Unlocking biological complexity: the role of machine learning in integrative multi-omics by Ravindra Kumar, Rajrani Ruhel, Andre J. van Wijnen

“…Integrative multi-omics approaches use multi-layered datasets such as genomic, transcriptomic, proteomic, and metabolomic data to understand biological processes much more comprehensively compared to the single-omics analysis and to provide a comprehensive view of cellular and molecular processes. …”
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Revisiting the role of cancer-associated fibroblasts in tumor microenvironment by Xiaolei Lan, Wenyang Li, Kai Zhao, Jianpeng Wang, Shifang Li, Hai Zhao

“…Although current detection methods, such as antibodies, mRNA probes, and single-cell transcriptomics, offer insights into CAF biology, they lack standardization and fail to provide reliable quantitative measures. …”
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Disorders in brassinosteroids signal transduction triggers the profound molecular alterations in the crown tissue of barley under drought. by Anetta Kuczyńska, Martyna Michałek, Piotr Ogrodowicz, Michał Kempa, Paweł Krajewski, Vladimiro Cardenia, Maria Teresa Rodriguez-Estrada, Marina Pérez-Llorca, Sergi Munné-Bosch, Krzysztof Mikołajczak

“…The advanced molecular tools provide critical inputs in uncovering the regulatory mechanisms underlying plants' adaptation to abiotic stress. …”
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Investigative needle core biopsies support multimodal deep-data generation in glioblastoma by Kenny K. H. Yu, Sreyashi Basu, Gerard Baquer, Ryuhjin Ahn, Jennifer Gantchev, Sonali Jindal, Michael S. Regan, Zaki Abou-Mrad, Michael C. Prabhu, Marc J. Williams, Alicia D. D’Souza, Seth W. Malinowski, Kelsey Hopland, Yuval Elhanati, Sylwia A. Stopka, Alexei Stortchevoi, Charles Couturier, Zhong He, Jingjing Sun, Yulong Chen, Alexsandra B. Espejo, Kin Hoe Chow, Smitha Yerrum, Pei-Lun Kao, Brittany Parker Kerrigan, Lisa Norberg, Douglas Nielsen, The GBM TeamLab, Vinay K. Puduvalli, Jason Huse, Rameen Beroukhim, Betty Y. S. Kim, Sangeeta Goswami, Adrienne Boire, Sarah Frisken, Michael J. Cima, Matthias Holdhoff, Calixto-Hope G. Lucas, Chetan Bettegowda, Stuart S. Levine, Tejus A. Bale, Cameron Brennan, David A. Reardon, Frederick F. Lang, E. Antonio Chiocca, Keith L. Ligon, Forest M. White, Padmanee Sharma, Viviane Tabar, Nathalie Y. R. Agar

“…We also examine biopsies taken from different locations and provide a framework for measuring spatial and genomic heterogeneity. …”
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Pathway metrics accurately stratify T cells to their cells states by Dani Livne, Sol Efroni

“…Designed to be open-source, extensible, and computationally efficient, PathSingle is available at https://github.com/zurkin1/PathSingle under the MIT license. This tool provides researchers with a versatile framework for uncovering biologically meaningful insights from high-dimensional single-cell transcriptomics data, facilitating a deeper understanding of cellular regulation and function.…”
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Single Cell Isolation from Human Diabetic Fibrovascular Membranes for Single-Cell RNA Sequencing by Katia Scheri, Thomas Tedeschi, Amani Fawzi

“…Single-cell transcriptomic analyses have emerged as very powerful tools to query the gene expression changes at the single-cell level in physiological and pathological conditions. …”
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CRISPRi screening reveals E. coli’s anaerobic-like respiratory adaptations to gentamicin: membrane depolarization by CpxR by Donghui Choe, Eunju Lee, Yoseb Song, Sun Chang Kim, Ki Jun Jeong, Bernhard Palsson, Byung-Kwan Cho, Suhyung Cho

“…Our study provides insights into cellular defense mechanisms, offering potential strategies for combating antibiotic resistance.IMPORTANCEBacteria can adapt to a variety of stressful environments, including antibiotic exposure. …”
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Comparative Study of PPARγ Targets in Human Extravillous and Villous Cytotrophoblasts by Fulin Liu, Christine Rouault, Mickael Guesnon, Wencan Zhu, Karine Clément, Séverine A. Degrelle, Thierry Fournier

“…Downstream annotation analysis revealed the similarities and differences between RT-EVCTs and RT-VCTs with respect to the biological processes, molecular functions, cellular components, and KEGG pathways affected by the treatment, as well as predicted binding sites for both protein-protein interactions and transcription factor-target gene interactions. These results provide a broad perspective of PPARγ-activated processes in trophoblasts; further analysis of the transcriptomic signatures of RT-EVCTs and RT-VCTs should open new avenues for future research and contribute to the discovery of possible drug-targeted genes or pathways in the human placenta.…”
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Bioactivity-Guided Isolation of Antistroke Compounds from <i>Gymnadenia conopsea</i> (L.) R. Br. by Juan Qin, Shiyi Xue, Chao Xu, Jian Jin, Jianbin Wang, Hailian Yuan, Liang Liu

“…Compounds <b>1–2</b>, <b>10–11</b>, <b>13–15</b>, and <b>17</b> provided varying degrees of protection against OGD/R injury in the PC12 cells at concentrations of 12.5, 25, and 50 µM. …”
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Targeting SLC7A11-mediated cysteine metabolism for the treatment of trastuzumab-resistant HER2-positive breast cancer by Yijia Hua, Ningjun Duan, Chunxiao Sun, Fan Yang, Min Tian, Yanting Sun, Shuhan Zhao, Jue Gong, Qian Liu, Xiang Huang, Yan Liang, Ziyi Fu, Wei Li, Yongmei Yin

“…Targeting metabolic reprogramming would provide novel insights for therapeutic strategies. …”
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Species- and strain-specific microbial modulation of interferon, innate immunity, and epithelial barrier in 2D air–liquid interface respiratory epithelial cultures by Mian Horvath, Ruoyu Yang, Diana Cadena Castaneda, Megan Callender, Elizabeth S. Aiken, Anita Y. Voigt, Ryan Caldwell, José Fachi, Blanda Di Luccia, Zoe Scholar, Peter Yu, Andrew Salner, Marco Colonna, Karolina Palucka, Julia Oh

“…To explore how the microbiome’s biodiversity affects microbe-epithelial interactions, we screened 58 phylogenetically diverse microbes for their transcriptomic effect on human primary bronchial air–liquid interface (ALI) cell cultures. …”
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Specific types of male infertility are correlated with T cell exhaustion or senescence signatures by Giada Amodio, Giorgia Giacomini, Luca Boeri, Massimiliano Raffo, Simone Cilio, Edoardo Pozzi, Federico Belladelli, Fausto Negri, Anna Maria Ferrara, Alessia d’Arma, Francesca Romana Santoni de Sio, Luca Pagliardini, Enrico Papaleo, Eugenio Ventimiglia, Massimo Alfano, Francesco Montorsi, Andrea Salonia, Silvia Gregori

“…These findings provide evidence that subtypes of male infertility are characterized by specific immune signatures and unravel the potential link between infertility and the risk of developing secondary diseases.…”
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An outlier approach: advancing diagnosis of neurological diseases through integrating proteomics into multi-omics guided exome reanalysis by Martin Man-Chun Chui, Anna Ka-Yee Kwong, Hiu Yu Cherie Leung, Chingyiu Pang, Ines F. Scheller, Sheila Suet-Na Wong, Cheuk-Wing Fung, Vicente A. Yépez, Julien Gagneur, Christopher Chun-Yu Mak, Brian Hon-Yin Chung

“…There is an increasing interest in transcriptomics and, more recently, proteomics for variant detection and interpretation. …”
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Current understanding on inferior quality of liver grafts by donation after circulatory death based on multi-omics data by Yifeng Zhou, Ting Que, Lu Yu, Lu Yu, Lu Yu, Shuping Que, Jun Xu, Jun Xu, Jun Xu, Zhengtao Liu, Zhengtao Liu, Zhengtao Liu, Zhengtao Liu

“…Finally, we discussed the challenges in current research and future directions to provide scientific evidence for clinical practice and promote the application of DCD donors in organ transplantation.…”
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Metabolic profiling of two white-rot fungi during 4-hydroxybenzoate conversion reveals biotechnologically relevant biosynthetic pathways by Lummy Maria Oliveira Monteiro, Carlos del Cerro, Teeratas Kijpornyongpan, Allison Yaguchi, Anna Bennett, Bryon S. Donohoe, Kelsey J. Ramirez, Alex F. Benson, Hugh D. Mitchell, Samuel O. Purvine, Lye Meng Markillie, Meagan C. Burnet, Kent J. Bloodsworth, Benjamin P. Bowen, Thomas V. Harwood, Katherine Louie, Trent Northen, Davinia Salvachúa

“…Their metabolic responses were assessed via transcriptomics, proteomics, lipidomics, metabolomics, and microscopy analyses. …”
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Molecular and spatial analysis of tertiary lymphoid structures in Sjogren’s syndrome by Saba Nayar, Jason D. Turner, Saba Asam, Eanna Fennell, Matthew Pugh, Serena Colafrancesco, Onorina Berardicurti, Charlotte G. Smith, Joe Flint, Ana Teodosio, Valentina Iannizzotto, David H. Gardner, Joel van Roon, Ilya Korsunsky, Dawn Howdle, Roche Fibroblast Network Consortium, Andreas P. Frei, Kara G. Lassen, Simon J. Bowman, Wan-Fai Ng, Adam P. Croft, Andrew Filer, Benjamin A. Fisher, Christopher D. Buckley, Francesca Barone

“…The identification of cellular properties associated with these structures and the molecular and functional interactions identified by this analysis may provide key therapeutic cues for tertiary lymphoid structures associated conditions in autoimmunity and cancer.…”
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Regulating the metabolic flux of pyruvate dehydrogenase bypass to enhance lipid production in Saccharomyces cerevisiae by Cairong Lei, Xiaopeng Guo, Miaomiao Zhang, Xiang Zhou, Nan Ding, Junle Ren, Meihan Liu, Chenglin Jia, Yajuan Wang, Jingru Zhao, Ziyi Dong, Dong Lu

“…This enhancement aimed to improve the biosynthesis of acetyl-CoA-derived compounds, such as terpenoids and fatty acid-derived molecules, in Saccharomyces cerevisiae. Through transcriptomic and lipidomic analyses, we identified ALD4 as a key regulatory gene influencing lipid metabolism. …”
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KDM1A epigenetically enhances RAD51 expression to suppress the STING-associated anti-tumor immunity in esophageal squamous cell carcinoma by Qingyuan Yang, Shiyin Wei, Cen Qiu, Chenjie Han, Zunguo Du, Ning Wu

“…Cell growth was assessed by colony formation assays in vitro and subcutaneous xenograft models in vivo. High-throughput transcriptomics and spatial immune proteomics were performed using bulk RNA sequencing and digital spatial profiling techniques, respectively. …”
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VIBE: an R-package for VIsualization of Bulk RNA Expression data for therapeutic targeting and disease stratification by Indu Khatri, Saskia D. van Asten, Leandro F. Moreno, Brandon W. Higgs, Christiaan Klijn, Christiaan Klijn, Francis Blokzijl, Iris C. R. M. Kolder

“…Here, we introduce VIBE (VIsualization of Bulk RNA Expression data), an R package which provides a thorough exploration of both individual and combined gene expression, supplemented by pathway-guided analyses. …”
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Dysfunctional immunity in the comorbidity of vitamin A deficiency and tuberculosis identifies therapeutic potential of vitamin A supplementation by Dr. Faye Lanni, Revanth Krishna, David Forrest Ackart, Victoria Mitcham, Sarah K Cooper, Connor King, Hadley Gary, Dr. Chuangqi Wang, Dr Brendan Podell

“…Conclusion: Collectively, these data indicate a potential compensatory role for CD8 cytotoxic T cell function in the absence of vitamin A and provides a link between dysfunctional CD4 T cells and neutrophil pulmonary pathology. …”
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