Publications by Slavica Dimitrieva Janeva

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

Philipp Bucher, Slavica Dimitrieva Janeva

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 ...

Academic Press Inc Elsevier Science2014

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

Slavica Dimitrieva Janeva

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To ev ...

Public Library of Science2014

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

Philipp Bucher, Slavica Dimitrieva Janeva

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 ...

Oxford University Press2013

Critical assessment of automated flow cytometry data analysis techniques

Philipp Bucher, Pascal Meyer, Giovanna Ambrosini, Nima Aghaeepour, Slavica Dimitrieva Janeva, René Dreos

Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessm ...

Nature Publishing Group2013

Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes

Slavica Dimitrieva Janeva

Recent advancements in DNA sequencing technologies, accompanied by parallel development of sophisticated computational methods, offer an unprecedented opportunity to explore and study the genetic material of many organisms. However, despite the tremendous ...

EPFL2013

Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements

Philipp Bucher, Slavica Dimitrieva Janeva

Motivation: Genomic context analysis, also known as phylogenetic profiling, is widely used to infer functional interactions between proteins but rarely applied to non-coding cis-regulatory DNA elements. We were wondering whether this approach could provide ...

Oxford University Press2012

Practicality and time complexity of a sparsified RNA folding algorithm

Philipp Bucher, Slavica Dimitrieva Janeva

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 ...

2012