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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...these epigenetic features change throughout normal neurodevelopment. Finally, we highlight single-gene neurodevelopmental disorders that illustrate the interdependence of epigenetic features, showing how disruptions in DNA methylation or architecture can ripple across the entire epi. As such, we emphasize...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Lê Cao
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
..., Canberra 2601, Australia; 3Bioinformatics and Cellular Genomics, St Vincent’s Institute, Fitzroy, Victoria 3065, Australia Gene networks provide a fundamental framework for understanding the molecular mechanisms that govern gene expression. Advances in single-cell RNA sequencing (scRNA-seq) have enabled...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...by these priors, PRISM-GRN remains inherently data-driven. It leverages the observed omics data to refine and adjust the regulatory network, allowing for the identification of novel or context-specific interactions that may not be captured by prior knowledge alone. Therefore, we implemented PRISM-GRN on another...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...that jointly interact in trans. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...flexible penalization based on the number of edges found in the network, which aids in the identification of a network structure that improves the discovery of true gene-gene interactions while reducing false positives (Huang et al. 2020). Here, we focus on improving the statistical power of network...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...neurodevelopmental disorders.Over the past two decades, the cost of sequencing the complete of an organism has rapidly declined. Advances in parallel DNA sequencing technologies have enabled the generation of reference s for thousands of biological organisms, across viral, archaeal, bacterial, and eukaryotic species...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...identification to the community discovery problem in a network in which the Infomap algorithm is utilized (for details, see Selection of Community Discovery Algorithms of the Supplemental Materials). Instead of running Infomap on the entire Hi-C contact matrix, we first extract submatrices by a fixed...
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Method: Spatial Cellular Networks from omics data with SpaCeNet
- Stefan Schrod,
- Niklas Lück,
- Robert Lohmayer,
- Stefan Solbrig,
- Dennis Völkl,
- Tina Wipfler,
- Katherine H. Shutta,
- Marouen Ben Guebila,
- Andreas Schäfer,
- Tim Beißbarth,
- Helena U. Zacharias,
- Peter J. Oefner,
- John Quackenbush,
- and Michael Altenbuchinger
Genome Res. September 2024 34: 1371-1383; Published in Advance September 4, 2024, doi:10.1101/gr.279125.124
..., Massachusetts 02115, USA; 5Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; 6Campus Institute Data Science (CIDAS), University of Göttingen, 37077 Göttingen, Germany; 7Peter L. Reichertz Institute for Medical Informatics of TU...
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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
...Chuanyuan Wang and Zhi-Ping Liu Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China Corresponding author: zpliu@sdu.edu.cnAbstractA gene regulatory network (GRN) intricately encodes the interconnectedness of identities...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...antigens and neutralization of authentic measles virus.The immune system is a complex network of cells, tissues, and organs that work together to defend the body against infections and foreign substances. It is broadly categorized into two main components: the innate immune system, which responds quickly...
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