Vital-IT / High Performance Computing Center

Supported Projects

Message of the Day.
A course on "Computational Analysis of Ultra-High-Throughput (UHT) Sequencing Data" will use the Vital-IT infrastructure from the:
13th Sep. 2010 until the 17th Sep. 2010.
The load on our computing infrastructure may be higher during this time.
Please contact us if you need more information.

(VF, 05.08.2010)

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Vital-IT provides Bioinformatic knowledge support, High Performance Computing and storage to a wide range of Life Science research projects.
On this page you will find a brief description of the most important of these projects

We provide resources to approximately 73 research projects which span 12 bioinformatic fields.

Please click on the categories below for more information.

Behavioural view

Currently 1 project(s) in this category.

PI	Affiliation	Description	Publication
L. Keller	UNIL	Automated observation of the ants behaviour in a colony

Ecology view

Currently 1 project(s) in this category.

PI	Affiliation	Description	Publication
A. Guisan	UNIL	Spatial ecology and predictive biodistribution

Genetic view

Currently 6 project(s) in this category.

PI	Affiliation	Description	Publication
M. Bochud	UNIL-CHUV	conduct family-based association studies	Variants in MTNR1B influence fasting glucose levels. Prokopenko J, Bochud M,, Abecasis GR. Nat Genet. 2009 Jan;41(1):77-81. 2008 Dec 7.
C. Rivolta	UNIL-CHUV	Quantitative linkage analysis
S. Bergmann	UNIL	Genome wide association studies CoLaus analysis, ChaVI.	Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Willer CJ, Bergman S, Hirschhorn JN; Jan;41(1):25-34. 2008
S. Antonarakis	UNIGE	Quantitative trait mapping of human chromosome 21 genes	Deutsch S, Lyle R, Dermitzakis ET, Attar H, Subrahmanyan L, Gehrig C, Parand L, Gagnebin M, Rougemont J, Jongeneel CV, Antonarakis SE. "Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes", Hum Mol Genet 14: 3741-3749 (2005)
S. Antonarakis	UNIGE	Phylogenetic analysis of ENCODE data	Nikolaev S, Montoya-Burgos JI, Margulies EH, NISC Comparative Sequencing Program, Rougemont J, Nyffeler B, Antonarakis SE. "Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data", PLoS Genet. 3(1): e2 (2007).
J-L. Blouin	UNIGE	Diagnostic analysis of myocardial genetic studies

Genomic view

Currently 29 project(s) in this category.

PI	Affiliation	Description	Publication
P. Hauser	UNIL-CHUV	Metagenomics and annotation of P. carinii
M. Monod	UNIL-CHUV	Development of a database of proteases
A. Telenti	UNIL-CHUV	Detection of positively selected sites in the HIV-1 Gag gene
A. Telenti	UNIL-CHUV	Association study between genetic polymorphism and treatment efficiency for the Swiss HIV cohort study.	AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. Martin O, Valsesia A, Telenti A, Xenarios I, Stevenson BJ. Bioinformatics. 2009 Mar 1;25(5):662-3.
L. Keller	UNIL	Design of a DNA chip and analysis of results	Wang J, Jemielity S, Uva P, Wurm Y, Graff J, Keller L. "An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta", Genome Biol. 8(1): R9 (2007)
L. Keller	UNIL	Next generation genomes sequencing and assembly of S. invictaÂ
J. Goudet	UNIL	Population genomics	quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. Neuenschwander S, Hospital F, Guillaume F, Goudet J. Bioinformatics. 2008 Jul 1;24(13):1552-3
I. Sanders	UNIL	Sequencing and annotation of asexual fungal genome
H. Kaessmann	UNIL	Analysis of the chicken genome	Hillier LW et al. "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution", Nature 432: 695-716 (2004)
H. Kaessmann	UNIL	Analysis of retroposed genes	Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H. "Emergence of young human genes after a burst of retroposition in primates", PLoS Biol 3:e357 (2005)
C. Hardkte	UNIL	Next generation sequencing and annotation of A. thaliana ecotypes
D. Duboule	UNIGE-EPFL	Large scale study of genomic region under long-range interaction
S. Antonarakis	UNIGE	Chromosome capture using 5C and chromosomal landscapeÂ
P. Descombes	UNIGE	Gene Expression analysis and infrastructure for the NCCR Frontiers in Genetics
L. Lopez-Molina	UNIGE	Sequence analysis of genes differentially expressed in an Arabidopsis thaliana mutant
L. Lopez-Molina	UNIGE	Study of A. thaliana cis-regulatory regions using gene expression profiling and genome mining
J. Schrenzel	UNIGE	Genome annotation and assembly of S.aureus and comparison of EDANA vs SHARGC	De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Hernandez D, FranÃ§ois P, Farinelli L, OsterÃ¥s M, Schrenzel J. Genome Res. 2008 May;18(5):802-9.
E. Zdobnov	UNIGE	Comparative genomic	Tapparel C, Junier T, Gerlach D, Cordey S, Van Belle S, Perrin L, Zdobnov EM, Kaiser L "New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features", BMC Genomics 8: 224 (2007).
D. Blanc	UNIGE	Genome sequencing using next generation sequencing of S.aureus
B. Galliot	UNIGE	Transcriptome analysis of hydra using next generation sequencing technologies
S. Cole	EPFL	M. leprae sequencing and comparative genomics (collaborative work with BBCF)
P. Bucher	EPFL	Chip-Seq data analysis and computation
J. Rougemont	EPFL	Genomic and multi-omics database	MIMAS 3.0 is a Multiomics Information Management and Annotation System. Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M. BMC Bioinformatics. 2009 May 18;10:151.
J. Rougemont	EPFL	Microbial comparative database	The Microbe browser for comparative genomics. Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J.Nucleic Acids Res. 2009 Jul 1;37
J. Rougemont	EPFL	Improving Illumina base calling algorithm	Probabilistic base calling of Solexa sequencing data. Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F. BMC Bioinformatics. 2008 Oct 13;9:431.
F. Naef	EPFL	Statistical analysis of ChIP on chip data	Parisi F, Wirapati P, Naef F. "Identifying synergistic regulation involving c-Myc and sp1 in human tissues", Nucleic Acids Res. 35(4): 1098-1107 (2007)
F. Naef	EPFL	Gillespie-simulation of circadian oscillatorsÂ
D. Trono	EPFL	Retroviral integration sites	Genotypic features of lentivirus transgenic mice. auvain MO, Dorr AP, Stevenson B, Quazzola A, Naef F, Wiznerowicz M, SchÃ¼tz F, Jongeneel V, Duboule D, Spitz F, Trono D. J. Virol. 2008 Jul;82(14):7111-9.
B. Deplancke	EPFL	Computational resources for analyzing and studying TF binding affinities.

Metagenomic view

Currently 1 project(s) in this category.

PI	Affiliation	Description	Publication
C. van Mering	UNIZH	Sequence analysis of metagenomic data

PK-PD view

Currently 1 project(s) in this category.

PI	Affiliation	Description	Publication
C. Csajka	UNIL-CHUV	Pharmacokinetics study of anti-HIV drugs.

Phylogeny view

Currently 10 project(s) in this category.

PI	Affiliation	Description	Publication
W. Herr	UNIL
N. Salamin	UNIL	Estimation of speciation rate based on phylogenetic trees using a MCMC approach.
N. Perrin	UNIL	Molecular evolution of sex-specific genes in frogs
M. Robinson-Rechavi	UNIL	Gene family reconstruction for phylogenetic analysis
M. Robinson-Rechavi	UNIL	Validation of an ontology for the comparison of expression profiles between species
L. Fumagalli	UNIL	Phylogenetic analysis of MHC genes in owls.
J. Pawlowski	UNIGE		Burki F, Pawlowski J. "Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts", Mol Biol Evol. 10: 1922-30 (2006)
D. Soldati	UNIGE	Phylogenetic analysis of myosins	Foth BJ, Goedecke MC, Soldati D. "New insights into myosin evolution and classification", PNAS 103: 3681-3686
B. Moret	EPFL	A benchmark suites for phylogenetics algorithms
B. Moret	EPFL	Web interface to RAxML	A rapid bootstrap algorithm for the RAxML Web servers. Stamatakis A, Hoover P, Rougemont J. Syst Biol. 2008 Oct;57(5):758-71.

Population Genetics view

Currently 1 project(s) in this category.

PI	Affiliation	Description	Publication
N. Perrin	UNIL	Dynamical simulation of population genetics using stochastic models	Guillaume F, Rougemont J. "Nemo: an evolutionary and population genetics programming framework", Bioinformatics 22: 2556-2557 (2006).

Proteomic view

Currently 3 project(s) in this category.

PI	Affiliation	Description
M. Quadroni	UNIL	Analysis of mass spectromic data and development of computational methodologies for non-labeled techniques
J.C. Sanchez	UNIGE	Use of mass spectrometry analysis methods, including the trans proteomic pipeline
M. Moniatte	EPFL	Supporting mass spectrometry data analysis

Sequence Analysis view

Currently 3 project(s) in this category.

PI	Affiliation	Description	Publication
W. Herr	UNIL	Chip-Seq analysis, MEME motif discovery
R. Benton	UNIL	Comparative genomics of novel chemosensor in Drosophila	Variant ionotropic glutamate receptors as chemosensory receptors in Drosophila. Benton R, Vannice KS, Gomez-Diaz C, Vosshall LB. Cell. 2009 Jan 9;136(1):149-62.
N. Hernandez	UNIL	Chip-Seq analysis and proteomics of maf1

Structural Biology view

Currently 7 project(s) in this category.

PI	Affiliation	Description	Publication
O. Michielin	UNIL-LICR	Structural study of the PPAR protein	Feige JN, Gelman L, Rossi D, et al.. "The endocrine disruptor mono-ethyl-hexyl-phthalate is a selective PPARgamma modulator which promotes adipogenesis", J Biol Chem. Apr 27 (2007)
O. Michielin	UNIL-LICR	Molecular dynamics simulation of the TCR/MHC/peptide binding	Fagerberg T, Cerottini JC, Michielin O. "Structural Prediction of Peptides Bound to MHC Class I", J Mol Biol 356: 521-546 (2006).
O. Michielin	UNIL-LICR	Optimization of a genetic algorithm for docking small molecules into protein active site.	Grosdidier A, Zoete V, Michielin O. "EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization", Proteins. 67(4): 1010-1025 (2007)
O. Michielin	UNIL-LICR	Optimization of generalized born equation on accelerated hardware	SchÃ¼pbach T, Zoete V, Tsakam-SotchÃ© B, Michielin O.Fourier transform convolution integrals applied to generalized Born molecular volume. J Comput Chem. 2009 Jun 25
A. Stasiak	UNIL	Chromosomal territories and computational modeling
J. Gruenberg	UNIGE	Molecular study of lipid bilayers using molecular dynamics
G. van der Goot	EPFL	Structural study of anthrax toxin and molecular modeling

Systems Biology view

Currently 10 project(s) in this category.

PI	Affiliation	Description	Publication
N. Hernandez	UNIL	Modeling three cycle together, cell cycle, circadian and metabolic using next generation sequencing technologies (SystemsX.ch)
C. Fankhauser	UNIL	Plant Growth and modeling of regulatory network (SystemsX.ch)
P. Kunzst	SIB	Systems Biology information technology supporting function
M. Pagni	SIB	Development of genome scale metabolic network of yeast and A.thaliana (SystemsX.ch)
S. Maerkl	EPFL	Collaboration with the BBCF as key partner
N. Mermod	EPFL	Gene expression modeling using stochastic processes	Steady-state expression of self-regulated genes. Fournier T, Gabriel JP, Mazza C, Pasquier J, Galbete JL, Mermod N. Bioinformatics. 2007 Dec 1;23(23):3185-92.
G. van der Goot	EPFL	Study of lipid composition and siRNA screen across different organisms (SystemsX.ch)
G. Di Micheli	EPFL	Stochastic modeling and logic synthesis	Modeling stochasticity and robustness in gene regulatory networks. Garg A, Mohanram K, Di Cara A, De Micheli G, Xenarios I. Bioinformatics. 2009 Jun 15;25(12):i101-9.
F. Naef	EPFL	Stochastic simulation of biological network	Stoll G, Rougemont J, Naef F. "Few crucial links assure checkpoint efficiency in the yeast cell-cycle network", Bioinformatics 22: 2539-2546 (2006)
F. Naef	EPFL	Simulation and analysis of circadian rythms	Rougemont J, Naef F. "Collective synchronization in populations of globally coupled phase oscillators with drifting frequencies", Phys. Rev. E 73:011104 (2006)

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