List of works - Ben Lehner

5,000 RNAi experiments on a chip.

scientific article published in November 2004

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

scientific article published on 16 June 2016

A first-draft human protein-interaction map

scientific article

A protein interaction framework for human mRNA degradation

scientific article

A simple principle concerning the robustness of protein complex activity to changes in gene expression

scientific article

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.

scientific article published on 27 January 2008

Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins encoded within the human MHC class III region

scientific article

Antisense transcripts in the human genome

scientific article (publication date: February 2002)

Author Correction: Changes in gene expression predictably shift and switch genetic interactions

scientific article published on 17 September 2019

Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience

scientific article

Biophysical ambiguities prevent accurate genetic prediction

scientific article published on 01 October 2020

Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types

scientific article published on 30 July 2015

Cancer: Exploiting collateral damage

scientific article published in August 2012

Changes in gene expression predictably shift and switch genetic interactions

scientific article published on 29 August 2019

Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome

scientific article

Chromatin organization is a major influence on regional mutation rates in human cancer cells.

scientific article published in August 2012

Co-option of the piRNA pathway for germline-specific alternative splicing of C. elegans TOR.

scientific article published on 15 September 2014

Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution

scientific article published on 2 August 2006

Compensatory Cell Movements Confer Robustness to Mechanical Deformation during Embryonic Development

scientific article published on 10 August 2016

Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis

scientific article published on 28 October 2014

Conflict between Noise and Plasticity in Yeast ⬇️

scientific article published on November 4, 2010

Conserved noncoding elements and the evolution of animal body plans

scientific article published on July 2009

Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution

scientific article

Determining protein structures using deep mutagenesis

scientific article published on 17 June 2019

Determining protein structures using genetics

article

DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies

scientific article published on 17 August 2020

Differential DNA mismatch repair underlies mutation rate variation across the human genome

scientific article

Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses

scientific article published on 6 May 2015

Empirical mean-noise fitness landscapes reveal the fitness impact of gene expression noise

scientific article published on 18 July 2019

Empirical noise-mean fitness landscapes and the evolution of gene expression

article

Epigenetic epistatic interactions constrain the evolution of gene expression

scientific article published on January 2013

Evolutionary plasticity of genetic interaction networks

article by Julia Tischler et al published 23 March 2008 in Nature Genetics

Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans

scientific article published in Science

Fluctuation and response in biology

scientific article

Generating transgenic nematodes by bombardment and antibiotic selection

Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast

scientific article published in 2010

Genotype to phenotype: lessons from model organisms for human genetics

scientific article published on 29 January 2013

Harmonious genetic combinations rewire regulatory networks and flip gene essentiality

scientific article published on 14 August 2019

Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers

scientific article published on 03 December 2021

Human epidermal stem cell function is regulated by circadian oscillations.

scientific article

Human genes with CpG island promoters have a distinct transcription-associated chromatin organization

scientific article published on 27 November 2012

Hydroxymethylated cytosines are associated with elevated C to G transversion rates

scientific article

Impaired DNA replication derepresses chromatin and generates a transgenerationally inherited epigenetic memory

scientific article published on 16 August 2017

In search of antisense

scientific article

Inferring gene function from evolutionary change in signatures of translation efficiency

scientific article published on 3 March 2014

Integrated genome-scale prediction of detrimental mutations in transcription networks

scientific article

Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity.

scientific article published in July 2009

Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours

scientific article published on 19 November 2018

Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference

scientific article published on 20 January 2006

MUFFINN: cancer gene discovery via network analysis of somatic mutation data

scientific article

Model-based approach for tracking embryogenesis in Caenorhabditis elegans fluorescence microscopy data.

scientific article

Modelling genotype-phenotype relationships and human disease with genetic interaction networks

scientific article

Molecular mechanisms of epistasis within and between genes

scientific article published on 22 June 2011

Mutations primarily alter the inclusion of alternatively spliced exons

scientific article published on 28 October 2020

Network evolution hinges on history

scientific article published in Nature

Network-guided genetic screening: building, testing and using gene networks to predict gene function

scientific article published on 29 April 2008

Noise control is a primary function of microRNAs and post-transcriptional regulation

Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner

scientific article

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

scientific article published on January 2007

Predicting genetic modifier loci using functional gene networks

scientific article

Predicting mutation outcome from early stochastic variation in genetic interaction partners.

scientific article published on 7 December 2011

Predicting phenotypic variation from genotypes, phenotypes and a combination of the two.

scientific article published on 26 March 2013

Predicting phenotypic variation in yeast from individual genome sequences

scientific article published on 13 November 2011

Protein domains enriched in mammalian tissue-specific or widely expressed genes

article

RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions

Rapid selection of transgenic C. elegans using antibiotic resistance

scientific article published on 22 August 2010

Reaching the limit

scientific article published on 10 August 2018

Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells

scientific article published on 14 August 2015

Selection to minimise noise in living systems and its implications for the evolution of gene expression

scientific article published on 4 March 2008

Single and dual drug selection for transgenes following bombardment of Caenorhabditis species

scientific article published on 20 May 2014

Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming

scientific article published on 12 March 2019

Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation

Single cell functional genomics reveals the importance of mitochondria in cell-to-cell variation in proliferation, drug resistance and mutation outcome

Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage

scientific article

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

article

Systematic discovery of germline cancer predisposition genes through the identification of somatic second hits.

scientific article

Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways

Systems Biology of Caenorhabditis elegans

Systems biology: where it's at in 2005

scientific article

The effects of genetic variation on gene expression dynamics during development

scientific article published on 24 November 2013

The genetic landscape of a physical interaction.

scientific article published on 11 April 2018

The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

scientific article published on 28 October 2019

The impact of rare germline variants on human somatic mutation processes

scientific article published in 2022

The mutational landscape of a prion-like domain

scientific article published on 13 September 2019

The roles of intersubunit interactions in exosome stability

scientific article published on 23 June 2003

The rules and impact of nonsense-mediated mRNA decay in human cancers

scientific article published on 12 September 2016

Tissue specificity and the human protein interaction network

scientific article published on 7 April 2009

Transgenerational transmission of environmental information in C. elegans

scientific article

Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution

scientific article published on 09 September 2008

List of works by Ben Lehner

5,000 RNAi experiments on a chip.

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

A first-draft human protein-interaction map

A protein interaction framework for human mRNA degradation

A simple principle concerning the robustness of protein complex activity to changes in gene expression

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.

Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins encoded within the human MHC class III region

Antisense transcripts in the human genome

Author Correction: Changes in gene expression predictably shift and switch genetic interactions

Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience

Biophysical ambiguities prevent accurate genetic prediction

Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types

Cancer: Exploiting collateral damage

Changes in gene expression predictably shift and switch genetic interactions

Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome

Chromatin organization is a major influence on regional mutation rates in human cancer cells.

Co-option of the piRNA pathway for germline-specific alternative splicing of C. elegans TOR.

Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution

Compensatory Cell Movements Confer Robustness to Mechanical Deformation during Embryonic Development

Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis

Conflict between Noise and Plasticity in Yeast ⬇️

Conserved noncoding elements and the evolution of animal body plans

Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution

Determining protein structures using deep mutagenesis

Determining protein structures using genetics

DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies

Differential DNA mismatch repair underlies mutation rate variation across the human genome

Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses

Empirical mean-noise fitness landscapes reveal the fitness impact of gene expression noise

Empirical noise-mean fitness landscapes and the evolution of gene expression

Epigenetic epistatic interactions constrain the evolution of gene expression

Evolutionary plasticity of genetic interaction networks

Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans

Fluctuation and response in biology

Generating transgenic nematodes by bombardment and antibiotic selection

Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast

Genotype to phenotype: lessons from model organisms for human genetics

Harmonious genetic combinations rewire regulatory networks and flip gene essentiality

Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers

Human epidermal stem cell function is regulated by circadian oscillations.

Human genes with CpG island promoters have a distinct transcription-associated chromatin organization

Hydroxymethylated cytosines are associated with elevated C to G transversion rates

Impaired DNA replication derepresses chromatin and generates a transgenerationally inherited epigenetic memory

In search of antisense

Inferring gene function from evolutionary change in signatures of translation efficiency

Integrated genome-scale prediction of detrimental mutations in transcription networks

Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity.

Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours

Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference

MUFFINN: cancer gene discovery via network analysis of somatic mutation data

Model-based approach for tracking embryogenesis in Caenorhabditis elegans fluorescence microscopy data.

Modelling genotype-phenotype relationships and human disease with genetic interaction networks

Molecular mechanisms of epistasis within and between genes

Mutations primarily alter the inclusion of alternatively spliced exons

Network evolution hinges on history

Network-guided genetic screening: building, testing and using gene networks to predict gene function

Noise control is a primary function of microRNAs and post-transcriptional regulation

Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

Predicting genetic modifier loci using functional gene networks

Predicting mutation outcome from early stochastic variation in genetic interaction partners.

Predicting phenotypic variation from genotypes, phenotypes and a combination of the two.

Predicting phenotypic variation in yeast from individual genome sequences

Protein domains enriched in mammalian tissue-specific or widely expressed genes

RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions

Rapid selection of transgenic C. elegans using antibiotic resistance

Reaching the limit

Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells

Selection to minimise noise in living systems and its implications for the evolution of gene expression

Single and dual drug selection for transgenes following bombardment of Caenorhabditis species

Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming

Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation

Single cell functional genomics reveals the importance of mitochondria in cell-to-cell variation in proliferation, drug resistance and mutation outcome

Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

Systematic discovery of germline cancer predisposition genes through the identification of somatic second hits.

Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways

Systems Biology of Caenorhabditis elegans

Systems biology: where it's at in 2005