Tag: NAR

Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs

doi: 10.1093/nar/gkac019. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA. 2 Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA. 3 Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA….

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Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project

Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project We’re sorry, but GBIF doesn’t work properly without JavaScript enabled. Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser. Citation McVeigh R (2013)….

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Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells

Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM (2014) Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 186:98–109. doi.org/10.1016/j.jbiotec.2014.05.024 CAS  Article  PubMed  Google Scholar  Altamirano C, Illanes A, Casablancas A, Gámez X,…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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Identification of differentially expressed genes in AF

Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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Efficient target cleavage by Type V Cas12a effectors programmed with split CRISPR RNA

doi: 10.1093/nar/gkab1227. Online ahead of print. Regina Shebanova  1 , Natalia Nikitchina  1   2 , Nikita Shebanov  1 , Vladimir Mekler  3 , Konstantin Kuznedelov  3 , Egor Ulashchik  4 , Ruslan Vasilev  5   6 , Olga Sharko  4 , Vadim Shmanai  4 , Ivan Tarassov  2 , Konstantin Severinov  1   3   7 , Nina Entelis  2…

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Bioinformatics analysis of long non-coding RNA-associated competing endogenous RNA network in schizophrenia

1. Marder, S. R. & Cannon, T. D. Schizophrenia. N. Engl. J. Med. 381, 1753–1761. doi.org/10.1056/NEJMra1808803 (2019). Article  PubMed  CAS  Google Scholar  2. Keshavan, M. S. et al. Neuroimaging in Schizophrenia. Neuroimaging Clin. N. Am. 30, 73–83. doi.org/10.1016/j.nic.2019.09.007 (2020). Article  PubMed  Google Scholar  3. McCutcheon, R. A., Reis Marques, T….

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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Establishment of sunitinib-resistant CDX model of ccRCC

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

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Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress

doi: 10.1093/nar/gkab1224. Online ahead of print. Affiliations Expand Affiliations 1 Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland. 2 Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland. 3 Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria. 4 Rieveschl Laboratories…

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HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs

doi: 10.1093/nar/gkab1221. Online ahead of print. Yang Yang  1   2 , Liwei Zhang  3 , Chaoyang Xiong  2 , Jun Chen  2   4   5 , Li Wang  6 , Zengqi Wen  2   5 , Juan Yu  2 , Ping Chen  4 , Yanhui Xu  6 , Jingji Jin  1   7   8 , Yong Cai …

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Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium | BMC Biotechnology

1. Jiang P, Shi FX, Li MR, Liu B, Wen J, Xiao HX, et al. Positive selection driving cytoplasmic genome evolution of the medicinally important ginseng plant genus Panax. Front Plant Sci. 2018;9:359. doi.org/10.3389/fpls.2018.00359. Article  PubMed  PubMed Central  Google Scholar  2. Takeshi T, Marouane B, Takuya I, Kazusato O, Kimiko…

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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

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Identification of lipid metabolism-associated gene signature

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

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Genomic features of a carbapenem-resistant K. oxytoca strain

Introduction Antimicrobial resistance is a global issue associated with an increased and often unrestricted antibiotic use in clinical settings, which leads to the dissemination of carbapenem-resistant Enterobacterales (CRE) in healthcare facilities (World Health Organization, 2017).1 CRE constitutes a large group of bacteria with different mechanisms for drug resistance. Among them,…

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Mutational Analysis of Mitochondrial tRNA Genes

Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…

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Next Generation Sequencing in tissues: Fully in situ methods

Here, Synthetic Biology Platform Lead at the Wyss Institute for Biologically Inspired Engineering, Richie Kohman, continues exploring the breakthroughs of Next Generation Sequencing (NGS) Exploring the locations and identities of RNA within biological tissues can uncover important information about cell types and states as well as give insight into cellular…

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Genomic and phenotypic characteristics for Vibrio vulnificus

Background Fisheries and aquaculture are becoming increasingly intensive to meet recent human consumption, resulting in proliferation of marine pathogens and food security concerns.1,2 Vibrio species, as one of the most dangerous foodborne pathogens, cause vibriosis in human around the world.3 It has been reported that vibriosis resulted in 80,000 illnesses…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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Infective endocarditis caused by ESBL-EC

Tsuneaki Kenzaka,1,2 Yuto Shinkura,1 Shizuo Kayama,3– 5 Liansheng Yu,3– 5 Sayoko Kawakami,3 Motoyuki Sugai,3– 5 Satoru Kawasaki1 1Department of Internal Medicine, Hyogo Prefectural Tamba Medical Center, Tanba, Japan; 2Division of Community Medicine and Career Development, Kobe University Graduate School of Medicine, Kobe, Japan; 3Antimicrobial Resistance Research Center, National Institute of…

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Plasmid-Encoded VIM-2-pProducing Pseudomonas stutzeri | IDR

Introduction Pseudomonas stutzeri is an aerobic, nonfermenting, active, Gram-negative oxidase-positive bacterium with unique colony morphology.1,2 Burri and Stutzer first described it in 1985,3 and the specific metabolic properties, such as denitrification, degradation of aromatic compounds, and nitrogen fixation, distinguish it from other pseudomonads species.2,4 Historically, P. stutzeri was not commonly…

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