Bioinfo

Bioinformatician and Biologist AAB014 30963

Open uri20180222 173607 1i8f4nx?1519322965

Luciano Andres Abriata

molecular modeling structural bioinformatics biological nmr matlab javascript html vba python

Bioinformatician and Biologist AI2135 39642

Open uri20190321 156016 dn0u5y?1553159833

Zimbul Albo

Prof. Gräff Group

Bioinformatician and Biologist AI1144 30982

Open uri20180222 173704 qpk05a?1519323009

Daniel Alpern

Prof. Deplancke Group

Bioinformatician AAB018 30957

Open uri20170727 193613 ci5oyu?1501145333

Giovanna Ambrosini

Web development Web applications Genomics ChIP-seq Data analysis Bowtie BEDtools BAMtools UCSC browser Ensembl Ensembl Biomart MEME HOMER ChIP-Seq SSA PWMTools SNP2TFBS C C++ Fortran Perl Bash PHP Javascript R

Bioinformatician and Biologist

Paola Yatzin Arguello Pascualli

Prof. Gräff Group
Section of Life Sciences Engineering - Spring semester

Bioinformatician AI0151 30651

Open uri20170808 160361 ofgl34?1502189250

Florence Armand

Proteomics Core Facility

Proteomics Data analysis Data visualisation Statistics Maxquant Perseus Mascot Proteome Discoverer Scaffold Cytoscape Rstudio Jupyter notebook Anaconda navigator R Python Ruby Perl

Bioinformatician and Biologist 0.102 263008803

Simon Blanchoud

Image analysis tunicate genomics ASSET CAST Metassembler MAKER2

Bioinformatician and Biologist AI1148 30954

Maroun Bou Sleiman

Genomics Gene Expression Systems genetics NGS Rstudio R

Bioinformatician AAB017 30956

Philipp Bucher

EDMS - Teaching

DNA sequence analysis functional genomics gene regulation Developed tools see ccg.vital-it.ch Fortran Perl R

Bioinformatician and Biologist AI2135 39642

Allison Burns

Prof. Gräff Group
Doctoral Program in Neuroscience

RNA-seq R

Bioinformatician AI0140 39629

Olivier Burri

BioImaging Image Analysis Image Processing ImageJ Fiji Imaris CellProfiler CellProfiler Analyst R Matlab Arivis Vision 4D ZEN ImageJ Macro Language Groovy Javascript Java PHP Beanshell

Bioinformatician and Biologist AAB036 30964

Open uri20190429 40251 9fofkm?1556530472

Chan Cao

Prof. Dal Peraro Group

Bioinformatician AI0140 39629

Nicolas Chiaruttini

BioImaging and Optics Core Facility

Image Analysis FIJI ImageJ Java

Bioinformatician and Biologist SV1535 30938

Elisa Cora

Gene Expression Core Facility

Bioinformatician AAB022 30940

Open uri20170802 70693 7kmvl0?1501675362

Alexandre Coudray

Laboratory of Virology and Genetics
Doctoral Program in Computational and Quantitative Biology

Genomics Rstudio Bioconductor Bash python R

Bioinformatician AAB026 30903

Fabrice David

Bioinformatics Competence Center

Web development Database design Data integration Web robots Lipidomics Genomics Ruby on Rails PostgreSQL SQLite3 MySQL Bootstrap PovRAY UniProt GO Ensembl UCSC browser HTSstation ASAP GetPrime FlyGut SwissPalm Ruby Perl Python Javascript SQL

2017

V Gardeux, FPA David, A Shajkofci, PC Schwalie, B Deplancke
ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data.
Bioinformatics (Oxford, England), Volume 33, Issue 19,, September 30, 2017, https://doi.org/10.1093/bioinformatics/btx337

2020

FPA David, M Litovchenko, B Deplancke, V Gardeux
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses.
Nucleic acids research, Volume 48, Issue W1,, July 01, 2020, https://doi.org/10.1093/nar/gkaa412

Bioinformatician and Biologist SV2830 30785

Fabio De Martino

Prof. Brisken Group
Doctoral Program in Molecular Life Sciences

Vital-IT Cluster RNAseq analysis in R Tophat Bowtie2 featureCounts Limma edgeR KEGG R UNIX

Bioinformatician SV2842 39708

Open uri20170828 65487 1fl6zae?1503929328

Lucille Delisle

Prof. Duboule Group

Hi-C captureHi-C RNA-seq ChIP-seq ATAC-seq 4Cseq Bowtie2 hicup hiclib tophat2 DESeq2 MACS2 bash python R

Bioinformatician

Open uri20180222 175125 vx8jvj?1519323812

Mustafa Demir

Prof. van der Goot Group
Laboratory for Biological Geochemistry
Doctoral Program in Biotechnology and Bioengineering

Bioinformatician 37644

Robin Denhardt-Eriksson

Prof. van der Goot Group
Laboratory of Computational Systems Biotechnology (SB/SV/STI)
Doctoral Program in Chemistry and Chemical Engineering

Julia Python MATLAB

Bioinformatician and Biologist AI1146 31848

Teresa Didonna

Prof. Deplancke Group
Doctoral Program in Molecular Life Sciences

R Bash

Bioinformatician AAB022 30940

Open uri20170816 49058 1ddz36r?1502875503

Julien Duc

Laboratory of Virology and Genetics

Bioinformatician and Biologist AI1133 30750

Torgil Elias Friman

Prof. Suter Group
Doctoral program in biotechnology and biomedical engineering
Doctoral Program in Biotechnology and Bioengineering

Bioinformatician AAB036 30931

Andreas

Prof. Barth Group

Protein Modeling Molecular Dynamics Fluid Dynamics Rosetta LAMMPS C C++ Python

Bioinformatician AI1144 37207

Vincent Roland Julien Gardeux

Prof. Deplancke Group

Genomics Single-cell RNA-seq ChIP-seq Drop-seq Smart-seq BRB-seq Truseq SCRB-seq Cel-seq ATAC-seq Transcriptomics Rstudio Eclipse IGV UCSC Genome Browser STAR bedtools BAMTools SAMTools seqMiner deeptools MACS HOMER DAVID Enrichr limma DESeq2 SC3 voom edgeR scLVM Cytoscape GATK bwa bioconductor Gene Ontology KEGG Gene Atlas PharmaGKB Drugbank dbSNP GTex MySQL Vital-IT tSNE ZIFA SCDE PAGODA Monocle ASAP R Java Python C C++ Bash SQL

Biologist using Bioinformatics tools AI2351.B 30765

Charlotte Gehin

Laboratory of Molecular Neurobiology and Neuroproteomics

Rstudio CellProfiler ImageJ R

Bioinformatician AAB036 30931

Cédric Gobet

Prof. Naef Group

Biologist using Bioinformatics tools AI3151 31799

Open uri20180222 173788 19ru7xv?1519323053

Laurence Gouzi Abrami

Prof. van der Goot Group
COSEC - SV

Bioinformatician AAB018 31670

Open uri20170727 186520 19pspo9?1501141339

Romain Groux

Bucher Group
Doctoral Program in Biotechnology and Bioengineering
Doctoral Program in Computational and Quantitative Biology

Genomics ChIP-seq Data analysis Data visualization Bowtie Bowtie2 Rstudio ChIP-seq server bash python C C++ R

Bioinformatician AAB014 30902

Open uri20170727 186831 71d35r?1501141424

Delphine Grun

Laboratory of Virology and Genetics

Genomics RNA-Seq Chip-Seq Microarrays Data analysis bedtools hisat featurecounts MACS2 limma DESeq2 R Bash PHP

Bioinformatician AI0140 39629

Open uri20190315 180316 15lc7yb?1552652402

Romain Guiet

BioImaging and Optics Core Facility

BioImage Analyst Image Processing Image Analysis Biology Immunology Oncology Cell Motility Microscopy ImageJ FIJI Imaris Arivis CellProfiler ilastik QuPath MatLab Rstudio Jupyter Notebook (Omero) ImageJ Macro Language Groovy Java Python (R)

Bioinformatician and Biologist AAB219

Open uri20170818 138216 1l0zciv?1503057255

Christian Hammer

Fellay Group

Bioinformatician AI3137 31693

Open uri20181127 69508 rea5vt?1543319805

Zander Harteveld

Laboratory of Protein Design & Immunoengineering
Doctoral Program in Biotechnology and Bioengineering

structural protein design Rosetta scaffolding machine learning protein solubility prediction tool Rosetta Bash Python

Bioinformatician CHH4625 39870

Open uri20180328 119545 t2yiid?1522234143

Vassily Hatzimanikatis

SCGC - Teaching
SMA - Teaching
Laboratory of Computational Systems Biotechnology (SB/SV/STI)
Doctoral Program Chemistry and chemical engineering
IBI-SV - Administration
Doctoral school committee

Bioinformatician and Biologist SV 3820

Sachi Iiyama Inukai

Prof. Deplancke Group

transcription factors transcription factor–DNA binding gene regulation microRNAs DESeq2 SELEX-seq (R) HMMER MAFFT PAGAN BLAST Bowtie2 Cytoscape KEGG MEME python R

Bioinformatician AAB021

Christian Iseli

Bioinformatics and Biostatistics Core Facility

Biologist using Bioinformatics tools AI1351 30609

Open uri20180226 165900 1w6gb73?1519637587

Charlotte Kern

Prof. Schoonjans Group
Doctoral Program in Biotechnology and Bioengineering

Biologist using Bioinformatics tools 789401353

Daria Korotkova

Prof. van der Goot Group
Doctoral Program in Molecular Life Sciences

rna-seq analysis c c++ r python

Bioinformatician AAB022 37216

Lucien Fabrice Krapp

Prof. Dal Peraro Group
Doctoral Program in Physics

machine learning

Bioinformatician

Judith Franziska Kribelbauer

Prof. Deplancke Group

Bioinformatician and Biologist AAB008 31628

Fabien Kuttler

Biomolecular Screening Core Facility

Biologist using Bioinformatics tools AI1112

Jakob Josef Langer

Prof. Lutolf Group
Doctoral Program in Biotechnology and Bioengineering

Bioinformatician AAB219 31874

Open uri20190328 105990 4bxv16?1553780666

Dylan Lawless

Fellay Group

Genomics exome genome human rare disease immunology

Bioinformatician AAB026 30944

Open uri20170828 94215 1w3r6yq?1503947223

Marion Leleu

Genomics NGS Data analysis Data mining Biostatistics Microarray RNA-seq Single-cell ChIP-seq ATAC-seq DNase-seq 4C-seq Hi-C Metagenomics Bioconductor BLAST Bootstrap Bowtie2 Circos ChICAGO Cytoscape DAVID Eclipse Ensembl Biomart gFeatBrowser HiCUP HTSeq HTSstation Limma MACS2 MySQL RStudio SAMtools SQLite3 STAR TopHat TCGA Wellington Bash Javascript Perl PHP Python R SQL

Bioinformatician and Biologist AI1148 30954

Open uri20170928 11167 1mqtjiy?1506610331

Hao Li

Laboratory of Integrative Systems Physiology
Doctoral Program in Biotechnology and Bioengineering
Doctoral Program in Computational and Quantitative Biology

systems genetics data integration systems-genetics.org R

Bioinformatician and Biologist AI1144 37207

Maria Litovchenko

Prof. Deplancke Group
Doctoral Program in Biotechnology and Bioengineering

Bioinformatics Drosophila Fly Stem Cells Mitochondria Aging Single Cell Genomics RNA-seq ChIP-seq Drop-seq BRB-seq ATAC-seq Transcriptomics samtools vcftools bwa STAR bioconductor Rstudio NetBeans IGV UCSC Genome Browser bedtools bamools seqMiner deeptools MACS2 HOMER DAVID DESeq2 GATK Gene Ontology Vital-IT tSNE ASAP Bash R Java Python C++

Biologist using Bioinformatics tools SV1841 37113

Bastien Mangeat

Bioinformatician AAB022 24071

Flavia Marzetta

Laboratory of Virology and Genetics

Genomics R

Biologist using Bioinformatics tools AAB042 37241

Open uri20181127 69431 107m6pk?1543319769

Daniel Mauvoisin

Prof. Naef Group

Metabolism;Chronobiology French English

Bioinformatician and Biologist SV2842 30605

Alexandre Mayran

Prof. Duboule Group

Bioinformatician CHH4595 39892

Ljubisa Miskovic

Biologist using Bioinformatics tools AI1133

Romane Mizeret

Prof. Suter Group
Doctoral Program in Computational and Quantitative Biology

Bioinformatician AAB040 31621

Open uri20181127 69370 eoqn4q?1543319743

Felix Naef

miscallaneous data analysis

Bioinformatician AAB-2.19

Open uri20170818 145898 191b1vm?1503061991

Olivier Naret

Fellay Group
Doctoral Program in Biotechnology and Bioengineering

Unix Genomics GWAS Web development plink BOLT-LMM PRSice Node.js jQuery TensorFlow Git Eclipse PostgreSQL Ruby on Rails VCFtools SAMtools Bash C Java Javascript PHP Python R Ruby SQL

Bioinformatician SV2528 37274

Sina Nassiri

Prof. De Palma Group

functional data analysis immuno-genomics statistical learning

Bioinformatician and Biologist GRB0419 36376

Open uri20190318 3285 1z0pygg?1552931187

Hannes Markus Peter

Stream Biofilm and Ecosystem Research Laboratory
SSIE - Teaching

bacterial 16S virome

Bioinformatician AAB022 30940

Evarist Planet Letschert

Laboratory of Virology and Genetics

Biologist using Bioinformatics tools AI2147 31976

Open uri20190319 128289 4mdg78?1553013618

Florence Pojer

protein structural biology Xray crystallography EM phenix coot chimera ccp4i relion cryosparc xds modeller

Bioinformatician AAB219 31803

Konstantin Popadin

Fellay Group

evolutionary and population genetics R PERL BASH

Bioinformatician AAB015 31847

Open uri20170815 147223 ei4kio?1502812409

Alessio Prunotto

Prof. Dal Peraro Group
Doctoral Program in Biotechnology and Bioengineering

Bioinformatician AI1144 37207

Pernille Yde Rainer

Prof. Deplancke Group
Doctoral Program in Biotechnology and Bioengineering
Doctoral Program in Computational and Quantitative Biology

Bioinformatician AI 1148 30954

Alexis Rapin

Laboratory of Integrative Systems Physiology

Immunology Allergies Microbiome Web application renku RoR Qiime genocrunch R Python Ruby

Bioinformatician and Biologist

Open uri20181128 188659 1vchpe9?1543405145

Sadegh Saghafinia

Merck Serono Chair in Oncology
Doctoral Program in Molecular Life Sciences

Computational Cancer Biology Genomics Epigenetics RESET R Python

Bioinformatician

Halima Hannah Emilie Schede

La Manno Group
Section of Life Sciences Engineering - Master semester 4

Bioinformatician MAB3465 30336

Martina Scolamiero

Laboratory for Topology and Neuroscience

Topological Data Analysis Mapper algorithm Python

Biologist using Bioinformatics tools AI3150 31793

Open uri20180222 174013 tl816k?1519323191

Oksana Andrei Sergeeva

Prof. van der Goot Group

Biologist using Bioinformatics tools SV2830 30784

Open uri20180402 101761 108whpc?1522680819

Georgios Sflomos

Prof. Brisken Group

Biologist using Bioinformatics tools BM2136 38511

Amir Shahein

Laboratory of Biological Network Characterization
Doctoral Program in Biotechnology and Bioengineering

Biophysics Python

Biologist using Bioinformatics tools AI1125 30764

Shoujie Sun

Prof. Suter Group
Doctoral Program in Molecular Life Sciences

Live-cell-imaging molecular biology cellpose stardist trackmate imagej cellprofiler ilastik python imagej_macro

Bioinformatician SV2827 39674

Stephanie Jocelyne Sungalee

Prof. Oricchio Group

Analysis and processing of NGS data ChIP Seq RNASeq HiC structural variant calling. Python bash R

Bioinformatician AI1241 39631

Open uri20190320 60644 1569sxo?1553093545

David Suter

Bioinformatician AAB219 37148

Open uri20170818 138484 paruj2?1503057293

Christian Axel Wandall Thorball

Laboratory of Virology and Genetics
Fellay Group
Doctoral Program in Molecular Life Sciences

GWAS Exome sequencing Whole genome sequencing CNV HLA imputation GATK BCFtools BEDtools SAMtools PLINK EIGENSOFT GCTA Picard Tools SNP2HLA HLA-PRG CLAMMS GMMAT FaST-LMM snpEff PrediXcan SKAT BWA R Python Bash