Genome-Wide Methylation Sequencing to Identify DNA Methylation Markers for Early-stage Hepatocellular Carcinoma in Liver and Blood by Siyu Fu, Ruben G. Boers, Joachim B. Boers, Pam E. van der Meeren, Jean Helmijr, Vanja de Weerd, Michail Doukas, Maurice Jansen, Bettina E. Hansen, Roeland F. de Wilde, Dave Sprengers, Joost Gribnau, Saskia M. Wilting, José D. Debes, Andre Boonstra

“…The selected DMMs with and without ASAP/GAAD score were further evaluated in 180 blood samples. Additionally, MeD-seq was performed to validate the results on blood. …”
Get full text

Precise Genotype Selection in “PSL2-Xa21” Rice Introgression Lines Using Whole Genome Sequencing by Walailak Laothaworn, Natchanon Meesa, Kumrop Ratanasut, Tepsuda Rungrat, Kittisak Buddhachat, Kawee Sujipuli, Phithak Inthima

“…This study improved BB resistance in ‘PSL2’ by introgressing the Xa21 gene, a broad-spectrum resistance gene from the donor parent ‘IRBB21’ through backcross breeding combined with whole genome sequencing (WGS)-assisted selection. Three BC5F6 introgression lines were evaluated for agronomic performance and BB resistance under field conditions. …”
Get full text

Long-read genome and RNA sequencing resolve a pathogenic intronic germline LINE-1 insertion in APC by Alexandra A. Baumann, Lisanne I. Knol, Marie Arlt, Tim Hutschenreiter, Anja Richter, Thomas J. Widmann, Marcus Franke, Karl Hackmann, Sylke Winkler, Daniela Richter, Isabel Spier, Stefan Aretz, Daniela Aust, Joseph Porrmann, Doreen William, Evelin Schröck, Hanno Glimm, Arne Jahn

“…The variant segregated with the phenotype in several family members allowing its evaluation as likely pathogenic. This study supports the utility of long-read DNA sequencing and complementary RNA approaches to tackle unsolved cases of hereditary disease.…”
Get full text

Whole genome sequencing of promising Lactobacillus delbrueckii subsp. bulgaricus strains isolated from Egyptian dairy products for probiotic characteristics by Mostafa F. El-Hosseny, Mervat G. Hassan, M. O. Abdel-Monem, Mohammed G. Seadawy

“…Only three promising isolates were subjected for whole genome sequence with high-output next generation technology and the obtained data was subjected to a full bioinformatics analysis. …”
Get full text

Genome-wide identification and expression analysis of the MORF gene family in celery reveals their potential role in chloroplast development by Pei-Zhuo Liu, Ya-Hui Wang, Yue-Hua Sun, Yong-Ju Wei, Xu Sun, Meng-Yao Li, Guo-Fei Tan, Ai-Sheng Xiong

“…Chlorophyll is an important nutrient in celery and one of the main indexes of quality evaluation. RNA editing in chloroplasts is an important factor affecting chloroplast development and chlorophyll biosynthesis. …”
Get full text

Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches by Yari Van Laere, Yari Van Laere, Marie-Alice Fraiture, Andrea Gobbo, Sigrid C. J. De Keersmaecker, Kathleen Marchal, Kathleen Marchal, Nancy H. C. Roosens, Kevin Vanneste

“…We evaluated the potential of whole genome sequencing (WGS) and metagenomics approaches, including nanopore long-read sequencing, to verify both authenticity (i.e., the labeled strain) and biological purity (i.e., the absence of any undesired genetic material) of commercial Bacillus thuringiensis bioinsecticides. …”
Get full text

Cutibacterium acnes of single locus sequence type clade C strains exhibit low susceptibility to benzoyl peroxide by Natsumi Sakaguchi, Shoji Seyama, Ryota Oba, Nobukazu Hayashi, Hidemasa Nakaminami

“…We previously found that no clade C strains, as determined by single locus sequence typing (SLST), were found before the introduction of BPO in Japan. …”
Get full text

Using cerebrospinal fluid nanopore sequencing assay to diagnose tuberculous meningitis: a retrospective cohort study in China by Lihong Zhou, Xingwu Zou, Yan Yong, Qin Hu

“…Objective This study aimed to evaluate the efficiency of nanopore sequencing for the early diagnosis of tuberculous meningitis (TBM) using cerebrospinal fluid and compared it with acid-fast bacilli (AFB) smear, mycobacterial growth indicator tube culture and Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF).Design Single-centre retrospective study.Setting The Tuberculosis Diagnosis and Treatment Center of Zhejiang Chinese and Western Medicine Integrated Hospital.Participants We enrolled 64 adult patients with presumptive TBM admitted to our hospital from August 2021 to August 2023.Methods We calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of AFB smear, culture, Xpert MTB/RIF and nanopore sequencing to evaluate their diagnostic efficacy compared with a composite reference standard for TBM.Results Among these 64 patients, all tested negative for TBM by AFB smear. …”
Get full text

The clinical utility and prognostic value of next-generation sequencing for measurable residual disease assessment in acute myeloid leukemia by Yu Liu, Huanchen Cheng, Meng Sun, Tiejun Gong, Jun Ma

“…Background: Next-generation sequencing (NGS) offers a method for measurable residual disease (MRD) assessment by detecting leukemia-associated genetic mutations. …”
Get full text

The immunogenic potential of an optimized mRNA lipid nanoparticle formulation carrying sequences from virus and protozoan antigens by Renata S. Fernandes, Gabriela de Assis Burle-Caldas, Sarah Aparecida Rodrigues Sergio, Ana Flávia Bráz, Nathália Pereira da Silva Leite, Milton Pereira, Juliana de Oliveira Silva, Natália Satchiko Hojo-Souza, Bianca de Oliveira, Ana Paula S. Moura Fernandes, Flávio Guimarães da Fonseca, Ricardo Tostes Gazzinelli, Diego dos Santos Ferreira, Santuza M. Ribeiro Teixeira

Get full text

Bioremediation of Restaurant Wastewater using Immobilized Green Microalgae, (Botryococcus Sp.) on Sequence Batch Reactor Storage Design by Y. Apparao, N.M. Apandi, N.M. Sunar, S.N.H. Ariffin, R. Nagarajah, R. Afifee, S. Moganathan, P. Pietrusiewicz

“…This study aims to design a Sequence Batch Reactor (SBR) equipped with microalgae microbeads (Botryococcus sp.), to examine the applicability of SBR technology in greywater treatment specifically evaluating the efficiency of SBR performance and to measure the efficiency in removing pollutant greywater of microalgae beads. …”
Get full text

A long-read sequencing approach to high-resolution profiling of bacterioplankton diversity in a shallow freshwater lake by Stephanie O. Castro Márquez, Viktor R. Tóth, Sofiia Kolchanova, Walter W. Wolfsberger, Taras K. Oleksyk

“…Abstract Lake Balaton, a large shallow freshwater lake in Hungary, exhibits diverse bacterioplankton communities influenced by various environmental factors. This study aims to evaluate the bacterial diversity in Lake Balaton using the long-read approach to 16 S rRNA gene sequencing. …”
Get full text

Mode Locking, Farey Sequence, and Bifurcation in a Discrete Predator-Prey Model with Holling Type IV Response by Yun Liu, Xijuan Liu

“…These periods are arranged in a Farey tree sequence and embedded within quasi-periodic/chaotic regions. …”
Get full text

Whole-genome sequencing identifies novel loci for keratoconus and facilitates risk stratification in a Han Chinese population by Yinghao Yao, Xingyong Li, Lan Wu, Jia Zhang, Yuanyuan Gui, Xiangyi Yu, Yang Zhou, Xuefei Li, Xinyu Liu, Shilai Xing, Gang An, Zhenlin Du, Hui Liu, Shasha Li, Xiaoguang Yu, Myopia Associated Genetics Intervention and Consortiums, Hua Chen, Jianzhong Su, Shihao Chen

“…This study was conducted to identify novel genetic variants linked to KC and to evaluate the potential applicability of a polygenic risk model in the Han Chinese population. …”
Get full text

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. by Robert Kofler, Pablo Orozco-terWengel, Nicola De Maio, Ram Vinay Pandey, Viola Nolte, Andreas Futschik, Carolin Kosiol, Christian Schlötterer

“…Its source code can be downloaded from http://code.google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data.…”
Get full text

Loop-mediated isothermal amplification of specific endoglucanase gene sequence for detection of the bacterial wilt pathogen Ralstonia solanacearum. by Rok Lenarčič, Dany Morisset, Manca Pirc, Pablo Llop, Maja Ravnikar, Tanja Dreo

Get full text

Successful Transition to Whole-Genome Sequencing and Bioinformatics to Identify Invasive Streptococcus spp. Drug Resistance, Alaska, USA by Karen M. Miernyk, Sopio Chochua, Ben Metcalf, Alisa Reasonover, Brenna Simons-Petrusa

“… The Centers for Disease Control and Prevention’s Arctic Investigations Program evaluated whole-genome sequencing (WGS) workflows and bioinformatics pipelines developed by the Centers’ Streptococcus Laboratory. …”
Get full text

Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing by Mirena Ivanova, Frank M. Aarestrup, Saria Otani

“…The effects of sample multiplexing on the detection sensitivity of antimicrobial resistance genes (ARGs) and pathogenic bacteria in metagenomic sequencing remain underexplored in newer sequencing technologies such as Oxford Nanopore Technologies (ONT), despite its critical importance for surveillance applications. …”
Get full text

Assessment of the new Next Generation Sequencing (NGS) tools to identify genes associated with tolerance to water deficit in sugarcane by John Jaime Riascos Arcos, Héctor Fabio Espitia Navarro, Jershon López Gerena

“…The aim of this research was to evaluate the performance of the new Next Generation Sequencing (NGS) technologies in comparative transcriptomics experiments, aiming to identify genes associated with tolerance mechanisms to abiotic stress such water deficit or flooding in sugarcane. …”
Get full text

Unveiling the Future of Infective Endocarditis Diagnosis: The Transformative Role of Metagenomic Next-Generation Sequencing in Culture-Negative Cases by Shafiu A. Umar Shinge, Binbin Zhang, Baixin Zheng, Yongjia Qiang, Hussein M. Ali, Youmbi T. Vanessa Melchiade, Lu Zhang, Minnan Gao, Guibin Feng, Kuan Zeng, Yanqi Yang

“…This narrative review synthesizes evidence from 152 studies (2015–2024), evaluating mNGS within existing diagnostic frameworks for culture-negative IE. …”
Get full text