A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes by Min-Jung Kim, Si-Cho Kim, Young-Joon Kim

“…However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. …”
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Characterization of the ZDSD Rat: A Translational Model for the Study of Metabolic Syndrome and Type 2 Diabetes by Richard G. Peterson, Charles V. Jackson, Karen Zimmerman, Willem de Winter, Norman Huebert, Michael K. Hansen

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Spatiotemporal range dynamics and conservation optimization for endangered medicinal plants in the Himalaya by Fu-Lv Liu, Winnie Wanjiku Mambo, Jie Liu, Guang-Fu Zhu, Raees Khan, Abdullah, Shujaul Mulk Khan, Lu Lu

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Early tolerance and late persistence as alternative drug responses in cancer by Simona Punzi, Davide Cittaro, Guido Gatti, Gemma Crupi, Oronza A. Botrugno, Antonino Alex Cartalemi, Alon Gutfreund, Caterina Oneto, Valentina Giansanti, Chiara Battistini, Giovanni Santacatterina, Lucrezia Patruno, Ilaria Villanti, Martina Palumbo, Daniel J. Laverty, Francesca Giannese, Alex Graudenzi, Giulio Caravagna, Marco Antoniotti, Zachary Nagel, Ugo Cavallaro, Luisa Lanfrancone, Timothy A. Yap, Giulio Draetta, Nathalie Balaban, Giovanni Tonon

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A revised classification of Dryopteridaceae based on plastome phylogenomics and morphological evidence, with the description of a new genus, Pseudarachniodes by Zheng-Yu Zuo, Germinal Rouhan, Shi-Yong Dong, Hong-Mei Liu, Xin-Yu Du, Li-Bing Zhang, Jin-Mei Lu

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Development and validation of a nomogram for predicting immune-mediated colitis in lung cancer patients treated with immune checkpoint inhibitors: a retrospective cohort study in C... by Qianjie Xu, Xiaosheng Li, Yuliang Yuan, Guangzhong Liang, Zuhai Hu, Wei Zhang, Ying Wang, Haike Lei

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Combination of Two‐Stage Continuous Feeding and Optimized Synthetic Medium Increases Lipid Production in Lipomyces starkeyi by Chih‐Chan Wu, Kenji Okano, Pijar Religia, Yuki Soma, Masatomo Takahashi, Yoshihiro Izumi, Takeshi Bamba, Kohsuke Honda

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De novo transcriptome assembly of the Perna viridis: A novel invertebrate model for ecotoxicological studies by V. G. Vysakh, Sandhya Sukumaran, Gopalakrishnan A.

“…This dataset greatly expands the omics resources of bivalve databases and advances our knowledge of transcriptomics, molecular biology, environmental toxicology, and cancer research.…”
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In silico design of an epitope-based vaccine ensemble for fasliolopsiasis by Ruchishree Konhar, Ruchishree Konhar, Kanhu Charan Das, Kanhu Charan Das, Aiboklang Nongrum, Rohan Raj Samal, Shailesh Kumar Sarangi, Devendra Kumar Biswal, Devendra Kumar Biswal

“…Finding successful vaccination antigen combinations from these huge number of genes/proteins in the available omics datasets is the key in combating these neglected tropical diseases. …”
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Utility of Integrated Analysis of Pharmacogenomics and Pharmacometabolomics in Early Phase Clinical Trial: A Case Study of a New Molecular Entity by Jaeseong Oh, Sojeong Yi, Namyi Gu, Dongseong Shin, Kyung-Sang Yu, Seo Hyun Yoon, Joo-Youn Cho, In-Jin Jang

“…Through the integrated omics analysis, we could understand the mechanism of inter-individual variability in drug exposure and in adverse response. …”
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Comprehensive genome annotation of Trilocha varians, a new model species of Lepidopteran insects by Jung Lee, Toshiaki Fujimoto, Katsushi Yamaguchi, Shuji Shigenobu, Ken Sahara, Toru Shimada

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LcProt: Proteomics‐based identification of plasma biomarkers for lung cancer multievent, a multicentre study by Hengrui Liang, Runchen Wang, Ran Cheng, Zhiming Ye, Na Zhao, Xiaohong Zhao, Ying Huang, Zhanpeng Jiang, Wangzhong Li, Jianqi Zheng, Hongsheng Deng, Yu Jiang, Yuechun Lin, Yun Yan, Lei Song, Jie Li, Xin Xu, Wenhua Liang, Jun Liu, Jianxing He

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Inter-Laboratory Validation of Method to Determine Residual Enrofloxacin in Chicken Meat by Joo Hee Chung, Kun Cho, Seongnyeon Kim, So Hyeon Jeon, Jeoung Hwa Shin, Jueun Lee, Yun Gyong Ahn

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Tumor-Associated Macrophages and Neutrophils in Tumor Microenvironment by Jaehong Kim, Jong-Sup Bae

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Discovery of a novel viroid‐like circular RNA in colorectal cancer by Meini Wu, Wenliang Li, Ningzhu Hu, Changning Liu, Jianfang Li, Yanhan Li, Ning Xu, Jiandong Shi, Jing Sun, Jing Li, Yunzhang Hu

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Network analysis uncovers the master role of WRKY transcription factors in Arabidopsis thaliana response to N-acyl homoserine lactones by Yongming Duan, Min Han, Maja Grimm, Adam Schikora

“…Methods Weighted gene co-expression network analysis (WGCNA), multi-omics network analysis, and reverse transcription quantitative PCR (RT-qPCR) assays were used to identify key genes in AHL signaling. …”
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Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity by Antony Cougnoux, Loay Mahmoud, Per A. Johnsson, Alper Eroglu, Louise Gsell, Jakob Rosenbauer, Rickard Sandberg, Jean Hausser

“…Abstract Combining 3D cultures such as tumor spheroids and organoids with spatial omics holds great potential for tissue biology and cancer research. …”
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Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics by Honggui Wu, Maoxu Wang, Yinghui Zheng, X. Sunney Xie

“…Collectively, we developed the sensitive, high-throughput dscHi-C and its multi-omics derivative, dscHi-C-multiome, demonstrating their potential for large-scale cell atlas studies in development and disease.…”
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Non-negligible Occurrence of Errors in Gender Description in Public Data Sets by Jong Hwan Kim, Jong-Luyl Park, Seon-Young Kim

“…Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. …”
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A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions by Xi Xi, Jiaqi Li, Jinmeng Jia, Qiuchen Meng, Chen Li, Xiaowo Wang, Lei Wei, Xuegong Zhang

“…This method to analyze single-cell multi-omics data demonstrates how the interpretable design of neural networks can better decode biological systems.…”
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