publications

2017

Maternal age generates phenotypic variation in Caenorhabditis elegans
MF Perez, M Francesconi, C Hidalgo-Carcedo, B Lehner
Nature 552 (7683), 106

Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells
AJ Faure, JM Schmiedel, B Lehner
Cell systems 5 (5), 471-484. e4

Impaired DNA replication derepresses chromatin and generates a transgenerationally inherited epigenetic memory
A Klosin, K Reis, C Hidalgo-Carcedo, E Casas, T Vavouri, B Lehner
Science advances 3 (8), e1701143

Clustered mutation signatures reveal that error-prone DNA repair targets mutations to active genes
F Supek, B Lehner
Cell 170 (3), 534-547. e23

Transgenerational transmission of environmental information in C. elegans
A Klosin, E Casas, C Hidalgo-Carcedo, T Vavouri, B Lehner
Science 356 (6335), 320-323

3D structures of individual mammalian genomes studied by single-cell Hi-C
TJ Stevens, D Lando, S Basu, LP Atkinson, Y Cao, SF Lee, M Leeb, KJ Wohlfahrt, W Boucher, A O’Shaughnessy-Kirwan, J Cramard, AJ Faure, M Ralser, E Blanco, L Morey, M Sansó, MGS Palayret, B Lehner, L Di Croce, A Wutz, B Hendrich, D Klenerman, ED Laue
Nature 544 (7648), 59

2016

MUFFINN: cancer gene discovery via network analysis of somatic mutation data
A Cho, JE Shim, E Kim, F Supek, B Lehner, I Lee
Genome biology 17 (1), 129

The rules and impact of nonsense-mediated mRNA decay in human cancers
RGH Lindeboom, F Supek, B Lehner
Nature genetics 48 (10), 1112

Compensatory cell movements confer robustness to mechanical deformation during embryonic development
R Jelier, A Kruger, J Swoger, T Zimmermann, B Lehner
Cell systems 3 (2), 160-171

A concentration-dependent liquid phase separation can cause toxicity upon increased protein expression
B Bolognesi, NL Gotor, R Dhar, D Cirillo, M Baldrighi, GG Tartaglia, B Lehner
Cell reports 16 (1), 222-231

The complete local genotype–phenotype landscape for the alternative splicing of a human exon
P Julien, B Miñana, P Baeza-Centurion, J Valcárcel, B Lehner
Nature communications 7, 11558

Mechanisms, timescales and principles of trans-generational epigenetic inheritance in animals
A Klosin, B Lehner
Current opinion in genetics & development 36, 41-49

2015

Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage
D Van Dijk, R Dhar, AM Missarova, L Espinar, WR Blevins, B Lehner, LB Carey
Nature communications 6, 7972

Cancer type‐dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types
S Park, B Lehner
Molecular systems biology 11 (7), 824

Systems biology: network evolution hinges on history
AM New, B Lehner
Nature 523 (7560), 297

Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses
K Toufighi, JS Yang, NM Luis, SA Benitah, B Lehner, L Serrano, C Kiel
PLoS computational biology 11 (5), e1004256

Differential DNA mismatch repair underlies mutation rate variation across the human genome
F Supek, B Lehner
Nature 521 (7550), 81

Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis
AV Krüger, R Jelier, O Dzyubachyk, T Zimmerman, E Meijering, B Lehner
Developmental biology 398 (2), 153-162

Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells
M Francesconi, B Lehner
Molecular BioSystems 11 (10), 2690-2698

2014

Co-option of the piRNA pathway for germline-specific alternative splicing of C. elegans TOR
S Barberán-Soler, L Fontrodona, A Ribó, AT Lamm, C Iannone, J Cerón, B Lehner, J Valcárcel
Cell reports 8 (6), 1609-1616

Hydroxymethylated cytosines are associated with elevated C to G transversion rates
F Supek, B Lehner, P Hajkova, T Warnecke
PLoS genetics 10 (9), e1004585

Single and dual drug selection for transgenes following bombardment of Caenorhabditis species
JI Semple, B Lehner
Methods 68 (3), 409-416

Synonymous mutations frequently act as driver mutations in human cancers
F Supek, B Miñana, J Valcárcel, T Gabaldón, B Lehner
Cell 156 (6), 1324-1335

Inferring gene function from evolutionary change in signatures of translation efficiency
A Krisko, T Copic, T Gabaldón, B Lehner, F Supek
Genome biology 15 (3), R44

The effects of genetic variation on gene expression dynamics during development
M Francesconi, B Lehner
Nature 505 (7482), 208

2013

Human epidermal stem cell function is regulated by circadian oscillations
P Janich, K Toufighi, G Solanas, NM Luis, S Minkwitz, L Serrano, B Lehner, SA Benitah
Cell stem cell 13 (6), 745-753

Conserved substitution patterns around nucleosome footprints in eukaryotes and archaea derive from frequent nucleosome repositioning through evolution
T Warnecke, EA Becker, MT Facciotti, C Nislow, B Lehner
PLoS computational biology 9 (11), e1003373

Predicting phenotypic variation from genotypes, phenotypes and a combination of the two
A Burga, B Lehner
Current opinion in biotechnology 24 (4), 803-809

Genotype to phenotype: lessons from model organisms for human genetics
B Lehner
Nature Reviews Genetics 14 (3), 168

Systems Biology of Caenorhabditis elegans
A Fraser, B Lehner
Handbook of Systems Biology, 367-390

Epigenetic epistatic interactions constrain the evolution of gene expression
S Park, B Lehner
Molecular systems biology 9 (1), 645

2012

Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner
T Warnecke, F Supek, B Lehner
PLoS computational biology 8 (12), e1002846

Human genes with CpG island promoters have a distinct transcription-associated chromatin organization
T Vavouri, B Lehner
Genome biology 13 (11), R110

Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience
A Burga, B Lehner
The FEBS journal 279 (20), 3765-3775

Cancer: Exploiting collateral damage
B Lehner, S Park
Nature 488 (7411), 284

Chromatin organization is a major influence on regional mutation rates in human cancer cells
B Schuster-Böckler, B Lehner
Nature 488 (7412), 504

Generating transgenic nematodes by bombardment and antibiotic selection
JI Semple, L Biondini, B Lehner
Nature methods 9 (2), 118

Fitness trade-offs and environmentally induced mutation buffering in isogenic C. elegans
MO Casanueva, A Burga, B Lehner
Science 335 (6064), 82-85

2011

Predicting mutation outcome from early stochastic variation in genetic interaction partners
A Burga, MO Casanueva, B Lehner
Nature 480 (7376), 250

Predicting phenotypic variation in yeast from individual genome sequences
R Jelier, JI Semple, R Garcia-Verdugo, B Lehner
Nature genetics 43 (12), 1270

Molecular mechanisms of epistasis within and between genes
B Lehner
Trends in Genetics 27 (8), 323-331

Integrated genome-scale prediction of detrimental mutations in transcription networks
M Francesconi, R Jelier, B Lehner
PLoS genetics 7 (5), e1002077

Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome
T Vavouri, B Lehner
PLoS genetics 7 (4), e1002036

Fluctuation and response in biology
B Lehner, K Kaneko
Cellular and molecular life sciences 68 (6), 1005-1010

2010

Conflict between noise and plasticity in yeast
B Lehner
PLoS genetics 6 (11), e1001185

Rapid selection of transgenic C. elegans using antibiotic resistance
JI Semple, R Garcia-Verdugo, B Lehner
Nature methods 7 (9), 725

Predicting genetic modifier loci using functional gene networks
I Lee, B Lehner, T Vavouri, J Shin, AG Fraser, EM Marcotte
Genome research 20 (8), 1143-1153

Perturbing genes and predicting the outcome
B Lehner
The Febs Journal 277, 19

Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast
B Lehner
PloS one 5 (2), e9035

2009

Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity
T Vavouri, JI Semple, R Garcia-Verdugo, B Lehner
Cell 138 (1), 198-208

Conserved noncoding elements and the evolution of animal body plans
T Vavouri, B Lehner
Bioessays 31 (7), 727-735

Tissue specificity and the human protein interaction network
A Bossi, B Lehner
Molecular systems biology 5 (1), 260

2008

A simple principle concerning the robustness of protein complex activity to changes in gene expression
JI Semple, T Vavouri, B Lehner
BMC systems biology 2 (1), 1

Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution
T Vavouri, JI Semple, B Lehner
Trends in genetics 24 (10), 485-488

Network-guided genetic screening: building, testing and using gene networks to predict gene function
B Lehner, I Lee
Briefings in Functional Genomics and Proteomics 7 (3), 217-227

Evolutionary plasticity of genetic interaction networks
J Tischler, B Lehner, AG Fraser
Nature genetics 40 (4), 390

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans
I Lee, B Lehner, C Crombie, W Wong, AG Fraser, EM Marcotte
Nature genetics 40 (2), 181

Selection to minimise noise in living systems and its implications for the evolution of gene expression
B Lehner
Molecular systems biology 4 (1), 170

2007

Evolution and conservation of genetic interactions in C. elegans
J Tischler, B Lehner, AG Fraser
The Febs Journal 274, 249

Modelling genotype–phenotype relationships and human disease with genetic interaction networks
B Lehner
Journal of Experimental Biology 210 (9), 1559-1566

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans
T Vavouri, K Walter, WR Gilks, B Lehner, G Elgar
Genome biology 8 (2), R15

2006

RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions
B Lehner, J Tischler, AG Fraser
Nature protocols 1 (3), 1617

Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution
J Tischler, B Lehner, N Chen, AG Fraser
Genome biology 7 (8), R69

Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways
B Lehner, C Crombie, J Tischler, A Fortunato, AG Fraser
Nature genetics 38 (8), 896

Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference
B Lehner, A Calixto, C Crombie, J Tischler, A Fortunato, M Chalfie, AG Fraser
Genome biology 7 (1), R4

2005

Systems biology: where it’s at in 2005
B Lehner, J Tischler, AG Fraser
Genome biology 6 (8), 338

2004

5,000 RNAi experiments on a chip
B Lehner, AG Fraser
Nature methods 1 (2), 103

Protein domains enriched in mammalian tissue-specific or widely expressed genes
B Lehner, AG Fraser
Trends in Genetics 20 (10), 468-472

A first-draft human protein-interaction map
B Lehner, AG Fraser
Genome biology 5 (9), R63

A protein interaction framework for human mRNA degradation
B Lehner, CM Sanderson
Genome research 14 (7), 1315-1323

How to use RNA interference
B Lehner, AG Fraser, CM Sanderson
Briefings in Functional Genomics 3 (1), 68-83

In search of antisense
G Lavorgna, D Dahary, B Lehner, R Sorek, CM Sanderson, G Casari
Trends in biochemical sciences 29 (2), 88-94

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
B Lehner, JI Semple, SE Brown, D Counsell, RD Campbell, CM Sanderson
Genomics 83 (1), 153-167

The roles of intersubunit interactions in exosome stability
AM Estévez, B Lehner, CM Sanderson, T Ruppert, C Clayton
Journal Of Biological Chemistry 278 (37), 34943-34951

Antisense transcripts in the human genome
B Lehner, G Williams, RD Campbell, CM Sanderson
Trends in Genetics 18 (2), 63-65