YAP1 as a Novel Negative Biomarker of Immune Checkpoint Inhibitors for EGFR-Mutant Non-Small-Cell Lung Cancer by Ling-Chen Li, Xie-Wan Chen, Ling Fang, Chun-Li Jian, Yong-Xin Yu, Xing-Yun Liao, Jian-Guo Sun

“…All the clinical data of NSCLC were downloaded from Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) for GSE11969 and GSE72094. …”
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Epigenetic Alterations and an Increased Frequency of Micronuclei in Women with Fibromyalgia by Victoria Menzies, Debra E. Lyon, Kellie J. Archer, Qing Zhou, Jenni Brumelle, Kimberly H. Jones, G. Gao, Timothy P. York, Colleen Jackson-Cook

“…To determine if acquired epigenetic/genetic changes are associated with FM, we compared the frequency of spontaneously occurring micronuclei (MN) and genome-wide methylation patterns in women with FM (n=10) to those seen in comparably aged healthy controls (n=42 (MN); n=8 (methylation)). …”
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An increased proportion of transgenic plants in the progeny of rapeseed (<i>Brassica napus</i> L.) transformants by G. N. Raldugina, T. Z. Hoang, H. B. Ngoc, I. V. Karpichev

“…We also found that in individual transformants gfp is randomly inherited throughout the central peduncle; its presence in the genome of seedlings does not depend on the location of the pod. …”
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Integrated bioinformatics and experimental analysis of CHAF1B as a novel biomarker and immunotherapy target in LUAD by Wei Du, Xiao-Wei Wu, Qing-Feng Li, Bing-Yu Zhang, Jing Wu, Ya-Ping Xu, Xue Yi

“…Here, CHAF1B expression in LUAD was examined using the GEPIA2 and UALCAN databases. Using The Cancer Genome Atlas (TCGA) LUAD database, we analyzed the diagnostic and prognostic significance of CHAF1B and its association with immune infiltration and immunological checkpoints. …”
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Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions. by Karen Campos-León, Jack Ferguson, Thomas Günther, C David Wood, Steven W Wingett, Selin Pekel, Christy S Varghese, Leanne S Jones, Joanne D Stockton, Csilla Várnai, Michelle J West, Andrew Beggs, Adam Grundhoff, Boris Noyvert, Sally Roberts, Joanna L Parish

“…Analysis of CTCF binding in the host cell genome by ChIP-Seq revealed that while the total number of CTCF binding sites is not altered by the virus, there are a sub-set of CTCF binding sites that are either enriched or depleted of CTCF. …”
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SLC25A38 is required for mitochondrial pyridoxal 5’-phosphate (PLP) accumulation by Izabella A. Pena, Jeffrey S. Shi, Sarah M. Chang, Jason Yang, Samuel Block, Charles H. Adelmann, Heather R. Keys, Preston Ge, Shveta Bathla, Isabella H. Witham, Grzegorz Sienski, Angus C. Nairn, David M. Sabatini, Caroline A. Lewis, Nora Kory, Matthew G. Vander Heiden, Myriam Heiman

“…In this study, we used a genome-wide CRISPR interference screen in erythroleukemia cells and organellar metabolomics to identify the mitochondrial inner membrane protein SLC25A38 as a regulator of mitochondrial pyridoxal 5’-phosphate. …”
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Establishment and characterization of ovarian clear cell carcinoma patient-derived xenografts by Joseph J. Caumanns, Shang Li, Gert J. Meersma, Evelien W. Duiker, Ate G. J. van der Zee, G. Bea A. Wisman, Steven de Jong

“…SNP array and Infinium MethylationEPIC BeadChip array data analysis demonstrated the copy number alterations and DNA methylation signatures of genome-wide and tumor-driver genes in PDXs generally resembled their patients’ tumors. …”
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Enhanced Tolerance to Antifungals as a General Feature of Rho⁻ Mutants in Yeast Species: Implications to Positive Selection of Respiratory Deficiency by Zachary Johnson, Farhan Nadim, Mikhajlo K. Zubko

“…Although the mitochondrial genome is an attribute of all eukaryotes, some yeast species (called petite-positive) can replicate without mitochondrial DNA (mtDNA). …”
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High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes by Meilee Ling, Judit Szarvas, Vaida Kurmauskaitė, Vaidotas Kiseliovas, Rapolas Žilionis, Rapolas Žilionis, Baptiste Avot, Baptiste Avot, Patrick Munk, Frank M. Aarestrup

“…Our method involves extracting and amplifying single bacterial DNA within individual SPCs, followed by combinatorial split-and-pool single-amplified genome (SAG) barcoding and short-read sequencing. …”
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Plant genetic resources in India: management and utilization by K. Singh, K. Gupta, V. Tyagi, S. Rajkumar

“…Presently, our focus is on characterization of ex situ conserved germplasm and detailed evaluation of prioritized crops for enhanced utilization; assessment of impact of on-farm conservation practices on genetic diversity; genome-wide association mapping for identification of novel genes and alleles for enhanced utilization of PGR; identification and deployment of germplasm/landraces using climate analog data; validation of trait-specific introduced germplasm for enhanced utilization.…”
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Association Analysis of NALCN Polymorphisms rs1338041 and rs61973742 in a Chinese Population with Isolated Cervical Dystonia by Qingqing Zhou, Jing Yang, Bei Cao, Yongping Chen, Qianqian Wei, Ruwei Ou, Wei Song, Bi Zhao, Ying Wu, Huifang Shang

“…Background. A genome-wide association study (GWAS) demonstrated a possible association between cervical dystonia (CD) and a sodium leak channel, nonselective (NALCN) gene. …”
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Archival and Newly Isolated Historical <i>Bacillus anthracis</i> Strains Populate the Deeper Phylogeny of the A.Br.075(Sterne) Clade by Markus Antwerpen, Peter Braun, Wolfgang Beyer, Dirk Aldenkortt, Michael Seidel, Gregor Grass

“…The A.Br.075 (A-branch) clade (also known as A.Br.Sterne) is prominent not only because it comprises several outbreak strains but even more so because spore preparations of its namesake, the Sterne strain, are counted among the most utilized anthrax animal vaccines. In this study, we genome-sequenced and analyzed 56 additional <i>B. anthracis</i> isolates of the A.Br.075 clade. …”
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Virulence is not directly related to strain success in planta in Clavibacter nebraskensis by Molly Veregge, Cory D. Hirsch, Matthew J. Moscou, Liana Burghardt, Peter Tiffin, Devanshi Khokhani

“…Here, we used phenotypic assays and a high-throughput whole-genome sequencing approach to explore among-strain variation in virulence and multistrain reproductive success in planta. …”
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Mendelian randomization analysis of the causal relationship between trimethylamine N-oxide and its precursors and Parkinson’s disease by Bei Zhang, Ruijie Zhang, Huiming Ren, Qiongfeng Guan, Weinv Fan, Liyuan Han

“…Material and methods We aggregated data from three genome-wide association studies (International Parkinson’s Disease Genomics Consortium, Parkinson’s Research: The Organized Genetics Initiative and GenePD, and FinnGen) to extract single-nucleotide polymorphisms (SNPs) associated with circulating concentrations of TMAO, choline, carnitine, and betaine. …”
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Feature Selection in Cancer Classification: Utilizing Explainable Artificial Intelligence to Uncover Influential Genes in Machine Learning Models by Matheus Dalmolin, Karolayne S. Azevedo, Luísa C. de Souza, Caroline B. de Farias, Martina Lichtenfels, Marcelo A. C. Fernandes

“…Gene expression data from RNA-seq, extracted from The Cancer Genome Atlas (TCGA), were used to train ML models, including decision trees (DTs), random forest (RF), and XGBoost (XGB), which achieved accuracies of 98.69%, 99.82%, and 99.37%, respectively. …”
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A Mendelian randomization study: physical activities and chronic kidney disease by Rui Xiao, Li Dong, Bo Xie, Beizhong Liu

“…Our study examined the potential bidirectional relationship between physical activity and CKD by using a genetically informed method. Genome-wide association studies from the UK Biobank baseline data were used for physical activity phenotypes and included 460,376 participants. …”
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Seedling resistance of winter and spring bread wheat cultivars to <i>Pyrenophora tritici-repentis</i> by N. V. Mironenko, N. M. Kovalenko, O. A. Baranova, A. G. Khakimova, O. P. Mitrofanova

“…The disclosed diversity of bread wheat cultivars in their responses to the infection with isolates of different Ptr populations may be due to their differences in the alleles of Ptr resistance/susceptibility genes as well as the presence of still unknown effector genes in the pathogen’s genome. Cultivars resistant to two or three Ptr populations can be used by breeders as sources of seedling resistance.…”
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Integration of Mendelian Randomization to explore the genetic influences of pediatric sepsis: a focus on RGL4, ATP9A, MAP3K7CL, and DDX11L2 by Liuzhao Zhang, Quanwang Chu, Shuyue Jiang, Bo Shao

“…MR analysis utilized genome-wide significant SNPs as instrumental variables to assess causal relationships between gene expression and sepsis risk. …”
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CHST1 as a prognostic-related biomarker in gastric cancer correlating with immune infiltration by Long Gui, Jin-hao Yu, Jia-nan Tan, Guang-yu Zhong, Yong-xue Wang, Lin Zhong, Jiao-jiao Su, Dong Hou, Bin Yang, Fang-hai Han, Sheng-ning Zhou

“…In this study, we obtained the transcriptional profile and corresponding clinical information of CHST1 in gastric cancer (GC) tissues and normal tissues from The Cancer Genome Atlas database. Our functional experiments have demonstrated that CHST1 enhances the proliferation and metastasis of GC cells, both in vitro and in vivo. …”
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Writers, readers, and erasers of N6-Methyladenosine (m6A) methylomes in oilseed rape: identification, molecular evolution, and expression profiling by Chaofan Shan, Kui Dong, Dongyu Wen, Ziyi Ye, Fei Hu, Meryem Zekraoui, Jun Cao

“…During the course of evolution, whole genome duplication (WGD) and segmental duplication were the primary drivers of the expansion of m6A-related gene families. …”
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