Loss of NnT increases expression of oxidative phosphorylation complexes in C57BL/6J hearts by Williams, Jack L., Hall, Charlotte L., Meimaridou, Eirini, Metherell, Louise A.

“…We saw enrichment of oxidative phosphorylation genes in the C57BL/B6J in the heart and adrenal, possibly indicative of an evolved response in this substrain to loss of Nnt. …”
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Leveraging linguistic knowledge to enhance low-resource NLP applications by Zhu, Zixiao

“…Specifically, 1. In the promptless fine-tuning paradigm, we first focus on fine-tuning word embeddings for task-related words, thereby enriching the conceptual knowledge available to compositional neural networks during feature learning in emotion recognition. …”
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Understanding early molecular mechanisms of abnormal myelination in neurological conditions by characterising Ermin deficiency by Oh, Sher Li, Ziaei, Amin, Tan, Liang Juin, Utami, Kagistia Hana, Pouladi, Mahmoud A., Langley, Sarah Raye

“…We studied the transcriptome of Ermin-deficient mice using gene co-expression and differential gene expression analyses to investigate early transcriptional effects of Ermin deficiency across age and sex. …”
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Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study by Lim, Kah Wai, Jenjaroenpun, Piroon, Low, Zhen Jie, Khong, Zi Jian, Ng, Yi Siang, Kuznetsov, Vladimir Andreevich, Phan, Anh Tuan

“…Enrichment analysis of SLQS-positive genes and mapping of SLQS onto transcriptional/mutagenesis hotspots and cancer-associated genes, provided a statistical framework supporting the biological involvements of SLQS. …”
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Systematic assessment of COVID-19 host genetics using whole genome sequencing data by Schmidt, A, Casadei, N, Brand, F, Demidov, G, Vojgani, E, Abolhassani, A, Aldisi, R, Butler-Laporte, G, DeCOI host genetics group, Alawathurage, TM, Augustin, M, Bals, R, Bellinghausen, C, Berger, MM, Bitzer, M, Bode, C, Boos, J, Brenner, T, Cornely, OA, Eggermann, T, Erber, J, Feldt, T, Fuchsberger, C, Gagneur, J

“…We did not observe any suggestive causal variants in or around the established risk gene TLR7. Burden testing in the largest population subgroup (i.e., Europeans) suggested nominal enrichments of rare variants in coding and non-coding regions of interferon immune response genes in the overall analysis and male subgroup. …”

Development of immunomodulatory RNA therapeutics for immune disorders by Iyer, Vaishnavi Srinivasan

“…We describe the RCC (rapid CRISPR competitive) assay, where we exploit the heterogeneity of the CRISPR-Cas9 mediated genome editing together with sanger sequencing to study the role of the target gene based on both the enrichment or depletion of mutated sequences but also the type of mutation (frameshift or silent mutations). …”
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Molecular characterization of Bacillus, lactic acid bacteria and yeast as potential probiotic isolated from fermented food by Cissé, Hama, Kagambèga, Boureima, Sawadogo, Adama, Tankoano, Abel, Sangaré, Gaston, Traoré, Yves, Ouoba, Irene, Savadogo, Aly

“…These microorganisms are responsible for the fermentation of food through their enzymatic activity, leading to production of fermented food with desirable organoleptic characteristics, improved food safety, the enrichment of nutrients and the promotion of health of consumers.…”
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Immune checkpoint blockade sensitivity and progression-free survival associates with baseline CD8+ T cell clone size and cytotoxicity by Watson, RA, Tong, O, Cooper, R, Taylor, CA, Sharma, PK, de Los Aires, AV, Mahé, EA, Ruffieux, H, Nassiri, I, Middleton, MR, Fairfax, BP

“…At the level of CD8⁺ T cell clonotypes, we found a relationship between transcriptional changes and clone size, with large clones showing a greater number of differentially regulated genes enriched for pathways including T cell receptor (TCR) signaling. …”

DNA-Methylation Patterns in Trisomy 21 Using Cells from Monozygotic Twins by Sailani, M. Reza, Santoni, Federico A., Letourneau, Audrey, Borel, Christelle, Makrythanasis, Periklis, Hibaoui, Youssef, Popadin, Konstantin, Bonilla, Ximena, Guipponi, Michel, Gehrig, Corinne, Vannier, Anne, Carre-Pigeon, Frederique, Feki, Anis, Nizetic, Dean, Antonarakis, Stylianos E.

“…The identified DMRs are enriched for genes involved in embryonic organ morphogenesis (FDR = 1.60 e -03) and include genes of the HOXB and HOXD clusters. …”
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Genome-wide mapping of Hif-1α binding sites in zebrafish by Greenald, David, Jeyakani, Justin, Pelster, Bernd, Sealy, Ian, Mathavan, Sinnakaruppan, van Eeden, Fredericus J.

“…Results: We performed high-density oligonucleotide microarray analysis of the gene expression changes in von Hippel-Lindau mutant zebrafish, which identified up-regulation of well-known hypoxia response genes and down-regulation of genes primarily involved in lipid processing. …”
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Regulation of mRNA abundance by polypyrimidine tract-binding protein-controlled alternate 5′ splice site choice by Hamid, Fursham M., Makeyev, Eugene V.

“…Consistent with this mechanism, u5′ss is intrinsically weaker than d5′ss, with a similar tendency observed for other genes with Ptbp1-induced u5′ss bias. Interestingly, the brain-enriched Ptbp1 paralog Ptbp2/nPTB/brPTB stimulated the u5′ss utilization but with a considerably lower efficiency than Ptbp1. …”
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Uncertainty & robustness for single-cell studies by Shiffman, Miriam

“…We develop an accurate and efficient approximation to estimate this dropping-data robustness metric for the key outcomes of differential expression, for independent observation and pseudobulk analyses. Broadening these gene-level results to a high-level, biologically meaningful summary, we overcome the inherently non-differentiable and combinatorial nature of gene set enrichment analysis to provide an additional approximation for the dropping-data robustness of top gene sets. …”
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Elucidating the genomic and transcriptomic profiles contributing to the overall survival of acute myeloid leukaemia patients with normal karyotype in Malaysia by Ambayya @ Ampiah, A Angeli

“…The transcriptome sequencing yielded discoveries of differentially expressed genes (DEGs) profiles and functionally enriched pathways in several subgroup analyses as follows: AML-NK patients with the healthy normal groups (5126 DEGs), paired DX and CR1 (5621 DEGs), FLT3/NPM1 genotypes (750 DEGs), and OS of below and above five years (211 DEGs). …”
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Molecular determinants of chromatin accessibility at CpG islands in mouse embryonic stem cells by King, H

“…The accessibility of DNA sequences to such <em>trans</em>-acting factors is an important feature of gene regulatory elements, including promoters. In vertebrates, the majority of gene promoters coincide with CpG islands (CGIs), which remain free from DNA methylation and exhibit elevated CpG densities. …”

Glycosylphosphatidylinositol-specific, CD1d-restricted T cells in paroxysmal nocturnal hemoglobinuria by Gargiulo, L, Papaioannou, M, Sica, M, Talini, G, Chaidos, A, Richichi, B, Nikolaev, AV, Nativi, C, Layton, M, de la Fuente, J, Roberts, I, Luzzatto, L, Notaro, R, Karadimitris, A

“…Thus, a novel, autoreactive, CD1d-restricted, GPI-specific T-cell population, enriched in an invariant TCRα chain, is expanded in PNH patients and may be responsible for BMF in PNH.…”

Investigating the role of CDK1 in governing the transcriptional landscape in cancer cells by Pluta, AJ

“…The regulation of these genes by 1-NM-PP1 was then tested in the new cell lines, and through the use of other CDK1 inhibitors. …”

Low magnetic field exposure alters prostate cancer cell properties by Lange, Sigrun, Inal, Jameel, Kraev, Igor, Dart, Dafydd Alwyn, Uysal-Onganer, Pinar

“…This study investigated the effects of LMF exposure (20 nT) by magnetic shielding on the prostate cancer cell line PC3 compared to the prostate epithelial cell line PNT2 under short-term (4 h) conditions. …”
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Nuclei sorting-based genome-wide CRISPR screens to identify novel regulators of hepatic insulin signalling by Martin Perez, E

“…Amongst the top differentially enriched genes were binding partners TMED2 and TMED10. …”

Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging by Jakobsen, NA, Turkalj, S, Zeng, AGX, Stoilova, B, Metzner, M, Rahmig, S, Nagree, MS, Shah, S, Moore, R, Usukhbayar, B, Angulo Salazar, M, Gafencu, G-A, Kennedy, A, Newman, S, Kendrick, BJL, Taylor, AH, Afinowi-Luitz, R, Gundle, R, Watkins, B, Wheway, K, Beazley, D, Murison, A, Aguilar-Navarro, AG, Flores-Figueroa, E, Dakin, SG, Carr, AJ, Nerlov, C, Dick, JE, Xie, SZ, Vyas, P

“…Clonal hematopoiesis (CH) arises when hematopoietic stem cells (HSCs) acquire mutations, most frequently in the DNMT3A and TET2 genes, conferring a competitive advantage through mechanisms that remain unclear. …”

Understanding tumor cell plasticity in spatial transcriptomics with graph attention networks and walk-based pseudotime analysis by Zamora, Izabella

“…By estimating a differentiation path from epithelial to mesenchymal-like cells, we can identify intermediate states despite a limited set of tumor marker genes. This cellular differentiation path shows enrichment and depletion of certain cell types within local neighborhoods aligning with known correlations, and by leveraging inferred ligand-receptor interactions, we can pinpoint potential drivers of plasticity to test in vitro. …”
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