A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins by Sodbo Sharapov, Anna Timoshchuk, Olga Zaytseva, Denis E. Maslov, Anna Soplenkova, Elizaveta E. Elgaeva, Evgeny S. Tiys, Massimo Mangino, Clemens Wittenbecher, Lennart Karssen, Maria Timofeeva, Arina Nostaeva, Frano Vuckovic, Irena Trbojević-Akmačić, Tamara Štambuk, Sofya Feoktistova, Nadezhda A. Potapova, Viktoria Voroshilova, Frances Williams, Dragan Primorac, Jan Van Zundert, Michel Georges, Karsten Suhre, Massimo Allegri, Nishi Chaturvedi, Malcolm Dunlop, Matthias B. Schulze, Tim Spector, Yakov A. Tsepilov, Gordan Lauc, Yurii S. Aulchenko

“…By integrating glycomics, proteomics, transcriptomics, and genomics, we provide a resource that facilitates deeper exploration of disease pathogenesis and supports the discovery of glycan-based biomarkers.…”
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Cell type and regulatory analysis in amphioxus illuminates evolutionary origin of the vertebrate head by Anna Markos, Jan Kubovciak, Simona Mikula Mrstakova, Anna Zitova, Jan Paces, Simona Machacova, Zbynek Kozmik-Jr, Zbynek Kozmik, Iryna Kozmikova

“…Abstract To shed light on the enigmatic origin of the vertebrate head, our study employs an integrated approach that combines single-cell transcriptomics, perturbations in signaling pathways, and cis-regulatory analysis in amphioxus. …”
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Dynamic metabolic regulation of histone modifications during the yeast metabolic cycle. by Bárbara Guzmán-Dinamarca, Raúl Conejeros, Marcelo Rivas-Astroza

“…These findings support the concept that metabolism provides timely cosubstrates essential for histone PTMs.…”
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Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. by Jasmina Ponjavic, Peter L Oliver, Gerton Lunter, Chris P Ponting

“…Besides protein-coding mRNAs, eukaryotic transcriptomes include many long non-protein-coding RNAs (ncRNAs) of unknown function that are transcribed away from protein-coding loci. …”
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Berberine as a Bioactive Alkaloid: Multi-Omics Perspectives on Its Role in Obesity Management by Bartłomiej Zieniuk, Magdalena Pawełkowicz

“…We further discuss nanoformulations and multi-omics approaches, which integrate data from genomics, transcriptomics, proteomics, and metabolomics, provide new insights into berberine’s mechanisms, and may guide personalized therapeutic applications. …”
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PAN2HGENE-tool for comparative analysis and identifying new gene products. by Mônica Silva de Oliveira, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sá, Adonney Allan de Oliveira Veras

“…Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various organisms. …”
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scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling. by Qile Yang, Ksenia R Safina, Kieu Diem Quynh Nguyen, Zewen Kelvin Tuong, Nicholas Borcherding

“…Single-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) and single-cell RNA sequencing (scRNA-seq) provide a transformative approach to profiling immune responses at unprecedented resolution across diverse pathophysiologic contexts. …”
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Single Molecule Fluorescence In Situ Hybridization Using RNAscope to Study Hematopoietic and Vascular Interactions in the Zebrafish Embryo and Larva by Léa Torcq, Anne Schmidt

“…Our experimental approach uses RNAscope technology, which allows combining high-sensitivity mRNA detection with high-resolution fluorescence confocal imaging to achieve spatial transcriptomics. Importantly, the small size of the probes allows better penetration inside tissues, which is a significant improvement in comparison to long mRNA probes; this is an invaluable advantage for reaching deeply embedded niches such as the ones of the pronephros region in the larva and, in addition, provides an increased signal-to-noise ratio.…”
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Machine-learning meta-analysis reveals ethylene as a central component of the molecular core in abiotic stress responses in Arabidopsis by Raul Sanchez-Munoz, Thomas Depaepe, Marketa Samalova, Jan Hejatko, Isiah Zaplana, Dominique Van Der Straeten

“…This remains a challenge given the complex nature of the underlying molecular mechanisms. To provide a comprehensive picture of stress-mitigation mechanisms, an exhaustive analysis of publicly available stress-related transcriptomic data has been conducted. …”
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OsWNK9 regulates the expression of key transcription factors, phytohormonal, and transporters genes to improve salinity stress tolerance in rice by Yogesh Negi, Kundan Kumar

“…In the present study, we used transcriptomic analysis to provide molecular insights into the tolerance mechanism exhibited by the overexpression line of OsWNK9 (Oe-OsWNK9) under salinity stress. …”
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RNA-Seq reveals infection-induced gene expression changes in the snail intermediate host of the carcinogenic liver fluke, Opisthorchis viverrini. by Sattrachai Prasopdee, Javier Sotillo, Smarn Tesana, Thewarach Laha, Jutharat Kulsantiwong, Matthew J Nolan, Alex Loukas, Cinzia Cantacessi

“…The examination of differences in gene expression profiling between uninfected and O. viverrini-infected B. siamensis goniomphalos could provide clues on fundamental pathways involved in the regulation of snail-parasite interplay.…”
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Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures. by Niu Du, Pardis Gholami, David I Kline, Christopher L DuPont, Andrew G Dickson, Dominick Mendola, Todd Martz, Andrew E Allen, B Greg Mitchell

“…A method to estimate Φ for both net carbon uptake and net oxygen evolution simultaneously can provide important insights into energy and mass fluxes. …”
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Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. by Anna Laddach, Joseph Chi Fung Ng, Franca Fraternali

“…We validate the association between these molecular features and variant pathogenicity by comparing against existing in silico variant impact annotations. This study provides molecular details into how different proteins exhibit resilience and/or sensitivity towards missense variants and provides the rationale to prioritise variant-enriched proteins and protein domains for therapeutic targeting and development. …”
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Influence of light on the infection of Aureococcus anophagefferens CCMP 1984 by a "giant virus". by Eric R Gann, P Jackson Gainer, Todd B Reynolds, Steven W Wilhelm

“…A hypothetical mechanism for the reduced efficiency of the infection cycle in low light due to ribosome biogenesis was predicted from pre-existing transcriptomes. Overall, these studies provide a framework for understanding light effects on infection dynamics over the course of the summer months when A. anophagefferens blooms occur.…”
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Multimodal AI/ML for discovering novel biomarkers and predicting disease using multi-omics profiles of patients with cardiovascular diseases by William DeGroat, Habiba Abdelhalim, Elizabeth Peker, Neev Sheth, Rishabh Narayanan, Saman Zeeshan, Bruce T. Liang, Zeeshan Ahmed

“…Advancements in multi-omics technologies, namely RNA sequencing and whole-genome sequencing, have provided translational researchers with a comprehensive view of the human genome. …”
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Analysis of the underlying mechanism of Ziziphi Spinosae Semen for treating anxiety disorder in a zebrafish sleep deprivation model by Jian Zhang, Junli Feng, Chenyu Feng

“…These findings will contribute to the understanding of how ZSS alleviates SD-induced anxiety, and provide a theoretical basis for the clinical application of ZSS.…”
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Characterization of T cells in the progression of dry eye disease using single-cell RNA sequencing in mice by Zhizhi Zhang, Liwei Zhang, Baihua Chen

“…Results CD4+ and CD8+ T cells exhibited an initial decline on Day 3 (D3) and followed by a recovery on Day 7 (D7). Single-cell transcriptomics provided insights into 15 distinct subsets of T cells with heterogeneous functional states. …”
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Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells by John D. Blair, Austin Hartman, Fides Zenk, Philipp Wahle, Giovanna Brancati, Carol Dalgarno, Barbara Treutlein, Rahul Satija

“…We show that Phospho-seq can provide insights into cellular states and trajectories, shed light on gene regulatory relationships, and help explore the causes and effects of diverse cell signaling in neurodevelopment.…”
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From chemoproteomic‐detected amino acids to genomic coordinates: insights into precise multi‐omic data integration by Maria F Palafox, Heta S Desai, Valerie A Arboleda, Keriann M Backus

“…Abstract The integration of proteomic, transcriptomic, and genetic variant annotation data will improve our understanding of genotype–phenotype associations. …”
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Amonabactin Synthetase G Regulates <i>Aeromonas hydrophila</i> Pathogenicity Through Modulation of Host Wnt/β-catenin Signaling by Yiyang Tang, Xiaofeng Liu, Chuyi Zeng, Yujun Liu, Ye Yang, Jiayi Hu, Pingyuan Li, Zejun Zhou

“…Complementation of Δ<i>AmoG</i> with AmoG (Δ<i>AmoG</i>-C) was performed to confirm the observed phenotypes. Transcriptomic and qRT-PCR analyses were used to investigate gene expression changes in infected fish. …”
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