Integrative proteomic-transcriptomic analysis revealed the lifestyles of Lactobacillus paracasei H4-11 and Kluyveromyces marxianus L1-1 under co-cultivation conditions by Na Liu, Likang Qin, Haiying Zeng, Anyan Wen, Song Miao

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Advances in omics technologies for traditional Chinese medicine in the prevention and treatment of metabolic bone diseases by Wenjun Cai, Wenjun Cai, Lili Jiang, Changwei Zhao, Changwei Zhao, Xiaoling Zhou, Xiaoling Zhou

“…Evidence indicates that TCM monomers, single botanical drugs, and herbal formulations are effective, safe, and well-tolerated in MBD prevention and treatment. …”
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Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex by Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J. Eagles, Daianna Gonzalez-Padilla, Sean K. Maden, Joel E. Kleinman, Thomas M. Hyde, Stephanie C. Hicks, Kristen R. Maynard, Leonardo Collado-Torres

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Genome-wide association study and transcriptomic analysis reveal the crucial role of sting1 in resistance to visceral white-nodules disease in Larimichthys polyactis by Jiajie Zhu, Feng Liu, Ting Ye, Qian Li, Haowen Liu, Sifang Liu, Tianle Zhang, Dandan Guo, Junquan Zhu, Bao Lou

“…However, genetic resistance mechanisms to VWND remain elusive in this species.MethodsThis study combined genome-wide association study (GWAS) and transcriptome analysis to unravel resistance loci and transcriptional regulation in L. polyactis.ResultsAs a result, GWAS on 946 infected fish genotyped by 100 K lipid chips identified 22 suggestive significantly associated single-nucleotide polymorphisms (SNPs), annotated 60 candidate genes, where DNA-sensing pathway were enriched. …”
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ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets by Ye Zheng, Daniel P. Caron, Ju Yeong Kim, Seong-Hwan Jun, Yuan Tian, Florian Mair, Kenneth D. Stuart, Peter A. Sims, Raphael Gottardo

“…Abstract Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) enables paired measurement of surface protein and mRNA expression in single cells using antibodies conjugated to oligonucleotide tags. …”
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Single and multi-omic characterization of a porcine model of ethanol-induced hepatic fibrosis by Mark Hieromnimon, Daniel P. Regan, R. Peter Lokken, Lawrence B. Schook, Ron C. Gaba, Kyle M. Schachtschneider

“…Liver sections from five fibrosis induced and five age-matched controls were harvested for RNA-seq (mRNA and lncRNA), small RNA-seq (miRNA), and reduced representation bisulfite sequencing (RRBS; DNA methylation). Single- and multi-omic analysis was performed to investigate the transcriptomic and epigenomic mechanisms associated with fibrosis deposition in this model. …”
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Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution by John F. Fullard, Prashant NM, Donghoon Lee, Deepika Mathur, Karen Therrien, Aram Hong, Clara Casey, Zhiping Shao, Marcela Alvia, Stathis Argyriou, Tereza Clarence, David Burstein, Sanan Venkatesh, Pavan K. Auluck, Lisa L. Barnes, David A. Bennett, Stefano Marenco, PsychAD Consortium, Kiran Girdhar, Vahram Haroutunian, Gabriel E. Hoffman, Georgios Voloudakis, Jaroslav Bendl, Panos Roussos

“…To facilitate a deeper understanding of these diseases and pave the way for more effective treatments, we have generated a population-scale multi-omics dataset consisting of genotype and single-nucleus transcriptome data from the prefrontal cortex of frozen human brain specimens. …”
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Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) vari... by Guangxia Duan, Chaoni Liang, Jundong Su, Yan Liang, Wanming Li, Jinbo Zhang, Yigong Zhang

“…Exploring the mechanism of chickpea adaptation to the saline environment can effectively supplement the problem of single source of plant protein. Results The present study analyzed the transcriptomic and metabolomic profiles of two distinct chickpea varieties, DY3 and DY1, with contrasting salinity tolerance capacities. …”
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Hepatocellular carcinoma hosts cholinergic neural cells and tumoral hepatocytes harboring targetable muscarinic receptors by Charlotte A. Hernandez, Claire Verzeroli, Armando Andres Roca Suarez, Abud-José Farca-Luna, Laurie Tonon, Roger Esteban-Fabró, Roser Pinyol, Marie-Laure Plissonnier, Ievgeniia Chicherova, Anaëlle Dubois, Pascale Bellaud, Marine Seffals, Bruno Turlin, Alain Fautrel, Gabriel Ichim, Michel Rivoire, Guillaume Passot, Zuzana Macek-Jilkova, Thomas Decaens, Alain Viari, Barbara Testoni, Sandra Rebouissou, Josep M. Llovet, Fabien Zoulim, Romain Parent

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Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis by Qiuting Deng, Pengfei Cai, Yingjie Luo, Zhongjin Zhang, Wen Ma, Zijie Huang, Xiaoya Chen, Shijie Hao, Weiguang Ma, Jiangshan Xu, Chunqing Wang, Mengnan Cheng, Xiumei Lin, Ru Zhou, Shanshan Duan, Junjie Chen, Ronghai Li, Xuyang Shi, Chang Liu, Liang Wu, Peng Gao, Jianting Li, Xiao Yang, Xiangdong Wang, Jun Xie, Longqi Liu, Yue Yuan, Chuanyu Liu

“…Here, we present high-throughput single-cell chromatin accessibility and transcriptome sequencing (HT-scCAT-seq), a method that simultaneously profiles transcriptome and chromatin accessibility. …”
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Single-Cell Sequencing and Machine Learning Integration to Identify Candidate Biomarkers in Psoriasis: INSIG1 by Zhou X, Ning J, Cai R, Liu J, Yang H, Bai Y

“…Bulk transcriptome and scRNA-seq data were integrated to identify differentially expressed genes (DEGs). …”
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Stereotyped Subclones Revealed by High‐Density Single‐Cell Lineage Tracing Support Robust Development by Xiaoyu Zhang, Zizhang Li, Jingyu Chen, Wenjing Yang, Xingxing He, Peng Wu, Feng Chen, Ziwei Zhou, Chenze Ren, Yuyan Shan, Xiewen Wen, Vassily A. Lyubetsky, Leonid Yu. Rusin, Xiaoshu Chen, Jian‐Rong Yang

“…An integrated analysis of high‐density cell lineage trees (CLTs) and single‐cell transcriptomes of differentiating colonies enabled the resolution of known cell types and developmental hierarchies. …”
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Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 by Hsiu-Chun Chuang, Ruidong Li, Huang Huang, Szu-Wen Liu, Christine Wan, Subhra Chaudhuri, Lili Yue, Terence Wong, Venina Dominical, Randy Yen, Olivia Ngo, Nam Bui, Hubert Stoppler, Tangsheng Yi, Silpa Suthram, Li Li, Kai-Hui Sun

“…Taken together, HT Smart-seq3 overcomes key technical challenges, offering distinct advantages that position it as a promising solution for the characterization of single-cell transcriptomes and immune repertoires, particularly well-suited for low-input, low-RNA content samples.…”
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Single-cell analysis of dup15q syndrome reveals developmental and postnatal molecular changes in autism by Yonatan Perez, Dmitry Velmeshev, Li Wang, Matthew L. White, Clara Siebert, Jennifer Baltazar, Guolong Zuo, Juan Andrés Moriano, Songcang Chen, David M. Steffen, Natalia Garcia Dutton, Shaohui Wang, Brittney Wick, Maximilian Haeussler, Stormy Chamberlain, Arturo Alvarez-Buylla, Arnold Kriegstein

“…Abstract Duplication 15q (dup15q) syndrome is a leading genetic cause of autism spectrum disorder, offering a key model for studying autism-related mechanisms. Using single-cell and single-nucleus RNA sequencing of cortical organoids from dup15q patient-derived iPSCs and post-mortem brain samples, we identify increased glycolysis, disrupted layer-specific marker expression, and aberrant morphology in deep-layer neurons during fetal-stage organoid development. …”
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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

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Multi-omics approach in tea polyphenol research regarding tea plant growth, development and tea processing: current technologies and perspectives by Jingwen Li, Yu Wang, Joon Hyuk Suh

“…The perspectives on future research and applications for improvement of tea polyphenols as well as current challenges of multi-omics studies for tea polyphenols are also discussed.…”
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Topic modeling analysis of the Allen Human Brain Atlas by Letizia Pizzini, Filippo Valle, Matteo Osella, Michele Caselle

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The Transcriptional Program of <i>Staphylococcus aureus</i> Phage K Is Affected by a Host <i>rpoC</i> Mutation That Confers Phage K Resistance by Rohit Kongari, Melissa D. Ray, Susan M. Lehman, Roger D. Plaut, Deborah M. Hinton, Scott Stibitz

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Integration of single-cell sequencing and mendelian randomization reveals novel causal pathways between monocytes and hepatocellular carcinoma by Jiang Yu, Jing Yu, Zhou Kang, Yong Peng

“…Methods This investigation employed single-cell transcriptomic analysis of human hepatic innate lymphoid cells (ILCs) to identify monocyte subpopulations and their cellular markers. …”
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Single-cell sequencing and machine learning reveal the role of dioxin-interacting genes in HCC prognosis and immune microenvironment by Senyan Wang, Qi Liu, Xiaoyan Sun, Minghui Hou, Wenjuan Wei, Hao Song, Jing Xu, Danyang Lu, Jing Fu, Xiaofang Zhao, Hongyang Wang

“…To address this gap, single-cell and bulk transcriptomic analyses, combined with machine learning, identified dioxin-interacting differentially expressed genes (DI-DEGs) associated with immune evasion, metabolic reprogramming, and cell cycle regulation in HCC. …”
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