Inflammation-Related Mechanisms in Chronic Kidney Disease Prediction, Progression, and Outcome by Simona Mihai, Elena Codrici, Ionela Daniela Popescu, Ana-Maria Enciu, Lucian Albulescu, Laura Georgiana Necula, Cristina Mambet, Gabriela Anton, Cristiana Tanase

“…In this scenario, a huge step forward was made by the increasing progression of omics approaches, specially designed for identification of biomarkers useful for early diagnostic and follow-up. …”
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Disease prediction by network information gain on a single sample basis by Jinling Yan, Peiluan Li, Ying Li, Rong Gao, Cheng Bi, Luonan Chen

“…Moreover, our method was validated by successfully predicting disease deteriorations and identifying their potential therapeutic targets from four real omics datasets, i.e., an influenza dataset and three cancer datasets.…”
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Posttreatment Blood Pressure as a Key Predictor in a 5‐Year Stroke Prediction Model by Nan Zhang, Jiarong Mei, Fangfang Fan, Yan Zhang, Ziyi Zhou, Jianping Li

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DisCo P-ad: Distance-Correlation-Based <i><b>p</b></i>-Value Adjustment Enhances Multiple Testing Corrections for Metabolomics by Debmalya Nandy, Debashis Ghosh, Katerina Kechris

“…While our focus is on metabolomics, DisCo P-ad can also readily be applied to other high-dimensional omics studies.…”
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Non‐Invasive Tumor‐Naïve Minimal Residual Disease Detection of Liver Cancer by Incorporating Circulating Tumor DNA Features and Alpha‐Fetoprotein: A Prospective Study by Qingqi Ren, Shiyong Li, Guolin Zhong, Yunfei Li, Dao‐Ling Huang, Liangliang Zhang, Yumin Feng, Guanghui Long, Mao Mao

“…Conclusion This prospective study highlights the prognostic value of ctDNA‐based tumor‐naïve MRD detection through a multi‐omics assay in early‐stage liver cancer patients.…”
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Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas by Yixin Wang, Jian Wang, Robert J. Gruninger, Tim A. McAllister, Mingzhou Li, Le Luo Guan

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Association between gestational weight gain and adverse pregnancy outcomes: cohort analysis from South Asia and Sub-Saharan Africa by Anisur Rahman, Fyezah Jehan, Gary M Shaw, Sunil Sazawal, Salahuddin Ahmed, Abdullah H Baqui, David K Stevenson, Monjur Rahman, Jesmin Pervin, Shaki Aktar, Rasheda Khanam, Sayedur Rahman, Nitya Wadhwa, Ge Zhang, Huan Xu, Usma Mehmood, Shinjini Bhatnagar, Jeffrey S A Stringer, Bellington Vwalika, Waqasuddin Khan, Nabidul Haque Chowdhury, Imran Nisar, Javairia Khalid, Nima Aghaeepour, U Tin Nu, Yuri V Sebastião, Ramachandran Thiruvengadam, Ayushi, Bapu Koundinya Desiraju, Fatma Kabole, Muhammad Farrukh Qazi, Margaret Kasaro, Bihila Abdalla Bakari

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Desmin‐related myopathy characterized by non‐compaction cardiomyopathy, cardiac conduction defect, and coronary artery dissection by Ran Tamiya, Yuki Saito, Daisuke Fukamachi, Koichi Nagashima, Yoshihiro Aizawa, Kimie Ohkubo, Takumi Hatta, Akira Sezai, Masashi Tanaka, Taisuke Ishikawa, Naomasa Makita, Naokata Sumitomo, Yasuo Okumura

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A Highly Efficient System for Separating Glandular and Non-glandular Trichome of Cucumber Fruit for Transcriptomic and Metabolomic Analysis by Lei Sun, Zhongxuan Feng, Fang Wang, Yu Qi, Menghang An, Lin Yang, Min Feng, Mingqi Wang, Huazhong Ren, Xingwang Liu

“…However, current methods for separating trichomes encounter challenges such as low efficiency and insufficient accuracy, limiting their applicability in multi-omics sequencing studies. This protocol introduces an efficient system designed for the precise separation of glandular and non-glandular trichomes from cucumber fruit. …”
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Disease-associated genetic variants in the regulatory regions of human genes: mechanisms of action on transcription and genomic resources for dissecting these mechanisms by E. V. Ignatieva, E. A. Matrosova

“…Dissecting the regulatory roles of polymorphic loci have been impossible without close integration of modern experimental approaches with computer analysis of a growing wealth of genetic and biological data obtained using omics technologies. The review provides a brief description of a number of the most well-known public genomic information resources containing data obtained using omics technologies, including (1) resources that accumulate data on the chromatin states and the regions of transcription factor binding derived from ChIP-seq experiments; (2) resources containing data on genomic loci, for which allele-specific transcription factor binding was revealed based on ChIP-seq technology; (3) resources containing in silico predicted data on the potential impact of genetic variants on the transcription factor binding sites.…”
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Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958 by Yang Shuqiong, Liu Jiafei, Cao Lingling, Chen Jibao, Duan Pengfei

“…Further to help comprehending the molecular mechanisms underlying drought adaptability and tolerance of maize, an integrated multi-omics analysis of transcriptome, sRNAome, and degradome was performed on the seedling roots of an elite hybrid Zhengdan958 under drought stress. …”
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Strategies to Improve the Quality and Freshness of Human Bone Marrow-Derived Mesenchymal Stem Cells for Neurological Diseases by Da Yeon Lee, Sung Eun Lee, Do Hyeon Kwon, Saraswathy Nithiyanandam, Mi Ha Lee, Ji Su Hwang, Shaherin Basith, Jung Hwan Ahn, Tae Hwan Shin, Gwang Lee

“…As studies on the traditional characteristics of hBM-MSCs before transplantation into the brain are very limited, omics and machine learning approaches are needed to evaluate cell conditions with indepth and comprehensive analyses. …”
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Targeting CXCL8 signaling sensitizes HNSCC to anlotinib by reducing tumor-associated macrophage-derived CLU by Xin Hu, Yikang Ji, Mi Zhang, Zhihui Li, Xinhua Pan, Zhen Zhang, Xu Wang

“…Understanding the spatial heterogeneity of glucose deficiency can reveal the molecular mechanisms regulating cancer metabolism and identify therapeutic targets to improve effective nutrient-starvation therapies. Methods Multiple omics data from RNA-seq, proteomics and spatial transcriptome analyses of HNSCC samples were integrated to analyze the spatial heterogeneity of glucose deficiency. …”
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Mitochondrial Heterogeneity: Evaluating Mitochondrial Subpopulation Dynamics in Stem Cells by D. C. Woods

“…While it has been well established that mitochondria in different tissues have distinctive ultrastructural features consistent with differential bioenergetic demands, recent and emerging technical advances in flow cytometry, imaging, and “-omics”-based bioinformatics have only just begun to explore the complex and divergent properties of mitochondria within tissues and cell types. …”
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Computational frameworks transform antagonism to synergy in optimizing combination therapies by Jinghong Chen, Anqi Lin, Aimin Jiang, Chang Qi, Zaoqu Liu, Quan Cheng, Shuofeng Yuan, Peng Luo

“…This review systematically analyzes computational methods for predicting drug combination effects through multi-omics data integration. We comprehensively assess key algorithms including DrugComboRanker and AuDNNsynergy, and evaluate integration approaches encompassing kernel regression and graph networks. …”
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Importance of Human Faecal Biobanking: From Collection to Storage by Lewandowska Izabela, Grzech Katarzyna, Krzysztoń-Russjan Jolanta

“…The review includes research on faecal microbiota transplantation (FMT), microbiome analysis, ‘-omics’ research, cancer and parasites. The primary topic addressed in this research is the impact of storage conditions and freezing methods for faecal samples on the stability and diversity of the gut microbiome. …”
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Bioinformatics services for analyzing massive genomic datasets by Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Ho-Yeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byunghee Kang, Sunguk Shin, Lian Kim, Seung-Won Lee, Dougu Nam, Jihyun F. Kim, Namshin Kim, Seon-Young Kim, Sanghyuk Lee, Tae-Young Roh, Byungwook Lee

“…Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. …”
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Allele frequency of pathogenic variants causing acid sphingomyelinase deficiency and Gaucher disease in the general Japanese population by Shuhei Sako, Kimihiko Oishi, Hiroyuki Ida, Eri Imagawa

“…Here, we reviewed the allele frequencies of pathogenic variants causing ASMD and GD in the Japanese population and populations with various ancestry backgrounds using the Japanese Multi-Omics Reference Panel 54KJPN and the Genome Aggregation Database v4.0.0. …”
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A COMPREHENSIVE REVIEW ON-APPLICATION AND FUTURE PROSPECT OF CYTOPLASMIC MALE STERILITY by Sujan Chapagain

“…Moreover, the review elucidates on the recent advancements in biotechnology, omics technologies, and breeding approaches, which promise to further harness the potential of CMS in addressing global food security challenges. …”
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Integrating New Approach Methodologies to Address Environmental Pancreatic Toxicity and Metabolic Disorders by Yue Ge

“…New Approach Methodologies (NAMs)—including high-throughput screening (HTS), OMICS technologies, computational modeling, and advanced in vitro systems—offer transformative tools to tackle these challenges. …”
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