Utilization of primary tumor samples for cancer neoantigen discovery by Yong Li, Steven A Rosenberg, Paul Robbins, Billel Gasmi, Todd D Prickett, Jared J Gartner, Devikala Gurusamy, Stephanie L Goff, Vid Leko, Victoria Hill, Frank J Lowery, Bradley Sinclair White, Sivasish Sindiri, Maria Parkhust, Noam Levin, Eric Groh, Shoshana T Levi, Amy R Copeland, Sanghyun Peter Kim

“…For the treatment of the latter, selecting cells for therapy typically involves laborious screening of TIL for recognition of autologous tumor-specific mutations, detected through next-generation sequencing of freshly resected metastatic tumors. Our study explored the feasibility of using archived formalin-fixed, paraffin-embedded (FFPE) primary tumor samples for cancer neoantigen discovery, to potentially expedite this process and reduce the need for resections normally required for tumor sequencing.Method Whole-exome sequencing was conducted on matched primary and metastatic colorectal cancer samples from 22 patients. …”
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Comparison of human-induced pluripotent stem cell-derived macrophages with peripheral blood-derived macrophages using single-cell genomics by ZHANG Yutong, HOU Guojun, SHEN Nan

“…Sequencing data for both IPSDMs and PBDMs were processed and analyzed using the seurat package in R software, with PBDMs annotated using the singleR package. …”
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Treatment Patterns of Follicular Lymphoma in the United States: A Claims Analysis by Scott F. Huntington, Sreevalsa Appukkuttan, Wenyi Wang, Yuxian Du, Sari Hopson, Svetlana Babajanyan

“…**Background:** A consensus is lacking on optimal treatment sequencing for follicular lymphoma (FL), the most common indolent lymphoma. …”
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Genomic, transcriptomic and metabolomic analyses of Amorphophallus albus provides insights into the evolution and resistance to southern blight pathogen by Longfei Duan, Longfei Duan, Jianfeng Qin, Gaoxin Zhou, Chuan Shen, Baofu Qin

“…IntroductionAmorphophallus albus, a perennial herb in the Araceae family, is a valuable cash crop known for its high production of konjac glucomannan and high disease resistance.MethodsIn this study, we present a high-quality, chromosome-scale genome assembly of A. albus using a combination of PacBio HiFi sequencing, DNBSEQ short-read sequencing, and Hi-C technology. …”
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Runaway Train: A Leaky Radiosensitive SCID with Skin Lesions and Multiple Lymphomas by Børre Fevang, Unn Merete Fagerli, Hanne Sorte, Harald Aarset, Håkon Hov, Marit Langmyr, Thomas Morten Keil, Ellen Bjørge, Pål Aukrust, Asbjørg Stray-Pedersen, Tobias Gedde-Dahl

“…The case underscores the importance of next-generation sequencing in the diagnosis of patients with suspected severe immunodeficiency.…”
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HIF-3α-Induced miR-630 Expression Promotes Cancer Hallmarks in Cervical Cancer Cells by Forming a Positive Feedback Loop by Qiaohui Gao, Zhenghua Ren, Shengyuan Jiao, Juan Guo, Xia Miao, Jin Wang, Junye Liu

“…Methods. We conducted RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) experiments to investigate the targets of HIF-3α or miR-630. …”
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Identification of Houge type of X-linked syndromic mental retardation caused by CNKSR2 truncated variants by Si-Hua Chang, Jie-Yuan Jin, Yi-Qiao Hu, Run-Yan Wang, Rong Xiang, Xia Wang

“…Methods Two Chinese MRXSHG families were recruited, and their genetic causes were investigated using whole-exome sequencing (WES), Sanger sequencing, and bioinformatics analysis. …”
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Health benefits of Grifola frondosa polysaccharide on intestinal microbiota in type 2 diabetic mice by Xiaoxiang Gao, Dan Liu, Luying Gao, Yuezhen Ouyang, Yuxi Wen, Chao Ai, Yuqing Chen, Chao Zhao

“…The changes of microbiota in faeces of the diabetic mice upon high fat diet were determined and the V3 region of the 16S rRNA was sequenced by Illumina MiSeq high-throughput sequencing platform. …”
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Multivariate stochastic modeling for transcriptional dynamics with cell-specific latent time using SDEvelo by Xu Liao, Lican Kang, Yihao Peng, Xiaoran Chai, Peng Xie, Chengqi Lin, Hongkai Ji, Yuling Jiao, Jin Liu

“…Abstract Recently, RNA velocity has driven a paradigmatic change in single-cell RNA sequencing (scRNA-seq) studies, allowing the reconstruction and prediction of directed trajectories in cell differentiation and state transitions. …”
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Soil Alveolata diversity in the undisturbed steppe and wheat agrocenoses under different tillage by N. B. Naumova, P. A. Barsukov, O. A. Baturina, O. A. Rusalimova, M. R. Kabilov

“…Microeukaryotes are vital for maintaining soil quality and ecosystem functioning, however, their communities are less studied than bacterial and fungal ones, especially by high throughput sequencing techniques. Alveolates are important members of soil microbial communities, being consumers and/or prey for other microorganisms. …”
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Genotype B of deformed wing virus and related recombinant viruses become dominant in European honey bee colonies by Fabrice Sircoulomb, Eric Dubois, Frank Schurr, Pierrick Lucas, Marina Meixner, Alicia Bertolotti, Yannick Blanchard, Richard Thiéry

“…Chimeric sequencing reads were used to locate the recombinant junctions along the DWV genome. …”
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Uncovering glycolysis-driven molecular subtypes in diabetic nephropathy: a WGCNA and machine learning approach for diagnostic precision by Chenglong Fan, Guanglin Yang, Cheng Li, Jiwen Cheng, Shaohua Chen, Hua Mi

“…Finally, the expression patterns of these hub genes were validated using single-cell sequencing data and quantitative real-time polymerase chain reaction (qRT-PCR). …”
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Impact of Notch3 Activation on Aortic Aneurysm Development in Marfan Syndrome by Kathryn Jespersen, Chenxin Li, Rishi Batra, Christopher A. Stephenson, Paul Harding, Kylie Sestak, Ryan T. Foley, Harrison Greene, Trevor Meisinger, Jason R. Cook, B. Timothy Baxter, Wanfen Xiong

“…Results. The murine RNA-sequencing data were validated with mouse and human MFS aortic tissue, demonstrating elevated Notch3 activation in MFS. …”
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2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. by Luis E Hernandez-Castro, Marta Paterno, Anita G Villacís, Björn Andersson, Jaime A Costales, Michele De Noia, Sofía Ocaña-Mayorga, Cesar A Yumiseva, Mario J Grijalva, Martin S Llewellyn

“…Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. …”
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An Extremely Rare SRD5A2 Gene c.485A>C Mutation in a Compound Heterozygous Newborn with Disorders of Sex Development First Identified in Vietnam by Phan Tuong Quynh Le, Thanh Nha Uyen Le, Thi Thanh Binh Nguyen, Minh Thao Nguyen, Thi Minh Thi Ha

“…This compound heterozygous mutation was first detected by next-generation sequencing. By Sanger sequencing, we confirmed that the c.485A>C mutation was maternal inherited, whereas the c.680G>A mutation was paternal inherited. …”
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Novel MFSD8 Variants in a Chinese Family with Nonsyndromic Macular Dystrophy by Qin Xiang, Yanna Cao, Hongbo Xu, Zhijian Yang, Liang Tang, Ju Xiang, Jianming Li, Hao Deng, Lamei Yuan

“…Ophthalmic examinations were performed, and genomic DNA was extracted from available family members. Whole exome sequencing of two members (the proband and her unaffected mother) and Sanger sequencing in available family members were performed to screen potential pathogenic variants. …”
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Voluntary wheel running ameliorated the deleterious effects of high-fat diet on glucose metabolism, gut microbiota and microbial-associated metabolites by Ling Zhang, Wenyu Zou, Yongyan Hu, Honghua Wu, Ying Gao, Junqing Zhang, Jia Zheng

“…An integrative 16S rDNA sequencing and metabolites profiling was synchronously performed to characterize the effects of voluntary wheel running on gut microbiota and metabolites. …”
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Native Microbiota of Rapeseed Cake as Potential Source of Industrial Producers by Olga P. Sverdlova, Elizaveta V. Podshivalova, Natalya Yu. Sharova, Daria D. Belova

“…The metagenomic analysis of the microbial taxonomy involved sequencing on the Illumina platform. The experiment revealed 16 types of colonies with different morphology. …”
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scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder by Xiaoxu Cui, Renkai Wu, Yinghao Liu, Peizhan Chen, Qing Chang, Pengchen Liang, Changyu He

“…Abstract Background Single-cell RNA sequencing (scRNA-seq) has transformed biological research by offering new insights into cellular heterogeneity, developmental processes, and disease mechanisms. …”
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MOLECULAR STUDY OF THE RED-LEGGED HAM BEETLE NECROBIA RUFIPES (DE GEER, 1775) (COLEOPTERA: CLERIDAE) FROM THE ERBIL PROVINCE OF THE KURDISTAN REGION, IRAQ by H. M. Muhammad, P. A. Jalil, N. A. Mawlood, K. M. Taha

“…This research presented the Ts:Tv mutation ratio through a sequencing technique for the species with reliable results. …”
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