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List of works by Uri Gophna

<i>Escherichia coli</i> Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations

scientific article published in 2022

A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis

scientific article published in December 2005

A genetic investigation of the KEOPS complex in halophilic Archaea

scientific article

A halocin-H4 mutant Haloferax mediterranei strain retains the ability to inhibit growth of other halophilic archaea

scientific article published on 14 September 2013

A likelihood framework to analyse phyletic patterns

scientific article published on December 2008

A novel ColV plasmid encoding type IV pili

scientific article published in January 2003

A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness

scientific article

A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness

scientific article

Alterations of Enteric Microbiota in Patients with a Normal Ileal Pouch Are Predictive of Pouchitis

scientific article published on 9 September 2016

An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes

scientific article

Analysis of coevolving gene families using mutually exclusive orthologous modules

scientific article published on 17 April 2011

Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus.

scientific article

Antibiotic resistance: turning evolutionary principles into clinical reality

scientific article published on 25 January 2020

Archaea in and on the Human Body: Health Implications and Future Directions

scientific article

Association between translation efficiency and horizontal gene transfer within microbial communities

scientific article (publication date: June 2011)

Bacterial flagella and Type III secretion: case studies in the evolution of complexity.

scientific article

Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events

scientific article (publication date: 17 July 2003)

By their genes ye shall know them: genomic signatures of predatory bacteria

scientific article published on 29 November 2012

CEACAM1 recognition by bacterial pathogens is species-specific

scientific article

CRISPR loci reveal networks of gene exchange in archaea

scientific article published on 21 December 2011

CRISPR/Cas systems in archaea: What array spacers can teach us about parasitism and gene exchange in the 3rd domain of life. ⬇️

scientific article published on January 2012

Can Colonoscopy Aspirates be a Substitute for Fecal Samples in Analyses of the Intestinal Microbiota?

scientific article

Carriage of Colibactin-producing Bacteria and Colorectal Cancer Risk

scientific article published on 04 June 2020

Cell Surface Glycosylation Is Required for Efficient Mating of Haloferax volcanii

scientific article published on 5 July 2017

Cell fusion and hybrids in Archaea: prospects for genome shuffling and accelerated strain development for biotechnology.

scientific article published on 30 October 2012

Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids

scientific article published on 21 June 2017

Community structure dynamics during startup in microbial fuel cells - The effect of phosphate concentrations

scientific article published on 6 April 2016

Competition between social cheater viruses is driven by mechanistically different cheating strategies

scientific article published on 21 August 2020

Competitive and cooperative metabolic interactions in bacterial communities.

scientific article published on 13 December 2011

Complex histories of genes encoding 3-hydroxy-3-methylglutaryl-CoenzymeA reductase

scientific article

Complexity, connectivity, and duplicability as barriers to lateral gene transfer

scientific article published on January 2007

Composition and dynamics of the gill microbiota of an invasive Indo-Pacific oyster in the eastern Mediterranean Sea.

scientific article

Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious

scientific article

Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen

article

Coordinated change at the colony level in fruit bat fur microbiomes through time

scientific article published on 10 December 2018

Curli fibers mediate internalization of Escherichia coli by eukaryotic cells

scientific article

DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival.

scientific article

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

scientific article

Deriving enzymatic and taxonomic signatures of metagenomes from short read data

scientific article

Detecting Horizontal Gene Transfer between Closely Related Taxa

scientific article

Detection of spatial and temporal influences on bacterial communities in an urban stream by automated ribosomal intergenic ribosomal spacer analysis

scientific article published on 24 August 2011

Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis

scientific article

Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations

scientific article published on 01 December 2019

Distinct Microbiotas are Associated with Ileum-Restricted and Colon-Involving Crohn's Disease.

scientific article published on 8 January 2016

Dynamics of bacterial composition in the locust reproductive tract are affected by the density-dependent phase

scientific article published on 01 April 2020

Effect of ribosome-targeting antibiotics on streptomycin-resistant Mycobacterium mutants in the rpsL gene

scientific article published on 10 May 2013

Eisenbergiella tayi gen. nov., sp. nov., isolated from human blood

scientific article

Escherichia coli isolates from patients with bacteremic urinary tract infection are genetically distinct from those derived from sepsis following prostate transrectal biopsy

scientific article

Evolutionary plasticity of methionine biosynthesis

scientific article published in August 2005

Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae

scientific article

Extensive gene diversity in septicemic Escherichia coli strains

scientific article

Extracellular DNA metabolism in Haloferax volcanii

scientific article published on 20 February 2014

Fecal microbiome signatures of pancreatic cancer patients

scientific article published on 14 November 2019

Finally, Archaea Get Their CRISPR-Cas Toolbox

scientific article published on 5 April 2017

Fine-scale temporal dynamics of a fragmented lotic microbial ecosystem

scientific article published on 18 January 2012

Gastric microbiota is altered in oesophagitis and Barrett's oesophagus and further modified by proton pump inhibitors.

scientific article

Genotype Is a Stronger Determinant than Sex of the Mouse Gut Microbiota

scientific article published on 23 December 2010

Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations

scientific article

Harnessing the landscape of microbial culture media to predict new organism-media pairings

scientific article

Have archaeal genes contributed to bacterial virulence?

scientific article published on May 2004

High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon.

scientific article published on 2 March 2017

Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions

scientific article published on January 2011

Impact of a homing intein on recombination frequency and organismal fitness

scientific article published on 26 July 2016

In and out: an analysis of epibiotic vs periplasmic bacterial predators

scientific article

In situ transplant analysis of free-living bacteria in a lotic ecosystem

scientific article published on 17 December 2012

In vivo analysis of various substrates utilized by cystathionine gamma-synthase and O-acetylhomoserine sulfhydrylase in methionine biosynthesis

scientific article published on 27 June 2003

In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii

scientific article

Integration of a foreign gene into a native complex does not impair fitness in an experimental model of lateral gene transfer

scientific article published on 16 June 2010

Interactions between the intestinal microbiota and bile acids in gallstones patients

scientific article published on 6 July 2015

Investigating a lotic microbial community following a severe detergent spill

scientific article

Lateral Gene Transfer in Evolution

article

Lateral acquisition of genes is affected by the friendliness of their products

scientific article

Low species barriers in halophilic archaea and the formation of recombinant hybrids

scientific article

Matrix-Assisted Refolding of Single-Chain Fv– Cellulose Binding Domain Fusion Proteins

scientific article published on 01 November 1999

Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms

scientific article

Menaquinone and iron are essential for complex colony development in Bacillus subtilis

scientific article

Metabolic-network-driven analysis of bacterial ecological strategies

scientific article published on 05 June 2009

Multilocus sequence typing (MLST) of Escherichia coli O78 strains

scientific article published in May 2003

Native homing endonucleases can target conserved genes in humans and in animal models

scientific article

Neutrality of foreign complex subunits in an experimental model of lateral gene transfer.

scientific article

No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales

scientific article published on 24 February 2015

OmpA of a septicemic Escherichia coli O78--secretion and convergent evolution.

scientific article

Oscillospira and related bacteria - From metagenomic species to metabolic features

scientific article published on 28 December 2016

Oscillospira: a Central, Enigmatic Component of the Human Gut Microbiota

scientific article published on 17 March 2016

Parity and disparity between two Chama oysters: the reproductive biology of the Indo-Pacific C. pacifica Broderip, invasive to the Mediterranean Sea; and C. savignyi Lamy, indigenous to the Red Sea

scientific article published in 2011

Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation

article

Phylo SI: a new genome-wide approach for prokaryotic phylogeny

scientific article

Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea

scientific article published on 6 April 2013

Pouch Inflammation Is Associated With a Decrease in Specific Bacterial Taxa.

scientific article published on 27 May 2015

Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy

scientific article published on 09 October 2019

Reconstructing ancestral gene content by coevolution

scientific article (publication date: 2010)

Reply

Reply to "The importance of accurate phenotyping and pouchitis risk and dietary assessment when investigating the microbial factors behind antibiotic dependent pouchitis"

scientific article published on 14 April 2020

Reviewing the right papers

scientific article published on 01 January 2020

Ribosomal mutations affecting the translation of genes that use non-optimal codons

scientific article published on 8 August 2014

Role of fibronectin in curli-mediated internalization

scientific article published on June 2002

Role of fibronectin in curli-mediated internalization

scholarly article by U Gophna published in June 2002

Sequence features of E. coli mRNAs affect their degradation

scientific article

Sexually transmitted Escherichia coli urethritis and orchiepididymitis.

scientific article

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli

scientific article published on 28 January 2016

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

article

The Guts of Dietary Habits

scientific article

The contribution of common rpsL mutations in Escherichia coli to sensitivity to ribosome targeting antibiotics.

scientific article published on 31 July 2013

The correlation between Clostridium-difficile infection and human gut concentrations of Bacteroidetes phylum and clostridial species

scientific article published on 19 September 2013

The evolution of modularity in bacterial metabolic networks.

scholarly article

The formation of Escherichia coli curli amyloid fibrils is mediated by prion-like peptide repeats.

scientific article

The gill microbiota of invasive and indigenous Spondylus oysters from the Mediterranean Sea and northern Red Sea.

scientific article published on 25 June 2015

The gut microbiota of toll-like receptor 2-deficient mice exhibits lineage-specific modifications.

scientific article

The large-scale organization of the bacterial network of ecological co-occurrence interactions.

scientific article

The lpf operon of invasive Escherichia coli

scientific article published on August 2005

The origins of eukaryotic-like proteins in Legionella pneumophila

scientific article published on 26 May 2010

The ubiquitous conserved glycopeptidase Gcp prevents accumulation of toxic glycated proteins

scientific article published on 24 August 2010

The unbearable ease of expression-how avoidance of spurious transcription can shape G+C content in bacterial genomes

scientific article published on 01 December 2018

Virulence and the heat shock response

scientific article

Virulence factors of septicemic Escherichia coli strains

scientific article

Weighted genome trees: refinements and applications

scientific article published on February 2005

Yersinia HPI in septicemic Escherichia coli strains isolated from diverse hosts

scholarly article by U Gophna published in March 2001

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