-1096; Published in Advance April 8, 2021, doi:10.1101/gr.260851.120
...) or for hundreds of epigenomic features (Zhou and Troyanskaya 2015; Kelley et al. 2016). These models tend to be cell type–specific, resulting in reduced performance when applied to other cell types (Banovich et al. 2018). We have previously shown that specialized deep learning models can outperform generic ones...
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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
...with a given complex trait are expected to be enriched specifically in noncoding regulatory elements of the trait-relevant cell types; for example, T2D-associated genetic variants are enriched in regulatory elements specific to pancreatic islets and beta cells (Parker et al. 2013; Pasquali et al. 2014...
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Resource: Dynamic DNA methylation across diverse human cell lines and tissues
- Katherine E. Varley,
- Jason Gertz,
- Kevin M. Bowling,
- Stephanie L. Parker,
- Timothy E. Reddy,
- Florencia Pauli-Behn,
- Marie K. Cross,
- Brian A. Williams,
- John A. Stamatoyannopoulos,
- Gregory E. Crawford,
- Devin M. Absher,
- Barbara J. Wold,
- and Richard M. Myers
Genome Res. March 2013 23: 555-567; Published in Advance January 16, 2013, doi:10.1101/gr.147942.112
...of genes, and are enriched for cancer-specific EZH2 binding and H3K27me3 (repressive chromatin). In noncancer samples, there are cell-type specific methylation signatures preserved in primary cell lines and tissues as well as methylation differences induced by cell culture. The relationship between...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...in one or more of these canonical gene sets (e.g., a single pathway or ontology term), this is considered a co-occurrence (Fig. 3D). We found significant co-occurrence of GCOD oligogenic gene partners in cell type signature gene sets (OR = 1.5, Fisher's exact test P = 0.00004), canonical pathways (OR = 1...
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Resource: Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types
- Peng Xu and
- Bin Zhang
Genome Res. October 2023 33: 1806-1817; Published in Advance October 31, 2023, doi:10.1101/gr.278063.123
...and the cytosolic iron–sulfur protein assembly component CIAO3 (previously known as NARFL) (Fig. 3F–H). Both 19p13.3 and 16p13.3 were located in euchromatic regions with open chromatin status.We used cell-type marker genes from the single-cell database PanglaoDB to explore whether cell-type marker genes were...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...-cell study in T2D at that time. Using the Smart-seq2 protocol, they generated transcriptional profiles of individual pancreatic endocrine and exocrine cells of healthy and T2D donors and simultaneously defined the transcriptional signatures of both abundant and rare cell types in the pancreas, including...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...between cell types, implying the influence of cell-specific factors in dictating turnover rate. The apparent influence of miRNA regions most important for targeting, together with the effect of one target on miR-7 accumulation, suggest that targets fulfill this role. Analysis of the tailing and trimming...

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