Mechanisms and technologies in cancer epigenetics by Zaki A. Sherif, Olorunseun O. Ogunwobi, Habtom W. Ressom

“…From the granular insights of single-cell epigenomics to the holistic view offered by multi-omics approaches, we examine how these tools are reshaping our understanding of tumor heterogeneity and evolution. …”
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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

“…Moreover, the greatest variation between genotypes in accumulation of BRs in the crown tissue exposed to drought was observed for castasterone. Presented multi-omics, high-throughput results enhanced the understanding of molecular response to drought in crown tissue. …”
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Development of the myocite biobank: Cost-efficient model of public sector investigator-driven biobank for idiopathic inflammatory myositis by R Naveen, Anamika Kumari Anuja, Mohit Kumar Rai, Vikas Agarwal, Latika Gupta

“…Background: Biobanking refers to the cryopreservation of the various biologic samples for future research. In the era of omics, biobanking has emerged as a vital process to aid research, more so for rare diseases. …”
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From Ontology to Semantic Similarity: Calculation of Ontology-Based Semantic Similarity by Mingxin Gan, Xue Dou, Rui Jiang

“…Advances in high-throughput experimental techniques in the past decade have enabled the explosive increase of omics data, while effective organization, interpretation, and exchange of these data require standard and controlled vocabularies in the domain of biological and biomedical studies. …”
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HCNetlas: A reference database of human cell type-specific gene networks to aid disease genetic analyses. by Jiwon Yu, Junha Cha, Geon Koh, Insuk Lee

“…Cell type-specific actions of disease genes add a significant layer of complexity to the genetic architecture underlying diseases, obscuring our understanding of disease mechanisms. Single-cell omics have revealed the functional roles of genes at the cellular level, identifying cell types critical for disease progression. …”
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A reference genome for the eastern bettong (Bettongia gaimardi) [version 2; peer review: 2 approved, 1 approved with reservations] by Richard J Edwards, Luke W Silver, Sam Banks, Carolyn J Hogg, Adrian D. Manning, Linda Neaves

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Application of Metabolomics in Thyroid Cancer Research by Anna Wojakowska, Mykola Chekan, Piotr Widlak, Monika Pietrowska

“…However, in some cases, cytological and histological patterns are inconclusive; hence, classification based on histopathology could be supported by molecular biomarkers, including markers identified with the use of high-throughput “omics” techniques. Beside genomics, transcriptomics, and proteomics, metabolomic approach emerges as the most downstream attitude reflecting phenotypic changes and alterations in pathophysiological states of biological systems. …”
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Effects of Pooling Samples on the Performance of Classification Algorithms: A Comparative Study by Kanthida Kusonmano, Michael Netzer, Christian Baumgartner, Matthias Dehmer, Klaus R. Liedl, Armin Graber

“…We evaluate a variety of experimental designs using mock omics datasets with varying levels of pool sizes and considering effects from feature selection. …”
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The Hsf1-sHsp cascade has pan-antiviral activity in mosquito cells by Jieqiong Qu, Michelle Schinkel, Lisa Chiggiato, Samara Rosendo Machado, Gijs J. Overheul, Pascal Miesen, Ronald P. van Rij

“…Blocking virus replication in mosquitoes is a promising approach to prevent arbovirus transmission, the development of which requires in-depth knowledge of virus-host interactions and mosquito immunity. By integrating multi-omics data, we find that heat shock factor 1 (Hsf1) regulates eight small heat shock protein (sHsp) genes within one topologically associated domain in the genome of the Aedes aegypti mosquito. …”
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Key Role of Human ABC Transporter ABCG2 in Photodynamic Therapy and Photodynamic Diagnosis by Toshihisa Ishikawa, Hiroshi Nakagawa, Yuichiro Hagiya, Naosuke Nonoguchi, Shin-ichi Miyatake, Toshihiko Kuroiwa

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Outcome Prediction in Infectious Disease by Khie Chen Lie, Yosia Yonggara, Adeline Pasaribu, Sharifah Shakinah, Leonard Nainggolan

“…Current research explores a range of prognostic tools, from traditional scoring systems and biomarkers to cutting-edge omics technologies and artificial intelligence. These tools can differ significantly across patient populations and clinical settings, such as the emergency department (ED) and intensive care unit (ICU). …”
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The clove (Syzygium aromaticum) genome provides insights into the eugenol biosynthesis pathway by Sonia Ouadi, Nicolas Sierro, Simon Goepfert, Lucien Bovet, Gaetan Glauser, Armelle Vallat, Manuel C. Peitsch, Felix Kessler, Nikolai V. Ivanov

“…The clove genome is a new contribution to omics resources for the Myrtaceae family and an important tool for clove research.…”
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Autoimmune Hepatitis: Progress from Global Immunosuppression to Personalised Regulatory T Cell Therapy by Nwe Ni Than, Hannah C. Jeffery, Ye H. Oo

“…Future direction of diagnosis and treatment for AIH should be guided by “omics” and the immunology profile of the individual patient and clinicians should aim to deliver personalised medicine for their patients. …”
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Unveiling the prognostic value of ARID3A in breast cancer through bioinformatic analysis by Wen-Run Cai, Xu-Gang Sun, Yue Yu, Xin Wang, Xu-Chen Cao, Xiao-Feng Liu

“…Subtype-specific expression and co-expression, particularly with REXO1, were evaluated using LinkedOmics, TIMER, and bc-GenExMiner. Functional enrichment analysis was conducted via LinkedOmics. …”
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Metabolomic and lipidomic pathways in aneurysmal subarachnoid hemorrhage by Bosco Seong Kyu Yang, Spiros L. Blackburn, Philip L. Lorenzi, Huimahn A. Choi, Aaron M. Gusdon

“…Aneurysmal subarachnoid hemorrhage (aSAH) results in a complex systemic response that is critical to the pathophysiology of late complications and has important effects on outcomes. Omics techniques have expanded our investigational scope and depth into this phenomenon. …”
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Comparative and phylogenetic analyses of the chloroplast genomes of mangrove plants by Jigui Yuan, Wei Gu, Haijie Yang, Mei Wang

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In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae by Márk Kovács-Valasek, Csaba Fekete, Andrea Kovács-Valasek

“…In the global effort to discover or design new effective antibiotics to fight infectious diseases, the increasingly available multi-omics data with novel bioinformatics tools open up new horizons for the exploration of the genetic potential of bacteria to synthesize bioactive secondary metabolites. …”
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Exploration of Nitrate Reductase Metabolic Pathway in Corynebacterium pseudotuberculosis by Sintia Almeida, Cassiana Sousa, Vinícius Abreu, Carlos Diniz, Elaine M. S. Dorneles, Andrey P. Lage, Debmalya Barh, Vasco Azevedo

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A Comprehensive Methodological Review of Major Developments in Bioinformatics Pipelines for Transcriptomic Data Analysis by Awais ALi, Syed Luqman Ali, Abdelkarem Omneya

“…Our findings provide valuable guidance for using omics tools effectively and developing better analysis methods. …”
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Evaluation of the Risk of Recurrence in Patients with Local Advanced Rectal Tumours by Different Radiomic Analysis Approaches by Alaa Khadidos, Adil Khadidos, Olfat M. Mirza, Tawfiq Hasanin, Wegayehu Enbeyle, Abdulsattar Abdullah Hamad

“…The word radiomics, like all domains of type omics, assumes the existence of a large amount of data. …”
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