A Topological Approach to Enhancing Consistency in Machine Learning via Recurrent Neural Networks by Muhammed Adil Yatkin, Mihkel Kõrgesaar, Ümit Işlak

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Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two Lineages of Helicobacter pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution by Abeer Babiker Idris, Hadeel Gassim Hassan, Maryam Atif Salaheldin Ali, Sulafa Mohamed Eltaher, Leena Babiker Idris, Hisham N. Altayb, Amin Mohamed Abass, Mustafa Mohammed Ahmed Ibrahim, El-Amin Mohamed Ibrahim, Mohamed A. Hassan

“…Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was applied, and the resulted sequences were matched with the sequences of the National Center for Biotechnology Information (NCBI) nucleotide database. …”
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Designing a Long Acting Erythropoietin by Fusing Three Carboxyl-Terminal Peptides of Human Chorionic Gonadotropin β Subunit to the N-Terminal and C-Terminal Coding Sequence by Fuad Fares, Avri Havron, Eyal Fima

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Revealing the core suppression effects of various Di (2-ethylhexyl) phthalate exposure on early meiosis progression in postnatal male mice via single-cell RNA sequencing by Baoquan Han, Lei Hua, Shuai Yu, Wei Ge, Cong Huang, Yu Tian, Chunxiao Li, Jiamao Yan, Tian Qiao, Jiachen Guo, Dongliang Lu, Bin Wang, Diya Cai, Yunqi Zhang, Shaolin Liang, Jianjuan Zhao, Qi Hou, Wei Shen, Zhongyi Sun

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Utilizing sc-linker to integrate single-cell RNA sequencing and human genetics to identify cell types and driver genes associated with non-small cell lung cancer by Yangfan Zhou, Liang Zhao, Meimei Cai, Doudou Luo, Yizhen Pang, Jianhao Chen, Qicong Luo, Qin Lin

“…Methods In this study, we utilized the sc-linker framework developed by Jagadeesh, which is an integrated framework that combines single-cell RNA sequencing (scRNA-seq), epigenomic single nucleotide polymorphism (SNP)-to-gene mapping, and GWAS summary statistics to infer potential cell types and diseases affected by genetic variations. …”
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Identification and Characterization of Genes Associated with Intestinal Ischemia-Reperfusion Injury and Oxidative Stress: A Bioinformatics and Experimental Approach Integrating High-Throughput Sequencing, Machine Learning, and Validation by Xie Y, Yang M, Huang J, Jiang Z

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Collection of SARS-CoV-2 Virus from the Air of a Clinic within a University Student Health Care Center and Analyses of the Viral Genomic Sequence by John A. Lednicky, Sripriya N. Shankar, Maha A. Elbadry, Julia C. Gibson, Md. Mahbubul Alam, Caroline J. Stephenson, Arantzazu Eiguren-Fernandez, J. Glenn Morris, Carla N. Mavian, Marco Salemi, James R. Clugston, Chang-Yu Wu

“…Such efforts currently rely on sequencing the genome of SARS-CoV-2 in patient specimens (direct sequencing) or of virus isolated from patient specimens in cell cultures. …”
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Are Collagen Protons Visible with the Zero Echo Time (ZTE) Magnetic Resonance Imaging Sequence: A D₂O Exchange and Freeze-Drying Study by Tan Guo, Dina Moazamian, Arya A. Suprana, Saeed Jerban, Eric Y. Chang, Yajun Ma, Michael Carl, Min Chen, Jiang Du

“…Finally, the samples were brought to room temperature and visualized using the identical 3D ZTE and UTE sequences. All hydrated bone and tendon specimens showed high signals with ZTE and UTE sequences. …”
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Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia by Andriansjah Rukmana, Cynthia Gozali, Linda Erlina

“…This study aimed to determine the association between the TB lineage distribution using whole-genome sequencing and bedaquiline, clofazimine, and linezolid phenotypic profile resistance among M. tuberculosisrifampicin-resistant isolates from West Java. …”
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Single‐cell RNA‐sequencing and spatial transcriptomic analysis reveal a distinct population of APOE− cells yielding pathological lymph node metastasis in papillary thyroid cancer by Guohui Xiao, Rongli Xie, Jianhua Gu, Yishu Huang, Min Ding, Dongjie Shen, Jiqi Yan, Jianming Yuan, Qiong Yang, Wen He, Siyu Xiao, Haizhen Chen, Dan Xu, Jian Wu, Jian Fei

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Chemical-guided SHAPE sequencing (cgSHAPE-seq) informs the binding site of RNA-degrading chimeras targeting SARS-CoV-2 5’ untranslated region by Zhichao Tang, Shalakha Hegde, Siyuan Hao, Manikandan Selvaraju, Jianming Qiu, Jingxin Wang

“…To locate the binding site, we developed a sequencing-based method namely cgSHAPE-seq, in which an acylating probe was directed to crosslink with the 2’-OH group of ribose at the binding site to create read-through mutations during reverse transcription. cgSHAPE-seq unambiguously determined a bulged G in SL5 as the primary binding site, which was validated through mutagenesis and in vitro binding experiments. …”
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Coinfection of severe acute respiratory syndrome coronavirus 2 and polyomavirus in a patient with coronavirus disease 2019 detected by enrichment next-generation sequencing: a case report by Gunadi, Esensi Tarian Geometri, Pramana Adhityo, Ali Zainal Abidin, Marcellus, Dyah Ayu Puspitarani, Fadila Dyah Trie Utami, Kristy Iskandar, Hendra Wibawa, Mohamad Saifudin Hakim

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Cost-effectiveness of targeted next-generation sequencing (tNGS) for detection of tuberculosis drug resistance in India, South Africa and Georgia: a modeling analysisResearch in context by Suvesh Shrestha, Angelina Addae, Cecily Miller, Nazir Ismail, Alice Zwerling

Subjects: “…Targeted next-generation sequencing (tNGS)…”
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Single-cell RNA-sequencing and genome-wide Mendelian randomisation along with abundant machine learning methods identify a novel B cells signature in gastric cancer by Qi Ma, Jie Gao, Yuan Hui, Zhi-Ming Zhang, Yu-Jie Qiao, Bin-Feng Yang, Ting Gong, Duo-Ming Zhao, Bang-Rong Huang

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A novel gene signature for predicting outcome in colorectal cancer patients based on tumor cell-endothelial cell interaction via single-cell sequencing and machine learning by Lina Pang, Qingxia Sun, Wenyue Wang, Mingjie Song, Ying Wu, Xin Shi, Xiaonan Shi

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The Effectiveness of an Anoxic-Oxic-Anoxic-Oxic Sequencing Batch Reactor System (A2/O2-SBR) to Treat Electroplating Wastewater and the Bacterial Community within the System by Tanta Suriyawong, Sasidhorn Buddhawong, Thanit Swasdisevi, Suntud Sirianuntapiboon

Subjects: “…sequencing batch reactor…”
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Complete Genome Sequence of Photobacterium damselae Subsp. damselae Strain SSPD1601 Isolated from Deep-Sea Cage-Cultured Sebastes schlegelii with Septic Skin Ulcer by Yongxiang Yu, Zheng Zhang, Yingeng Wang, Meijie Liao, Xiaojun Rong, Bin Li, Kai Wang, Jing Chen, Hao Zhang

“…The SSPD1601 genome consists of two chromosomes and two plasmids, totaling 4,252,294 bp with 3,751 coding sequences (CDSs), 196 tRNA genes, and 47 rRNA genes. …”
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Genetic analysis of nucleotide sequences of neuraminidase gene of highly pathogenic avian influenza A/H5N8 virus isolates recovered in the Russian Federation in 2020 by P. B. Akshalova, N. G. Zinyakov, A. V. Andriyasov, P. D. Zhestkov, Z. B. Nikonova, S. N. Kolosov, I. A. Chvala

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Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland by Anna Tumeo, Francesca McDonagh, Aneta Kovarova, Kate Ryan, Christina Clarke, Georgios Miliotis

“…Phylogenetic analysis was performed using whole-genome-multilocus-sequence-typing (wgMLST). Results: E. coli E230738 genome was identified to belong to phylogroup-A/ST10 complex and to harbour 63 ARGs, 17 of which acquired. …”
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Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples by Sonali P. Barwe, Anilkumar Gopalakrisnapillai, Nitin Mahajan, Todd E. Druley, E. Anders Kolb, Erin L. Crowgey

Subjects: “…error-corrected sequencing…”
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