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• Silver-Loaded Turbinaria turbinata Oil Nanoemulsions: Antimicrobial and Anticancer Potential Revealed Through In Vitro Assays and Molecular Docking.
  Nanoemulsions are promising nanotechnology-based delivery systems that may improve the stability, bioavailability, and cellular uptake of therapeutic agents. Silver nanoparticles (AgNPs) have been reported to exhibit high antibacterial and anticancer activitie…
  pubmed Hamouda RA, Alhumairi AM, Alreemi RM 2026 Jul 13 置信度 0.82
• Synthetic Microbial Community Biosensors: From Engineered Ecosystems to Modular Detection Platforms with AI-Driven Intelligence.
  Synthetic microbial community (SynCom) biosensors are emerging from the convergence of whole-cell biosensing, synthetic ecology, and computational design. Conventional whole-cell biosensors (WCBs) use a single microbial chassis to convert analyte recognition i…
  pubmed Hu L, Yang Y, Xia S, Mao W 等 2026 Jul 6 置信度 0.82
• Shear Stress Modeling and Machine Learning for Nanomedicine Development: A Mechanistic Pathway to Pharmacokinetic Prediction.
  Clinical translation of nanomedicines remains constrained by a persistent gap between static preclinical assays and the dynamic shear environment of the human vasculature. This review argues that fluid shear stress is an underappreciated contributor to clinica…
  pubmed Modh H, Leong D, Dindhoria K, Malinovskaya J 等 2026 Jul 27 置信度 0.82
• Polychip-A High-Throughput Droplet Microfluidics Platform for Interrogating Microbial Interactions.
  Microbial interactions are fundamental to ecology, health, and disease, yet high-throughput tools to study these complex relationships remain scarce. We introduce Polychip, a fully integrated, high-throughput droplet microfluidics platform that revolutionizes …
  pubmed Han JJ, Guzman AR, Zhou A, Zhang H 等 2026 Jul 27 置信度 0.82
• A systematic study of conventional, sensor-induced, and machine learning-based methods for milk quality analysis and adulterant detection.
  Milk is important constituent of daily food worldwide. Quality of milk is compromised because of multiple issues like sub-standard practices in dairy industry, frequent adulterations, microbial contaminations, storage and climatic conditions. The problem gets …
  pubmed Prakash S, Gautam KA, Gupta KK, Raghav PS 等 2026 Aug 置信度 0.82
• Assessment of Neutralizing Antibodies Against COVID-19: The Impact of Vaccination in Western Rajasthan.
  The COVID-19 pandemic has been a major public health disaster, wreaking havoc on people's finances, physical health, and emotional well-being. However, many cases go undetected because they are asymptomatic. The purpose of the study is to identify neutralizing…
  pubmed Choudhary V, Khatri PK, Khinvasara P, Aseri GK 等 2026 Aug 置信度 0.82
• Haemophilus influenzae tryptophan biosynthesis is required for lung infection.
  Tryptophan plays a key role in regulating human lung homeostasis and immunity through the indoleamine 2,3-dioxygenase (IDO) and aryl hydrocarbon receptor (AhR) signalling pathways. In patients with chronic obstructive pulmonary disease (COPD), altered IDO and …
  pubmed Asensio-López J, Rapún-Araiz B, Euba B, Domínguez-San Pedro A 等 2026 置信度 0.82
• Association between gut microbiota composition and liver dysfunction in school-aged children exposed to triclosan.
  Growing epidemiological evidence implicate endocrine-disrupting chemicals (EDCs) in the development of liver dysfunction across populations. However, the effects of mixed EDC exposure on children's liver function remains critically limited. This study investig…
  pubmed Li A, Li M, Xu W, Zhang Y 等 2026 Sep 置信度 0.82
• Data driven optimization of PGPR biomass yield for development of carrier based bioformulation for ameliorating salt stress in Salvia hispanica (chia) seedlings.
  Scale up of plant growth promoting rhizobacteria based bioformulation, remains challenging because of the complex and nonlinear nature of interactions between the components of formulation affecting plant growth promoting rhizobacteria (PGPR) biomass, resultin…
  pubmed Singh S, Rai S, Vishvakarma R, Saxena A 等 2026 Jul 24 置信度 0.82
• Longitudinal zone- and cell type-specific pattern-triggered immune responses in Arabidopsis roots.
  Roots, composed of diverse cell types across longitudinal developmental zones, are vital for plant survival against microbial challenges. Leveraging single-cell transcriptomics and live-cell imaging of Arabidopsis roots, we reveal here that plant-derived phyto…
  pubmed Xu L, Ortiz-Morea FA, Kim SI, Ferrari C 等 2026 Jul 24 置信度 0.82
• Plasmodium vivax and Plasmodium falciparum mixed infections in human and mosquito hosts: The impact of multi-species infection on parasite densities and transmission to mosquitoes.
  In co-endemic regions, mixed Plasmodium vivax (Pv) and Plasmodium falciparum (Pf) infections are commonly reported. How mixed species infections compare to single species infections in terms of parasite densities and transmission to mosquitoes is poorly unders…
  pubmed Chali W, Ejigu LA, Atele T, Sisay S 等 2026 Jul 24 置信度 0.82
• Recurrent evolution of cryptic triploids in cultivated enset increases yield.
  The high incidence of polyploidy in crops could be explained if domestication involved the selection of polyploids (cytotypes with more than two sets of chromosomes). Ancestral horticulture could have targeted desirable traits including yield, robustness to st…
  pubmed Dussert Y, Borrell JS, Stocks J, Hunt HV 等 2026 Jul 置信度 0.82
• Comparative genomics of herpes simplex virus 2 isolated from a maternal-neonatal dyad reveals high consensus sequence homology as well as minor variant diversity.
  Neonatal herpes simplex virus disease most often occurs following mother-to-neonate transmission during childbirth. However, genomic differences between the maternal and neonatal viral populations are poorly understood. Here, we performed deep whole-genome seq…
  pubmed Rass RA, Simons LM, Bowen CD, Carter HS 等 2026 Jul 24 置信度 0.82
• Single-cell insights into hepatic fibroblasts and stellate cells: heterogeneity in matrix remodelling in development, health, and disease.
  Hepatic fibroblasts and hepatic stellate cells (HSCs) are dynamic regulators of liver development, homeostasis, and disease beyond structural roles. Advances in single-cell transcriptomics have provided new evidence on their heterogeneity, plasticity, and dive…
  pubmed Campinoti S, Kirubendran K, Wei L, Medic M 等 2026 置信度 0.82
• Engineering Strategies and Operations of Frozen Yogurt Formulated With GABA-Enriched Yogurt: A Review.
  Frozen yogurt formulated with γ-aminobutyric acid (GABA)-enriched yogurt represents a promising functional dairy matrix in response to growing interest in foods associated with cognitive health and neurological well-being. Although GABA has been associat…
  pubmed Wan-Mazlan WMF, Ushidee-Radzi MA, Shin-Yee C, Yusof YA 等 2026 Jul 置信度 0.82
• Comparative assessment of large language models for microbial phenotype assignment.
  Large language models (LLMs) are increasingly used to extract knowledge from text, yet their coverage and reliability in biology remain unclear. Microbial phenotypes are especially important to assess, as comprehensive data remain sparse except for well-studie…
  pubmed Münch PC, Safaei N, Mreches R, Binder M 等 2026 Jul 23 置信度 0.82
• The Metaproteomics Initiative: five years of community-driven progress.
  The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed…
  pubmed Van Den Bossche T, Grenga L, Alves G, Arntzen MØ 等 2026 Jul 23 置信度 0.82
• The need for standardization and improved open (meta)data practices in metaproteomics.
  Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reprod…
  pubmed Van Den Bossche T, Wolf M, Armengaud J, Arntzen MØ 等 2026 Jul 23 置信度 0.82
• Gut microbiome composition differs between aortic stenosis and aortic regurgitation patients.
  The gut microbiome has emerged as an important modulator of cardiovascular diseases, yet data on aortic valve disorders, particularly aortic stenosis (AS), remain limited. This study aimed to characterize gut microbiome differences in patients with bicuspid (B…
  pubmed Bartsch B, Nesic S, Al Zaidi M, Jamin RN 等 2026 Jul 23 置信度 0.82
• In Skin Biopsies of Localized Cutaneous Leishmaniasis Patients from Ethiopia, Expression of Anti-Inflammatory Cytokines was Greater than that of Proinflammatory Cytokines.
  The immunopathology of cutaneous leishmaniasis (CL) caused by Leishmania aethopica is not well understood. This study aimed to characterize the host's localized immune response in formalin-fixed paraffin-embedded (FFPE) skin biopsies taken from skin lesions of…
  pubmed Yimam S, Ayele AA, Girma S, Hassen M 等 2026 Jul 23 置信度 0.82
• Genomic language models (gLMs): Emerging applications, challenges, and future directions in computational genomics.
  Genomic language models (gLMs) are rapidly becoming important tools for learning biological information directly from sequence data. By adapting concepts from natural language processing, these models aim to capture contextual dependencies, regulatory grammar,…
  pubmed Mashhour MA, Wahed MA, Mabrouk MS 2026 Jul 22 置信度 0.82
• Harnessing high-throughput phenotyping and artificial intelligence for soybean breeding: From trait assessment to data-driven decisions.
  Soybean ( Glycine max (L.) Merrill) is a highly important crop widely used for food, edible oil, animal feed, and microbial fermentation products. Traditional phenotypic measurement methods are often time-consuming, labor-intensive, destructive to plants, and …
  pubmed Chagas JTB, Araújo MS, Pavan JPS, Françani AO 等 2026 Sep 置信度 0.82
• SynBioGPT2: A dynamic reasoning framework enables high-fidelity design of microbial cell factories.
  The rational design of microbial cell factories is essential for sustainable biomanufacturing, yet the traditional Design-Build-Test-Learn (DBTL) cycle is bottlenecked by the highly non-linear and interconnected nature of biological systems. Although large lan…
  pubmed Mao Z, Du J, Guan J, Wang W 等 2026 Sep 置信度 0.82
• Seasonal variation in the bacterial microbiome of questing nymphal ticks in Missouri, United States.
  Seasonal environmental variation may influence the composition of tick-associated bacterial communities. This study assessed seasonal differences in the microbiome of questing nymphal ticks collected from Missouri, United States.
  pubmed DeSalle AJ, Agbajelola VI, Ericsson AC, Shyu CR 等 2026 置信度 0.82
• Synergistic Effects of Cepharanthine and Amphotericin B Against Candida albicans by Targeting PMP3-Mediated Sphingolipid Biosynthesis and Membrane Disruption.
  Candida albicans is a major opportunistic fungal pathogen causing various mucosal infections, including oral candidiasis, poses challenges in current antifungal therapy because of limited number of drugs, increased pathogen resistance, and notable toxicity ass…
  pubmed Wang S, Zhang Q, Li Q, Wang G 等 2026 Jul 23 置信度 0.82
• Optimizing Soil Health and Productivity in Intensive Rice-Wheat Systems Using Conjoint Application of Sewage Sludge.
  This study assessed the long-term sustainability of integrating sewage sludge (SSL) with recommended (100%) or reduced (75%) doses of chemical fertilizers to enhance soil health, crop productivity, and reduce dependency on synthetic fertilizer inputs in the in…
  pubmed Jatav SS, Singh SK, Nath D, Kumari V 等 2026 Jul 23 置信度 0.82
• A novel SaeS-targeting antivirulence antagonist screened against methicillin-resistant Staphylococcus aureus.
  The SaeRS two-component system is a major virulence regulator in Staphylococcus aureus , and its sensor kinase SaeS represents a potential target for small-molecule intervention.
  pubmed Yao J, Ai D, Duan H 2026 置信度 0.82
• Editorial: Metabolic engineering and synthetic biology for sustainable microbial cell factories.
  pubmed Sankaranarayanan M, Loganathan K, Pasotti L 2026 置信度 0.82
• Isotopic Evidence for Reaction Pathways and Quantum Tunneling in Methanotrophy.
  The isotope composition of residual methane after microbial oxidation can provide rigorous constraints on proposed methanotrophic pathways. However, mechanistic interpretation of the abundances of naturally occurring partially substituted methane isotopomers r…
  pubmed Xia X, Gao Y 2026 Jul 22 置信度 0.82
• PFAS in textiles: a critical review on contamination pathways, analytical methods, toxicity assessment, and feasible control strategies.
  The widespread application of PFAS in textile industry has triggered serious human health risks worldwide, leading to typical adverse health outcomes such as thyroid dysfunction, neurodevelopmental disorders in children and reproductive damage. This paper revi…
  pubmed Zhao X, Deng C, Huang K, Wang H 等 2026 Jul 23 置信度 0.82
• Integrated experimental and computational characterization of bioactive metabolites from Streptomyces paradoxus GH53 with antimicrobial, antioxidant, and antitumor activities.
  Streptomyces species are widely recognized as valuable sources of secondary metabolites with diverse biological activities. In this study, the isolate GH53 was identified as Streptomyces paradoxus based on morphological characteristics and partial 16 S rR…
  pubmed El Sayed GH, Fahim AM, Fadel M, Selim MS 等 2026 Jul 23 置信度 0.82
• CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium.
  Microbes exist within complex community contexts, particularly for key functional species whose stable colonization critically depends on specific ecological partners. However, conventional microbial correlation analyses predominantly rely on isolated pairwise…
  pubmed Zhang J, Xu W, Xing J, Sun Y 等 2026 Jul 3 置信度 0.82
• Harnessing Natural Diversity and Rational Design for Enhanced Plant Immunity.
  Plant pathogens cause crop loss. Genetic resistance, through natural genetic diversity or engineered resistance, can be highly effective in protecting plants from infection. Genetic resistance from wild relatives of crops has been successfully introduced into …
  pubmed Diplock N, Lewis JD 2026 Jul 22 置信度 0.82
• Circadian Clock Gates Verticillium dahliae Defence in Cotton by Modulating JAZs Expression.
  The circadian clock plays critical roles in orchestrating temporal regulation of diverse physiological processes. However, its role in mediating root-associated immunity against soil-borne pathogens in crops remains poorly understood. Here, we show that cotton…
  pubmed Wang P, Liu M, Zhao C, Lu Q 等 2026 Jul 22 置信度 0.82
• Faster turnover of taxonomic over functional bacterial composition during vermicomposting indicates increasing functional redundancy.
  Microbial taxonomy underpins microbial functionality; consequently, changes in taxonomic composition are expected to influence community functional profiles. However, functional redundancy-the ability of different microorganisms to perform similar functions-ca…
  pubmed Aira M, Pérez-Losada M, Crandall KA, Domínguez J 2026 置信度 0.82
• ALPAR: automated learning pipeline for antimicrobial resistance.
  The field of machine learning in antimicrobial resistance (AMR) research has experienced rapid growth, fueled by advancements in high-throughput genome sequencing and the growing capacity of computational resources. However, the complexity and lack of standard…
  pubmed Yurtseven A, Joeres R, Kalinina OV 2026 Aug 3 置信度 0.82
• Anticancer effects of alpha-helical peptide epinecidin-1 and its variants in combination with doxorubicin.
  In this study, we evaluated the in silico and in vitro anticancer activity of the antimicrobial peptide epinecidin-1 (Epi-1) and its lysine-substituted variants (Variant-1 (Var-1) & Variant-2 (Var-2)). Computational docking demonstrated energetically favou…
  pubmed Jeyarajan S, Ranjith S, Anbarasu A, Kandasamy I 等 2026 Jul 22 置信度 0.82
• Pharmacological potential of the marine peptide cyclo(L-phenylalanyl-L-prolyl) against both multidrug-resistant, gram-negative Acinetobacter baumannii and gram-positive Staphylococcus aureus: structure - activity relationship, computational and experimental studies.
  The marine cyclic dipeptide, cyclo(phenylalanine-proline) (cFP), exhibits promising antimicrobial and antibiofilm activities. The balanced reactivity and stability of the compound, which are conducive to multi-target interactions, were identified using the den…
  pubmed Shankar S, Vadivel M, Kumar U, Nayak SS 等 2026 Jul 22 置信度 0.82
• Integrative multicohort analysis reveals consistent sex differences in gut microbiota of multiple sclerosis patients.
  Biological sex is a key determinant in the onset and progression of multiple diseases. In multiple sclerosis (MS), females exhibit higher disease prevalence, earlier onset, and more pronounced inflammatory activity, whereas males tend to experience a more seve…
  pubmed Soler-Sáez I, Galiana-Roselló C, Grillo-Risco R, Falony G 等 2026 Jul 22 置信度 0.82
• Development of self-healing model of rock fracture for PFC simulation.
  Rock mass fractures often lead to structural instability, posing significant safety risks in underground engineering such as mines and tunnels, including water seepage, air leakage, and damage to concrete structures. This study aims to enhance grouting-based r…
  pubmed Hu Y, Liu J, Wang D, Liu W 等 2026 Jul 22 置信度 0.82
• Biofilm Formation on Indwelling Medical Devices: A Review of Health and Economic Implications.
  Indwelling medical devices represent an impressive stride in modern surgical practice and are widely used in procedures that support the body's natural physiological functions. The global demand for these devices has surged, primarily driven by a range of clin…
  pubmed Abebe GM 2026 置信度 0.82
• From Virtual Modelling to Smarter Endodontic Innovation: In Silico Research for Translational Decision Making.
  To discuss how in silico research may function as an early translational decision layer in endodontics by supporting the prioritisation of hypotheses, technologies and experimental conditions before biological and clinical validation.
  pubmed da Silva-Filho JE, Gurgel-Filho ED 2026 Jul 22 置信度 0.82
• Computing for Comparative Microbial Genomics
  crossref 2008-12-15T06:05:14Z 置信度 0.70
• Microbial computing: Review and Perspectives.
  Engineering microbial computers has been a longstanding endeavor in synthetic biology. Like other unconventional computing disciplines, the goal is to bring computation into real-world scenarios. Several potential applications in bioproduction, bioremediation,…
  europepmc 2026 置信度 0.80
• A microbial signature for Crohn's disease
  OBJECTIVE: A decade of microbiome studies has linked IBD to an alteration in the gut microbial community of genetically predisposed subjects. However, existing profiles of gut microbiome dysbiosis in adult IBD patients are inconsistent among published studies,…
  openalex Victoria Pascal, Marta Pozuelo, Natalia Borruel, Francesc Casellas 等 2017-02-07 置信度 0.72 MicrobiomeDysbiosisCohortCohort studyImmunology
• Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
  The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tediou…
  openalex Alexander F. Auch, Mathias von Jan, Hans‐Peter Klenk, Markus Göker 2010-01-28 置信度 0.72 GenomeBiologyComputational biologyDNA sequencingGenome project
• CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
  openalex Alex Chklovski, Donovan H. Parks, Ben J. Woodcroft, Gene W. Tyson 2023-07-27 置信度 0.72 GenomeMetagenomicsComputational biologyScalabilityBacterial genome size
• Actual Causes of Death in the United States, 2000
  CONTEXT: Modifiable behavioral risk factors are leading causes of mortality in the United States. Quantifying these will provide insight into the effects of recent trends and the implications of missed prevention opportunities. OBJECTIVES: To identify and quan…
  openalex Ali H. Mokdad 2004-03-09 置信度 0.72 MedicineCause of deathEnvironmental healthEpidemiologyInjury prevention
• Microbial Dysbiosis in Colorectal Cancer (CRC) Patients
  UNLABELLED: The composition of the human intestinal microbiota is linked to health status. The aim was to analyze the microbiota of normal and colon cancer patients in order to establish cancer-related dysbiosis. PATIENTS AND METHODS: Stool bacterial DNA was e…
  openalex Iradj Sobhani, Julien Tap, Françoise Roudot‐Thoraval, Jean Pierre Roperch 等 2011-01-27 置信度 0.72 Faecalibacterium prausnitziiPrevotellaBiologyPyrosequencingBifidobacterium
• Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
  The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structur…
  openalex Karthik Anantharaman, Christopher T. Brown, Laura Hug, Itai Sharon 等 2016-10-24 置信度 0.72 Biogeochemical cyclePhylumMetagenomicsOrganismBiology
• Microbial lipases and their industrial applications: a comprehensive review
  Lipases are very versatile enzymes, and produced the attention of the several industrial processes. Lipase can be achieved from several sources, animal, vegetable, and microbiological. The uses of microbial lipase market is estimated to be USD 425.0 Million in…
  openalex Prem Chandra, Enespa, Ranjan Singh, Pankaj Kumar Arora 2020-08-26 置信度 0.72 Biochemical engineeringBiotechnologyBiologyEngineering
• GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
  GET_HOMOLOGUES is an open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians. It can cluster homologous gene families using…
  openalex Bruno Contreras‐Moreira, Pablo Vinuesa 2013-10-05 置信度 0.72 Cluster analysisComparative genomicsComputer scienceSyntenySoftware
• Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate
  Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and ec…
  openalex Nicholas A. Bokulich, J.H. Thorngate, Paul M. Richardson, David A. Mills 2013-11-25 置信度 0.72 WineTerroirVintageVineyardViticulture
• Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study
  BACKGROUND: High systemic estrogen levels contribute to breast cancer risk for postmenopausal women, whereas low levels contribute to osteoporosis risk. Except for obesity, determinants of non-ovarian systemic estrogen levels are undefined. We sought to identi…
  openalex Roberto Flores, Jianxin Shi, Barbara J. Fuhrman, Xia Xu 等 2012-12-01 置信度 0.72 FecesEstroneEstrogenPhysiologyMicrobiome
• phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
  BACKGROUND: the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increas…
  openalex Paul J. McMurdie, Susan Holmes 2013-04-22 置信度 0.72 UniFracComputer scienceData scienceData miningVisualization
• Estimating and mapping ecological processes influencing microbial community assembly
  Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population size…
  openalex James Stegen, Xueju Lin, Jim Fredrickson, Allan Konopka 2015-05-01 置信度 0.72 Biological dispersalEcologySelection (genetic algorithm)PopulationHomogeneous
• Taxonomical and functional microbial community selection in soybean rhizosphere
  This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversi…
  openalex Lucas William Mendes, Eiko E. Kuramae, Acácio Aparecido Navarrete, Johannes A. van Veen 等 2014-02-20 置信度 0.72 BiologyRhizosphereMicrobial ecologyGeomicrobiologySelection (genetic algorithm)
• From Microbial Communities to Distributed Computing Systems
  A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive…
  openalex Behzad D Karkaria, Neythen J. Treloar, C. Barnes, Alex J. H. Fedorec 2020-07-22 置信度 0.72 Computer scienceDistributed computing
• Metabolic dependencies drive species co-occurrence in diverse microbial communities
  Microbial communities populate most environments on earth and play a critical role in ecology and human health. Their composition is thought to be largely shaped by interspecies competition for the available resources, but cooperative interactions, such as met…
  openalex Aleksej Zelezniak, Sergej Andrejev, Olga Ponomarova, Daniel R. Mende 等 2015-05-04 置信度 0.72 Competition (biology)BiologyEcologyInterdependenceHabitat
• Microbial strain-level population structure and genetic diversity from metagenomes
  Among the human health conditions linked to microbial communities, phenotypes are often associated with only a subset of strains within causal microbial groups. Although it has been critical for decades in microbial physiology to characterize individual strain…
  openalex Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower 等 2017-02-06 置信度 0.72 BiologyFaecalibacterium prausnitziiMetagenomicsGeneticsGenetic diversity
• Loss in microbial diversity affects nitrogen cycling in soil
  Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial com…
  openalex Laurent Philippot, Aymé Spor, Catherine Hénault, David Bru 等 2013-03-07 置信度 0.72 BiologySpecies richnessEcosystemEcologyBiogeochemical cycle
• A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
  MOTIVATION: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data. RESULTS: A5…
  openalex David A. Coil, Guillaume Jospin, Aaron E. Darling 2014-10-22 置信度 0.72 Adapter (computing)Computer sciencePipeline (software)ContigSource code
• CMEIAS Color Segmentation: An Improved Computing Technology to Process Color Images for Quantitative Microbial Ecology Studies at Single-Cell Resolution
  Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper…
  crossref Colin A. Gross, Chandan K. Reddy, Frank B. Dazzo 2009-12-18T00:46:43Z 置信度 0.70
• Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
  Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA…
  openalex Susan M. Huse, Les Dethlefsen, Julie A. Huber, David B. Mark Welch 等 2008-11-20 置信度 0.72 BiologyHypervariable regionPyrosequencingRibosomal RNAEvolutionary biology
• Relative roles of niche and neutral processes in structuring a soil microbial community
  Most attempts to identify the processes that structure natural communities have focused on conspicuous macroorganisms whereas the processes responsible for structuring microbial communities remain relatively unknown. Two main theories explaining these processe…
  openalex Alex J. Dumbrell, Michaela Nelson, Thorunn Helgason, Calvin Dytham 等 2009-11-19 置信度 0.72 BiologyStructuringNicheMicrobial ecologyMicrobial population biology
• IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets
  IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately e…
  openalex Claire Bertelli, Matthew R. Laird, Kelly P. Williams, Britney Y. Lau 等 2017-04-20 置信度 0.72 BiologyGenomeVisualizationGenomicsAdaptability
• Microbial Computing Using Geobacter Biofilm Electrodes: Output Stability and Consistency.
  The direction of our work is towards a proof of concept of a novel biological processing unit and a new paradigm of computation based on neurone-like and transistor-like behaviour in the same units. This paper describes a non accumulating, steady state microbi…
  openalex John Greenman, Ioannis Ieropoulos, Colin McKenzie 2006-01-01 置信度 0.72 BiofilmGeobacter sulfurreducensGeobacterConsistency (knowledge bases)Stability (learning theory)
• Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer
  openalex Maria Gloria Domínguez-Bello, Kassandra M. De Jesús-Laboy, Nan Shen, Laura M. Cox 等 2016-02-01 置信度 0.72 MedicineVaginal deliveryMicrobiomeObstetricsPregnancy
• Microbial species delineation using whole genome sequences
  Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignmen…
  openalex Neha Varghese, Supratim Mukherjee, Natalia Ivanova, Konstantinos T. Konstantinidis 等 2015-07-06 置信度 0.72 BiologyGenomeComputational biologyEvolutionary biologyWhole genome sequencing
• Computed microtomography and mechanical property analysis of soy protein porous hydrogel prepared by homogenizing and microbial transglutaminase cross-linking
  openalex Jian Guo, Yu‐Cong Jin, Xiaoquan Yang, Shujuan Yu 等 2012-11-07 置信度 0.72 PorositySoy proteinTissue transglutaminaseMaterials scienceChemical engineering
• Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks
  Abstract We are firmly in the era of biological big data. Millions of omics datasets are publicly accessible and can be employed to support scientific research or build a holistic view of an organism. Here, we introduce a workflow that converts all public gene…
  openalex Anand V. Sastry, Saugat Poudel, Kevin Rychel, Reo Yoo 等 2021-07-02 置信度 0.72 WorkflowRegulonComputer sciencePipeline (software)Python (programming language)
• Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves
  BACKGROUND: Plate readers can measure the growth curves of many microbial strains in a high-throughput fashion. The hundreds of absorbance readings collected simultaneously for hundreds of samples create technical hurdles for data analysis. RESULTS: Growthcurv…
  openalex Kathleen Sprouffske, Andreas Wagner 2016-04-19 置信度 0.72 LicenseComputer scienceR packageGrowth curve (statistics)Measure (data warehouse)
• Establishing microbial composition measurement standards with reference frames
  Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial load, or absolute number of microorganisms, to accurately determine taxonomic shifts. Therefore, most st…
  openalex James T. Morton, Clarisse Marotz, Alex Washburne, Justin D. Silverman 等 2019-06-20 置信度 0.72 Relative species abundanceMicrobiomeFalse positive paradoxIntuitionAbundance (ecology)
• The comprehensive microbial resource
  The Comprehensive Microbial Resource or CMR (http://cmr.jcvi.org) provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displ…
  openalex Tanja M. Davidsen, Erin Beck, Anuradha Ganapathy, Robert A. Montgomery 等 2009-11-05 置信度 0.72 AnnotationGenomeBiologyGenBankGenome project
• Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice
  The above- and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and rhizosphere microbiota of rice cultivars using a metaproteogenomic approach to get insight into the physi…
  openalex Claudia Knief, Nathanaël Delmotte, Samuel Chaffron, Manuel Stark 等 2011-12-22 置信度 0.72 PhyllosphereRhizosphereBiologyBotanyBacteria
• The vocabulary of microbiome research: a proposal
  The advancement of DNA/RNA, proteins, and metabolite analytical platforms, combined with increased computing technologies, has transformed the field of microbial community analysis. This transformation is evident by the exponential increase in the number of pu…
  openalex Julian R. Marchesi, Jacques Ravel 2015-07-24 置信度 0.72 MicrobiomeMetagenomicsBiologyVocabularyField (mathematics)
• Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development
  Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-indivi…
  openalex Adam R. Burns, W. Zac Stephens, Keaton Stagaman, Sandi Wong 等 2015-08-21 置信度 0.72 BiologyMetacommunityBiological dispersalDanioHost (biology)
• Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
  Disruption of healthy microbial communities has been linked to numerous diseases, yet microbial interactions are little understood. This is due in part to the large number of bacteria, and the much larger number of interactions (easily in the millions), making…
  openalex Sophie Weiss, Will Van Treuren, Catherine Lozupone, Karoline Faust 等 2016-02-23 置信度 0.72 BiologyMicrobiomeMetagenomicsCorrelationSampling (signal processing)
• The Microbial Loop
  openalex Lawrence R. Pomeroy, Peter leB. Williams, Farooq Azam, John E. Hobbie 2007-06-01 置信度 0.72 Environmental science
• From hairballs to hypotheses–biological insights from microbial networks
  Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these networks is not straightforward, and the biological …
  openalex Lisa Röttjers, Karoline Faust 2018-07-24 置信度 0.72 Spurious relationshipModularity (biology)BiologyInferenceContext (archaeology)
• Challenges in microbial ecology: building predictive understanding of community function and dynamics
  The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and ma…
  openalex Stefanie Widder, Rosalind J. Allen, Thomas Pfeiffer, Thomas P. Curtis 等 2016-03-29 置信度 0.72 BiologyEcologyMicrobial ecologyFunction (biology)Microbial population biology
• Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling
  Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empiric…
  openalex Maria Mooshammer, Wolfgang Wanek, Ieda Hämmerle, Lucia Fuchslueger 等 2014-04-16 置信度 0.72 DecomposerMineralization (soil science)Nitrogen cycleCyclingNitrogen
• Greengenes2 unifies microbial data in a single reference tree
  Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By i…
  openalex Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell 等 2023-07-27 置信度 0.72 Tree (set theory)BiologyComputational biologyComputer scienceMathematics
• Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
  The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists a…
  openalex Ilias Lagkouvardos, Sandra E. Fischer, Neeraj Kumar, Thomas Clavel 2017-01-11 置信度 0.72 Computer scienceScripting languageSoftwareMetagenomicsAmplicon sequencing
• Land use driven change in soil pH affects microbial carbon cycling processes
  Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategi…
  openalex Ashish A. Malik, Jérémy Puissant, Kate M. Buckeridge, Tim Goodall 等 2018-08-29 置信度 0.72 Soil carbonSoil waterEnvironmental scienceTopsoilCarbon fibers
• Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
  Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial "rare biosphere" to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 t…
  openalex Ashley Shade, Stuart E. Jones, J. Gregory Caporaso, Jo Handelsman 等 2014-07-16 置信度 0.72 TaxonRare speciesEcologyMicrobial population biologyBiology
• Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
  Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes …
  openalex Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni 等 2020-05-19 置信度 0.72 GenomeMetagenomicsPhylogenetic treeBiologyClade
• Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
  16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and phylum spectr…
  openalex Anna Klindworth, Elmar Pruesse, Timmy Schweer, Jörg Peplies 等 2012-08-28 置信度 0.72 BiologyAmplicon16S ribosomal RNAPrimer (cosmetics)Genetics
• A Novel Sparse Compositional Technique Reveals Microbial Perturbations
  By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source li…
  openalex Cameron Martino, James T. Morton, Clarisse Marotz, Luke Thompson 等 2019-02-11 置信度 0.72 Beta diversityMicrobiomeSalientCompositional dataRobustness (evolution)
• The composition of the zebrafish intestinal microbial community varies across development
  The assembly of resident microbial communities is an important event in animal development; however, the extent to which this process mirrors the developmental programs of host tissues is unknown. Here we surveyed the intestinal bacteria at key developmental t…
  openalex W. Zac Stephens, Adam R. Burns, Keaton Stagaman, Sandi Wong 等 2015-09-04 置信度 0.72 BiologyZebrafishDanioMicrobial population biologyVertebrate
• Application of Neural Computing Methods for Interpreting Phospholipid Fatty Acid Profiles of Natural Microbial Communities
  The microbial community compositions of surface and subsurface marine sediments and sediments lining burrows of marine polychaetes and hemichordates from the North Inlet estuary (near Georgetown, S.C. ) were analyzed by comparing ester-linked phospholipid fatt…
  openalex Peter A. Noble, Jonas S. Almeida, Charles R. Lovell 2000-02-01 置信度 0.72 BurrowSedimentLinear discriminant analysisEstuaryArtificial neural network
• Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
  openalex Andrew Maltez Thomas, Paolo Manghi, Francesco Asnicar, Edoardo Pasolli 等 2019-04-01 置信度 0.72 MetagenomicsColorectal cancerCohortComputational biologyCancer
• Bracken: estimating species abundance in metagenomics data
  Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within…
  openalex Jennifer Lu, Florian P. Breitwieser, Peter Thielen, Steven L. Salzberg 2017-01-02 置信度 0.72 MetagenomicsBiologyAbundance (ecology)PopulationDNA sequencing
• The subgingival microbial flora during pregnancy
  The subgingival bacterial flora from 2 gingival sites was cultured and characterized monthly in twenty periodontitis‐free women during pregnancy and again post‐partum. Monthly plaque samples were also cultured in eleven age and disease matched non‐pregnant wom…
  openalex Kenneth S. Kornman, Walter J. Loesche 1980-04-01 置信度 0.72 GingivitisBacteroidesPeriodontitisPregnancyFlora (microbiology)
• A general species delimitation method with applications to phylogenetic placements
  MOTIVATION: Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys and DNA metabarcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intens…
  openalex Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis, Alexandros Stamatakis 2013-08-29 置信度 0.72 Coalescent theoryPhylogenetic treeMarkov chain Monte CarloComputer scienceBayesian probability
• Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
  One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination …
  openalex Daniel Straub, Nia Blackwell, Adrián Langarica-Fuentes, Alexander Peltzer 等 2020-10-23 置信度 0.72 Amplicon16S ribosomal RNABiologyAmplicon sequencingGenetics
• micropan: an R-package for microbial pan-genomics
  BACKGROUND: A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species. Due to the extensive within-species diversity in the microbial world, the pan-genome is often many times larger than a single geno…
  openalex Lars Snipen, Kristian Hovde Liland 2015-03-11 置信度 0.72 GenomeR packageBiologyComputational biologyComparative genomics
• Computation Of Microbial Ecosystems in Time and Space (COMETS): An open source collaborative platform for modeling ecosystems metabolism
  Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and designing microbial …
  arxiv Ilija Dukovski, Djordje Bajić, Jeremy M Chacón, Michael Quintin 等 2020-09-03T15:14:44Z 置信度 0.78 q-bio.QM
• Reducing assembly complexity of microbial genomes with single-molecule sequencing
  Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gap…
  arxiv Sergey Koren, Gregory P Harhay, Timothy PL Smith, James L Bono 等 2013-04-13T00:25:43Z 置信度 0.78 q-bio.GN
• Design Mining Microbial Fuel Cell Cascades
  Microbial fuel cells (MFCs) perform wastewater treatment and electricity production through the conversion of organic matter using microorganisms. For practical applications, it has been suggested that greater efficiency can be achieved by arranging multiple M…
  arxiv Richard J. Preen, Jiseon You, Larry Bull, Ioannis A. Ieropoulos 2016-10-18T17:36:26Z 置信度 0.78 cs.NEcs.AI