Publications associées à Computational Identification of MicroRNAs and Their Targets

Inferring the Evolutionary History of Primate microRNA Binding Sites: Overcoming Motif Counting Biases

The first microRNAs (miRNAs) were identified as essential, conserved regulators of gene expression, targeting the same genes across nearly all bilaterians. However, there are also prominent examples of conserved miRNAs whose functions appear to have shifte ...

Oxford Univ Press2014

Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations

Ursula Röthlisberger, Pablo Campomanes Ramos

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals a ...

2014

Wire Mesh Design

Mark Pauly, Bailin Deng, Akash Garg

We present a computational approach for designing wire meshes, i.e., freeform surfaces composed of woven wires arranged in a regular grid. To facilitate shape exploration, we map material properties of wire meshes to the geometric model of Chebyshev nets. ...

Association for Computing Machinery2014

Mapping the fine structure of a eukaryotic promoter input-output function

Sebastian Maerkl, Nicolas Dénervaud, Arun Stephen Rajkumar

The precise tuning of gene expression levels is essential for the optimal performance of transcriptional regulatory networks. We created 209 variants of the Saccharomyces cerevisiae PHO5 promoter to quantify how different binding sites for the transcriptio ...

Nature Publishing Group2013

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Alina Isakova, Jovan Simicevic, Jean-Daniel Feuz, Antonina Iagovitina

The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression b ...

Nature / European Molecular Biology Organization2013

Detection of RNAP-DNA complexes using solid state nanopores

Aleksandra Radenovic, Michael Graf, Camille Alice Raillon

Transcription is the first step in gene expression where DNA is copied into RNA. It is extensively studied at the bulk level especially the regulation mechanism, which in cancerous cells is impaired. We were interested in studying E. coli RNAP enzyme at th ...

IEEE2013

Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide

Ursula Röthlisberger, Thomas Rizzo, Ivano Tavernelli, Natalia Nagornova, Matteo Guglielmi

We benchmark the performance of various computational approaches, ranging from the classical nonpolarizable force fields AMBER FF96 and FF99SB, the polarizable force fields AMBER FF02polEP and AMOEBAbio09 to the semiempirical DFT method SCC-DFTB. The test ...

Wiley-Blackwell2013

Critical assessment of automated flow cytometry data analysis techniques

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

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

The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community

Martin Kussmann, Ruedi Aebersold

The biology and disease oriented branch of the Human Proteome Project (B/D-HPP) was established by the Human Proteome Organization (HUPO) with the main goal of supporting the broad application of state-of-the-art measurements of proteins and proteomes by l ...

Amer Chemical Soc2013

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Computational Identification of MicroRNAs and Their Targets

Mathematical models and computational methods for the analysis of genome-scale protein synthesis

Inferring the Evolutionary History of Primate microRNA Binding Sites: Overcoming Motif Counting Biases

Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations

Wire Mesh Design

Mapping the fine structure of a eukaryotic promoter input-output function

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

Detection of RNAP-DNA complexes using solid state nanopores

Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide

Critical assessment of automated flow cytometry data analysis techniques

The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community

Graph Chatbot

Chattez avec Graph Search

Mathematical models and computational methods for the analysis of genome-scale protein synthesis

Inferring the Evolutionary History of Primate microRNA Binding Sites: Overcoming Motif Counting Biases

Wire Mesh Design

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

Detection of RNAP-DNA complexes using solid state nanopores

Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations

Mapping the fine structure of a eukaryotic promoter input-output function

The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community

Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide

Critical assessment of automated flow cytometry data analysis techniques