Browse Papers

Search the literature by keyword, topic, or author. Filter to articles with full text available.

Full text All articles Nanopore Basecalling

10297 results

Full text 2026

Adaptive transcriptional remodeling of Streptococcus mutans under simulated microgravity and silver stress reveals evolutionary innovation in artificial environments

Fernander MC, McClure KR, Sanders BT, et al.

Understanding how microorganisms adapt to novel physical and chemical environments requires integrating evolutionary, regulatory, and phenotypic perspectives. Here, we examined Streptococcus mutans populations previously evolved for 100 days under simulated microgravity (sMG) or combined microgravity …

Read PDF

Transcriptomics

Full text 2026

Epithelial-mesenchymal plasticity and immunosuppression in canine carcinomas reveals cross-species upregulation of CD109

Bakhle K, Nelissen S, Li L, et al.

Epithelial-mesenchymal plasticity (EMP) is activated in carcinoma cells to drive metastasis and chemoresistance. Recently, we demonstrated that EMP activation results in an immunosuppressive tumor microenvironment and immunotherapy resistance in a syngeneic orthotopic murine model. However, …

Read PDF

Bioinformatics

Full text 2026

Transgenic hookworm secretes anti-tetrodotoxin human single chain antibody

Singh KS, Bharti S, Rosa BA, et al.

Biologics, protein- and peptide-based drugs derived from living organisms or cell lines have emerged as effective therapies across a broad range of indications. However, parenteral administration and the need for frequent dosing increase costs and …

Read PDF

Bioinformatics

Full text 2026

Dose-dependent hormone actions at estrogen receptor enhancers specify distinct molecular and biological outcomes

Kim HB, Nandu T, Kim YJ, et al.

Adult women are typically exposed to 17β-estradiol (E2) concentrations of ~100 to 200 pM, yet most cell-based studies use 100 nM. We determined the molecular effects of E2 concentrations spanning six orders of magnitude (1 …

Read PDF

Epigenetics

Full text 2026

Single-nucleus profiling reveals a core disease signature and cell type-specific vulnerabilities in early Rett syndrome

Li Y, Anderson AG, Qi G, et al.

Rett syndrome (RTT) is an X-linked neurological disorder caused by MECP2 mutations, creating distinct cellular environments in females (mosaic) versus males (nonmosaic). Despite female patients representing most cases, how mosaicism contributes molecularly to RTT pathogenesis, …

Read PDF

Transcriptomics

Full text 2026

Peroxin Pex8 couples stress responses, antifungal tolerance, and virulence regulation in Candida albicans

Xi B, Wu Y.

Candida albicans, a World Health Organization critical-priority fungal pathogen, represents the predominant cause of candidemia. Therapeutic failure is sometimes driven by antifungal tolerance, a phenotype distinct from resistance, whose underlying mechanisms remain incompletely defined. Here, …

Read PDF

Transcriptomics

Full text 2026

Gene body methylation buffers noise in gene expression in plants

Unknown

No abstract available.

Read PDF

Epigenetics

Full text 2025

ENO1-related gene signature predicts prognosis and therapeutic response in diffuse large B-cell lymphoma

Yan W, Liu X, Gao B, et al.

<h4>Purpose</h4>Alpha-enolase (ENO1), the enzyme catalyzing 2-phosphoglycerate conversion to phosphoenolpyruvate, is highly expressed in diffuse large B-cell lymphoma (DLBCL) and correlates with adverse clinical outcomes. Thus, understanding the relationship between ENO1-related gene (ERG) network and DLBCL …

Read PDF

Transcriptomics

Full text 2026

Single-Cell RNAseq Identifies Heterogeneity in Myoblasts From Older Adults With Differences Related to Muscle Mass and Function

Burton MA, Garratt ES, Sharkh HY, et al.

<h4>Background</h4>Ageing is associated with the loss of muscle mass and function, with consequences for metabolic health, frailty and independence in later life. The aim of this study was to investigate the transcriptional heterogeneity of human …

Read PDF

Transcriptomics

Full text 2025

High-precision cell-type mapping and annotation of single-cell spatial transcriptomics with STAMapper

Shen Q, Dong K, Zhang S, et al.

In this paper, we develop a heterogeneous graph neural network, STAMapper, to transfer the cell-type labels from single-cell RNA-sequencing (scRNA-seq) data to single-cell spatial transcriptomics (scST) data. We collect 81 scST datasets consisting of 344 …

Read PDF

Single-Cell Transcriptomics

Full text 2025

c-Rel drives pancreatic cancer metastasis through fibronectin-integrin signaling-induced isolation stress resistance and EMT

Bakırdöğen D, Görgülü K, Xin J, et al.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with limited treatment options and a high recurrence rate. Recurrence often occurs with metastasis, for which cancer cells must adapt to isolation stress to …

Read PDF

Transcriptomics

Full text 2026

Transcriptomic changes associated with heat-induced susceptibility in wheat plants to Hessian fly (Diptera: Cecidomyiidae)

Zhu L, Maldani M, Subramanyam S, et al.

Wheat (Triticum aestivum L.) resistance to Hessian fly (HF, Mayetiola destructor) conferred by HF resistance (R) genes, is often vulnerable to heat stress. This study aims to investigate the molecular basis of heat-induced susceptibility in …

Read PDF

Transcriptomics

Full text 2026

Transcriptomic response to different heme sources in Trypanosoma cruzi epimastigotes

Tevere E, Mediavilla MG, Di Capua CB, et al.

Heme is an essential molecule for most organisms, yet some parasites, like Trypanosoma cruzi, the causative agent of Chagas disease, cannot synthesize it. These parasites must acquire heme from their hosts, making this process critical …

Read PDF

Transcriptomics

Full text 2026

Single cell RNA transcriptome response to fentanyl use in persons with HIV infection

Roskin KM, Meeds HL, Krishnan JM, et al.

The US is experiencing a major drug epidemic largely attributed to synthetic opioids including fentanyl. We considered how illicit fentanyl use in persons living with HIV impacted gene expression profiles in the peripheral blood. Whole …

Read PDF

Transcriptomics

Full text 2026

Integrated Molecular, Genomic, and Clinical Characterization of Pediatric and Adolescent Translocation Renal Cell Carcinoma: A Report from the Children's Oncology Group

Groenendijk A, Aronow BJ, Cost N, et al.

Background: Translocation morphology renal cell carcinoma (tRCC) accounts for nearly half of all pediatric RCC cases. Biological study AREN14B4-Q aimed to characterize the molecular landscape of tRCC using samples acquired from patients enrolled in the …

Read PDF

Transcriptomics

Full text 2026

Microgravity effects on secondary metabolism of plant-affecting bacteria

Sharma G, Ahmed MMA, Ali T, et al.

Despite their miniscule mass, microgravity has been shown to impose physiological stresses on bacteria, leading to altered gene regulation and metabolic output in unpredictable ways. Changes in metabolic output can ultimately impact the production of …

Read PDF

Transcriptomics

Full text 2025

Elevated synaptic PKA activity and abnormal striatal dopamine signaling in Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder

Song BJ, Ge Y, Nicolella A, et al.

Loss-of-function mutations in AKAP11 (a protein kinase A (PKA)-binding protein) greatly increase the risk of bipolar disorder and schizophrenia. To determine the neurobiological functions of AKAP11, we conduct multi-omic and neurobiological analyses of Akap11 mutant …

Read PDF

Transcriptomics

Full text 2025

Optimized murine sample sizes for RNA sequencing studies revealed from large scale comparative analysis

Halasz G, Schmahl J, Negron N, et al.

Determining the appropriate sample size (N) for bulk RNA sequencing experiments is critical for obtaining reliable results. We show in two N = 30 profiling studies, comparing wild-type mice and mice in which one copy …

Read PDF

Transcriptomics

Full text 2026

Targeting pathogenic Th17.1 cells via JAK-STAT3 pathway: A novel approach with tofacitinib for refractory myasthenia gravis

Zhao R, Yan C, Zhong H, et al.

There remains a critical unmet need for effective, accessible, and well-tolerated therapies for myasthenia gravis (MG) who are refractory to current immunotherapies. The janus kinase and signal transducer and activator of transcription (JAK-STAT) signaling pathway …

Read PDF

Bioinformatics

Full text 2025

RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing

Bouirdene SG, Gotty S, Leclercq M, et al.

RNA sequencing (RNA-seq) is a widely used method in transcriptomics research, offering insights into gene expression, variant discovery, and, when deconvoluted, the cellular composition of complex tissues. However, existing RNA-seq pipelines frequently emphasize gene expression …

Read PDF

Transcriptomics

Browse Papers

Adaptive transcriptional remodeling of <i>Streptococcus mutans</i> under simulated microgravity and silver stress reveals evolutionary innovation in artificial environments

Epithelial-mesenchymal plasticity and immunosuppression in canine carcinomas reveals cross-species upregulation of CD109

Transgenic hookworm secretes anti-tetrodotoxin human single chain antibody

Dose-dependent hormone actions at estrogen receptor enhancers specify distinct molecular and biological outcomes

Single-nucleus profiling reveals a core disease signature and cell type-specific vulnerabilities in early Rett syndrome

Peroxin Pex8 couples stress responses, antifungal tolerance, and virulence regulation in <i>Candida albicans</i>

Gene body methylation buffers noise in gene expression in plants

ENO1-related gene signature predicts prognosis and therapeutic response in diffuse large B-cell lymphoma

Single-Cell RNAseq Identifies Heterogeneity in Myoblasts From Older Adults With Differences Related to Muscle Mass and Function

High-precision cell-type mapping and annotation of single-cell spatial transcriptomics with STAMapper

c-Rel drives pancreatic cancer metastasis through fibronectin-integrin signaling-induced isolation stress resistance and EMT

Transcriptomic changes associated with heat-induced susceptibility in wheat plants to Hessian fly (Diptera: Cecidomyiidae)

Transcriptomic response to different heme sources in <i>Trypanosoma cruzi</i> epimastigotes

Single cell RNA transcriptome response to fentanyl use in persons with HIV infection

Integrated Molecular, Genomic, and Clinical Characterization of Pediatric and Adolescent Translocation Renal Cell Carcinoma: A Report from the Children's Oncology Group

Microgravity effects on secondary metabolism of plant-affecting bacteria

Elevated synaptic PKA activity and abnormal striatal dopamine signaling in Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder

Optimized murine sample sizes for RNA sequencing studies revealed from large scale comparative analysis

Targeting pathogenic Th17.1 cells via JAK-STAT3 pathway: A novel approach with tofacitinib for refractory myasthenia gravis

RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing