Complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770 from coal mine of Hongcheon on Republic of Korea by Min-Kyu Park, Yeong-Jun Park, Myung-Suk Kang, Min-Ha Kim, Soo-Young Kim, Jae-Ho Shin

“…Abstract Objectives The data were collected to obtain the complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770, isolated from the rhizosphere of Sasamorpha in a heavy metal-contaminated coal mine in Hongcheon, Republic of Korea. …”
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The Potential Therapeutic Targets of Anlotinib in Osteosarcoma: Characterization Based on Patient‐Derived Xenografts and Next‐Generation Sequencing by Zuoyao Long, Yajie Lu, Minghui Li, Jing Li, Guojing Chen, Fengwei Wang, Qi Wang, Liangbi Xiang, Zhen Wang

“…ABSTRACT Background The aim of this study was to analyze the potential therapeutic targets of anlotinib using the patient‐derived xenografts (PDX) and evaluate the efficacy of the combination of chemotherapy and anlotinib in osteosarcoma patients before surgery. …”
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Integrating single-cell RNA sequencing, WGCNA, and machine learning to identify key biomarkers in hepatocellular carcinoma by Gang Wang, Jiaxing Zhang, Yirong Li, Yuyu Zhang, Weiwei Dong, Hengquan Wu, Jinglan Wang, Peiqing Liao, Ziqiang Yuan, Tao Liu, Wenting He

“…Abstract The microarray and single-cell RNA-sequencing (scRNA-seq) datasets of hepatocellular carcinoma (HCC) were downloaded from the Gene Expression Omnibus (GEO) database. …”
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Epidemiological surveillance and phylogenetic diversity of Orthohantavirus hantanense using high-fidelity nanopore sequencing, Republic of Korea. by Kyungmin Park, Jongwoo Kim, Juyoung Noh, Seong-Gyu Kim, Hee-Kyung Cho, Kijin Kim, Ye-Rin Seo, Taehun Lim, Seonghyeon Lee, Jaeyeon Lee, Seung In Lim, Young Hoon Joo, Buddle Lee, Seok Hyeon Yun, Changbo Park, Won-Keun Kim, Jin-Won Song

“…This study aimed to evaluate the application of advanced nanopore sequencing and bioinformatics to generate complete genome sequences of HTNV, with the objective of accurately identifying infection sources and analyzing their genetic diversity.…”
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New insights on taxonomy, phylogeny and population genetics of Leishmania (Viannia) parasites based on multilocus sequence analysis. by Mariana C Boité, Isabel L Mauricio, Michael A Miles, Elisa Cupolillo

“…The Leishmania genus comprises up to 35 species, some with status still under discussion. The multilocus sequence typing (MLST)--extensively used for bacteria--has been proposed for pathogenic trypanosomatids. …”
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Exploring the Microbial Landscape of Bone and Joint Infections: An Analysis Using 16S rRNA Metagenome Sequencing by Maimaiti Z, Liu L

“…Zulipikaer Maimaiti, Liang Liu Department of Orthopedics, Beijing Luhe Hospital, Capital Medical University, Beijing, 101149, People’s Republic of ChinaCorrespondence: Liang Liu, Email Liuliang@ccmu.edu.cnBackground: Bone and joint infections (BJIs) are challenging to diagnose. This study evaluated the utility of 16S rRNA gene sequencing in diagnosing BJIs, comparing it with conventional bacterial culture to explore microbial diversity in orthopedic infections.Methods: Thirty patients with BJIs were enrolled from January 2019 to September 2020 at a single orthopedic center. …”
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Global pneumococcal sequence cluster lineage for invasive pneumococcal isolates in Denmark from summer 2019 to 2023 by Hans-Christian Slotved, Thor Bech Johannesen, Marc Stegger, Kurt Fuursted

“…This study explores the dynamics of Global Pneumococcal Sequence Clusters (GPSCs) in Denmark from 2019 to 2023 using whole-genome sequencing (WGS) on IPD isolates from all age groups received at Statens Serum Institut (SSI). …”
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The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies. by Muthannan A Ramakrishnan, Zheng Jin Tu, Sushmita Singh, Ashok K Chockalingam, Marie R Gramer, Ping Wang, Sagar M Goyal, My Yang, David A Halvorson, Srinand Sreevatsan

“…<h4>Methodology and principal findings</h4>We evaluated quasispecies and mixed infections by de novo sequencing the whole genomes of 10 virus isolates, including eight avian influenza viruses grown in embryonated chicken eggs (six waterfowl isolates - five H3N2 and one H4N6; an H7N3 turkey isolate; and a bald eagle isolate with H1N1/H2N1 mixed infection), and two tissue cultured H3N2 swine influenza viruses. …”
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Facilitating Cross-border Viral Sequencing Through Nucleic Acid Sample Transport Using Dry Cards by Lili Wang, Qikai Yin, Alie Brima Tia, Fengyu Tian, Liping Gao, Kai Nie, Kang Xiao, Xuejun Ma, Xiaoping Dong, Doris Harding, Xiaozhou He, George F. Gao

“…(1) Background: A safe and effective nucleic acid sample transportation method was developed that is suitable for underdeveloped areas which lack advanced sequencing capabilities, specifically for virus genomic sequencing and infectious disease monitoring. (2) Methods: This study evaluated the use of Flinders Technology Associates (FTA) cards for transporting amplified whole-genome DNA from 120 SARS-CoV-2-positive nasopharyngeal swab samples in Sierra Leone. …”
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Resolving an Asteroseismic Catastrophe: Structural Diagnostics from p-mode Phase Functions off the Main Sequence by J. M. Joel Ong, Christopher J. Lindsay, Claudia Reyes, Dennis Stello, Ian W. Roxburgh

“…On the main sequence, the asteroseismic small frequency separation δν _02 between radial and quadrupole p -modes is customarily interpreted to be a direct diagnostic of internal structure. …”
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Whole mitochondrial DNA sequencing improves resolution of population structure for Pacific green turtles (Chelonia mydas) by Amy Frey, Erin L. LaCasella, Michael P. Jensen, Michael P. Jensen, Peter H. Dutton

“…Understanding these population dynamics is crucial for effective conservation and management, as distinct nesting populations may face different threats. This study evaluates the use of whole mitochondrial genome sequencing to improve genetic resolution of population structure and enhance the accuracy of mixed stock analysis (MSA). …”
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Detection of single nucleotide polymorphisms associated with litter size in goats using genotyping-by-sequencing and association analysis by Satoshi Kubota, Thara Wongdee, Pramote Paengkoum

“…Methods Nine reproductive traits were evaluated, including litter size and age at the first, second, and third parities, as well as intervals between parities, in 31 female goats (2 purebred and 29 crossbred goats in various combinations of seven breeds). …”
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Genetic landscape of Romanian children with inborn errors of immunity via gene panels, exome, and genome sequencing by Cristina-Loredana Pantea, Mihaela Bataneant, Cristian G. Zimbru, Bogdan Dragulescu, Catalin Vasile Munteanu, Adela Chirita-Emandi

“…Sanger sequencing, next generation sequencing panels with genes associated with IEI (1–474 genes), WES and WGS were used. …”
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Candidate gene mutations of patients with astrocytoma who present with seizures: evidence from whole exome sequencing by Kanitpong Phabphal, Pongsakorn Choochuen, Pongsakorn Choochuen, Anukoon Kaewborisutsakul, Thara Tunthanathip, Surasak Sangkhathat

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Impact of Pseudomonas aeruginosa biofilm formation by different sequence types on treating lower limb vascular infections by Yudi Wang, Qian Xiao, Qiong Yang, Yulin Long, Zhibiao Jiang, Tantao Zhang, Ying Hu, Bingru Gao, Xuanyu Chen, Ting Wang, Linlin Xiao

“…By employing multilocus sequence typing, antimicrobial susceptibility testing, biofilm gene quantification, growth kinetics assays, Galleria mellonella virulence experiments, and phylogenetic reconstruction, we systematically evaluated the relationships between these strains'biofilm formation and virulence. …”
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Validation of high-throughput sequencing-based test system for detection of microsatellite instability in colorectal cancer samples by A. A. Lebedeva, A. N. Taraskina, A. I. Kavun, E. V. Belova, T. V. Grigor'eva, O. A. Kuznetsova, D. A. Kravchuk, L. D. Belyaeva, V. E. Nikulin, E. D. Khomenko, V. A. Mileyko, A. A. Tryakin, M. Yu. Fedyanin, M. V. Ivanov

“…MSI identification using high-throughput sequencing (next generation sequencing, NGS) is of special interest because it allows to analyze a large number of microsatellites and simultaneously study alterations in therapeutically significant genes.Aim. …”
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An immune scoring system predicts prognosis and immune characteristics in lung adenocarcinoma brain metastases by RNA sequencing by Gang Xiao, Guilong Tanzhu, Xuan Gao, Lifeng Li, Zhiyuan Liu, Xuefeng Xia, Rongrong Zhou

“…We comprehensively evaluated the immunological role of GYMS based on gene expression profile of LUAD BrMs by systematically correlating GYMS with immunological characteristics and immunotherapy responsiveness in the BrMs. …”
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A structure-based tool to interpret the significance of kinase mutations in clinical next generation sequencing in cancer by Amith Rangarajan, Ilona Sviezhentseva, Emma Gunderson, Yana Pikman, Yana Pikman, Matthew P. Jacobson, Beth Apsel Winger, Beth Apsel Winger

“…IntroductionClinical workflows to analyze variants of unknown significance (VUSs) found in clinical next generation sequencing (NGS) are labor intensive, requiring manual analysis of published data for each variant. …”
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Diagnostic performance of the DISQVER metagenomic sequencing tool for the identification of pathogens in febrile neutropenic patients: the ADNEMIA trial by Geneviève Héry-Arnaud, Christophe Burucoa, Marie Kempf, David Boutoille, Yohann Foucher, Philippe Lanotte, Maxime Pichon, Stéphane Corvec, Cécile Le Brun, Helene Pailhories

“…However, blood culture (the reference test) is limited for several reasons: such as fastidious culture, antibiotic treatment prior to sampling or insufficient sample volume. Sequencing technologies have led to the development of diagnostic approaches based on the detection of circulating DNA in blood. …”
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A Breast Cancer Polygenic Risk Score Validation in 15,490 Brazilians Using Exome Sequencing by Flávia Eichemberger Rius, Rodrigo Santa Cruz Guindalini, Danilo Viana, Júlia Salomão, Laila Gallo, Renata Freitas, Cláudia Bertolacini, Lucas Taniguti, Danilo Imparato, Flávia Antunes, Gabriel Sousa, Renan Achjian, Eric Fukuyama, Cleandra Gregório, Iuri Ventura, Juliana Gomes, Nathália Taniguti, Simone Maistro, José Eduardo Krieger, Yonglan Zheng, Dezheng Huo, Olufunmilayo I. Olopade, Maria Aparecida Azevedo Koike Folgueira, David Schlesinger

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