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Philipp Bucher

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Related publications (158)

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Related publications (158)

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

Cathrin Brisken, Giovanna Ambrosini, Georgios Sflomos, Ayyakkannu Ayyanan, Laura Battista, Philipp Bucher, Maryse Fiche, Valentina Scabia, 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 ...

PUBLIC LIBRARY SCIENCE2021

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

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

Cathrin Brisken, Giovanna Ambrosini, Marian Caikovski, Philipp Bucher, Renuga Devi Rajaram, Patrik Aouad, Dalya Ataca, Marie Shamseddin, Céline Berthe Constantin, 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 ...

2020

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

Giovanna Ambrosini, Philipp Bucher, 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

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

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

Giovanna Ambrosini, Philipp Bucher, 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 ...

Springer2019

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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 ...

2019

Chromatin 3D interactions mediate genetic effects on gene expression

David Hacker, Giovanna Ambrosini, Philipp Bucher

NATURE PUBLISHING GROUP2019

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

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2019

Chromatin three-dimensional interactions mediate genetic effects on gene expression

SPar-K: a method to partition NGS signal data

Philipp Bucher, Romain Fernand Pietro Groux

OXFORD UNIV PRESS2019