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Visualitza Documents OpenAIRE (Open Access Infrastructure for Research in Europe) per autoria "Lehner, Ben, 1978-"

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

Seuma, Mireia; Lehner, Ben, 1978-; Bolognesi, Benedetta (Nature Research, 2022)

Multiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal disease mechanisms. To date, MAVEs have focussed on a single mutation type-amino acid (AA) substitutions-despite the diversity ...
Biophysical ambiguities prevent accurate genetic prediction

Li, Xianghua; Lehner, Ben, 1978- (Nature Research, 2020)

A goal of biology is to predict how mutations combine to alter phenotypes, fitness and disease. It is often assumed that mutations combine additively or with interactions that can be predicted. Here, we show using simulations ...
Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types

Park, Solip; Lehner, Ben, 1978- (Wiley Blackwell, 2015)

Cancers, like many diseases, are normally caused by combinations of genetic alterations rather than by changes affecting single genes. It is well established that the genetic alterations that drive cancer often interact ...
Changes in gene expression predictably shift and switch genetic interactions

Li, Xianghua; Lalić, Jasna; Baeza Centurión, Pablo, 1989-; Dhar, Riddhiman; Lehner, Ben, 1978- (Nature Research, 2019)

Non-additive interactions between mutations occur extensively and also change across conditions, making genetic prediction a difficult challenge. To better understand the plasticity of genetic interactions (epistasis), we ...
Co-option of the piRNA pathway for germline-specific alternative splicing of C. elegans TOR

Barberán-Soler, Sergio; Fontrodona, Laura; Ribó Rubio, Anna; Lamm, Ayelet T.; Iannone, Camilla, 1984-; Cerón, Julián; Lehner, Ben, 1978-; Valcárcel, J. (Juan) (Cell Press, 2014)

Many eukaryotic genes contain embedded antisense transcripts and repetitive sequences of unknown function. We report that male germline-specific expression of an antisense transcript contained in an intron of C. elegans ...
Determining protein structures using deep mutagenesis

Schmiedel, Jörn M.; Lehner, Ben, 1978- (Nature Research, 2019)

Determining the three-dimensional structures of macromolecules is a major goal of biological research, because of the close relationship between structure and function; however, thousands of protein domains still have ...
Differential DNA mismatch repair underlies mutation rate variation across the human genome

Supek, Fran; Lehner, Ben, 1978- (Nature Publishing Group, 2015)

Cancer genome sequencing has revealed considerable variation in somatic mutation rates across the human genome, with mutation rates elevated in heterochromatic late replicating regions and reduced in early replicating ...
DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies

Faure, Andre J.; Schmiedel, Jörn M.; Baeza Centurión, Pablo, 1989-; Lehner, Ben, 1978- (BioMed Central, 2020)

Deep mutational scanning (DMS) enables multiplexed measurement of the effects of thousands of variants of proteins, RNAs, and regulatory elements. Here, we present a customizable pipeline, DiMSum, that represents an ...
Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses

Toufighi, Kiana, 1980-; Yang, Jae-Seong; Luis, Nuno Miguel, 1982-; Aznar Benitah, Salvador; Lehner, Ben, 1978-; Serrano Pubull, Luis, 1982-; Kiel, Christina (Public Library of Science (PLoS), 2015)

The molecular details underlying the time-dependent assembly of protein complexes in cellular networks, such as those that occur during differentiation, are largely unexplored. Focusing on the calcium-induced differentiation ...
Empirical mean-noise fitness landscapes reveal the fitness impact of gene expression noise

Schmiedel, Jörn M.; Carey, Lucas, 1980-; Lehner, Ben, 1978- (Nature Research, 2019)

The effects of cell-to-cell variation (noise) in gene expression have proven difficult to quantify because of the mechanistic coupling of noise to mean expression. To independently quantify the effects of changes in mean ...
Harmonious genetic combinations rewire regulatory networks and flip gene essentiality

New, Aaron M.; Lehner, Ben, 1978- (Nature Research, 2019)

We lack an understanding of how the full range of genetic variants that occur in individuals can interact. To address this shortcoming, here we combine diverse mutations between genes in a model regulatory network, the ...
Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers

Park, Solip; Supek, Fran; Lehner, Ben, 1978- (Nature Research, 2021)

The classic two-hit model posits that both alleles of a tumor suppressor gene (TSG) must be inactivated to cause cancer. In contrast, for some oncogenes and haploinsufficient TSGs, a single genetic alteration can suffice ...
Human epidermal stem cell function is regulated by circadian oscillations

Janich, Peggy, 1981-; Toufighi, Kiana, 1980-; Solanas, Guiomar; Luis, Nuno Miguel, 1982-; Minkwitz, Susann; Serrano Pubull, Luis, 1982-; Lehner, Ben, 1978-; Aznar Benitah, Salvador (Elsevier, 2013)

Human skin copes with harmful environmental factors that are circadian in nature, yet how circadian rhythms modulate the function of human epidermal stem cells is mostly unknown. Here we show that in human epidermal stem ...
Human genes with CpG island promoters have a distinct transcription-associated chromatin organization

Vavouri, Tanya; Lehner, Ben, 1978- (BioMed Central, 2012)

Background: More than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. These genes show differences in their patterns of transcription initiation, and have been ...
Impaired DNA replication derepresses chromatin and generates a transgenerationally inherited epigenetic memory

Klosin, Adam; Reis, Kadri, 1985-; Hidalgo-Carcedo, Cristina; Casas, Eduard; Vavouri, Tanya; Lehner, Ben, 1978- (American Association for the Advancement of Science (AAAS), 2017)

Impaired DNA replication is a hallmark of cancer and a cause of genomic instability. We report that, in addition to causing genetic change, impaired DNA replication during embryonic development can have major epigenetic ...
Intergenerational and transgenerational epigenetic inheritance in animals

Perez, Marcos Francisco, 1987-; Lehner, Ben, 1978- (Nature Research, 2019)

Animals transmit not only DNA but also other molecules, such as RNA, proteins and metabolites, to their progeny via gametes. It is currently unclear to what extent these molecules convey information between generations and ...
Mapping the energetic and allosteric landscapes of protein binding domains.

Faure, Andre J.; Domingo Espinós, Júlia, 1991-; Schmiedel, Jörn M.; Hidalgo-Carcedo, Cristina; Diss, Guillaume; Lehner, Ben, 1978- (2022)

Allosteric communication between distant sites in proteins is central to biological regulation but still poorly characterized, limiting understanding, engineering and drug development1-6. An important reason for this is ...
Mutations primarily alter the inclusion of alternatively spliced exons

Baeza Centurión, Pablo, 1989-; Miñana Gómez, Belén; Valcárcel, J. (Juan); Lehner, Ben, 1978- (eLife, 2020)

Genetic analyses and systematic mutagenesis have revealed that synonymous, non-synonymous and intronic mutations frequently alter the inclusion levels of alternatively spliced exons, consistent with the concept that altered ...
Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation

Dhar, Riddhiman; Missarova, Alsu, 1990-; Lehner, Ben, 1978-; Carey, Lucas, 1980- (eLife, 2019)

Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially ...
Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming

Francesconi, Mirko; Di Stefano, Bruno, 1984-; Berenguer, Clara; de Andrés-Aguayo, Luisa; Plana-Carmona, Marcos; Mendez-Lago, Maria; Guillaumet-Adkins, Amy; Rodríguez Esteban, Gustavo; Gut, Marta; Gut, Ivo Glynne; Heyn, Holger; Lehner, Ben, 1978-; Graf, T. (Thomas) (eLife, 2019)

Forced transcription factor expression can transdifferentiate somatic cells into other specialised cell types or reprogram them into induced pluripotent stem cells (iPSCs) with variable efficiency. To better understand the ...