Genetic parameters and identification of genomic regions and candidate genes associated with vaginal discharge score in Holstein cattle based on genomic and transcriptomic analyses by Junxing Zhang, Liyun Han, Hui Sheng, Hailiang Zhang, Luiz F. Brito, Shanshan Li, Guoshang Ji, Xingang Dan, Bei Cai, Yamei Hu, Yachun Wang, Yun Ma

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Prioritization of Kidney Cell Types Highlights Myofibroblast Cells in Regulating Human Blood Pressure by Mahboube Ganji-Arjenaki, Zoha Kamali, Soroush Sardari, Martin de Borst, Harold Snieder, Ahmad Vaez, Evangelos Evangelou, Helen R. Warren, He Gao, Georgios Ntritsos, Niki Dimou, Tonu Esko, Reedik Mägi, Lili Milani, Peter Almgren, Thibaud Boutin, Stéphanie Debette, Jun Ding, Franco Giulianini, Elizabeth G. Holliday, Anne U. Jackson, Ruifang Li -Gao, Wei -Yu Lin, Jian'an Luan, Massimo Mangino, Christopher Oldmeadow, Bram Peter Prins, Yong Qian, Muralidharan Sargurupremraj, Nabi Shah, Praveen Surendran, Sébastien Thériault, Niek Verweij, Sara M. Willems, Jing -Hua Zhao, Philippe Amouyel, John Connell, Renée de Mutsert, Alex S.F. Doney, Martin Farrall, Cristina Menni, Andrew D. Morris, Raymond Noordam, Guillaume Paré, Neil R. Poulter, Denis C. Shields, Alice Stanton, Simon Thom, Gonçalo Abecasis, Najaf Amin, Dan E. Arking, Kristin L. Ayers, Caterina M. Barbieri, Chiara Batini, Joshua C. Bis, Tineka Blake, Murielle Bochud, Michael Boehnke, Eric Boerwinkle, Dorret I. Boomsma, Erwin P. Bottinger, Peter S. Braund, Marco Brumat, Archie Campbell, Harry Campbell, Aravinda Chakravarti, John C. Chambers, Ganesh Chauhan, Marina Ciullo, Massimiliano Cocca, Francis Collins, Heather J. Cordell, Gail Davies, Martin H. de Borst, Eco J. de Geus, Ian J. Deary, Joris Deelen, Fabiola Del Greco M, Cumhur Yusuf Demirkale, Marcus Dörr, Georg B. Ehret, Roberto Elosua, Stefan Enroth, A. Mesut Erzurumluoglu, Teresa Ferreira, Mattias Frånberg, Oscar H. Franco, Ilaria Gandin, Paolo Gasparini, Vilmantas Giedraitis, Christian Gieger, Giorgia Girotto, Anuj Goel, Alan J. Gow, Vilmundur Gudnason, Xiuqing Guo, Ulf Gyllensten, Anders Hamsten, Tamara B. Harris, Sarah E. Harris, Catharina A. Hartman, Aki S. Havulinna, Andrew A. Hicks, Edith Hofer, Albert Hofman, Jouke-Jan Hottenga, Jennifer E. Huffman, Shih-Jen Hwang, Erik Ingelsson, Alan James, Rick Jansen, Marjo -Riitta Jarvelin, Roby Joehanes, Åsa Johansson, Andrew D. Johnson, Peter K. Joshi, Pekka Jousilahti, J. Wouter Jukema, Antti Jula, Mika Kähönen, Sekar Kathiresan, Bernard D. Keavney, Kay-Tee Khaw, Paul Knekt, Joanne Knight, Ivana Kolcic, Jaspal S. Kooner, Seppo Koskinen, Kati Kristiansson, Zoltan Kutalik, Maris Laan, Marty Larson, Lenore J. Launer, Benjamin Lehne, Terho Lehtimäki, David C.M. Liewald, Li Lin, Lars Lind, Cecilia M. Lindgren, YongMei Liu, Ruth J.F. Loos, Lorna M. Lopez, Yingchang Lu, Leo-Pekka Lyytikäinen, Anubha Mahajan, Chrysovalanto Mamasoula, Jaume Marrugat, Jonathan Marten, Yuri Milaneschi, Anna Morgan, Andrew P. Morris, Alanna C. Morrison, Peter J. Munson, Mike A. Nalls, Priyanka Nandakumar, Christopher P. Nelson, Teemu Niiranen, Ilja M. Nolte, Teresa Nutile, Albertine J. Oldehinkel, Ben A. Oostra, Paul F. O'Reilly, Elin Org, Sandosh Padmanabhan, Walter Palmas, Aarno Palotie, Alison Pattie, Brenda W.J.H. Penninx, Markus Perola, Annette Peters, Ozren Polasek, Peter P. Pramstaller, Quang Tri Nguyen, Olli T. Raitakari, Rainer Rettig, Kenneth Rice, Paul M. Ridker, Janina S. Ried, Harriëtte Riese, Samuli Ripatti, Antonietta Robino, Lynda M. Rose, Jerome I. Rotter, Igor Rudan, Daniela Ruggiero, Yasaman Saba, Cinzia F. Sala, Veikko Salomaa, Nilesh J. Samani, Antti-Pekka Sarin, Reinhold Schmidt, Helena Schmidt, Nick Shrine, David Siscovick, Albert V. Smith, Harold Snieder, Siim Sõber, Rossella Sorice, John M. Starr, David J. Stott, David P. Strachan, Rona J. Strawbridge, Johan Sundström, Morris A. Swertz, Kent D. Taylor, Alexander Teumer, Martin D. Tobin, Maciej Tomaszewski, Daniela Toniolo, Michela Traglia, Stella Trompet, Jaakko Tuomilehto, Christophe Tzourio, André G. Uitterlinden, Ahmad Vaez, Peter J. van der Most, Cornelia M. van Duijn, Germaine C. Verwoert, Veronique Vitart, Uwe Völker, Peter Vollenweider, Dragana Vuckovic, Hugh Watkins, Sarah H. Wild, Gonneke Willemsen, James F. Wilson, Alan F. Wright, Jie Yao, Tatijana Zemunik, Weihua Zhang, John R. Attia, Adam S. Butterworth, Daniel I. Chasman, David Conen, Francesco Cucca, John Danesh, Caroline Hayward, Joanna M.M. Howson, Markku Laakso, Edward G. Lakatta, Claudia Langenberg, Olle Melander, Dennis O. Mook-Kanamori, Colin N.A. Palmer, Lorenz Risch, Robert A. Scott, Rodney J. Scott, Peter Sever, Tim D. Spector, Pim van der Harst, Nicholas J. Wareham, Eleftheria Zeggini, Daniel Levy, Patricia B. Munroe, Christopher Newton-Cheh, Morris J. Brown, Andres Metspalu, Bruce M. Psaty, Louise V. Wain, Paul Elliott, Mark J. Caulfield

“…Enrichment of heritability for systolic BP (SBP) was observed in myofibroblast cells in mature human kidney cortex, and enrichment of heritability for diastolic BP (DBP) was observed in descending vasa recta and peritubular capillary endothelial cells as well as stromal myofibroblast cells. The new finding of myofibroblast, the significant cell type for both BP traits, was consistent in 8 replication efforts using 7 sets of independent data, including in human fetal kidney, in East-Asian (EAS) ancestry, using mouse single-cell RNA sequencing (scRNA-seq) data, and when using another prioritization method. …”
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Identification of PRKCQ-AS1 as a Keratinocyte-Derived Exosomal lncRNA That Promotes Th17 Differentiation and IL-17 secretion in Psoriasis Through Bioinformatics, Machine L... by Gao P, Gao X, Lin L, Zhang M, Luo D, Chen C, Li Y, He Y, Liu X, Shi C, Yang R

“…The expression distribution in single-cell RNA sequencing data suggested that exosomal PRKCQ-AS1 may originate from keratinocytes, and co-expression analysis supported its role in STAT3 activation within lymphocytes. …”
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Integrating Mendelian randomization and multi-transcriptomic analyses to unveil the genetic association risk of regulatory T cell-mediated free cholesterol and gastric cancer by Fanyu Peng, Haitao Liu, Yesong Guo, Jing Wen, Yizhi Ge, Yanhong Luo

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Overexpression of MMP14 is associated with poor prognosis and immune cell infiltration in colon cancer by Na Li, Nan Zhang, Guanghui Wang

“…Single-cell transcriptome data were analyzed to explore MMP14 expression and immune microenvironment changes. mRNA expression profiles and clinical data were retrieved from public databases (TCGA and GEO). …”
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Integrating multi-omics data reveals the antitumor role and clinical benefits of gamma-delta T cells in triple-negative breast cancer by Guixin Wang, Shuo Wang, Wenbin Song, Chenglu Lu, Zhaohui Chen, Long He, Xiaoning Wang, Yizeng Wang, Cangchang Shi, Zhaoyi Liu, Yue Yu, Xin Wang, Yao Tian, Yingxi Li

“…Bulk RNA sequencing was included to uncover the heterogeneity in signaling pathways, as well as radiotherapy and immunotherapy responses, among patients with varying levels of γδT cell abundance. …”
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Unveiling SSR4: a promising biomarker in esophageal squamous cell carcinoma by Jiaqi Zhang, Fang Jia, Chuqiao Li, Shunzhe Song, Aixia Gong

“…Accordingly, we aim to determine the interconnection between SSR4 expression and clinical characteristics of ESCC.MethodsThis differential expression and prognostic significance of SSR4 was performed using bulk RNA-seq data and 110 patients with complete follow-up information. …”
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The impact of dropouts in scRNAseq dense neighborhood analysis by Alisa Pavel, Manja Gersholm Grønberg, Line H. Clemmensen

“…Single cell RNA sequencing (scRNAseq) provides the possibility to investigate transcriptomic profiles on a single cell level. …”
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Comprehensive characterization of NK cell-related genes in cutaneous melanoma identified a novel prognostic signature for predicting the prognosis, immunotherapy, and chemotherapy... by Haili Ma, Jian Liu, Huan Jin, Min Zhang, Qian Liang, Zhiqiang Guo

“…This study aimed to develop a predictive model based on NK cell-associated immune genes (NKIGs) for patients with cutaneous melanoma (CM) and to assess its utility in predicting prognosis and guiding personalized treatment. Methods RNA-sequencing data and clinical information of CM patients were retrieved from The Cancer Genome Atlas (TCGA) database, while expression profiles from normal skin specimens were obtained from the Genotype-Tissue Expression (GTEx) database. …”
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Sphingosine-1-phosphate stimulates colorectal cancer tumor microenvironment angiogenesis and induces macrophage polarization via macrophage migration inhibitory factor by Fang Wu, Zhaode Feng, Xuan Wang, Yingcong Guo, Bingcong Wu, Shuheng Bai, Ning Lan, Min Chen, Juan Ren

“…In order to elucidate the contribution of S1P to the complexity of the tumor microenvironment, we employed intercellular communication analysis and functional enrichment analysis at the single-cell transcriptome (scRNA-seq) level. …”
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Comprehensive analysis of disulfidptosis-related genes and the immune microenvironment in heart failure by Linna Zhao, Juanjuan Zhang, Juanjuan Zhang, Qiuhang Song, Cheng Dai, Yiping Qin, Aiying Li, Aiying Li

“…Nonetheless, the effect of disulfidoptosis on the immune microenvironment of HF is not well comprehended. In this paper, bioinformatics analysis was performed to investigate how disulfidptosis-related genes (DRGs) affect the immune microenvironment of HF.MethodsThe expression of four DRGs was initially examined using bulk RNA-Seq and single-cell RNA sequencing data. …”
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Identification and validation of pyroptosis patterns in AML via comprehensive bioinformatics analysis by Zeyu Deng, Hongkai Zhu, Zhao Cheng, Ruijuan Li, Hongling Peng

“…This classification was validated in an independent cohort (GSE10358, n = 91). Single-cell RNA sequencing data (GSE116256, n = 15) revealed that the ELANElow subtype is characterized by an immunologically active microenvironment, marked by an expansion of cytotoxic T cells and naive CD4 + /CD8 + T cells. …”
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Targeting macrophages and ion homeostasis in T2D: new genes and therapeutic pathways identified by Lisha Mou, Lisha Mou, Tony Bowei Wang, Ying Lu, Ying Lu, Zijing Wu, Zijing Wu, Yuxian Chen, Ziqi Luo, Xinyu Wang, Zuhui Pu, Zuhui Pu

“…This study explored the intersection of macrophage-specific gene expression and abnormal blood monovalent inorganic cation concentration-related genes (ABRGs) in T2D patients via single-cell RNA sequencing (scRNA-seq) and machine learning to identify key genes and potential therapeutic targets.MethodsScRNA-seq data from the pancreatic islet cells of 27 nondiabetic (ND) patients and 17 T2D patients were analyzed to identify differentially expressed genes (DEGs) in macrophages. …”
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Comparative Transcriptomics Analysis of Foot-and-Mouth Disease Virus-Infected Cell Model Systems by Haibin Ma, Zhenzhen Zheng, Min Liu, Mengsi Zhang, Xiaoyun Qu, Jingqiang Ren, Ming Liao

“…The FMDV genome, composed of single-stranded RNA, consists of approximately 8500 nucleotides and harbors a single open reading frame (ORF) encoding both structural and non-structural proteins vital for the virus’s pathogenicity and replication. …”
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Comparative plastome analysis of Arundinelleae (Poaceae, Panicoideae), with implications for phylogenetic relationships and plastome evolution by Li-Qiong Jiang, Bryan T. Drew, Watchara Arthan, Guo-Ying Yu, Hong Wu, Yue Zhao, Hua Peng, Chun-Lei Xiang

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Molecular characterization and phylogenetic analyses of the mitogenome of Wan-Xi white goose, a native goose breed in China by Lunbin Xia, Shaoshuai Bi, Yafei Zhang, Cunwu Chen, Naidong Chen

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BRD4 as the key lactylation related gene in heart failure identified through bioinformatics analysis by Kaiyuan Li, Lingyu Han, Xiaowen Wang, Zhipeng Zheng, Min Sha, Jun Ye, Li Zhu

“…Immune cell infiltration and single-cell data analyses indicated that BRD4 exhibits a strong association with immune cells, including mast cells, T cells, and macrophages, and demonstrates significantly elevated expression in these immune cells as well as in cardiomyocytes. …”
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Analysis of changes in intercellular communications in Alzheimer’s disease reveals conserved changes in glutamatergic transmission in mice and humans by Katrina Bartas, Megan Nguyen, Wei Zhao, May Hui, Qing Nie, Kevin T. Beier

“…Abstract Analysis of system-wide cellular communication changes in Alzheimer’s disease (AD) has recently been enabled by single nucleus RNA sequencing (snRNA-seq) and new computational methods. …”
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Comparative analysis of 18 chloroplast genomes reveals genomic diversity and evolutionary dynamics in subtribe Malaxidinae (Orchidaceae) by Lin Li, Wenting Yang, Qiang Liu, Xingyou Jiang, Kunlin Wu, Lin Fang, Mingzhi Li, Songjun Zeng, Shijin Li

“…Detailed sequence alignment of the chloroplast genome revealed that structural variants are primarily concentrated within single-copy regions. …”
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Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas. by Michael E Berens, Anup Sood, Jill S Barnholtz-Sloan, John F Graf, Sanghee Cho, Seungchan Kim, Jeffrey Kiefer, Sara A Byron, Rebecca F Halperin, Sara Nasser, Jonathan Adkins, Lori Cuyugan, Karen Devine, Quinn Ostrom, Marta Couce, Leo Wolansky, Elizabeth McDonough, Shannon Schyberg, Sean Dinn, Andrew E Sloan, Michael Prados, Joanna J Phillips, Sarah J Nelson, Winnie S Liang, Yousef Al-Kofahi, Mirabela Rusu, Maria I Zavodszky, Fiona Ginty

“…Multiplexed immunofluorescence (MxIF) was used to generate single cell data for 43 protein markers representing all cancer hallmarks, Genomic sequencing (exome and RNA (normal and tumor) and magnetic resonance imaging (MRI) quantitative features (protocols were T1-post, FLAIR and ADC) from whole tumor, peritumoral edema and enhancing core vs equivalent normal region were also collected from patients. …”
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