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Frederic Bastian is listed as Associate Group Leader at SIB Swiss Institute of Bioinformatics, a with 233 employees, based in Lausanne Metropolitan Area, Switzerland. AeroLeads shows a work email signal at sib.swiss and a matched LinkedIn profile for Frederic Bastian.
Frederic Bastian previously worked as Bioinformatics Scientist - Junior Project Manager at Swiss Institute Of Bioinformatics and Bioinformatics Scientist at Sib Swiss Institute Of Bioinformatics. Frederic Bastian holds Doctor Of Philosophy (Phd), Life Sciences from Doctoral School Of The Faculty Of Biology And Medicine - University Of Lausanne.
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My motivation is to build bioinformatics resources allowing to understand gene expression, and gene expression evolution in the context of animal anatomy evolution.Since 2011, I have worked on the development of the gene expression database Bgee (https://bgee.org/), developed at the SIB Swiss Institute of Bioinformatics and Department of Ecology and Evolution at the University of Lausanne. We try to integrate all possible sources of expression data in a consistent framework, in order to build a detailed and faithful representation of gene expression patterns in many animal species. The development of such a database requires work at the intersection of data curation, ontology development, software development, data quality control, and data reproducibility.I am a supporter of open science principles, supporting notably copyright-free software and data sharing, disclosure and versioning of data analysis pipelines, open peer-reviews in journals, and pre-publication platforms.
Listed skills include Bioinformatics, Comparative Genomics, Molecular Biology, Evolutionary Biology, and 11 others.
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Région De Lausanne, Suisse
I work in the team developing the gene expression database Bgee (https://bgee.org), my role is team leader. Our aim is to contribute to the understanding of gene expression, and to help biologist users by developing bioinformatics tools useful to their research. We work as a Teal organization. I work for the SIB Swiss Institute of Bioinformatics, embedded in the Department of Ecology and Evolution at University of Lausanne.
Lausanne Area, Switzerland
I lead the development of Bgee (http://bgee.org/), under the supervision of Prof. Marc Robinson-Rechavi, at the University of Lausanne. This work is notably funded by the Swiss Institute of Bioinformatics. Bgee is a database to perform high-throughput and automated comparisons of gene expression patterns between species. We have the aim of producing a database useful to disciplines such as comparative genomics, Evo-Devo, or transcriptome studies, whilst providing an improved integration of homology and related concepts into bioinformatics through ontologies and ontology tools.Project management: - leader of the Bgee team (developer, biocurator)- provide project vision, standards, roadmap- trained in Project Management through the Swiss Institute of Bioinformatics (course provided by Iteral management SA)Bioinformatics: - development of the Bgee pipeline to store and perform high-throughput analyses of transcriptomics data of various types, notably Illumina RNA-Seq and Affymetrix microarray: use of Java, perl, R, Bioconductor, Ensembl API, Intermine, etc.Ontology development: - participation in the development of the Uberon ontology: use of OWL2, OWL API, owltools. - developer of the repository of developmental stage ontologies: http://developmental-stage-ontologies.googlecode.com/- developer of the similarity annotations, used to define evolutionary relations between anatomical entities described in the Uberon ontology: http://sourceforge.net/p/bgee/- developer of the confidence code ontology: http://svn.code.sf.net/p/bgee/code/trunk/release/ontologies/conf_information.oboApplication development: - development of the Bgee application: use of Java 7, Maven, MySQL, unit/regression testing, best practices in programming. I love effective design patterns.- development of the Bgee database: use of MySQL, big data optimizations- committer to owltools, a tool to manipulate ontologies - developer of log4jbc-log4j2, a JDBC logging library
Lausanne Area, Switzerland
Developer of the Bgee database (http://bgee.org/).
Région De Lausanne, Suisse
I have a double affiliation University of Lausanne / Swiss Institute of Bioinformatics, see SIB profile.
Lausanne Area, Switzerland
During my PhD, my aim was to provide new tools to increase our capacity to analyse gene expression patterns, and to study on a large-scale basis the evolution of gene expression in animals.To this end, I developed the database Bgee (Base for Gene Expression Evolution, http://bgee.unil.ch). Bgee is a database to perform high-throughput and automated comparisons of gene expression patterns between species. The aim was producing a database useful to disciplines such as comparative genomics, Evo-Devo, or transcriptome studies, whilst providing an improved integration of homology and related concepts into bioinformatics through ontologies and ontology tools.I was then able to tackle unanswered questions in evolutionary biology, such as analyzing the fate of gene expression evolution of thousands of duplicates in vertebrates with high granularity.
Lausanne Area, Switzerland
- preliminary analysis of EST and microarray data to study muscle dysfunctions.- installation of a local version of the ArrayExpress database (ORACLE) and application (Tomcat) for the CRESCENDO european consortium.- modification of a Java software to enable the CRESCENDO partners to inser microarray data into the ArrayExpress database- teaching in bioinformaticsDepartment of Ecology and EvolutionGroup: Evolutionary BioinformaticsGroup leader: Marc Robinson-RechaviLanguage: Java, PerlDBMS: ORACLE, MySQLOS: Mac OS X, Linux (Ubuntu)
Paris Area, France
Development of a web-application and a database, using ontologies, to manage wet lab in situ hybridization data, and analyse gene expression patterns."Populations, Genetique et Evolution", CNRS Gif/YvetteGroup: "Genome, Developpement et Evolution"Group leader: Didier CasaneTasks: - implementation of Minimum Information standards to manage in situ hybridization data (MISFISHIE)- Implementation of anatomical ontologies- Development of tools to manage in situ hybridization data, and map gene expression patterns to ontologiesLanguage: object-oriented PHP5DBMS: MySQLOS: Linux (Debian)
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Fabio Madness
Colleague at Sib Swiss Institute Of BioinformaticsFaro, Portugal
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DU
Deepak Unni
Colleague at Sib Swiss Institute Of BioinformaticsBasel, Switzerland
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Leonore Wigger
Colleague at Sib Swiss Institute Of BioinformaticsLausanne, Vaud, Switzerland
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JB
Jocelyne Bocquet
Colleague at Sib Swiss Institute Of BioinformaticsLausanne, Vaud, Switzerland
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MH
Mathilde Heusghem
Colleague at Sib Swiss Institute Of BioinformaticsGeneva, Switzerland
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JG
Julien Gobeill
Colleague at Sib Swiss Institute Of BioinformaticsGeneva, Switzerland
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SG
Sébastien Géhant
Colleague at Sib Swiss Institute Of BioinformaticsSwitzerland
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PL
Philippe Le Mercier
Colleague at Sib Swiss Institute Of BioinformaticsGeneva, Switzerland
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LV
Laure Verbregue
Colleague at Sib Swiss Institute Of BioinformaticsGeneva, Switzerland
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MB
Matthew Berkeley
Colleague at Sib Swiss Institute Of BioinformaticsGeneva, Switzerland
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Graduated with Honors, 1st rank Ontologies in Biology, Molecular Evolution, Phylogenetic Methods, High Throughput Data Generation, Machine.
Bioinformatics, Genetics of Plant Development, Modeling, Population Biology and Evolution
Graduated with Honors, ranked 3rd Bioinformatics, Genetics, Molecular Biology, Biochemistry, Statistics, Modeling, Angiosperm Biology.
Quick answers generated from the profile data available on this page.
Frederic Bastian works for SIB Swiss Institute of Bioinformatics.
Frederic Bastian is listed as Associate Group Leader at SIB Swiss Institute of Bioinformatics.
AeroLeads has found 1 work email signal at @sib.swiss for Frederic Bastian at SIB Swiss Institute of Bioinformatics.
Frederic Bastian is based in Lausanne Metropolitan Area, Switzerland while working with SIB Swiss Institute of Bioinformatics.
Frederic Bastian has worked for Sib Swiss Institute Of Bioinformatics, Swiss Institute Of Bioinformatics, University Of Lausanne, and Cnrs.
Frederic Bastian's colleagues at SIB Swiss Institute of Bioinformatics include Fabio Madness, Deepak Unni, Leonore Wigger, Jocelyne Bocquet, and Mathilde Heusghem.
You can use AeroLeads to view verified contact signals for Frederic Bastian at SIB Swiss Institute of Bioinformatics, including work email, phone, and LinkedIn data when available.
Frederic Bastian holds Doctor Of Philosophy (Phd), Life Sciences from Doctoral School Of The Faculty Of Biology And Medicine - University Of Lausanne.
Frederic Bastian is listed with skills including Bioinformatics, Comparative Genomics, Molecular Biology, Evolutionary Biology, Ontologies, Transcriptomics, Java, and Programming.
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