The acceptability of blood spot screening and genome sequencing in newborn screening: a systematic review examining evidence and frameworks by Duncan Chambers, Susan Baxter, Anastasios Bastounis, Katherine Jones, Burak Kundakci, Anna Cantrell, Andrew Booth

“…We included quantitative and qualitative studies that investigated the acceptability to parents/carers of newborn blood spot screening or genetic sequencing. Quantitative studies were narratively synthesised, and theories/frameworks identified and evaluated. …”
Get full text

Immune repertoire sequencing reveals differences in treatment response to camrelizumab plus platinum-based chemotherapy in advanced ESCC by Xiaoling Zhang, Xiaoling Zhang, Xiaoling Zhang, Wenqi Zhao, Yunyi Du, Fei Su, Yuexiang Zhang, Hui Wang, Yongai Li, Min Liu, Yangjun Gao, Linlin Cai, Tingting Feng, Mei Wang, Chunmei Yao, Ning Xu, Yu Wang, Guohua Song, Guohua Song, Guohua Song, Wenqing Hu, Jun Zhao

“…This study evaluated the efficacy and safety of camrelizumab combined with platinum-based chemotherapy (taxanes [T] or fluorouracil agents [F] plus platinum [P] drugs) as the first-line treatment in advanced esophageal squamous cell carcinoma (ESCC), using immune repertoire sequencing (IRS) to explore treatment response mechanism. …”
Get full text

Identification of potential molecular targets of luteolin in the treatment of hepatocellular carcinoma based on network pharmacology and transcriptome sequencing technology by Yunqi Han, Huijun Wu, Xin Zhang, Wei Lv, Yang Xiong, Xinyuan Tian, Yunfeng Xiao, Hongwei Cui

“…The anti-HCC effects of LUT were evaluated in vitro by assessing its impact on SMMC-7721 and HepG2 cell viability, apoptosis, migration, and invasion. …”
Get full text

Landscape of antisense genes in the human genome and identification of new human hepatic antisense RNAs by long-read sequencing by Juan Jose Rojo-Carrillo, Pedro Garrido-Rodríguez, Maria Llamas-López, Rosa Cifuentes-Riquelme, Jose Padilla, Bruno Ramos-Molina, Maria Luisa Lozano, Belen de la Morena-Barrio, Maria Eugenia de la Morena-Barrio, Javier Corral

“…Results We performed an in-depth review of AS genes in Ensembl and evaluated the expression of AS genes in human liver by third-generation RNA sequencing methods. …”
Get full text

Vulnerability-Based Economic Loss Rate Assessment of a Frame Structure Under Stochastic Sequence Ground Motions by Zheng Zhang, Yunmu Jiang, Zixin Liu

Get full text

Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers. by Xinzhong Li, Andrew J Buckton, Samuel L Wilkinson, Shibu John, Roddy Walsh, Tomas Novotny, Iveta Valaskova, Manu Gupta, Laurence Game, Paul J R Barton, Stuart A Cook, James S Ware

“…<h4>Methodology/principal findings</h4>We evaluated two next-generation sequencing (NGS) platforms for molecular diagnostics. …”
Get full text

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs. by Alexander T Dilthey, Pierre-Antoine Gourraud, Alexander J Mentzer, Nezih Cereb, Zamin Iqbal, Gil McVean

“…Extensive hyperpolymorphism and sequence similarity between the HLA genes, however, pose problems for accurate read mapping and make HLA type inference from whole-genome sequencing data a challenging problem. …”
Get full text

Non-contrast enhanced visualization of the equine foot vasculature in a cadaver model using time-of-flight sequence by Bianca A. Underberg, Bianca A. Underberg, Sabine Kaessmeyer, Daniela Schweizer, Barbara Drews, Elke Van der Vekens

“…Visibility of the coronary plexus, sublamellar plexus, palmar plexus, terminal arch and its respective branches, solar plexus, and the marginal circumflex vessels was evaluated in a total of 74 sequences.ResultsTwelve EF of 10 horses were scanned. …”
Get full text

Full-length 16S rRNA Sequencing Reveals Gut Microbiome Signatures Predictive of MASLD in children with obesity by Yu-Cheng Lin, Chi-Chien Wu, Yun-Er Li, Chun-Liang Chen, Chia-Ray Lin, Yen-Hsuan Ni

“…The AUC for the model based on FL16S sequencing data (86.98%) was significantly higher than that based on V3-V4 sequencing data (70.27%), as determined by DeLong's test (p = 0.008). …”
Get full text

The complete genome sequence of “Candidatus Liberibacter asiaticus” strain 9PA and the characterization of field strains in the Brazilian citriculture by Michele F. S. Dutra, Priscila A. Silva, Jianchi Chen, Nelson A. Wulff

“…Our study presents the first fully sequenced Brazilian strain of CLas, designated as 9PA, and includes an analysis of two prophages occurring in this strain. …”
Get full text

Metagenomic next-generation sequencing of cerebrospinal fluid: a diagnostic approach for varicella zoster virus-related encephalitis by Jin Tang, Kaimeng Wang, Haoming Xu, Jingzhe Han

“…In this study, we used metagenomic next-generation sequencing (mNGS) to rapidly and accurately detect and identify the VZV pathogen directly from cerebrospinal fluid (CSF) samples, aiming to achieve a definitive diagnosis for encephalitis patients.MethodsIn this retrospective study, we analyzed the clinical characteristics and laboratory evaluations of 28 patients at the Harrison International Peace Hospital in Hebei, China, between 2018 and 2024. …”
Get full text

EPI-DynFusion: enhancer-promoter interaction prediction model based on sequence features and dynamic fusion mechanisms by Ao Zhang, Jianhua Jia, Mingwei Sun, Xin Wei

“…This model begins by encoding DNA sequences using pre-trained DNA embeddings and extracting local features through convolutional neural networks (CNNs). …”
Get full text

Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing by Takuya Hosoda, Masahiro Suzuki, Takahiro Matsuno, Kenjiro Matsui, Koji Ohyama, Yohei Doi

“…To address this limitation, we evaluated whole-genome sequencing (WGS) as an alternative method for identifying anaerobic bacteria in blood cultures. …”
Get full text

KeyMPs: One-Shot Vision-Language Guided Motion Generation by Sequencing DMPs for Occlusion-Rich Tasks by Edgar Anarossi, Yuhwan Kwon, Hirotaka Tahara, Shohei Tanaka, Keisuke Shirai, Masashi Hamaya, Cristian C. Beltran-Hernandez, Atsushi Hashimoto, Takamitsu Matsubara

“…To address this limitation, we propose Keyword Labeled Primitive Selection and Keypoint Pairs Generation Guided Movement Primitives (KeyMPs), a framework that combines VLMs with sequencing of DMPs. KeyMPs use VLMs&#x2019; high-level reasoning capability to select a reference primitive through keyword labeled primitive selection and VLMs&#x2019; spatial awareness to generate spatial scaling parameters used for sequencing DMPs by generalizing the overall motion through keypoint pairs generation, which together enable one-shot vision-language guided motion generation that aligns with the intent expressed in the multimodal input. …”
Get full text

Insertion sequences accelerate genomic convergence of multidrug resistance and hypervirulence in Klebsiella pneumoniae via capsular phase variation by Da-Wei Wei, Yuqin Song, Yi Li, Gang Zhang, Qi Chen, Linhuan Wu, Jiangqing Huang, Xueru Tian, Chao Wang, Jie Feng

“…Capsule-deficient mutants were analyzed using genetic sequencing to identify the types and insertion sites of insertion sequences (IS). …”
Get full text

Screening, Genome Sequencing and Tolerance Mechanism Analysis of Bile Acid-resistant Pediococcus pentosaceus 32M07 by Qingping HONG, Ziqing DI, Daqing SUN, Xinrui DU, Hongfei LI, Yuxi YAO, Xianglin GE

“…To further investigate the bile acid metabolism and tolerance mechanisms of probiotics, the bile acid resistance of 165 strains of lactic acid bacteria was evaluated and characterized. The strain 32M07, which demonstrated the highest bile salt hydrolase activity, was subjected to whole-genome sequencing and an analysis of its bile acid resistance mechanisms. …”
Get full text

Benchmarking Differential Abundance Tests for 16S microbiome sequencing data using simulated data based on experimental templates. by Eva Kohnert, Clemens Kreutz

“…MetaSPARSim: a 16S rRNA gene sequencing count data simulator. BMC Bioinformatics. 2019;20:416. https://doi.org/10.1186/s12859-019-2882-6 PMID: 31757204) MIDASim (He M, Zhao N, Satten GA. …”
Get full text

Non-Invasive Prenatal Testing with Next Generation Sequencing Methods in Birth Defect Pregnancy: A Pilot Study by Anom Suardika, Anak Agung Ngurah Jaya Kusuma, Ni Gusti Ayu Manik Ermayanti, Endang Sri Widiyanti, I Gusti Ngurah Agung Satria Wibawa, Divika Silvana, Anak Agung Gede Raka Budayasa, Ni Nyoman Ayu Dewi, I Made Jawi, H. Sunny Sun, Yen-An Tang

“…KEYWORDS: G-banding karyotyping, next generation sequencing, non-invasive prenatal testing…”
Get full text

Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients by Ning Zheng, Hai-Long Yu, Bing-Jie Zhang, Dan Wang, Ya-Liang Ji, Lu-Lu Dai, Wen Li, Sheng-Hui Li, Zhi-Liang Hu, Zhi-Liang Hu, Yi-Shan Zheng

“…Principal coordinates analysis was used to evaluate disease-related variation, and virus–bacteria associations in BALF were investigated via Spearman correlation.ResultsSequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. …”
Get full text

Pathogenesis of Graves’ Disease Determined Using Single-Cell Sequencing with Thyroid Autoantigen Peptide Stimulation in B Cells by Genki Kobayashi, Takuro Okamura, Yoshitaka Hashimoto, Kimiko Sakai, Madoka Sumi, Dan Imai, Nobuko Kitagawa, Masahide Hamaguchi, Michiaki Fukui

“…This study reports the use of single-cell RNA sequencing to evaluate B cells in the peripheral blood mononuclear cells (PBMCs) and intrathyroidal blood mononuclear cells of patients with Graves’ disease (GD) undergoing thyroidectomy. …”
Get full text