Genomic Analysis Methods of Microorganisms by Canan Kebabçıoğlu, Osman Erganiş

“…MLVA determines the genetic relationships of bacterial strains and biovar-level differences and assesses the copy number of repeated DNA sequences. Sequencing provides genetic data by identifying DNA sequences; Sanger sequencing is the basis for next-generation approaches. …”
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A Robotic Brain Scheme: Proposal Originated by a Modular Robotic Control by J. Negrete-Martínez

“…Finally, the planning and sequencing modules are imperative implementations in a robotic brain.…”
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Chromosome-scale genome assembly of Korean goosegrass (Eleusine indica) by Solji Lee, Changsoo Kim

“…We then combined Pore-C sequencing technology to successfully anchor 255 contigs to nine pseudochromosomes. …”
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How data science and AI-based technologies impact genomics by Jing Lin, Kee Yuan Ngiam

“…However, the accumulation of genomic data from sequencing and clinical data from electronic health records (EHRs) poses significant challenges for data scientists. …”
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Evaluation of various RNA-seq approaches for identification of gene outrons in the flatworm Opisthorchis felineus by N. I. Ershov, D. E. Maslov, N. P. Bondar

“…In the current study, we tested various experimental approaches for identifying the sequences of outrons in O. felineus using massive parallel sequencing. …”
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Gene Polymorphism of Antigen B Subunit 2 and Pathogenesis of Cystic Echinococcosis in Murine Model by Hadi M. Alsakee, Hussein M. Abdulla, Reshna K. Albarzanji

“…Minor sequence polymorphisms, 1.67%, are observed in one of the isolates, whereas remarkable DNA sequence polymorphisms are noticed in three of the isolates. …”
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RETRACTED ARTICLE: Single-cell omics and machine learning integration to develop a polyamine metabolism-based risk score model in breast cancer patients by Xiliang Zhang, Hanjie Guo, Xiaolong Li, Wei Tao, Xiaoqing Ma, Yuxing Zhang, Weidong Xiao

“…Methods We used a multi-omics approach combining bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) to study polyamine metabolism. …”
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A scalable tool for analyzing genomic variants of humans using knowledge graphs and graph machine learning by Shivika Prasanna, Ajay Kumar, Deepthi Rao, Eduardo J. Simoes, Praveen Rao

“…Advances in high-throughput genome sequencing have enabled large-scale genome sequencing in clinical practice and research studies. …”
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Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae) by Yanlei Liu, Kai Chen, Lihu Wang, Xinqiang Yu, Chao Xu, Zhili Suo, Shiliang Zhou, Shuo Shi, Wenpan Dong

“…Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. …”
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The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards by Chunxiao Wang, Yu Yang, Xiaoqing Xu, Dou Wang, Xianghui Shi, Lei Liu, Yu Deng, Liguan Li, Tong Zhang

“…However, the relative abundances derived from sequencing impede comparisons across samples and studies. …”
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Mitochondrial trifunctional protein deficiency caused by a deep intronic deletion leading to aberrant splicing by Thomas Cassini, Sarah Silverstein, Molly Behan, Cynthia J. Tifft, May Christine Malicdan, David R. Adams, Undiagnosed Diseases Network, Sun‐Young Ahn, Debra S. Regier

“…Both siblings were also diagnosed with focal segmental glomerulosclerosis (FSGS) and bone marrow failure and ultimately died of hypoxemic respiratory failure. Initial sequencing of the TFP‐associated genes HADHA and HADHB showed only a paternally inherited variant in HADHB, NM_000183.3:c.1059del (p.Gly354AspfsTer10). …”
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Distinct relative abundances in pathogens detected in mechanically ventilated patients with suspected pneumonia in the intensive care unit at King Abdulaziz University Hospital by Haifa Algethamy, Diyaa H. Bokhary, Ibrahim Abushoshah, Abdulrahman A. Alalyani, Maan K. Baamer, Dalya M. Attallah, Ruba M. Alotaibi, Shehla N. Amin, Shaza A. Mass, Nisreen R. Tashkandy

“…DNA from 83 deep endotracheal aspirate lung samples was subjected to PacBio sequencing to identify pathogens in comparison with conventional diagnostic techniques. …”
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Transcriptomic analysis of the root system of Platycodon grandiflorum in response to the fallen leaves of Acer truncatum by FENG Chaoqun, RUAN Kunfei, SHI Shaotong, LI Sen, CHENG Shaoying, LIU Zhonghua

“…[Objective] The aim of this study was to explore the effect of Acer truncatum fallen leaves in Beijing on the accumulation of medicinal active ingredients of Platycodon grandiflorum and to reveal the molecular mechanism of active ingredient synthesis in P . grandiflorum roots through transcriptome sequencing. [Methods] We performed transcriptome sequencing using Illumina high throughput sequencing technology. …”
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Isolation and characterization of mercuric reductase by newly isolated halophilic bacterium, Bacillus firmus MN8 by M. Noroozi, M.A. Amoozegar, A.A. Pourbabaei, N.S. Naghavi, Z. Nourmohammadi

“…Moreover, tracking and sequencing merA gene and kinetic properties of mercuric reductase in the selected strain were performed in this study. …”
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DeepRetention: A Deep Learning Approach for Intron Retention Detection by Zhenpeng Wu, Jiantao Zheng, Jiashu Liu, Cuixiang Lin, Hong-Dong Li

“…These metrics are not able to describe the pattern of sequencing depth of intronic reads, which is an intuitive and informative characteristic of retained introns. …”
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A Novel Pathogenic Splicing Mutation of OFD1 is Responsible for a Boy with Joubert Syndrome Exhibiting Orofaciodigital Spectrum Anomalies, Polydactyly and Retinitis Pigmentosa by Chen L, Zhao MF, Deng HW, Liao M, Fan LL, Zhong QB, Wang J, Li K, Wu ZH, Yin JY

“…Here, we identified a child who presented with Joubert syndrome exhibiting orofaciodigital spectrum anomalies, polydactyly, and retinitis pigmentosa. Whole exome sequencing and Sanger sequencing revealed a splicing mutation (NM_003611.2, c.2387+1G>A) in the OFD1 gene of the patient and his mother. mRNA sequencing further confirmed this mutation. …”
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A case report of confirmed difficult pulmonary tuberculosis based on the hybrid capture-based tNGS method by Weiqian Chen, Huimin Chen, Ze Liu, Xinle Chi, Yaomeng Chen, Huan Ye, Wenjie Huang, Chenlei Cao, Wei Weng

“…Currently, with the increasing popularity, iteration, and decreasing costs of Next-generation sequencing (NGS) testing technology, NGS is being more widely applied in the diagnosis of pulmonary tuberculosis. …”
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Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions by Vanesa R. Marcelino, Laszlo Irinyi, John-Sebastian Eden, Wieland Meyer, Edward C. Holmes, Tania C. Sorrell

“…Abstract High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. …”
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Endosperm culture-based allotriploid hybrid production from an interspecific cross of Haemanthus spp.: new insights into polyploidization and hybridization by Arisa Nakano, Masahiro Mii, Yoichiro Hoshino

“…In addition, chloroplast DNA sequencing revealed maternal inheritance in the endosperm-derived plantlets, consistent with embryo-derived plantlets. …”
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Comparisons of performances of structural variants detection algorithms in solitary or combination strategy. by De-Min Duan, Chinyi Cheng, Yu-Shu Huang, An-Ko Chung, Pin-Xuan Chen, Yu-An Chen, Jacob Shujui Hsu, Pei-Lung Chen

“…However, the precise identification and characterization of SVs remain challenging. While long-read sequencing offers superior accuracy for SV detection, short-read sequencing remains essential due to practical and cost considerations, as well as the need to analyze existing short-read datasets. …”
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