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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...category, and the user has the option to explore the full set of G4s for each with additional annotations.Quadrupia offers experimental validation for the G4 sequences of selected s in three forms: (1) genomic coordinate matches to experimentally validated G4 sequences, as described in the study by Marsico...
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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
...a lot of attention owing to their critical role in tumor metastasis. Around 40% to 80% of patients with metastatic breast cancers have been found to have CTCs in their blood (Kwa and Esteva 2018). The detection and characterization of CTCs obtained from patient blood offer clinically relevant insights...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...of high-dimensional RNA structures in determining sequencing efficiency and their impact on data quality. Our findings offer valuable insights into the underlying mechanisms of RNA structure–mediated sequencing bias. This deeper understanding enables more accurate and reliable RNA-seq analyses...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...with CRISPR for targeted sequencing and expanding direct RNA-seq technologies will offer deeper insights into genomic and transcriptomic complexities. The integration of long-read sequencing into clinical diagnostics represents a crucial frontier, with several sequencing centers beginning to validate...
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Method: Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
- Vishvak Raghavan,
- Yumin Zheng,
- Yue Li,
- and Jun Ding
Genome Res. July 2025 35: 1646-1663; Published in Advance May 2, 2025, doi:10.1101/gr.279771.124
.... This makes them insensitive in complex environments where the detailed dynamics of cell interactions matter. We introduce CellAgentChat, an agent-based model (ABM) designed to decipher CCIs from single-cell RNA sequencing and spatial transcriptomics data. This approach models biological systems...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...Corresponding authors: mjliu@gate.sinica.edu.tw, tingying@gate.sinica.edu.twAbstractmRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling...
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Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...offers new insights for analyzing ageing effect with spatial transcriptomics.31 Keywords: Spatial Transcriptomics, Foundation Model, Data Denoising, Data32 Imputation, Survival Analysis, Ageing33 Introduction34 Spatially-resolved transcriptomic (SRT) technologies have enabled the investigation of35...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...Vittad. (Murat et al. 2018a), which have been sequenced with a combination of Pacific Biosciences (PacBio) RSII and Illumina short reads. To overcome these limitations and elucidate the impact of transposons bursts in Tuberaceae genomic architecture, we generated a high-quality assembly of the critically...
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Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
- Lin Li,
- Xianbin Su,
- and Ze-Guang Han
Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
..., the development of spatial transcriptomics (ST) technologies has enabled the depiction of spatial coregulation patterns of gene programs within a specific tissue (Rao et al. 2021; Moses and Pachter 2022; Walker et al. 2022). However, current computational methods for systematically deciphering gene programs...
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Method: Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics
- Zhen Li,
- Xiaoyang Chen,
- Xuegong Zhang,
- Rui Jiang,
- and Shengquan Chen
Genome Res. October 2023 33: 1757-1773; Published in Advance October 30, 2023, doi:10.1101/gr.277891.123
...discoveries in different areas of biological research (Crosetto et al. 2015; Dries et al. 2021; Larsson et al. 2021; Zhuang 2021; Moses and Pachter 2022). Advanced spatial transcriptomic (ST) techniques, including Visium (10x Genomics), Slide-seq (Rodriques et al. 2019), and Stereo-seq (Chen et al. 2022a...
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