Publications by Philipp Bucher

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Telomeres protect the eukaryotic chromosome ends from degradation and fusion. They are maintained by the ribonucleoprotein telomerase, the core of which is composed of a reverse transcriptase (TERT) and a RNA subunit. In the yeast Saccharomyces cerevisiae, a third critical telomerase subunit, the Ever Shorter Telomeres 1 (EST1) gene product, recruits or activates telomerase at the 3' end of telomeres. Est1p has so far only been known in budding yeast, and mechanisms that mediate telomerase access and activa

Scarce work has been done in the analysis of the composition of conserved non-coding elements (CNEs) that are identified by comparisons of two or more genomes and are found to exist in all metazoan genomes. Here we present the analysis of CNEs with a metho ...

BACKGROUND: High-throughput gene expression profiling technologies generating a wealth of data, are increasingly used for characterization of tumor biopsies for clinical trials. By applying machine learning algorithms to such clinically documented data set ...

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 ...

Background: In cell differentiation, a less specialized cell differentiates into a more specialized one, even though all cells in one organism have (almost) the same genome. Epigenetic factors such as histone modifications are known to play a significant r ...

Background: In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in ...

Background: Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not a ...

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 ...

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 ...

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 ...

Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n^3). Recently, it has been claimed that RNA folding can be achie ...

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 ...

Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences. At the example of public STAT1 ChIP-seq data sets, we ...

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrati ...

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single C ...

Applications of optimal matching analysis in the social sciences are typically based on sequences of specific social statuses that model the residential, family, or occupational trajectories of individuals. Despite the broadly recognized interdependence of ...

UCNEbase (http://ccg.vital-it.ch/UCNEbase) is a free, web-accessible information resource on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs). It currently covers 4351 such elements in 18 different species. The majority ...

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 ...

Pancreas development is initiated by the specification and expansion of a small group of endodermal cells. Several transcription factors are crucial for progenitor maintenance and expansion, but their interactions and the downstream targets mediating their ...

The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit diff ...

Philipp Bucher

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A human homolog of yeast est1 associates with telomerase and uncaps chromosome ends when overexpressed

Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers

Can survival prediction be improved by merging gene expression data sets?

Opposing chromatin remodelers control transcription initiation frequency and start site selection

A maximum-likelihood approach for building cell-type trees by lifting

Study of cell differentiation by phylogenetic analysis using histone modification data

ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites

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

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

Chromatin three-dimensional interactions mediate genetic effects on gene expression

Practicality and time complexity of a sparsified RNA folding algorithm

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

MER41 repeat sequences contain inducible STAT1 binding sites

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

Principles of ChIP-seq Data Analysis Illustrated with Examples

Multichannel Sequence Analysis Applied To Social Science Data

UCNEbase – a database of ultra-conserved non-coding elements and genomic regulatory blocks

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

RNA Profiling and Chromatin Immunoprecipitation-Sequencing Reveal that PTF1a Stabilizes Pancreas Progenitor Identity via the Control of MNX1/HLXB9 and a Network of Other Transcription Factors

ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries