Genome research

01 16 October 2026

DOI 10.1101/gr.281897.126

Conditional diffusion for single-cell Hi-C data imputation and enhancement with scHiC-Diff

Open DOI

Wuhao Liu, Zhaoyu Fang, Xuyan Du et al.

Single-cell high-throughput chromosome conformation capture (scHi-C) enables the analysis of cell-to-cell variability in three-dimensional (3D) genome organization, but its utility is severely limited by pervasive technical dropouts, lea...

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02 16 October 2026

DOI 10.1101/gr.281820.125

Glucocorticoid regulation of the human noncoding genome

Open DOI

Thai Tran, Robert Kwiat, Qilin Cao et al.

Glucocorticoids (GCs) are widely used anti-inflammatory and immunosuppressive agents known to induce substantial changes in gene expression, yet their effects on noncoding RNAs such as long noncoding RNAs (lncRNAs) or microRNAs (miRNAs) ...

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03 16 October 2026

DOI 10.1101/gr.282034.126

Pangenome and transcriptomics reveal the genomic basis associated with interspecific variation of sexually dimorphic nuptial spines in moustache toads

Open DOI

Jun Li, Yan Feng, Shaodi Huang et al.

Sexual dimorphism is a widespread phenotypic innovation that plays a crucial role in species diversification, yet its genetic origins and evolutionary trajectories remain poorly understood in vertebrates. Leptobrachium provides a tractab...

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04 16 October 2026

DOI 10.1101/gr.282119.126

Liver X receptors participate in the fasting response by assisting CEBPB binding to enhancers and promoting the fasting transcriptional program

Open DOI

Tali Gorbonos, Maria C Romero Florian, Hadar Shalev et al.

Upon fasting, a group of transcription factors (TFs) activates an extensive transcriptional program in the liver to alter hepatocyte metabolism and cope with fasting. This is achieved by TF-mediated activation of enhancers, which become ...

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05 13 October 2026

DOI 10.1101/gr.281732.125

The divergent 3D genome landscapes of aging and neurodegenerative mouse models

Open DOI

Ekaterina Kashuk, Dmitrii Smirnov, Ekaterina Eremenko et al.

Chromatin structure is essential for gene regulation and genome stability, as neurons must preserve their 3D genome organization throughout life. This structure gradually deteriorates with aging and is further disrupted in neurodegenerat...

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06 13 October 2026

DOI 10.1101/gr.281770.125

Reconstruction of contact signals from repeated elements with Hicberg

Open DOI

Sébastien Gradit, Samuel Ortion, Pauline Larrous et al.

Throughout evolution, genomes have acquired various repetitive elements, such as transposons, ribosomal DNA, duplicated genes, and tandem repeats. These sequences pose significant challenges to current high-throughput sequencing pipeline...

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07 13 October 2026

DOI 10.1101/gr.282338.126

Identity-by-descent captures shared environmental factors at biobank scale

Open DOI

Franco Marsico, Silvia Buonaiuto, Ernestine K. Amos-Abanyie et al.

Genealogical ties leave traces beyond shared genetic material: relatives tend to share environmental exposures and cultural practices that persist across generations. Here, using genomic and electronic health record data from 13,143 indi...

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08 13 October 2026

DOI 10.1101/gr.281969.126

Parental genome reprogramming drives allelic convergence while preserving parent-of-origin memory during human early embryonic development

Open DOI

Fanqing Xu, Qian Liu, Zhengrong Du et al.

Human sperm and oocytes carry highly distinct DNA methylation landscapes, yet parental DNA methylation ultimately converges to a largely equivalent state, raising the question of when and how the allelic DNA methylome is reprogrammed tow...

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09 9 October 2026

DOI 10.1101/gr.281292.125

Single-cell transcriptome analysis reveals onco-fetal reprogramming with implications for drug resistance and clinical outcome

Open DOI

Yongle Xu, Shaoyi Chen, Zhenglin Lu et al.

Onco-fetal reprogramming of the tumor ecosystem induces fetal-like characteristics, leading to tumor growth and malignant progression. Here, we develop a robust computational pipeline to systematically identify onco-fetal (OF) cells, usi...

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10 9 October 2026

DOI 10.1101/gr.281566.125

Protein large language model–assisted one-to-one gene homology mapping in cross-species single-cell transcriptome integration

Open DOI

Ze-Yu Kuang, Yuan-Chen Sun, Na-Na Wei et al.

Cross-species integration of single-cell transcriptomes requires establishing gene correspondences to enable comparative analysis of expression profiles across organisms. Current approaches predominantly rely on Ensembl homology tables; ...

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