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2026
Microstructural changes in locus coeruleus-cortical projections in aged bonnet macaques are independent of myelin loss
Neurobiology of Aging
2025
Effect of copper exposure on the silkworm Bombyx mori: Insights into the changes of metabolism, gut microbial composition and gene expression
Insect Molecular Biology
2025
Are bacterial communities and aggregation in fragile soils influenced by the management system?
Farming System
2025
SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx
mBio
2025
Transcriptome remodeling drives acclimation to iron availability in the marine N 2 -fixing cyanobacterium Trichodesmium erythraeum IMS101
mSystems
2025
Predicted m6A and m5C marks in honeybee larval transcriptomes imply functional differences in caste development
Apidologie
2025
Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages
Cell Reports
2025
The Drosophila Zinc Finger Protein Aef1 Colocalizes with Enhancers and Is Involved in the Transcriptional Regulation of Numerous Genes
Acta Naturae
2025
Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs
Frontiers in Microbiology
2025
Impact of intensive agricultural management on soil biota in mountain ecosystems of the Brazilian Atlantic Forest
Applied Soil Ecology
2025
Methods in Molecular Biology
2025
Genetic and biochemical determinants in potentially toxic metals resistance and plant growth promotion in Rhizobium sp LBMP-C04
World Journal of Microbiology and Biotechnology
2025
Effect of co-inoculation with plant growth-promoting bacteria on the microbiome of soybean roots
Frontiers in Sustainable Food Systems
2025
Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing
ISME Communications
2025
Multi-omic analysis of SDHB-deficient pheochromocytomas and paragangliomas identifies metastasis and treatment-related molecular profiles
Nature Communications
2025
Shared environments can facilitate microbial transmission and alter metabolic outcomes
Gut Microbes
2025
Immunization induces inflammation in the mouse heart during spaceflight
BMC Genomics
2025
Multi-omics integration identifies molecular markers and biological pathways for carcass and meat quality traits in Nellore cattle
Scientific Reports
2025
Integrating Plasma Cell-Free DNA Fragment End Motif and Size with Genomic Features Enables Lung Cancer Detection
Cancer Research
2025
Metatranscriptomic profiling reveals microbial succession and adaptation strategies during long-term lignocellulose degradation
International Biodeterioration & Biodegradation
2025
Markers or metagenomes: sequencing marine eukaryotic DNA for better biodiversity surveys
Metabarcoding and Metagenomics
2025
Revealing the Bacteriome in Crop–Livestock–Forest Integration Systems in the Cerrado of MATOPIBA, Brazil
Forests
2025
Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort
Nature Communications
2025
Misprocessing of α-Galactosidase A, Endoplasmic Reticulum Stress, and the Unfolded Protein Response
Journal of the American Society of Nephrology
2025
CaDAVEr: a metagenome-assembled genome catalog of microbial decomposers across vertebrate environments
Microbiology Resource Announcements
2024
Investigating the Evolution of Drosophila STING-Dependent Antiviral Innate Immunity by Multispecies Comparison of 2′3′-cGAMP Responses
Molecular Biology and Evolution
2024
Type VI secretion system drives bacterial diversity and functions in multispecies biofilms
Microbiological Research
2024
Transgenerational effects of early life stress on the fecal microbiota in mice
Communications Biology
2024
WNT signalling control by KDM5C during development affects cognition
Nature
2024
Transcriptional responses of Metarhizium pingshaense blastospores after UV-B irradiation
Frontiers in Microbiology
2024
Short-Term Effects of Poultry Litter and Cattle Manure on Soil’s Chemical Properties and Bacterial Community
Agronomy
2024
Integration of polygenic and gut metagenomic risk prediction for common diseases
Nature Aging
2024
The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data
Metabarcoding and Metagenomics
2024
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables
Nature Microbiology
2024
Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis
Frontiers in Microbiology
2024
Endogenous viral elements are targeted by RNA silencing pathways in banana
New Phytologist
2024
Effects of Trichoderma harzianum and Bacillus subtilis on the root and soil microbiomes of the soybean plant INTACTA RR2 PRO™
Frontiers in Plant Science
2024
Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions
International Journal of Medical Microbiology
2024
Detection of allele-specific expression in spatial transcriptomics with spASE
Genome Biology
2024
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing
PLOS Computational Biology
2024
Exploratory comparative transcriptomic analysis reveals potential gene targets associated with Cry1A.105 and Cry2Ab2 resistance in fall armyworm (Spodoptera frugiperda)
Functional & Integrative Genomics
2024
Human Herpesvirus-6B Infection and Alterations of Gut Microbiome in Patients with Fibromyalgia: A Pilot Study
Biomolecules
2024
Peripheral neuronal activation shapes the microbiome and alters gut physiology
Cell Reports
2024
Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases
Microbiome
2024
Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest
Nature Communications
2024
Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda
Science of The Total Environment
2024
Sex-specific developmental gene expression atlas unveils dimorphic gene networks in C. elegans
Nature Communications
2024
Ehf and Fezf2 regulate late medullary thymic epithelial cell and thymic tuft cell development
Frontiers in Immunology
2024
PTEN-regulated PI3K-p110 and AKT isoform plasticity controls metastatic prostate cancer progression
Oncogene
2024
Systems Biology Approaches for Host-Pathogen Interaction Analysis
2024
Temperature-driven coordination of circadian transcriptional regulation
PLOS Computational Biology
2024
Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults
European Journal of Nutrition
2024
Genetic diversity accelerates canine distemper virus adaptation to ferrets
Journal of Virology
2024
Associations between gut microbiota and incident fractures in the FINRISK cohort
npj Biofilms and Microbiomes
2024
Fungal community structure in bees: influence of biome and host species
Symbiosis
2024
Growth promotion and modulation of the soybean microbiome INTACTA RR PRO with the application of the fungi Trichoderma harzianum and Purpureocillum lilacinum
Scientific Reports
2024
A pilot case-control study on the fecal microbiota of pediatric functional abdominal pain-not otherwise specified and the role of early life stress
Microbiome Research Reports
2024
Influence of Growth Support on the Diversity, Composition, and Functionality of Microbial Communities Associated with Tillandsia recurvata
Microbial Ecology
2024
Successful Invasion Into New Environments Without Evidence of Rapid Adaptation by a Predatory Marine Gastropod
Molecular Ecology
2024
Autonomous eDNA collection using an uncrewed surface vessel over a 4200‐km transect of the eastern Pacific Ocean
Environmental DNA
2023
Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2
Nature Cell Biology
2023
Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture
International Journal of Biological Macromolecules
2023
Age-associated H3K9me2 loss alters the regenerative equilibrium between murine lung alveolar and bronchiolar progenitors
Developmental Cell
2023
Artificial Intelligence-Driven Morphology-Based Enrichment of Malignant Cells from Body Fluid
Modern Pathology
2023
Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis
Cancers
2023
Long-term continuous cultivation of Kenyan infant fecal microbiota using the host adapted PolyFermS model
Scientific Reports
2023
Integrating massive RNA-seq data to elucidate transcriptome dynamics in Drosophila melanogaster
Briefings in Bioinformatics
2023
Transcription factor SOX15 regulates stem cell pluripotency and promotes neural fate during differentiation by activating the neurogenic gene Hes5
Journal of Biological Chemistry
2023
Reductive carboxylation epigenetically instructs T cell differentiation
Nature
2023
Differential Expression of miRNAs Involved in Response to Candidatus Liberibacter asiaticus Infection in Mexican Lime at Early and Late Stages of Huanglongbing Disease
Plants
2023
Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in the activation of circumjacent pathways upon DNA damage
Molecular Oncology
2023
Validation of a batch cultivation protocol for fecal microbiota of Kenyan infants
BMC Microbiology
2023
A comprehensive investigation of histotype‐specific microRNA and their variants in Stage I epithelial ovarian cancers
International Journal of Cancer
2023
The gut microbiome is a significant risk factor for future chronic lung disease
Journal of Allergy and Clinical Immunology
2023
Emergence and fate of stem cell–likeTcf7+CD8+T cells during a primary immune response to viral infection
Science Immunology
2023
In Vivo Emergence of Dual Resistance to Rifampin and Levofloxacin in Osteoarticular Cutibacterium avidum
Microbiology Spectrum
2023
A scoping review on deep learning for next-generation RNA-Seq. data analysis
Functional & Integrative Genomics
2023
Exome sequencing reveals IFT172 variants in patients with non-syndromic cholestatic liver disease
PLOS ONE
2023
Alterations in microRNA of extracellular vesicles associated with major depression, attention-deficit/hyperactivity and anxiety disorders in adolescents
Translational Psychiatry
2023
Genome‐wide analysis of the chromatin sites targeted by HEX 70a storage protein in the honeybee brain and fat body
Insect Molecular Biology
2022
Functional Fermented Milk with Fruit Pulp Modulates the In Vitro Intestinal Microbiota
Foods
2022
Intronization Signatures in Coding Exons Reveal the Evolutionary Fluidity of Eukaryotic Gene Architecture
Microorganisms
2022
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy
mSystems
2022
The DNA/RNA helicase DHX9 contributes to the transcriptional program of the androgen receptor in prostate cancer
Journal of Experimental & Clinical Cancer Research
2022
Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes
Journal of Translational Medicine
2022
Specificities and Commonalities of Carbapenemase-Producing Escherichia coli Isolated in France from 2012 to 2015
mSystems
2022
Modeling electron beam irradiation of methane
International Journal of Chemical Kinetics
2022
Honeybee Iflaviruses Pack Specific tRNA Fragments from Host Cells in Their Virions
ChemBioChem
2022
NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks
Communications Biology
2022
Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology
iScience
2022
The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ
npj Breast Cancer
2022
DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis
Nature Genetics
2022
Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course
Cell
2022
Haemolysis Detection in MicroRNA-Seq from Clinical Plasma Samples
Genes
2022
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Nature Microbiology
2022
CREBBP/EP300 acetyltransferase inhibition disrupts FOXA1-bound enhancers to inhibit the proliferation of ER+ breast cancer cells
PLOS ONE
2022
Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases
mSystems
2022
Lake Erie field trials to advance autonomous monitoring of cyanobacterial harmful algal blooms
Frontiers in Marine Science
2022
Novel Genetic Prognostic Signature for Lung Adenocarcinoma Identified by Differences in Gene Expression Profiles of Low- and High-Grade Histological Subtypes
Biomolecules
2022
Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults
Diabetes Care
2022
Feed Insects as a Reservoir of Granadaene-Producing Lactococci
Frontiers in Microbiology
2021
Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity
Inflammatory Bowel Diseases
2021
Links between gut microbiome composition and fatty liver disease in a large population sample
Gut Microbes
2021
Experimental Infection of the Biomphalaria glabrata Vector Snail by Schistosoma mansoni Parasites Drives Snail Microbiota Dysbiosis
Microorganisms
2021
Periodontitis associates with species-specific gene expression of the oral microbiota
npj Biofilms and Microbiomes
2021
Clostridioides difficileWhole-genome Sequencing Differentiates Relapse With the Same Strain From Reinfection With a New Strain
Clinical Infectious Diseases
2021
Atria: an ultra-fast and accurate trimmer for adapter and quality trimming
Gigabyte
2021
Advances in Experimental Medicine and Biology
2021
Enrichment and description of novel bacteria performing syntrophic propionate oxidation at high ammonia level
Environmental Microbiology
2021
Genome-resolved metagenomics using environmental and clinical samples
Briefings in Bioinformatics
2021
HIV Modifies the m6A and m5C Epitranscriptomic Landscape of the Host Cell
Frontiers in Virology
2021
Integrative genetic, genomic and transcriptomic analysis of heat shock protein and nuclear hormone receptor gene associations with spontaneous preterm birth
Scientific Reports
2021
Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates
Nature Communications
2021
A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
Genome Research
2021
An ADAR1-dependent RNA editing event in the cyclin-dependent kinase CDK13 promotes thyroid cancer hallmarks
Molecular Cancer
2021
Plasmid Acquisition Alters Vancomycin Susceptibility in Clostridioides difficile
Gastroenterology
2021
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes
Genome Research
2021
Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis
Multiple Sclerosis Journal
2021
Convergent genomic and pharmacological evidence of PI3K/GSK3 signaling alterations in neurons from schizophrenia patients
Neuropsychopharmacology
2021
Intestinal inflammation alters mucosal carbohydrate foraging and monosaccharide incorporation into microbial glycans
Cellular Microbiology
2021
Drosophila Fezf functions as a transcriptional repressor to direct layer-specific synaptic connectivity in the fly visual system
Proceedings of the National Academy of Sciences
2021
Transcriptomic analysis of Streptococcus agalactiae periprosthetic joint infection
MicrobiologyOpen
2021
A Comparison of DNA/RNA Extraction Protocols for High-Throughput Sequencing of Microbial Communities
BioTechniques
2021
Comparative Transcriptomic Analysis of Staphylococcus aureus Associated with Periprosthetic Joint Infection under in Vivo and in Vitro Conditions
The Journal of Molecular Diagnostics
2021
Genome-wide and size-based cell-free DNA indices as predictive biomarkers for locally advanced esophageal squamous cell carcinoma treated with preoperative or definitive chemoradiotherapy
Current Problems in Cancer
2021
Metagenome-assembled genome of a Chitinophaga sp. and its potential in plant biomass degradation, as well of affiliated Pandoraea and Labrys species
World Journal of Microbiology and Biotechnology
2021
Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms
Brain, Behavior, and Immunity
2021
Simplifying the development of portable, scalable, and reproducible workflows
eLife
2021
Unraveling the features of somatic transposition in the Drosophila intestine
The EMBO Journal
2021
m6A RNA methylation regulates the fate of endogenous retroviruses
Nature
2021
Identification of genuine and novel miRNAs in Amaranthus hypochondriacus from high-throughput sequencing data
Genomics
2021
Microbiota Modulates Cardiac Transcriptional Responses to Intermittent Hypoxia and Hypercapnia
Frontiers in Physiology
2021
TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex
eLife
2021
Systems Medicine
2021
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome
Microbiological Research
2021
EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences
Bioinformatics
2021
A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes
Computational and Structural Biotechnology Journal
2021
Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021
mSystems
2021
Vocal Fold Fibroblasts in Reinke’s Edema Show Alterations Involved in Extracellular Matrix Production, Cytokine Response and Cell Cycle Control
Biomedicines
2021
Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion
Cell
2021
Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation
RNA Biology
2021
Benchmarking microbial growth rate predictions from metagenomes
The ISME Journal
2020
An Efficient Trimming Algorithm based on Multi-Feature Fusion Scoring Model for NGS Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2020
Lecture Notes in Networks and Systems
2020
Poised potential is not an effective strategy to enhance bio-electrochemical denitrification under cyclic substrate limitations
Science of The Total Environment
2020
RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Nature
2020
Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic
Viruses
2020
Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling
eLife
2020
Read trimming is not required for mapping and quantification of RNA-seq reads at the gene level
NAR Genomics and Bioinformatics
2020
Noncoding RNA transcription alters chromosomal topology to promote isotype-specific class switch recombination
Science Immunology
2020
Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee
Frontiers in Microbiology
2020
Immunological pathways of macrophage response to Brucella ovis infection
Innate Immunity
2020
Simultaneous identification of clinically relevant RB1 mutations and copy number alterations in aqueous humor of retinoblastoma eyes
Ophthalmic Genetics
2020
Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans
Cell
2020
Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota
Scientific Data
2020
Mutational profiling of micro-dissected pre-malignant lesions from archived specimens
BMC Medical Genomics
2020
Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection
Journal of Experimental Medicine
2020
Targeting Mitochondria-Located circRNA SCAR Alleviates NASH via Reducing mROS Output
Cell
2020
Read trimming has minimal effect on bacterial SNP-calling accuracy
Microbial Genomics
2020
The CD38/NAD/SIRTUIN1/EZH2 Axis Mitigates Cytotoxic CD8 T Cell Function and Identifies Patients with SLE Prone to Infections
Cell Reports
2020
Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs
mSystems
2020
The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community
Genes
2020
Phylogenetic signature of fungal response to long-term chemical pollution
Soil Biology and Biochemistry
2020
Initial butyrate producers during infant gut microbiota development are endospore formers
Environmental Microbiology
2019
Revealing the pathogenic changes of PAH based on multiomics characteristics
Journal of Translational Medicine
2019
Environmentally induced plasticity of programmed DNA elimination boosts somatic variability inParamecium tetraurelia
Genome Research
2019
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
Genome Biology
2019
Physical and Molecular Landscapes of Mouse Glioma Extracellular Vesicles Define Heterogeneity
Cell Reports
2019
Multi omics analysis of fibrotic kidneys in two mouse models
Scientific Data
2019
Interplay between small RNA pathways shapes chromatin landscapes in C. elegans
Nucleic Acids Research
2019
Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes
Proceedings of the National Academy of Sciences
2019
Methods in Molecular Biology
2019
LC/MS analysis and deep sequencing reveal the accurate RNA composition in the HIV-1 virion
Scientific Reports
2019
Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity
Analytical Chemistry
2019
Sex Differences in Adrenal Bmal1 Deletion–Induced Augmentation of Glucocorticoid Responses to Stress and ACTH in Mice
Endocrinology
2019
Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome
Life Science Alliance
2019
Application of metagenomic shotgun sequencing to detect vector-borne pathogens in clinical blood samples
PLOS ONE
2019
Brca2 abrogation engages with the alternative lengthening of telomeres via break‐induced replication
The FEBS Journal
2018
BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues
BMC Genomics
2018
Studying Smaller and Neglected Organisms in Modern Evolutionary Venomics Implementing RNASeq (Transcriptomics)—A Critical Guide
Toxins
2018
CD8 Follicular T Cells Promote B Cell Antibody Class Switch in Autoimmune Disease
The Journal of Immunology
2018
Limitations of alignment-free tools in total RNA-seq quantification
BMC Genomics
2018
Improving saliva shotgun metagenomics by chemical host DNA depletion
Microbiome
2018
High‑throughput sequencing reveals differentially expressed lncRNAs and circRNAs, and their associated functional network, in human hypertrophic scars
Molecular Medicine Reports
2018
American Gut: an Open Platform for Citizen Science Microbiome Research
mSystems
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