Recent publications
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Front Physiol.: auth.: F.Schütz

Front Physiol. 2018 Nov 21;9:1638. doi: 10.3389/fphys.2018.01638. eCollection 2018.

ABPS: An R Package for Calculating the Abnormal Blood Profile Score.

Abstract

The Abnormal Blood Profile Score (ABPS) is used to identify blood doping in sport. It combines seven hematological markers, including hemoglobin level, reticulocytes percent, and haematocrit level, using two different machine learning algorithms in order to create a single score that has a better ability to identify doping than each parameter taken alone. The resulting score allows the detection of several types of doping using a single score and is part of the current Athlete Biological Passport program managed by World Anti-Doping Agency (WADA). We describe ≪ ABPS ≫, an R package that allows the calculation of this score. This is the first software implementation calculating this score that is released publicly. The package also contains functions to calculate the OFF-score (another score used for detection of doping), as well as several test datasets. The package is useful for laboratories conducting anti-doping analyses and for researchers working on anti-doping research projects. In particular, it has been successfully used in projects estimating the prevalence of blood doping.

KEYWORDS:

ABPS; anti-doping; blood doping; code:R; machine learning

PMID: 30519191

 

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Nucleic Acids Res.: co-auth.: group Stasiak

 2018 Dec 1. doi: 10.1093/nar/gky1140. [Epub ahead of print]

KnotProt 2.0: a database of proteins with knots and other entangled structures.

Abstract

The KnotProt 2.0 database (the updated version of the KnotProt database) collects information about proteins which form knots and other entangled structures. New features in KnotProt 2.0 include the characterization of both probabilistic and deterministic entanglements which can be formed by disulfide bonds and interactions via ions, a refined characterization of entanglement in terms of knotoids, the identification of the so-called cysteine knots, the possibility to analyze all or a non-redundant set of proteins, and various technical updates. The KnotProt 2.0 database classifies all entangled proteins, represents their complexity in the form of a knotting fingerprint, and presents many biological and geometrical statistics based on these results. Currently the database contains >2000 entangled structures, and it regularly self-updates based on proteins deposited in the Protein Data Bank (PDB).

PMID: 30508159

 

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Bioinformatics.: auth.: group Dessimoz

 2018 Dec 3. doi: 10.1093/bioinformatics/bty994. [Epub ahead of print]

iHam & pyHam: visualizing and processing hierarchical orthologous groups.

Train CM1,2,3Pignatelli M4,5Altenhoff A1,2Dessimoz C1,3,6,7,8.

Abstract

SUMMARY:

The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display, and interpret this type of information. To address this, we introduce iHam, an interactive JavaScript widget to visualise and explore gene family history encoded in HOGs, and pyHam, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species.

AVAILABILITY AND IMPLEMENTATION:

iHam’s code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam’s code is available at https://github.com/DessimozLab/pyHam and or via the pip package “pyham”.

PMID: 30508066

 

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2019 CIG research progress seminars

Schedule of our CIG research progress seminars in Spring 2019 from 16h-17h.

Génopode room 2020 (or GEN B, will be announced depending on the progress of the work in the building)
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Mon Dec 17, 2018 CIG Sem. A. Vjestica

CIG Seminars Fall 2018

Monday 12:15, Génopode, auditorium A, followed by sandwiches

Download the poster

Monday December 17, 2018
Aleksandar Vjestica, DMF, University of Lausanne, CH
«1+1=1 The formula of fateful sexual reproduction»
Host: Paul Franken

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CIG Seminars Spring 2019 Program

CIG Seminars Spring 2019

Monday 12:15, Génopode, auditorium B, followed by sandwiches

Download the poster

Monday January 21, 2019
Paola Picotti, ETHZ, CH
«To be announced»
Host: Manfredo Quadroni

Monday February 11, 2019
Guillaume Andrey, University of Geneva, CH
«The dynamics of 3D chromatin structures influence transcription and morphogenesis»
Host: Alexandre Reymond

Monday February 25, 2019
Jolanda van Leeuwen, CIG, University of Lausanne, CH
«Systematic assessment of genetic suppression interactions»
Host: Paul Franken

Monday March 11, 2019
Louis John Ptacek, University of California San Francisco, USA
«Genetics and biology of human circadian rhythms»
Host: Paul Franken

Monday March 18, 2019
Kent Duncan, University of Hamburg, DE
«Translational control in neuronal development, function, and disease»
Host: David Gatfield

Monday March 25, 2019
Sascha Hoogendoorn, University of Geneva, CH
«A CRISPR-based screen for Hedgehog signaling: insights into ciliary function and ciliopathies»
Host: Jolanda van Leeuwen

Monday April 8, 2019
Manuel Serrano, Institute of Research in Biomedicine, Barcelona, ES
«Tissue repair: An integrated view of senescence and reprogramming»
Host: Lluis Fajas

Monday May 13, 2019
Melanie Blokesch, EPFL, CH
«Ecology and evolution of the cholera-causing pathogen Vibrio cholerae»
Host: Richard Benton

Monday May 20, 2019
Manuel Irimia, Centre for Genomic Regulation, Barcelona, ES
«How can hundreds of cell types be built from a single genome? Evolutionary mechanisms for proteome specialization»
Hosts: PhD students and Postdocs

Monday May 27, 2019
Justin Crocker, EMBL Heidelberg, DE
«Decoding evolution and development: From gene-regulatory structure to function»
Host: Richard Benton

Monday June 17, 2019
Martine Collart, University of Geneva, CH
«Co-translational assembly of proteasome in Not1 granules»
Host: David Gatfield

Monday June 24, 2019
Mihaela Zavolan, University of Basel, CH
«Regulation of RNA processing in relation to the cellular state»
Hosts: PhD students and Postdocs