scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. by Fengdi Zhao, Xin Ma, Bing Yao, Qing Lu, Li Chen

“…In addition to demonstrating the highest power in three real sc-multiome data analyses, scaDA successfully identifies differentially accessible regions in microglia from sc-multiome data for an Alzheimer's disease (AD) study that are most enriched in GO terms related to neurogenesis and the clinical phenotype of AD, and AD-associated GWAS SNPs.…”
Get full text

Convergence of evolving artificial intelligence and machine learning techniques in precision oncology by Elena Fountzilas, Tillman Pearce, Mehmet A. Baysal, Abhijit Chakraborty, Apostolia M. Tsimberidou

“…By analyzing multi-dimensional, multiomic, spatial pathology, and radiomic data, these technologies enable a deeper understanding of the intricate molecular pathways, aiding in the identification of critical nodes within the tumor’s biology to optimize treatment selection. …”
Get full text

Examination of Molecular Effects of MYLK Deletion in a Patient with Extensive Aortic, Carotid, and Abdominal Dissections That Underlie the Genetic Dysfunction by Sarah K. Macklin, Katelyn A. Bruno, Charitha Vadlamudi, Haytham Helmi, Ayesha Samreen, Ahmed N. Mohammad, Stephanie Hines, Paldeep S. Atwal, Thomas R. Caulfield

“…We also provide the electrostatics calculations from the wild type and mutant variant. Through a combined multiomic approach of clinical, functional, and protein informatics, we arrive at a data fusion for determination of pathogenicity embedded within the genetic code for this particular genetic variant, which, as a platform, continues to broaden its scope across the field of variants of uncertain significance classification.…”
Get full text

Gut Microbiome: An Intersection between Human Genome, Diet, and Epigenetics by Abdullahi Y. Muhammad, Malik Amonov, Atif A. Baig, Farrukh J. Alvi

“…Recently, the association between the human genome and the gut microbiome has been analyzed and considered a multiomic approach, and extensive genome-wide association studies were conducted to further understand the complex relationship.…”
Get full text

Systematic dissection of pleiotropic loci and critical regulons in excitatory neurons and microglia relevant to neuropsychiatric and ocular diseases by Yunlong Ma, Dingping Jiang, Jingjing Li, Gongwei Zheng, Yao Deng, Xuanxuan Gou, Shuaishuai Gao, Cheng Chen, Yijun Zhou, Yaru Zhang, Chunyu Deng, Yinghao Yao, Haijun Han, Jianzhong Su

“…To investigate the biological connections between the eye and brain, we integrated bulk and single-cell multiomic profiles with GWAS summary statistics for eight neuropsychiatric and five ocular diseases. …”
Get full text

APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence by Jingyi Xie, Daniel G. Chen, William Chour, Rachel H. Ng, Rongyu Zhang, Dan Yuan, Jongchan Choi, Michaela McKasson, Pamela Troisch, Brett Smith, Lesley Jones, Andrew Webster, Yusuf Rasheed, Sarah Li, Rick Edmark, Sunga Hong, Kim M. Murray, Jennifer K. Logue, Nicholas M. Franko, Christopher G. Lausted, Brian Piening, Heather Algren, Julie Wallick, Andrew T. Magis, Kino Watanabe, Phil Mease, Philip D. Greenberg, Helen Chu, Jason D. Goldman, Yapeng Su, James R. Heath

“…Here, we describe Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT), an integrated experimental-computational framework designed for the high-throughput capture and analysis of CD8 T cells, with paired antigen, TCR sequence, and single-cell transcriptome. …”
Get full text

Copy number amplification of FLAD1 promotes the progression of triple-negative breast cancer through lipid metabolism by Xiao-Qing Song, Tian-Jian Yu, Yang Ou-Yang, Jia-Han Ding, Yi-Zhou Jiang, Zhi-Ming Shao, Yi Xiao

“…Through an integrated analysis of our TNBC multiomic dataset (n = 465) and subsequent experimental validation, we identify copy number amplification of the metabolic gene flavin-adenine dinucleotide synthetase 1 (FLAD1) as a crucial genetic event that drives TNBC progression. …”
Get full text

Uncovering functional lncRNAs by scRNA-seq with ELATUS by Enrique Goñi, Aina Maria Mas, Jovanna Gonzalez, Amaya Abad, Marta Santisteban, Puri Fortes, Maite Huarte, Mikel Hernaez

“…ELATUS enhances the detection of functional lncRNAs from scRNA-seq data, detecting their expression with higher concordance than standard methods with the ATAC-seq profiles in single-cell multiome data. Interestingly, the better results of ELATUS are due to its advanced performance with an inaccurate reference annotation such as that of lncRNAs. …”
Get full text

Single-cell and spatial characterization of plasmablast-like lymphoma cells in primary central nervous system lymphoma by Hiroki Kobayashi, Ryota Chijimatsu, Yusuke Naoi, Yoshihiro Otani, Ryo Mizuta, Kentaro Fujii, Joji Ishida, Hiroyuki Murakami, Hideki Ujiie, Kazuhiro Ikeuchi, Tomohiro Urata, Keisuke Seike, Hideaki Fujiwara, Noboru Asada, Nobuharu Fujii, Ken-ichi Matsuoka, Yasuharu Sato, Yoshinobu Maeda, Daisuke Ennishi

“…Here, we conducted single-cell and spatial multiomic analyses to elucidate the cellular and spatial heterogeneity and the microenvironment in PCNSL. …”
Get full text

Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice by Peiling Geng, Ni Zhao, Yufan Zhou, Reuben S. Harris, Yong Ge

“…Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. …”
Get full text

Oncolytic peptide LTX-315 induces anti-pancreatic cancer immunity by targeting the ATP11B-PD-L1 axis by Meng Wang, Xing Huang, Tingbo Liang, Tianyu Tang, Gang Zhang, Minghao Lu, Zhengtao Hong, Junming Huang, Xiao Zhi

“…Flow cytometry and immunohistochemistry were used to assess the immune microenvironment. Multiomic analysis was used to identify the potential target and down-streaming signaling pathway. …”
Get full text