The Transcriptional Signature of Active Tuberculosis Reflects Symptom Status in Extra-Pulmonary and Pulmonary Tuberculosis. by Simon Blankley, Christine M Graham, Jacob Turner, Matthew P R Berry, Chloe I Bloom, Zhaohui Xu, Virginia Pascual, Jacques Banchereau, Damien Chaussabel, Ronan Breen, George Santis, Derek M Blankenship, Marc Lipman, Anne O'Garra

“…<h4>Conclusions</h4>The transcriptional signature in extra-pulmonary TB demonstrated heterogeneity of gene expression reflective of symptom status, while the signature of pulmonary TB was distinct, based on a higher proportion of symptomatic individuals. …”
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Comparing statistical learning methods for complex trait prediction from gene expression. by Noah Klimkowski Arango, Fabio Morgante

“…For example, methods performing variable selection achieved higher prediction accuracy for starvation resistance in females, while they generally had lower accuracy for startle response in both sexes. …”
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Impact of β-defensin 103 (DEFB103) copy number variation on bull sperm parameters and post-insemination uterine gene expression. by Ozge Sidekli, Edward J Hollox, Sean Fair, Kieran G Meade

“…Sperm from low CN bulls exhibited higher binding to the oviductal epithelium, while high CN increased sperm membrane fluidity in vitro (p < 0.05). …”
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Impact of developmental state, p53 status, and interferon signaling on glioblastoma cell response to radiation and temozolomide treatment. by Artem Berezovsky, Oluwademilade Nuga, Indrani Datta, Kimberly Bergman, Thais Sabedot, Katherine Gurdziel, Susan Irtenkauf, Laura Hasselbach, Yuling Meng, Claudius Mueller, Emanuel F Petricoin, Stephen Brown, Neeraja Purandare, Sidhesh Aras, Tom Mikkelsen, Laila Poisson, Houtan Noushmehr, Douglas Ruden, Ana C deCarvalho

“…Differentiated CSC progenies retained the expression of key stemness genes and survival pathways, while activating the BMP-Smad signaling pathway and upregulating extracellular matrix components. …”
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Mitochondrial SLC25A10 promotes prostate cancer progression by inhibiting ferritinophagy by Guopeng Yu, Kailei Chen, Bin Xu, Qi Cao

“…Functional gain- and loss-of-function experiments demonstrated that SLC25A10 promotes tumor cell proliferation, migration, and invasion, while exacerbating mitochondrial dysfunction and impairing autophagic flux. …”
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Changes in phytohormone levels and gene expression of potato plants in response to potato virus Y and a nonvector insect by GE Yang, ZHONG Jian, ZHANG Yadong, HE Xiaoli, LIU Lining, Asim MUNAWAR, MAO Lijuan, ZHU Zengrong, XU Yi, ZHOU Wenwu

“…Compared with the healthy control plants, herbivory stimuli and PVY infection treatments produced 3 998 and 104 differentially expressed genes (DEGs), respectively; while 9 178 DEGs were induced by co-stressed treatment, suggesting that the co-stressed treatment may greatly affected the physiological responses in potato plants. …”
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Identification, expression profiling and potential functional roles of nuclear receptors in the social aphid Pseudoregma bambucicola by Jianjun Lu, Xiaolei Huang

“…The findings provide preliminary evidence for the functional significance of NR genes in social aphids, while offering novel insights for subsequent research exploration.…”
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Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes. by Sophie Garnier, Vinh Truong, Jessy Brocheton, Tanja Zeller, Maxime Rovital, Philipp S Wild, Andreas Ziegler, Cardiogenics Consortium, Thomas Munzel, Laurence Tiret, Stefan Blankenberg, Panos Deloukas, Jeannette Erdmann, Christian Hengstenberg, Nilesh J Samani, Heribert Schunkert, Willem H Ouwehand, Alison H Goodall, François Cambien, David-Alexandre Trégouët

“…In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. …”
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Refining the annotation of Rhodnius prolixus aspartic proteases A1 family genes through proteogenomics by Radouane Ouali, Sabrina Bousbata

“…Notably, 11 of these genes were confirmed at the protein level, while two were supported by transcriptomic data. …”
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Patient-specific data fusion defines prognostic cancer subtypes. by Yinyin Yuan, Richard S Savage, Florian Markowetz

“…In cancer studies, for example, data on copy number alterations indicate losses and amplifications of genomic regions in tumours, while transcriptomic data point to the impact of genomic and environmental events on the internal wiring of the cell. …”
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RegAB Homolog of Burkholderia pseudomallei is the Master Regulator of Redox Control and involved in Virulence. by Julia Phenn, Jan Pané-Farré, Nikolai Meukow, Annelie Klein, Anne Troitzsch, Patrick Tan, Stephan Fuchs, Gabriel E Wagner, Sabine Lichtenegger, Ivo Steinmetz, Christian Kohler

“…Further investigations of the RegAB regulon, using a global transcriptomic approach, identified 20 additional regulators under transcriptional control of RegAB, indicating a superordinate role of RegAB in the B. pseudomallei anaerobiosis regulatory network. …”
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A multi-omics technology to the study of lactic acid bacteria responses to environmental stress: the past, current and future trends by Yaqi Liu, Jingxian Sun, Xiaowen Liu, Mingpeng Zheng, Wen Ma, Gang Jin

“…To achieve a targeted improvement of their adaptability to various environments, a detail analysis of their evolutionary physiological processes is required. While several studies have been carried out in the past by using single-omics techniques to investigate their response to environmental stress, most researchers are now using a multi-omics approach to explore more detail in the biological regulatory networks and molecular mechanisms of lactic acid bacteria in response to environmental stress, thereby overcoming the limitations of single- omics analysis. …”
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Bayesian variable selection with graphical structure learning: Applications in integrative genomics. by Suprateek Kundu, Yichen Cheng, Minsuk Shin, Ganiraju Manyam, Bani K Mallick, Veerabhadran Baladandayuthapani

“…Significant advances in biotechnology have allowed for simultaneous measurement of molecular data across multiple genomic, epigenomic and transcriptomic levels from a single tumor/patient sample. …”
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Differential Analysis of Early-Onset and Late-Onset Colorectal Cancer Based on Multidimensional Evidence Integration: A Review by Xiaoying Mi MS, Peng Zheng MS, Xiangbai Wu MS

“…At the biomolecular level, PIK3CA mutation and TP53 deletion exhibits a higher mutation rate in EO-CRC compared to LO-CRC, while other common gene mutations such as APC, KRAS, and SMAD4 are relatively less frequent. …”
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Support Vector Machine – Recursive Feature Elimination for Feature Selection on Multi-omics Lung Cancer Data by Nuraina Syaza Azman, Azurah A Samah, Ji Tong Lin, Hairudin Abdul Majid, Zuraini Ali Shah, Nies Hui Wen, Chan Weng Howe

“…The results show that all 5 VAE models can obtain an accuracy and AUC score of 1.000, while only 2 out of 5 SDAE models (FS 1000 & 4000) can do so. 3 out of 5 SDAE models have an AUC score of 0.500, indicating zero capability in separating the binary class labels. …”
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STRIPAK complex defects result in pseudosexual reproduction in Cryptococcus neoformans. by Patricia P Peterson, Sarah Croog, Yeseul Choi, Sheng Sun, Joseph Heitman

“…Here, we further investigate the specific roles of the STRIPAK catalytic subunit Pph22 and its regulatory partner Far8 during sexual development. We show that while pph22Δ mutants are defective in α-a sexual reproduction, exhibiting impaired meiotic progression and a failure to produce viable spores, deletion of PPH22 results in exclusive pseudosexual reproduction, with progeny inheriting nuclear genomes solely from the wild-type parent. …”
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Ensemble modeling of SARS-CoV-2 immune dynamics in immunologically naïve rhesus macaques predicts that potent, early innate immune responses drive viral elimination by Catherine Byrne, Joshua T. Schiffer

“…We used multi-model inference and ensemble modeling approaches from ecology and weather forecasting to compare and combine various competing models.Results and discussionModel outputs suggest that the innate immune response plays a crucial role in controlling early infection, while SARS-CoV-2 specific CD4+ T cells correspond to later viral elimination, and anti-spike IgG antibodies do not impact viral dynamics. …”
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Integrative analysis of ceRNA networks and immune cell infiltration in thyroid cancer for enhanced diagnostic and prognostic insights by Chang Lv, Huazhe Wu, Dejun Yin, Wei Fang, Liming Zhou

“…DUXAP8 was positively correlated with activated mast cells and monocytes, while HCP5 was negatively correlated with resting NK cells. …”
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Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages by Małgorzata Orłowska, Drishtee Barua, Sebastian Piłsyk, Anna Muszewska

“…The expression of fucose-related protein-coding genes proteins was validated with the help of transcriptomic data originating from representatives of early diverging fungi. …”
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VPS72, a member of VPS protein family, can be used as a new prognostic marker for hepatocellular carcinoma by Jian Huang, Jin Gan, Jian Wang, Min Zheng, Han Xiao

“…The mRNA expression of VPSs displayed a negative correlation with OS, while exhibiting a positive correlation with tumor grade and stage. …”
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