Recent publications

Bioinformatics.: co-auth.: I.Xenarios

 2019 Dec 2. pii: btz882. doi: 10.1093/bioinformatics/btz882. [Epub ahead of print]

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference – application to H5N1 spread in the Mekong region.



The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially-explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences are geo-referenced at broad spatial scale such as, for example, the administrative unit of origin rather than more exact locations (e.g. GPS coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better possibility.


We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza (HPAI) H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities.


Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10.


Supplementary data are available at Bioinformatics online and on

PMID: 31790143

Welcome to Johanna !

I’m a postdoc in the Fankhauser lab where I am looking for genes that fine-tune phototropic responses of Arabidopsis seedlings to directional blue light. Before moving to Lausanne I lived in Edinburgh where I did my PhD with Andrew Millar on post-translational modifications in the plant circadian clock, and a postdoc with Karen Halliday on plant metabolism in phytochrome mutants.


The RTS radio program CQFD interviewed M.Jan from the Franken lab, Nov. 29, 2019

Le manque de sommeil a des conséquences à long terme. Il favorise le développement de maladies non transmissibles comme les troubles du métabolisme. Plus inquiétant encore: même si le manque de sommeil est rattrapé, les problèmes demeurent!
Cʹest ce que viennent de démontrer des chercheurs de lʹUniversité de Lausanne (Unil) et de lʹEcole polytechnique fédérale de Lausanne (EPFL).

Les détails avec Maxime Jan, bio-informaticien à lʹUnil, interrogé par Bastien Confino.


Lire la publication:

Ecouter l’interview de M. Jan du groupe P. Franken:

Dossier sur le sommeil:

Article sur le magazine de l’UNIL; L’actu:


Proc Natl Acad Sci U S A.: auth.: group Franken

 2019 Nov 27. pii: 201910590. doi: 10.1073/pnas.1910590116.

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


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 interaction to transcriptional and epigenomic regulatory dynamics requires sampling over time under conditions of unperturbed and perturbed sleep. We profiled mRNA expression and chromatin accessibility in the cerebral cortex of mice over a 3-d period, including a 6-h sleep deprivation (SD) on day 2. We used mathematical modeling to integrate time series of mRNA expression data with sleep-wake history, which established that a large proportion of rhythmic genes are governed by the homeostatic process with varying degrees of interaction with the circadian process, sometimes working in opposition. Remarkably, SD caused long-term effects on gene-expression dynamics, outlasting phenotypic recovery, most strikingly illustrated by a damped oscillation of most core clock genes, including Arntl/Bmal1, suggesting that enforced wakefulness directly impacts the molecular clock machinery. Chromatin accessibility proved highly plastic and dynamically affected by SD. Dynamics in distal regions, rather than promoters, correlated with mRNA expression, implying that changes in expression result from constitutively accessible promoters under the influence of enhancers or repressors. Serum response factor (SRF) was predicted as a transcriptional regulator driving immediate response, suggesting that SRF activity mirrors the build-up and release of sleep pressure. Our results demonstrate that a single, short SD has long-term aftereffects at the genomic regulatory level and highlights the importance of the sleep-wake distribution to diurnal rhythmicity and circadian processes.


circadian; epigenetics; gene expression; long-term effects; sleep

PMID: 31776259

Link to the RTS CQFD article and interview about this publication:

Link to the article on the “UNIL Actu” review:


Welcome to Giti !

Hi everybody!

I am Giti Ghazi Soltani and I just joined the Soyk lab as PhD student.

I started my University studies in Agricultural Sciences with a focus on Plant Pathology at the University of Tabriz, Iran.

I completed a Master’s degree in the University of Pierre and Marie Curie (UPMC) in Paris on taxonomy of a pollinator bee species. Then, I joined the group of Niko Geldner at UNIL in 2017, where I studied the role of a gene family in plant volatile perception in the model plant Arabidopsis thaliana.

In the Soyk lab, I am interested in identifying genes and genetic interactions that regulate meristem development and plant architecture in the model crop tomato.


P. Franken was on l’Actu, on Nov. 28, 2019

Manque de sommeil: comme si le temps s’arrêtait

Les perturbations du sommeil, que ce soit en termes de quantité ou de qualité, sont très répandues dans notre société moderne. Outre leur impact immédiat sur la performance cognitive et la vigilance, elles constituent un facteur de risque important dans le développement de maladies non transmissibles telles que les troubles du métabolisme. Une étude publiée dans la revue «PNAS», réalisée conjointement par des chercheurs de l’UNIL et de l’EPFL, met en lumière les conséquences moléculaires à moyen et long terme d’une privation de sommeil. Même une fois le sommeil perdu rattrapé, notre horloge interne demeure fatiguée.