Publications by Philipp Bucher

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Ayyakkannu Ayyanan, Laura Battista, Georgios Sflomos, Valentina Scabia, Maryse Fiche, Patrik Aouad, Fabio De Martino

Invasive lobular carcinoma (ILC) is the most frequent special histological subtype of breast cancer, typically characterized by loss of E‐cadherin. It has clinical features distinct from other estrogen receptor‐positive (ER+) breast cancers but the molecul ...

2021

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Philipp Bucher, René Dreos

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

2021

Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Laura Battista, Céline Berthe Constantin, Valentina Scabia, Marie Shamseddin, Csaba Ferenc László, Fabio De Martino

Hormonal contraception exposes women to synthetic progesterone receptor (PR) agonists, progestins, and transiently increases breast cancer risk. How progesterone and progestins affect the breast epithelium is poorly understood because we lack adequate mode ...

2021

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux

BackgroundPositional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological application ...

2020

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux, René Dreos, Patrick Meylan

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

2020

The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche

Philipp Bucher, Cathrin Brisken, Renuga Devi Rajaram, Giovanna Ambrosini, Marian Caikovski, Rachel Marcone, Céline Berthe Constantin, Dalya Ataca, Marie Shamseddin, Patrik Aouad, Csaba Ferenc László

Estrogens and progesterone control breast development and carcinogenesis via their cognate receptors expressed in a subset of luminal cells in the mammary epithelium. How they control the extracellular matrix, important to breast physiology and tumorigenes ...

Nature Research2020

Chromatin three-dimensional interactions mediate genetic effects on gene expression

Philipp Bucher, David Hacker, Giovanna Ambrosini, Sanjeev Kumar

Studying the genetic basis of gene expression and chromatin organization is key to characterizing the effect of genetic variability on the function and structure of the human genome. Here we unravel how genetic variation perturbs gene regulation using a da ...

American Association for the Advancement of Science2019

SPar-K: a method to partition NGS signal data

Philipp Bucher, Romain Fernand Pietro Groux

We present SPar-K (Signal Partitioning with K-means), a method to search for archetypical chromatin architectures by partitioning a set of genomic regions characterized by chromatin signal profiles around ChIP-seq peaks and other kinds of functional sites. ...

OXFORD UNIV PRESS2019

Common genetic variants associated with Parkinson's disease display widespread signature of epigenetic plasticity

Philipp Bucher, Giovanna Ambrosini, Amit Sharma, Tikam Chand Dakal

Parkinson disease (PD) is characterized by a pivotal progressive loss of substantia nigra dopaminergic neurons and aggregation of alpha-synuclein protein encoded by the SNCA gene. Genome-wide association studies identified almost 100 sequence variants link ...

Springer Nature2019

Opposing chromatin remodelers control transcription initiation frequency and start site selection

Philipp Bucher, René Dreos

Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy fol ...

NATURE PUBLISHING GROUP2019

Chromatin 3D interactions mediate genetic effects on gene expression

Philipp Bucher, David Hacker, Giovanna Ambrosini

NATURE PUBLISHING GROUP2019

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-r ...

2018

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

Philipp Bucher, Alexandre Coudray

To detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of soma ...

2018

SNP2TFBS-a database of regulatory SNPs affecting predicted transcription factor binding site affinity

Philipp Bucher, Giovanna Ambrosini, Sanjeev Kumar

NATURE PUBLISHING GROUP2018

MGA repository: a curated data resource for ChIP-seq and other genome annotated data

Rouayda Cavin Perier, Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux, René Dreos

Oxford University Press2018

Local regulatory networks across two tissues and applications to analyze rare non-coding variants

Philipp Bucher, Giovanna Ambrosini, Sanjeev Kumar

NATURE PUBLISHING GROUP2018

Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each

Philipp Bucher, Lukas Kühn, Otto Hagenbüchle, Giovanna Ambrosini, Barbara Grisoni-Neupert, Ramona Pauchard-Batschulat

Regulation of mRNA stability by RNA-protein interactions contributes significantly to quantitative aspects of gene expression. We have identified potential mRNA targets of the AU-rich element binding protein AUF1. Myc-tagged AUF1 p42 was induced in mouse N ...

2018

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Philipp Bucher, Didier Trono, Giovanna Ambrosini, Bart Deplancke, Romain Fernand Pietro Groux, Alina Isakova, Pernille Yde Rainer, Michaël Imbeault, Riccardo Dainese, Daniel Alpern

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Nature Publishing Group2017

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

Rouayda Cavin Perier, Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux, René Dreos

We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next gene ...

2017

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

Philipp Bucher, Giovanna Ambrosini, René Dreos

The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription ...

Public Library Science2016