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Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
- Dachang Dang,
- Shao-Wu Zhang,
- Ran Duan,
- and Shihua Zhang
Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
...characterize the locations of TAD boundaries and reflect their biological significance and cell type specificity.View larger version: In this window In a new window Figure 4. Comparison of TAD boundaries across different cell lines. (A) Hi-C contact maps and the corresponding TAD separation landscapes...
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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
...whether network modules were enriched for specific chromosome locations that are influenced by chromatin states. The Giemsa banding technique stains euchromatic and heterochromatic regions with different GC contents, which generates a map of chromosome cytobands (Verma and Rees 1974). Thus, we used...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...gene regulatory networks.In fact, the storage and passage of interactome information in genomic structure can be crucial for tissue specificity and stability of the regulatory networks. It is known that the tissue/cell-specific PPIs play essential roles in the functional organization of regulatory...
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Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
...18 showed relatively higher expression levels in cells specific to clusters 1, 2, and 3 (Supplemental Fig. S5B–E).Expression-based CNV inferenceDuplications and deletions that result in the addition or loss of significant chromosomal regions are referred to as CNVs. As proven by The Cancer Genome...
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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
..., Cummings Life Science Center, Chicago, IL 60637, USA Corresponding author: watersto@uw.eduAbstractRecently developed single-cell technologies allow researchers to characterize cell states at ever greater resolution and scale. Caenorhabditis elegans is a particularly tractable system for studying...
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Research: Transcription factor activity and nucleosome organization in mitosis
- Nicola Festuccia,
- Nick Owens,
- Thaleia Papadopoulou,
- Inma Gonzalez,
- Alexandra Tachtsidi,
- Sandrine Vandoermel-Pournin,
- Elena Gallego,
- Nancy Gutierrez,
- Agnès Dubois,
- Michel Cohen-Tannoudji,
- and Pablo Navarro
Genome Res. February 2019 29: 250-260; Published in Advance January 17, 2019, doi:10.1101/gr.243048.118
...by microscopy reflects the sum of site-specific interactions remains to be demonstrated. Diverse modes of binding, other than those involving base-specific interactions, may be responsible for the global decoration of the chromosomes by TFs, as we proposed earlier (Festuccia et al. 2017) and was clearly...
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Research: Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
- Anushka Gupta,
- Farnaz Shamsi,
- Nicolas Altemose,
- Gabriel F. Dorlhiac,
- Aaron M. Cypess,
- Andrew P. White,
- Nir Yosef,
- Mary Elizabeth Patti,
- Yu-Hua Tseng,
- and Aaron Streets
Genome Res. February 2022 32: 242-257; Published in Advance January 18, 2022, doi:10.1101/gr.275509.121
...RNA-seq for the characterization of cellular diversity in the adipose tissue.Adipose tissue is a complex, heterogenous organ responsible for maintaining energy balance in animals by storing energy during nutritional excess and providing energy during nutritional deprivation. This regulation of whole-body energy homeostasis...
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Research: Speciation network in Laurasiatheria: retrophylogenomic signals
- Liliya Doronina,
- Gennady Churakov,
- Andrej Kuritzin,
- Jingjing Shi,
- Robert Baertsch,
- Hiram Clawson,
- and Jürgen Schmitz
Genome Res. June 2017 27: 997-1003; Published in Advance March 15, 2017, doi:10.1101/gr.210948.116
.... (2002) is presented at the root of the “tree.” Laurasiatherian retrophylogenomic network Genome Research 999 www..org An analysis of the chromosomal distribution of retrotransposonmarkers did not reveal any “phylogenetic” clusters of retroelement locations in the derived ideogram, showing that markers...
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Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
- Etienne Routhier,
- Edgard Pierre,
- Ghazaleh Khodabandelou,
- and Julien Mozziconacci
Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
...by interpreting the DNA sequence. The application of deep neural networks to genomics is growing at a high pace, and it can now be considered as a state of the art computational approach to predict genomics annotations (Quang et al. 2015; Kelley et al. 2016, 2018; Kim et al. 2016; Min et al. 2016; Jones et al...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...epigenomic change in mammalian sperm methylomes and point to a divergence in trans-epigenetic mechanisms that govern the organization of epigenetic states at gene promoters.Mammalian DNA methylation is an epigenetic modification that occurs primarily on cytosines in the context of CpG dinucleotide and has...

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