Ben Lehner

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

A. Fraser, Ben Lehner, Catriona Crombie, 2006, Nature Genetics.

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

A. Fraser, E. Marcotte, Insuk Lee, 2008, Nature Genetics.

A first-draft human protein-interaction map

A. Fraser, Ben Lehner, 2004, Genome Biology.

The complete local genotype–phenotype landscape for the alternative splicing of a human exon

J. Valcárcel, Ben Lehner, P. Julien, 2016, Nature Communications.

The effects of genetic variation on gene expression dynamics during development

Ben Lehner, M. Francesconi, 2013, Nature.

Tissue specificity and the human protein interaction network

Ben Lehner, Alice Bossi, 2009, Molecular systems biology.

Predicting genetic modifier loci using functional gene networks.

A. Fraser, E. Marcotte, Insuk Lee, 2010, Genome research.

Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes

F. Supek, Ben Lehner, 2017, Cell.

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

Ben Lehner, 2008, Molecular systems biology.

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

J. Valcárcel, F. Supek, Ben Lehner, 2014, Cell.

Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome

Ben Lehner, T. Vavouri, 2011, PLoS genetics.

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

Ben Lehner, Ben Lehner, A. Burga, 2013, Current opinion in biotechnology.

Integrated Genome-Scale Prediction of Detrimental Mutations in Transcription Networks

Mirko Francesconi, Rob Jelier, Ben Lehner, 2011, PLoS genetics.

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

Ben Lehner, L. Carey, A. Missarova, 2019, eLife.

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

Ben Lehner, L. Carey, A. Missarova, 2018, bioRxiv.

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

David van Dijk, Ben Lehner, Riddhiman Dhar, 2015, Nature Communications.

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

Ben Lehner, M. Francesconi, 2015, Molecular bioSystems.

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

B. Schuster-Böckler, Ben Lehner, Benjamin Schuster-Böckler, 2012, Nature.

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

Ben Lehner, Solip Park, Ben Lehner, 2015, Molecular systems biology.

Technique review: how to use RNA interference.

A. Fraser, Ben Lehner, C. Sanderson, 2004, Briefings in functional genomics & proteomics.

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

Ben Lehner, Ayelet T. Lamm, Camilla Iannone, 2014, Cell reports.

Ben Lehner, Ben Lehner, 2010, PloS one.

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Ben Lehner, Ben Lehner, A. Burga, 2011, Nature.

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

F. Supek, Insuk Lee, Ben Lehner, 2016, Genome Biology.

Systems Biology of Caenorhabditis elegans

A. Fraser, Ben Lehner, 2013 .

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

E. Meijering, Ben Lehner, O. Dzyubachyk, 2015, Developmental biology.

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

Ben Lehner, T. Vavouri, 2012, Genome Biology.

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

A. Fraser, Ben Lehner, 2004, Trends in genetics : TIG.

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

F. Supek, Ben Lehner, R. Lindeboom, 2016, Nature Genetics.

3D structure of individual mammalian genomes studied by single cell Hi-C

Andre J. Faure, D. Klenerman, Ben Lehner, 2017, Nature.

Fluctuation and response in biology

K. Kaneko, Ben Lehner, 2010, Cellular and Molecular Life Sciences.

Inferring gene function from evolutionary change in signatures of translation efficiency

Ben Lehner, Toni Gabaldón, Fran Supek, 2014, Genome Biology.

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

F. Supek, Ben Lehner, Solip Park, 2018, Nature Communications.

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

Ben Lehner, Nansheng Chen, Andrew G Fraser, 2006, Genome Biology.

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

Ben Lehner, T. Vavouri, J. Semple, 2008, Trends in genetics : TIG.

The genetic landscape for amyloid beta fibril nucleation accurately discriminates familial Alzheimer’s disease mutations

Andre J. Faure, Ben Lehner, Marta Badia, 2020, bioRxiv.

The genetic landscape of a physical interaction

Ben Lehner, Guillaume Diss, Ben Lehner, 2018, eLife.

Antisense transcripts in the human genome.

Ben Lehner, Ben Lehner, R. Campbell, 2002, Trends in genetics : TIG.

Mutations primarily alter the inclusion of alternatively spliced exons

J. Valcárcel, Ben Lehner, B. Miñana, 2020, bioRxiv.

Compensatory Cell Movements Confer Robustness to Mechanical Deformation during Embryonic Development.

T. Zimmermann, Ben Lehner, J. Swoger, 2016, Cell systems.

Human epidermal stem cell function is regulated by circadian oscillations.

Ben Lehner, Kiana Toufighi, Nuno Miguel Luis, 2013, Cell stem cell.

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.

Ben Lehner, Damian Counsell, Ben Lehner, 2004, Genomics.

Changes in gene expression predictably shift and switch genetic interactions

Ben Lehner, Pablo Baeza-Centurion, R. Dhar, 2019, Nature Communications.

Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells.

Andre J. Faure, Jörn M. Schmiedel, Ben Lehner, 2017, Cell systems.

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

Andre J. Faure, Ben Lehner, Pablo Baeza-Centurion, 2020, Genome Biology.

Editorial Novapublishers CHAPTER TITLE : Applications of RNAi in C . elegans research

J. M. Monje, Ben Lehner, S. Schwartz, 2007 .

Applications of RNAi in C. Elegans Research

J. M. Monje, Ben Lehner, S. Schwartz, 2008 .

A Concentration-Depende nt Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression Graphical

Ben Lehner, D. Cirillo, G. Tartaglia, 2016 .

Biophysical ambiguities prevent accurate genetic prediction

Ben Lehner, Xianghua Li, 2020, Nature Communications.

Single cell expression analysis uncouples transdifferentiation and reprogramming

M. Gut, I. Gut, Ben Lehner, 2018, bioRxiv.

Systems biology: where it's at in 2005

A. Fraser, Ben Lehner, Julia Tischler, 2005, Genome Biology.

Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome

Ben Lehner, T. Vavouri, 2011, PLoS genetics.

Rapid selection of transgenic C. elegans using antibiotic resistance

Ben Lehner, J. Semple, Rosa Garcı́a-Verdugo, 2010, Nature Methods.

Maternal age generates phenotypic variation in C. elegans

Ben Lehner, M. Francesconi, Cristina Hidalgo-Carcedo, 2017, Nature.

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

Ben Lehner, Ben Lehner, 2007, Journal of Experimental Biology.

Systems biology: Network evolution hinges on history

Ben Lehner, Ben Lehner, A. New, 2015, Nature.

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

Jörn M. Schmiedel, D. Marks, Ben Lehner, 2017, bioRxiv.

Intergenerational and transgenerational epigenetic inheritance in animals

Ben Lehner, M. F. Perez, 2019, Nature Cell Biology.

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

Ben Lehner, Tanya Vavouri, Jennifer I. Semple, 2008 .

In search of antisense.

Ben Lehner, Rotem Sorek, Giovanni Lavorgna, 2004, Trends in biochemical sciences.

Scales and mechanisms of somatic mutation rate variation 1 across the human genome 2 3

F. Supek, Ben Lehner, 2020 .

Scales and mechanisms of somatic mutation rate variation across the human genome.

F. Supek, Ben Lehner, 2019, DNA repair.

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

Ben Lehner, Andre J. Faure, Jörn M. Schmiedel, 2020, bioRxiv.

Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing

Ben Lehner, Belén Miñana, Juan Valcárcel, 2019, Cell.

Molecular mechanisms of epistasis within and between genes.

Ben Lehner, Ben Lehner, 2011, Trends in genetics : TIG.

Hydroxymethylated Cytosines Are Associated with Elevated C to G Transversion Rates

Ben Lehner, Tobias Warnecke, Fran Supek, 2014, PLoS genetics.

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

Klaudia Walter, Ben Lehner, Tanya Vavouri, 2007, Genome Biology.

Vitellogenins - Yolk Gene Function and Regulation in Caenorhabditis elegans

Ben Lehner, M. F. Perez, 2019, Front. Physiol..

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

Ben Lehner, Fran Supek, F. Supek, 2019, Nature Genetics.

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

F. Supek, Ben Lehner, A. Castellanos, 2018, Nature Cell Biology.

Pairwise and higher order genetic interactions during the evolution of a tRNA

Ben Lehner, Guillaume Diss, Ben Lehner, 2018, Nature.

3 D structure of individual mammalian genomes studied by single cell HiC

Enrique Blanco, Tim J. Stevens, Wayne Boucher, 2017 .

Transgenerational transmission of environmental information in C. elegans

Cristina Hidalgo-Carcedo, Ben Lehner, Tanya Vavouri, 2017, Science.

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

F. Supek, Ben Lehner, Solip Park, 2021, Nature Communications.

Predicting phenotypic variation in yeast from individual genome sequences

Rob Jelier, Ben Lehner, Ben Lehner, 2011, Nature Genetics.

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

Ben Lehner, Fran Supek, F. Supek, 2015, Nature.

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

Mirko Francesconi, Ben Lehner, Holger Heyn, 2019, eLife.

Intrinsic Protein Disorder and Interaction Promiscuity Are Widely Associated with Dosage Sensitivity

Ben Lehner, Tanya Vavouri, Jennifer I. Semple, 2009, Cell.

How to use RNA interference

A. Fraser, Ben Lehner, C. Sanderson, 2004 .

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

A. Fraser, M. Chalfie, Ben Lehner, 2006, Genome Biology.

5,000 RNAi experiments on a chip

Ben Lehner, Andrew G Fraser, A. Fraser, 2004, Nature Methods.

The impact of rare germline variants on human somatic mutation processes

F. Supek, Ben Lehner, Mischan Vali-Pour, 2021, Nature Communications.

Epigenetic epistatic interactions constrain the evolution of gene expression

Ben Lehner, Solip Park, 2013, Molecular systems biology.

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

Ben Lehner, D. Cirillo, G. Tartaglia, 2016, Cell reports.

Genotype to phenotype: lessons from model organisms for human genetics

Ben Lehner, 2013, Nature Reviews Genetics.

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

Ben Lehner, Ben Lehner, A. Burga, 2012, The FEBS journal.

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

Ben Lehner, Ben Lehner, A. Burga, 2012, Science.

The Roles of Intersubunit Interactions in Exosome Stability*

Ben Lehner, C. Clayton, C. Sanderson, 2003, Journal of Biological Chemistry.

To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases.

F. Supek, Ben Lehner, R. Lindeboom, 2020, Trends in genetics : TIG.

Generating transgenic nematodes by bombardment and antibiotic selection

Ben Lehner, J. Semple, L. Biondini, 2012, Nature Methods.

Determining protein structures using deep mutagenesis

Jörn M. Schmiedel, Ben Lehner, J. Schmiedel, 2019, Nature Genetics.

The Causes and Consequences of Genetic Interactions (Epistasis).

Ben Lehner, Pablo Baeza-Centurion, Ben Lehner, 2019, Annual review of genomics and human genetics.

An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity

Andre J. Faure, Ben Lehner, Donate Weghorn, 2023, bioRxiv.

Dominance vs. epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles

Ben Lehner, Xianghua Li, X. Xie, 2022, bioRxiv.

Changes in gene expression shift and switch genetic interactions

Ben Lehner, Pablo Baeza-Centurion, R. Dhar, 2019, bioRxiv.

Conflict between Noise and Plasticity in Yeast

Ben Lehner, 2010, PLoS genetics.

Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses

Luis Serrano, Ben Lehner, Jae-Seong Yang, 2015, PLoS Comput. Biol..

Conserved noncoding elements and the evolution of animal body plans

Ben Lehner, T. Vavouri, 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.

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

Ben Lehner, L. Carey, J. Schmiedel, 2019, Nature Communications.

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

Ben Lehner, L. Carey, Joern M Schmiedel, 2018, bioRxiv.

Evolutionary plasticity of genetic interaction networks

Ben Lehner, Julia Tischler, A. Fraser, 2008, Nature Genetics.

Harmonious genetic combinations rewire regulatory networks and flip gene essentiality

Ben Lehner, A. New, 2019, Nature Communications.

Combinatorial genetic analysis of a regulatory network reveals the importance of higher order epistasis for gene deletion phenotypes

Ben Lehner, A. New, 2019 .

Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner

Ben Lehner, Tobias Warnecke, Fran Supek, 2012, PLoS Comput. Biol..

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

Insuk Lee, Ben Lehner, Insuk Lee, 2008, Briefings in functional genomics & proteomics.

Mechanisms, timescales and principles of trans-generational epigenetic inheritance in animals.

Ben Lehner, A. Klosin, 2016, Current opinion in genetics & development.

A protein interaction framework for human mRNA degradation.

Ben Lehner, Ben Lehner, C. Sanderson, 2004, Genome research.

The mutational landscape of a prion-like domain

Ben Lehner, Gian Gaetano Tartaglia, Andre J. Faure, 2019, Nature Communications.

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

Ben Lehner, T. Vavouri, Kadri Reis, 2017, Science Advances.

Global mapping of the energetic and allosteric landscapes of protein binding domains

Andre J. Faure, Ben Lehner, J. Schmiedel, 2021, bioRxiv.

Determining protein structures using genetics

Ben Lehner, Jörn M. Schmiedel, Ben Lehner, 2018, bioRxiv.

The energetic and allosteric landscape for KRAS inhibition

Andre J. Faure, Ben Lehner, Chenchun Weng, 2022, bioRxiv.

Maternal age generates phenotypic variation in Caenorhabditis elegans

Mirko Francesconi, Marcos Francisco Perez, Cristina Hidalgo-Carcedo, 2017, Nat..

Memory of ancestral mitochondrial stress

Ben Lehner, Sarah-Lena Offenburger, M. F. Perez, 2018, Nature Cell Biology.

An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation

Ben Lehner, Benedetta Bolognesi, Mireia Seuma, 2022, bioRxiv.

Cancer: Exploiting collateral damage

Ben Lehner, Solip Park, Ben Lehner, 2012, Nature.

Mapping the energetic and allosteric landscapes of protein binding domains

Andre J. Faure, Ben Lehner, J. Schmiedel, 2022, Nature.

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

Ben Lehner, Andrew G Fraser, Julia Tischler, 2006, Nature Protocols.

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

F. Supek, Ben Lehner, R. Lindeboom, 2019, Nature Genetics.

Neuronal perception of the social environment generates an inherited memory that controls the development and generation time of C. elegans

Ben Lehner, M. Francesconi, Alejandro Mata-Cabana, 2021, Current Biology.

Neuronal perception of the social environment intergenerationally controls germline development and generation time in C. elegans

Ben Lehner, M. Francesconi, M. Olmedo, 2020 .

Reaching the limit

Ben Lehner, Benedetta Bolognesi, 2018, eLife.

Mapping the energetic and allosteric landscapes of protein binding domains

Andre J. Faure, Ben Lehner, J. Schmiedel, 2022 .

An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity

Andre J. Faure, Ben Lehner, Donate Weghorn, 2023, bioRxiv.

SUNi mutagenesis: Scalable and uniform nicking for efficient generation of variant libraries

Taylor L. Mighell, Ben Lehner, Ignasi Toledano, 2023, bioRxiv.

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

F. Supek, Ben Lehner, Solip Park, 2018, Nature Communications.

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

Jörn M. Schmiedel, Ben Lehner, L. Carey, 2019, Nature Communications.

Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules

F. Supek, Ben Lehner, Ignasi Toledano, 2023, bioRxiv.

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

M. Gut, I. Gut, María Méndez-Lago, 2019, eLife.

Neuronal perception of the social environment generates an inherited memory that controls the development and generation time of C. elegans

Ben Lehner, M. Francesconi, M. Olmedo, 2021, Current Biology.

Molecular Systems Biology Epistasis is cancer type specific

Ben Lehner, Solip Park, 2015 .

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

Ben Lehner, T. Vavouri, J. Semple, 2008, BMC Systems Biology.