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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
..., Worcester, Massachusetts 01605, USA; 2Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; 3Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; 4Departments of Cell Biology and Pathology, Harvard Medical School...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...topic modeling, which reveals context-specific gene regulation linked to dynamic cellular processes and environmental responses, offering a deeper understanding of how gene regulation is modulated in the brain. These findings underscore the importance of genotype-environment interactions in genetic...
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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
.... However, analyses are generally restricted to one insect species and/or one or a few xenobiotic gene families (XGFs). We examine evidence for TE accumulation at XGFs by performing a comparative genomic analysis across 20 aphid s, considering major subsets of XGFs involved in metabolic resistance...
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Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
....aerts@med.kuleuven.be Abstract Transcription factors regulate their target genes by binding to regulatory regions in the genome. Although the binding preferences of TP53 are known, it remains unclear what distinguishes functional enhancers from nonfunctional binding. In addition, the genome is scattered with recognition...
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Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
- Yingxin Lin,
- Tung-Yu Wu,
- Xi Chen,
- Sheng Wan,
- Brian Chao,
- Jingxue Xin,
- Jean Y.H. Yang,
- Wing H. Wong,
- and Y.X. Rachel Wang
Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
.... However, this comes with the drawback that the relationships between the measured features (e.g., genes) and cellular phenotypes in trained models become more difficult to interpret. Although alternative architectures have been proposed involving linearizing part of the neural network (Svensson et al...
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Method: Dissecting and improving gene regulatory network inference using single-cell transcriptome data
- Lingfeng Xue,
- Yan Wu,
- and Yihan Lin
Genome Res. September 2023 33: 1609-1621; Published in Advance August 14, 2023, doi:10.1101/gr.277488.122
...inference using scRNA-seq data, that is, the challenge to accurately infer gene regulatory relationships from gene expression data only.To better understand this challenge, it would be helpful to closely examine gene regulation, and revisit the rationale underlying GRN inference using scRNA-seq data. During...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
...patients. The mutational status of commonly altered PDAC genes and PDAC subtype for each TCGA patient was highlighted (The Cancer Genome Atlas Research Network 2017).Survival analysisWe first fit a complex clinical model including diagnosis age, stage, grade, residual tumor...
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Method: Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus
- Bharat Panwar,
- Benjamin J. Schmiedel,
- Shu Liang,
- Brandie White,
- Enrique Rodriguez,
- Kenneth Kalunian,
- Andrew J. McKnight,
- Rachel Soloff,
- Gregory Seumois,
- Pandurangan Vijayanand,
- and Ferhat Ay
Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
...of different cell types, we here analyze six major circulating immune cell types from SLE patient blood. Our results show that presence of an interferon response signature stratifies patients into two distinct groups (IFNneg vs. IFNpos). Comparing these two groups using differential gene expression...
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12 Drosophila Genomes/Letter: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- Michael F. Lin,
- Joseph W. Carlson,
- Madeline A. Crosby,
- Beverley B. Matthews,
- Charles Yu,
- Soo Park,
- Kenneth H. Wan,
- Andrew J. Schroeder,
- L. Sian Gramates,
- Susan E. St. Pierre,
- Margaret Roark,
- Kenneth L. Wiley, Jr.,
- Rob J. Kulathinal,
- Peili Zhang,
- Kyl V. Myrick,
- Jerry V. Antone,
- Susan E. Celniker,
- William M. Gelbart,
- and Manolis Kellis
Genome Res. December 2007 17: 1823-1836; Published in Advance November 7, 2007, doi:10.1101/gr.6679507
...of comparative genomics to enhance our understanding of organization, even in a model organism as intensively studied as Drosophila melanogaster . The compilation of a complete and accurate catalog of all protein-coding genes is a critical step in fully understanding the functional elements in any...
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Method: Single-cell-level spatial gene expression in the embryonic neural differentiation niche
- Yi Huang,
- Xiaoming Yu,
- Na Sun,
- Nan Qiao,
- Yaqiang Cao,
- Jerome D. Boyd-Kirkup,
- Qin Shen,
- and Jing-Dong J. Han
Genome Res. April 2015 25: 570-581; Published in Advance January 9, 2015, doi:10.1101/gr.181966.114
...Single-cell-level spatial gene expression in the embryonic neural differentiation niche Yi Huang 1 , 2 , Xiaoming Yu 1 , 3 , Na Sun 1 , Nan Qiao 1 , Yaqiang Cao 1 , 2 , Jerome D. Boyd-Kirkup 1 , Qin Shen 4 , 5...

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