Publications by Ioannis Xenarios

Towards mouse genetic-specific RNA-sequencing read mapping

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using ...

2022

Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery

Nicolas Jean Philippe Guex, Fabrizio Benedetti, George Coukos, Ioannis Xenarios, Alexandre Harari

2021

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

Marion Leleu, Flavia Marzetta, Ioannis Xenarios, Ludovica Vanzan

Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation ...

2020

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

Didier Trono, Marion Leleu, Evaristo Jose Planet Letschert, George Coukos, Ioannis Xenarios, Laia Simo Riudalbas, Delphine Yvette L Grun, Alexandre Harari, Markus Müller, Lin Zhang, Marion Arnaud, Florian Huber

Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides derived from annotated ...

Nature Research2020

miR363-3p mediates maintenance of breast cancer stem cells (BCSCs) and predicts resistance to neoadjuvant chemotherapy and disease recurrence

Nicolas Mermod, Jean-Yves Meuwly, Cathrin Brisken, Valentina Scabia, Valérian Charles Robert Dormoy, Maryse Fiche, Ioannis Xenarios

AMER ASSOC CANCER RESEARCH2020

Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex

Felix Naef, Maxime Jan, Jake Yeung, Ioannis Xenarios

The timing and duration of sleep results from the interaction between a homeostatic sleep-wake-driven process and a periodic circadian process, and involves changes in gene regulation and expression. Unraveling the contributions of both processes and their ...

National Academy of Sciences2019

Gene expression across mammalian organ development

Maria del Carmen Sandi Perez, Ioannis Xenarios

The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early or ...

2019

Differential regulation of RNA polymerase III genes during liver regeneration

Felix Naef, Philippe Jacquet, Nicolas Jean Philippe Guex, Jonathan Aryeh Sobel, Cristian Carmeli, Olivier Martin, Irina Krier, Mauro Delorenzi, Nouria Hernandez, Bart Deplancke, Jacques Rougemont, François Mange, Laura Symul, Fabrice David, Sunil Kumar Raghav, Julien Delafontaine, Marion Leleu, Julia Catharina Cajan, Winship Herr, Kyle Gustafson, Maykel Lopes, Dominic Villeneuve, Ioannis Xenarios

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcriptio ...

Oxford University Press (OUP)2019

Neutrophils and Snail orchestrate the establishment of a protumor microenvironment in lung adenocarcinoma

Nicolas Jean Philippe Guex, Miguel Garcia, Nadine Fournier, Etienne Meylan, Alessandra Piersigilli, Julien Robert Rémi Faget, Svenja Johanna Groeneveld, Gael Luis Boivin, Ioannis Xenarios, Inti Zlobec

AMER ASSOC CANCER RESEARCH2018

MAR-Mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering

Christian Iseli, Nicolas Mermod, Thomas Junier, Samuel Neuenschwander, Ioannis Xenarios

Untargeted plasmid integration into mammalian cell genomes remains a poorly understood and inefficient process. The formation of plasmid concatemers and their genomic integration has been ascribed either to non-homologous end-joining (NHEJ) or homologous r ...

2017

Neutrophils and Snail Orchestrate the Establishment of a Pro-tumor Microenvironment in Lung Cancer

Nicolas Jean Philippe Guex, Miguel Garcia, Nadine Fournier, Etienne Meylan, Loïc Steiner, Alessandra Piersigilli, Julien Robert Rémi Faget, Svenja Johanna Groeneveld, Gael Luis Boivin, Ioannis Xenarios, Inti Zlobec

Understanding the immune compartment of tumors facilitates the development of revolutionary new therapies. We used a Kras(G12D)-driven mouse model of lung cancer to establish an immune signature and identified a contribution of Gr1 + neutrophils to disease ...

Cell Press2017

TIE-2-expressing monocytes are lymphangiogenic and associate specifically with lymphatics of human breast cancer

Nicolas Jean Philippe Guex, Luc Henry, Nathalie Rufer, Emanuela Marina Iancu, Hans-Anton Lehr, George Coukos, Ioannis Xenarios

In experimental mouse models of cancer, increasingly compelling evidence point toward a contribution of tumor associated macrophages (TAM) to tumor lymphangiogenesis. Corresponding experimental observations in human cancer remain scarce although lymphatic ...

Taylor & Francis Inc2016

An Extended, Boolean Model of the Septation Initiation Network in S-pombe Provides Insights into Its Regulation

Viesturs Simanis, Andrea Krapp, Elena Cano, Anastasia Chasapi, Ioannis Xenarios

Cytokinesis in fission yeast is controlled by the Septation Initiation Network (SIN), a protein kinase signaling network using the spindle pole body as scaffold. In order to describe the qualitative behavior of the system and predict unknown mutant behavio ...

Public Library of Science2015

Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN

Michaël Unser, Daniel Sage, Viesturs Simanis, Daniel Andreas Schmitter, Andrea Krapp, Jacques Rougemont, Anastasia Chasapi, Ioannis Xenarios

The Schizosaccharomyces pombe septation initiation network (SIN) regulates cytokinesis, and asymmetric association of SIN proteins with the mitotic spindle pole bodies (SPBs) is important for its regulation. Here, we have used semi-automated image analysis ...

Company Of Biologists Ltd2015

Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes

Amalio Telenti, Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren, Ioannis Xenarios

Loss-of-function variants in innate immunity genes are associated with Mendelian disorders in the form of primary immunodeficiencies. Recent resequencing projects report that stop-gains and frameshifts are collectively prevalent in humans and could be resp ...

Public Library Science2014

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Philipp Bucher, Amos Bairoch, Olivier Michielin, Heinz Stockinger, Mauro Delorenzi, Jacques Rougemont, Ioannis Xenarios

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRI ...

Oxford University Press2014

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis

Michaël Unser, Daniel Sage, Viesturs Simanis, Daniel Andreas Schmitter, Anastasia Chasapi, Ioannis Xenarios

Background: The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins ...

Biomed Central Ltd2013

Database resources for the tuberculosis community

Stewart Cole, Jocelyne Lew, Ioannis Xenarios

Access to online repositories for genomic and associated "-omics" datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as we ...

Churchill Livingstone2013

Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling

Jacques Rougemont, Christian Fankhauser, Ioannis Xenarios

Plant growth is strongly influenced by the presence of neighbors that compete for light resources. In response to vegetational shading shade-intolerant plants such as Arabidopsis display a suite of developmental responses known as the shade-avoidance syndr ...

Wiley-Blackwell2012

The Microbe browser for comparative genomics

Jacques Rougemont, Alexandre Gattiker, Marco Pagni, Ioannis Xenarios

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene pr ...

Oxford University Press2009