A5008872013- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Traumatic Brain Injury and Neurovascular Disturbances
- Molecular Biology Techniques and Applications
- Light effects on plants
- Genomic variations and chromosomal abnormalities
- RNA Research and Splicing
- Breast Cancer Treatment Studies
- Nonlinear Dynamics and Pattern Formation
- Pleural and Pulmonary Diseases
- Diagnosis and treatment of tuberculosis
- Circadian rhythm and melatonin
- Chromosomal and Genetic Variations
- Advanced Mathematical Modeling in Engineering
- Leprosy Research and Treatment
- Microbial Community Ecology and Physiology
- Fungal and yeast genetics research
- Computational Drug Discovery Methods
- Plant Molecular Biology Research
- RNA modifications and cancer
Inserm
1991-2023
Theories and Approaches of Genomic Complexity
2004-2023
École Polytechnique Fédérale de Lausanne
2010-2020
University of Geneva
1998-2020
SIB Swiss Institute of Bioinformatics
2007-2016
University of Lausanne
2011-2012
Institut de Neurobiologie de la Méditerranée
2005
Institut National de Recherche en Santé Publique
2005
OZ Biosciences (France)
2004
Heriot-Watt University
2000-2002
Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in computation bootstrap support values. Conducting a probably insufficient number 100 (BS) analyses with current ML programs on large datasets—either respect taxa or base pairs—can easily require month run time. Therefore, we have developed, implemented, thoroughly tested...
Stereotactic thalamotomy of the thalamic nucleus ventralis intermedius (VIM) is routinely used for movement disorders. During this procedure, it has been observed that high-frequency (100 Hz) stimulation VIM was able to stop extrapyramidal tremor. In patients with bilateral tremor origin, who were resistant drug therapy, therapeutic protocol associated (1) a radiofrequency most disabled side, and (2) continuous other side using stereotactically implanted electrodes, connected subcutaneous...
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete components with high success rates but assembly complete isoform structures poses a major challenge even when all constituent elements identified. Expression-level estimates also varied widely across methods, based on similar models. Consequently,...
Summary 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 developmental responses known shade‐avoidance syndrome (SAS). The phytochrome B (phyB) photoreceptor major sensor mediate this adaptive response. Control SAS occurs in part with phyB, which controls protein abundance phytochrome‐interacting factors 4 and 5 (PIF4 PIF5) directly. also requires...
Temporal mapping during a circadian day of binding sites for the BMAL1 transcription factor in mouse liver reveals genome-wide daily rhythms DNA and uncovers output functions that are controlled by oscillator.
The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, existence particular three-dimensional (3D) architectures remained to be assessed vivo. Using high-resolution chromatin conformation capture methodology, we examined configuration clusters embryonic mouse tissues where different genes are active. When cluster transcriptionally inactive, associate...
Highlights•The microbiota contributes to helminth-induced modulation of allergic asthma•Cecal microbial communities are altered in helminth-infected mice•Helminth infection increases microbial-derived short chain fatty acids•GPR41 mediates Treg cell suppressor functionSummaryIntestinal helminths potent regulators their host's immune system and can ameliorate inflammatory diseases such as asthma. In the present study we have assessed whether this anti-inflammatory activity was purely...
In the southern region of United States, such as in Louisiana and Texas, there are autochthonous cases leprosy among native-born Americans with no history foreign exposure. same region, well Mexico, wild armadillos infected Mycobacterium leprae.
Abstract Breast cancer is a heterogeneous disease. Comprehensive gene expression profiles obtained using DNA microarrays have revealed previously indistinguishable subtypes of noninflammatory breast (NIBC) related to different features mammary epithelial biology and significantly associated with survival. Inflammatory (IBC) rare, particular, aggressive form Here we investigated whether the five molecular described for NIBC (luminal A B, basal, ERBB2 overexpressing, normal breast-like) were...
Breast cancer is a heterogeneous disease whose evolution difficult to predict by using classic histoclinical prognostic factors. Prognostic classification can benefit from molecular analyses such as large-scale expression profiling. Using immunohistochemistry on tissue microarrays, we have monitored the of 26 selected proteins in more than 1,600 samples 552 consecutive patients with early breast cancer. Both an unsupervised approach and new supervised method were used analyze these profiles....
Abstract Inflammatory breast cancer (IBC) is a rare but aggressive form of with 5-year survival limited to ∼40%. Diagnosis, based on clinical and/or pathological criteria, may be difficult. Optimal systemic neoadjuvant therapy and accurate predictors response have yet defined for increasing rate survival. Using DNA microarrrays containing ∼8,000 genes, we profiled samples from 81 patients, including 37 IBC 44 noninflammatory (NIBC). Global unsupervised hierarchical clustering was able some...
Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization cell physiology in mammals. To understand transcriptional and epigenetic basis rhythms mouse liver genome-wide, we generated DNA occupancy profiles by RNA polymerase II (Pol II) as well histone modifications H3K4me3 H3K36me3. We used these data to quantify relationships phases amplitudes between different marks. found that rhythmic Pol recruitment at promoters rather than...
Abstract Summary: Nemo is an individual-based, genetically explicit and stochastic population computer program for the simulation of genetics life-history trait evolution in a metapopulation context. It comes as both C++ programming framework executable file. Its object-oriented design gives it flexibility extensibility needed to implement large variety forward-time evolutionary models. provides developers with abstract models allowing them their own traits life-cycle events. offers panel...
The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% the genes, including those ESX-1 secretion apparatus, a major determinant. Mutations phoP lead to compromised production pathogen-specific cell wall components and attenuation both ex vivo vivo. Using antibodies against native protein ChIP-seq experiments (chromatin immunoprecipitation followed by high-throughput sequencing) we demonstrated that PhoP binds...
The principal virulence determinant of Mycobacterium tuberculosis (Mtb), the ESX-1 protein secretion system, is positively controlled at transcriptional level by EspR. Depletion EspR reportedly affects a small number genes, both or negatively, including key component, espACD operon. also thought to be an substrate. Using EspR-specific antibodies in ChIP-Seq experiments (chromatin immunoprecipitation followed ultra-high throughput DNA sequencing) we show that binds least 165 loci on Mtb...
In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and molecular basis for their remains largely unknown. Here we identify two prevalent promoter types, both characterized upstream binding general transcription factor (TF) Rap1 followed RPG-specific Fhl1/Ifh1 pair, with one type also HMG-B Hmo1. We show that regulatory properties types are remarkably similar,...
In this paper, we propose privacy-enhancing technologies for medical tests and personalized medicine methods that use patients' genomic data. Focusing on genetic disease-susceptibility tests, develop a new architecture (between the patient unit) "privacy-preserving disease susceptibility test" (PDS) by using homomorphic encryption proxy re-encryption. Assuming whole genome sequencing to be done certified institution, store data encrypted their public keys at "storage processing unit" (SPU)....
Bisphenol A [BPA, 2,2,-bis (hydroxyphenyl) propane] is one of the highest-volume chemicals produced worldwide. It detected in body fluids more than 90% human population. Originally synthesized as an estrogenic compound, it currently utilized to manufacture food and beverage containers resulting uptake with drinks. There concern that exposure low doses BPA, defined less or equal 5 mg/kg weight /d, may have developmental effects on various hormone-responsive organs including mammary gland....