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Full text 2026

An example for potentially underrated causes of recessive disease in the Greater Middle East: integrative long-read genome and transcriptome sequencing pinpoint a deep-intronic homozygous HEXB candidate founder variant in GM2-gangliosidosis

Bolte A, Velmans C, Netzer C, et al.

<h4>Background</h4>Consanguinity provides shortcuts to identify homozygous recessive mutations. However, deep-intronic variants escape standard sequencing (panel; exome/WES), and their pathogenicity cannot be inferred from genomic data. We applied WES, long-read genome and long-read-RNA-sequencing (LR-WGS, LR-RNA-Seq) in …

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Transcriptomics
Full text 2026

Prediction of disease resilience of pigs using multi-omics data

Chen Y, Lonergan S, Lim KS, et al.

<h4>Background</h4>Genomic prediction is widely used in pig breeding, but phenotypic prediction of complex traits such as disease resilience remains limited because genotypes alone do not capture infection-induced regulatory responses, environmental and management effects, or their …

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Transcriptomics
Full text 2026

COBRAxy: constraint-based metabolic modeling in Galaxy

Lapi F, Milazzo L, Lin L, et al.

<h4>Motivation</h4>Metabolic network modeling is essential for understanding metabolic shifts occurring in complex physio-pathological processes. Currently, constraint-based modeling frameworks for metabolic networks primarily rely on Python or MATLAB libraries, requiring some coding skills. In contrast, more …

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Transcriptomics
Full text 2026

Hypergraph representations of single-cell RNA sequencing data for improved cell clustering

He W, Bolnick DI, Scarpino SV, et al.

<h4>Motivation</h4>Single-cell RNA sequencing (scRNA-seq) data analysis is often performed using network projections that produce co-expression networks. These network-based algorithms are attractive because regulatory interactions are fundamentally network-based and there are many tools available for downstream …

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Single-Cell Transcriptomics
Full text 2026

Differentially Expressed Gene Annotator (DEGAn): automated annotation and analysis of DEGs datasets with OS and PFS data

Agapito G, Cannataro M.

<h4>Motivation</h4>High-throughput transcriptomic platforms routinely generate large differentially expressed gene (DEG) datasets, but linking these matrices to clinical outcomes still often requires manual data integration and repeated gene-by-gene survival analyses. This limits scalability, reproducibility, and practical …

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Transcriptomics
Full text 2026

m6A-modified circFOXA1 promotes tumor immune evasion via enhancing PD-L1 deubiquitination in triple-negative breast cancer

Shen H, Li B, Wen X, et al.

Restoring CD8⁺T cell infiltration and potentiating anti-tumor immune responses in the tumor microenvironment (TME) is critical for developing effective immunotherapies against triple-negative breast cancer(TNBC), while the regulatory role of N⁶-methyladenosine (m⁶A)-modified circular RNAs (circRNAs) in …

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Bioinformatics Epigenetics Transcriptomics