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List of works by Elhanan Borenstein

Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis

scientific article

An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing

scientific article published on 11 July 2016

An algorithm for designing minimal microbial communities with desired metabolic capacities

scientific article published on 26 February 2016

An end to endless forms: epistasis, phenotype distribution bias, and nonuniform evolution

scientific article (publication date: October 2008)

BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data.

scientific article published in March 2018

Broker genes in human disease

scientific article

Characterising the taxonomic composition of children and livestock gut microbiomes and of environmental samples and the potential role for household-level microbiome sharing in western Kenya

article

Circuitry and dynamics of human transcription factor regulatory networks

scientific article published on 5 September 2012

Comparative analysis of functional metagenomic annotation and the mappability of short reads

scientific article

Competitive lottery-based assembly of selected clades in the human gut microbiome

scientific article published on 19 October 2018

Computational systems biology and in silico modeling of the human microbiome

scientific article published on 15 May 2012

Conservation of trans-acting circuitry during mammalian regulatory evolution

scientific article

Cultural niche construction in a metapopulation

scientific article published on 19 January 2006

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

scientific article

Direct evolution of genetic robustness in microRNA.

scholarly article

Emergent biosynthetic capacity in simple microbial communities

scientific article

Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis

scientific article published on 30 October 2013

Evolution of learning in fluctuating environments: when selection favors both social and exploratory individual learning.

scientific article

Evolutionary assembly patterns of prokaryotic genomes

scientific article published on 14 April 2016

Extensive strain-level copy-number variation across human gut microbiome species

scientific article published on 29 January 2015

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

scientific article published on 7 December 2006

Getting Personal About Nutrition

scientific article published on 14 January 2016

High-resolution characterization of the human microbiome

scientific article

Hsp90 promotes kinase evolution

scientific article

Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

Large-scale reconstruction and phylogenetic analysis of metabolic environments

scholarly article

MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

scientific article

Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome

scientific article

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

scientific article published on 19 January 2016

Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss.

scientific article

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

scientific article

Metabolic-network-driven analysis of bacterial ecological strategies

scientific article published on 05 June 2009

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis

scientific article

Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules

scientific article

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

scientific article

Microbiome sharing between children, livestock and household surfaces in western Kenya

scientific article published on 02 February 2017

Most networks in Wagner's model are cycling

scientific article (publication date: 2012)

Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders

scientific article

NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species

scientific article published on 4 June 2012

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

scientific article published on 17 May 2015

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

scientific article published on 4 January 2012

Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution

scientific article

Reverse Ecology: from systems to environments and back

scientific article

Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome

scientific article published on 08 February 2017

Similarly strong purifying selection acts on human disease genes of all evolutionary ages

scientific article

Social and individual learning of helping in humans and other species.

scientific article published on 23 October 2008

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

scientific article (publication date: 4 April 2012)

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome

scientific article published on 18 January 2017

Taxa-function robustness in microbial communities.

scientific article published on 2 March 2018

The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition

scientific article

The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data.

scientific article

The discovery of integrated gene networks for autism and related disorders

scientific article

The evolution of modularity in bacterial metabolic networks.

scholarly article

The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy

article

Topological signatures of species interactions in metabolic networks

scientific article published on February 2009

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

scientific article

Where next for microbiome research?

scientific article

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