http://www2.unil.ch/cbg/api.php?action=feedcontributions&user=Sven&feedformat=atomComputational Biology Group - User contributions [en]2015-04-19T19:05:50ZUser contributionsMediaWiki 1.19.1http://www2.unil.ch/cbg/index.php?title=Module_4:_How_does_feature_selection_impact_integrative_clustering_analysis%3FModule 4: How does feature selection impact integrative clustering analysis?2015-03-06T09:16:18Z<p>Sven: </p>
<hr />
<div>* Title: "How to make valid prognostic models with gene expression signatures?"<br />
<br />
* Paper to be examined: “The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups”, Nature 486(7403):346-52 (2012)[http://www.nature.com/nature/journal/v486/n7403/full/nature10983.html] <br />
<br />
* Key claim of the paper: "We have generated a robust, population-based molecular subgrouping of breast cancer based on multiple genomic views. [...] The joint clustering of CNAs and gene expression profiles further resolves the considerable heterogeneity of the expression-only subgroups." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
** H1: General introduction to the paper/motivation<br />
** H2: Write code to import the data and practice with the iClusterPlus R package with vignette example<br />
** H3: Reproduce results from Figure 4 on subsample(s) of the data<br />
** H4-5: Write code to import second dataset and reproduce clustering results<br />
** H6: Discussion: "What features discriminate the resulting clusters? Do we see the issue? How can we improve?"<br />
** H7-8: Based on discussion, modify feature selection and redo the analyses on one (two) datasets<br />
** H9: Summarize results (e.g. on this wiki)<br />
<br />
* Key bioinformatics concept of this module: <br />
** Feature selection (and its importance for cluster analyses)<br />
** integrative analysis<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Module_4:_How_does_feature_selection_impact_integrative_clustering_analysis%3FModule 4: How does feature selection impact integrative clustering analysis?2015-03-06T09:15:52Z<p>Sven: Created page with "* Title: "How to make valid prognostic models with gene expression signatures?" * Paper to be examined: “The genomic and transcriptomic architecture of 2,000 breast tumour..."</p>
<hr />
<div>* Title: "How to make valid prognostic models with gene expression signatures?"<br />
<br />
* Paper to be examined: “The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups”, Nature 486(7403):346-52 (2012)[http://www.nature.com/nature/journal/v486/n7403/full/nature10983.html] <br />
<br />
* Key claim of the paper: "We have generated a robust, population-based molecular subgrouping of breast cancer based on multiple genomic views. [...] The joint clustering of CNAs and gene expression profiles further resolves the considerable heterogeneity of the expression-only subgroups." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
<br />
** H1: General introduction to the paper/motivation<br />
** H2: Write code to import the data and practice with the iClusterPlus R package with vignette example<br />
** H3: Reproduce results from Figure 4 on subsample(s) of the data<br />
** H4-5: Write code to import second dataset and reproduce clustering results<br />
** H6: Discussion: "What features discriminate the resulting clusters? Do we see the issue? How can we improve?"<br />
** H7-8: Based on discussion, modify feature selection and redo the analyses on one (two) datasets<br />
** H9: Summarize results (e.g. on this wiki)<br />
<br />
* Key bioinformatics concept of this module: <br />
** Feature selection (and its importance for cluster analyses)<br />
** integrative analysis<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-03-06T09:08:38Z<p>Sven: </p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals of Forensics in Bioinformatics]]<br />
* [[Schedule for Forensics in Bioinformatics 2015]]<br />
* Modules<br />
** [[Module 1: Is the hourglass model for gene expression really supported by the data?]]<br />
** [[Module 2: How well does sequence similarity predict similarity in binding specificity?]]<br />
** [[Module 3: How to make valid prognostic models with gene expression signatures?]]<br />
** [[Module 4: How does feature selection impact integrative clustering analysis?]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello]]<br />
* Students<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=User:MauroUser:Mauro2015-02-26T09:22:35Z<p>Sven: </p>
<hr />
<div>'''Mauro Delorenzi'''<br />
<br />
* homepage: http://bcf.isb-sib.ch/Delorenzi/index.html<br />
* contact: mauro.delorenzi@unil.ch</div>Svenhttp://www2.unil.ch/cbg/index.php?title=User:MauroUser:Mauro2015-02-26T09:21:48Z<p>Sven: Created page with "* homepage: http://bcf.isb-sib.ch/Delorenzi/index.html * contact: mauro.delorenzi@unil.ch"</p>
<hr />
<div>* homepage: http://bcf.isb-sib.ch/Delorenzi/index.html<br />
* contact: mauro.delorenzi@unil.ch</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Module_3:_How_to_make_valid_prognostic_models_with_gene_expression_signatures%3FModule 3: How to make valid prognostic models with gene expression signatures?2015-02-26T09:19:20Z<p>Sven: </p>
<hr />
<div>* Title: "How to make valid prognostic models with gene expression signatures?"<br />
<br />
* Paper to be examined: “Gene Expression Profiling for Survival Prediction in Pediatric Rhabdomyosarcomas: A Report From the Children's Oncology Group”, J Clin Oncol. 2010 Mar 1;28(7):1240-6 (2010)[http://jco.ascopubs.org/content/28/7/1240.long] <br />
<br />
* Key claim of the paper: "Metagenes to discriminate patients with good prognosis from those with poor prognosis, with the potential to direct risk-adapted therapy." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
<br />
** H1: General introduction to the paper/motivation<br />
** H2-3: Write code to import the data and start computing "meta-genes"<br />
<br />
** H4-6: Aim to fit a predictive model for clinical outcome based on meta-genes<br />
<br />
** H7: Discussion: “Is a model that fits the data necessarily a good predictive model?” <br />
** H8: Sketch cross-validation approach<br />
** H9: Summarize results (e.g. on this wiki)<br />
<br />
* Key bioinformatics concept of this module: <br />
** Prognostic models<br />
** cross validation<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Module_3:_How_to_make_valid_prognostic_models_with_gene_expression_signatures%3FModule 3: How to make valid prognostic models with gene expression signatures?2015-02-26T09:19:01Z<p>Sven: </p>
<hr />
<div>==== '''MODULE 3' LESSON PLAN '' ====<br />
<br />
* Title: "How to make valid prognostic models with gene expression signatures?"<br />
<br />
* Paper to be examined: “Gene Expression Profiling for Survival Prediction in Pediatric Rhabdomyosarcomas: A Report From the Children's Oncology Group”, J Clin Oncol. 2010 Mar 1;28(7):1240-6 (2010)[http://jco.ascopubs.org/content/28/7/1240.long] <br />
<br />
* Key claim of the paper: "Metagenes to discriminate patients with good prognosis from those with poor prognosis, with the potential to direct risk-adapted therapy." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
<br />
** H1: General introduction to the paper/motivation<br />
** H2-3: Write code to import the data and start computing "meta-genes"<br />
<br />
** H4-6: Aim to fit a predictive model for clinical outcome based on meta-genes<br />
<br />
** H7: Discussion: “Is a model that fits the data necessarily a good predictive model?” <br />
** H8: Sketch cross-validation approach<br />
** H9: Summarize results (e.g. on this wiki)<br />
<br />
* Key bioinformatics concept of this module: <br />
** Prognostic models<br />
** cross validation<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Module_2:_How_well_does_sequence_similarity_predict_similarity_in_binding_specificity%3FModule 2: How well does sequence similarity predict similarity in binding specificity?2015-02-25T11:53:58Z<p>Sven: Created page with "* Title: "How well does sequence similarity predict similarity in binding specificity?" * Paper to be examined: “A Specificity Map for the PDZ Domain Family”, PLoS Biol ..."</p>
<hr />
<div>* Title: "How well does sequence similarity predict similarity in binding specificity?"<br />
<br />
* Paper to be examined: “A Specificity Map for the PDZ Domain Family”, PLoS Biol 6(9): e239 [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060239] <br />
<br />
* Key claim of the paper: "Similarity in sequence of binding motifs of PDZ domains can be used to identify 16 distinct specificity classes." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
<br />
**H1: General intro to the paper/motivation<br />
**H2-3: Write code to import the data and start computing similarity<br />
<br />
**H4-6: Write code to compute and compare different types of similarity values and do the clustering.<br />
<br />
**H7: Use a visualization software to look at the data.<br />
**H8: Start writing the report<br />
**H9: Broader view on the use and challenges with similarity metrics between biological objects <br />
<br />
* Key bioinformatics concept of this module: <br />
** Similarity measures between biological objects (here protein sequence and binding specificity)<br />
** Clustering <br />
<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-02-25T11:41:40Z<p>Sven: </p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals of Forensics in Bioinformatics]]<br />
* [[Schedule for Forensics in Bioinformatics 2015]]<br />
* Modules<br />
** [[Module 1: Is the hourglass model for gene expression really supported by the data?]]<br />
** [[Module 2: How well does sequence similarity predict similarity in binding specificity?]]<br />
** [[Module 3: Mauro's project]]<br />
** [[Module 4: Giovanni's project]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello]]<br />
* Students<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-02-25T11:38:31Z<p>Sven: </p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals of Forensics in Bioinformatics]]<br />
* [[Schedule for Forensics in Bioinformatics 2015]]<br />
* Modules<br />
** [[Module 1: Is the hourglass model for gene expression really supported by the data?]]<br />
** [[Module 2: David's project]]<br />
** [[Module 3: Mauro's project]]<br />
** [[Module 4: Giovanni's project]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello]]<br />
* Students<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Module_1:_Is_the_hourglass_model_for_gene_expression_really_supported_by_the_data%3FModule 1: Is the hourglass model for gene expression really supported by the data?2015-02-25T11:15:23Z<p>Sven: </p>
<hr />
<div>* Title: "Is the hourglass model for gene expression really supported by the data?"<br />
<br />
* Paper to be examined: “A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns”, Nature 9;468(7325):815-8 (2010)[http://www.nature.com/nature/journal/v468/n7325/full/nature09632.html] <br />
<br />
* Key claim of the paper: "Gene expression follows the so-called hour-glass pattern observed for morphological features of development, which are most similar to each other in the phylotypic stage in mid-development." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
<br />
** H1: General introduction to the paper/motivation<br />
** H2-3: Write code to import the data and start computing transcriptome age index (TAI)<br />
<br />
** H4-6: Aim to reproduce figure 1 of the paper – help/scripts will be given if needed.<br />
<br />
** H7: Discussion: “Are you convinced of this result? What might have gone wrong?” <br />
** H8: Redo analysis using log-transformed data<br />
** H9: Summarize results (e.g. on this wiki)<br />
<br />
* Key bioinformatics concept of this module: "Data normalization is important and can impact the results of subsequent analyses!"<br />
<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Module_1:_Is_the_hourglass_model_for_gene_expression_really_supported_by_the_data%3FModule 1: Is the hourglass model for gene expression really supported by the data?2015-02-25T11:13:43Z<p>Sven: </p>
<hr />
<div>* Title: "Is the hourglass model for gene expression really supported by the data?"<br />
<br />
* Paper to be examined: “A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns”, Nature 9;468(7325):815-8 (2010)[http://www.nature.com/nature/journal/v468/n7325/full/nature09632.html] <br />
<br />
* Key claim of the paper: "Gene expression follows the so-called hour-glass pattern observed for morphological features of development, which are most similar to each other in the phylotypic stage in mid-development." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
<br />
** H1: General introduction to the paper/motivation<br />
** H2-3: Write code to import the data and start computing transcriptome age index (TAI)<br />
<br />
** H4-6: Aim to reproduce figure 1 of the paper – help/scripts will be given if needed.<br />
<br />
** H7: Discussion: “Are you convinced of this result? What might have gone wrong?” <br />
** H8: Redo analysis using log-transformed data<br />
** H9: Summarize results (e.g. on this wiki)<br />
<br />
* Key bioinformatics concept of this module: "Data normalization is important and can impact the results of subsequent analyses!"</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Module_1:_Is_the_hourglass_model_for_gene_expression_really_supported_by_the_data%3FModule 1: Is the hourglass model for gene expression really supported by the data?2015-02-25T11:13:06Z<p>Sven: </p>
<hr />
<div>* Title: "Is the hourglass model for gene expression really supported by the data?"<br />
<br />
* Paper to be examined: “A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns”, Nature 9;468(7325):815-8 (2010)[http://www.nature.com/nature/journal/v468/n7325/full/nature09632.html] <br />
<br />
* Key claim of the paper: "Gene expression follows the so-called hour-glass pattern observed for morphological features of development, which are most similar to each other in the phylotypic stage in mid-development." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
<br />
** H1: General introduction to the paper/motivation<br />
** H2-3: Write code to import the data and start computing transcriptome age index (TAI)<br />
<br />
** H4-6: Aim to reproduce figure 1 of the paper – help/scripts will be given if needed.<br />
<br />
** H7: Discussion: “Are you convinced of this result? What might have gone wrong?” <br />
** H8: Redo analysis using log-transformed data (30’)!<br />
** H9: Summarize results (e.g. on this wiki)<br />
<br />
* Key bioinformatics concept of this module: "Data normalization is important and can impact the results of subsequent analyses!"</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Module_1:_Is_the_hourglass_model_for_gene_expression_really_supported_by_the_data%3FModule 1: Is the hourglass model for gene expression really supported by the data?2015-02-25T11:11:28Z<p>Sven: Created page with "* Title: "Is the hourglass model for gene expression really supported by the data?" * Paper to be examined: “A phylogenetically based transcriptome age index mirrors ontog..."</p>
<hr />
<div>* Title: "Is the hourglass model for gene expression really supported by the data?"<br />
<br />
* Paper to be examined: “A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns”, Nature 9;468(7325):815-8 (2010)[http://www.nature.com/nature/journal/v468/n7325/full/nature09632.html] <br />
<br />
* Key claim of the paper: "Gene expression follows the so-called hour-glass pattern observed for morphological features of development, which are most similar to each other in the phylotypic stage in mid-development." <br />
<br />
* Data and Code<br />
<br />
* Schedule: <br />
<br />
** H1: General introduction to the paper/motivation<br />
** H2-3: Write code to import the data and start computing transcriptome age index (TAI)<br />
<br />
** H4-6: Aim to reproduce figure 1 of the paper – help/scripts will be given if needed.<br />
<br />
** H7: Discussion: “Are you convinced of this result? What might have gone wrong?” <br />
** H8: Redo analysis using log-transformed data (30’)!<br />
** H9: Summarize results (e.g. on this wiki)</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-02-25T10:58:34Z<p>Sven: </p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals of Forensics in Bioinformatics]]<br />
* [[Schedule for Forensics in Bioinformatics 2015]]<br />
* Modules<br />
** [[Module 1: Is the hourglass model for gene expression really supported by the data?]]<br />
** [[Module 2: David's project]]<br />
** [[Module 3: Mauro's project]]<br />
** [[Module 4: Giovanni's project]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello (to be confirmed)]]<br />
* Students<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Course_idea_and_teaching_goals_of_Forensics_in_BioinformaticsCourse idea and teaching goals of Forensics in Bioinformatics2015-02-25T10:57:18Z<p>Sven: </p>
<hr />
<div>The general idea of the "Forensics in Bioinformatics" is to expose the students to published bioinformatics analyses that will be re-examined critically in a hands-on fashion. Specifically, we will consider four individual cases, corresponding to four teaching modules. The teacher of each module will introduce a paper and its context, and then guide the students to study in detail one or several of its bioinformatics analysis with the goal to reproduce their results. This will typically involve some programming, where the students can apply and develop their skills in using Python and/or R programming. <br />
<br />
The rationale of our “Forensics in Bioinformatics” as an integral part of the “mention Bioinformatics” in the life science Master is three fold:<br />
<br />
* It is quite common that Master or PhD projects build on existing work and it is usually a good start to critically examine some of the key results. This course will train students in how to validate bioinformatics analyses. <br />
<br />
* Focusing on published analyses provides a good focus, because usually the analysis pipelines are well described and the data are readily available.<br />
<br />
* On some occasions students might find minor or even major mistakes in published analyses. The bioinformatics community would profit from revealing such issues and we will motivate our students to think about how they can share their “question marks” (e.g. on this wiki). <br />
<br />
Through the individual modules the course aims to teach key concepts of bioinformatics, including:<br />
<br />
* data normalization<br />
* similarity measures<br />
* clustering<br />
* data (over-)fitting<br />
* cross validation<br />
<br />
Students will be asked to provide a written report for one of the modules, detailing their code and explaining their results. This grade will be based on this report.<br />
<br />
In summary this course puts emphasis on developing the analysis and programming skills of UNIL Master students and is a requirement for those studying towards a mention in bioinformatics. By dissecting (rather than reviewing) papers they will really understand how the analyses were done, preparing them for their own future projects.<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Course_idea_and_teaching_goals_of_Forensics_in_BioinformaticsCourse idea and teaching goals of Forensics in Bioinformatics2015-02-25T10:55:36Z<p>Sven: </p>
<hr />
<div>The general idea of the "Forensics in Bioinformatics" is to expose the students to published bioinformatics analyses that will be re-examined critically in a hands-on fashion. Specifically, we will consider four individual cases, corresponding to four teaching modules. The teacher of each module will introduce a paper and its context, and then guide the students to study in detail one or several of its bioinformatics analysis with the goal to reproduce their results. This will typically involve some programming, where the students can apply and develop their skills in using Python and/or R programming. <br />
<br />
The rationale of our “Forensics in Bioinformatics” as an integral part of the “mention Bioinformatics” in the life science Master is three fold:<br />
<br />
* It is quite common that Master or PhD projects build on existing work and it is usually a good start to critically examine some of the key results. This course will train students on how to validate bioinformatics analyses. <br />
<br />
* Focusing on published analyses provides a good focus, because usually the analysis pipelines are well described and the data are readily available.<br />
<br />
* On some occasions students might find minor or even major mistakes in published analyses. The bioinformatics community would profit from revealing such issues and we will motivate our students to think about how they can share their “question marks” (e.g. on this wiki). <br />
<br />
The course aims to teach also key concepts of bioinformatics, including:<br />
<br />
* data normalization<br />
* similarity measures<br />
* clustering<br />
* data (over-)fitting<br />
* cross validation<br />
<br />
Students will be asked to provide a written report for one of the modules, detailing their code and explaining their results. This grade will be based on this report.<br />
<br />
In summary this course puts emphasis on developing the analysis and programming skills of UNIL Master students and is a requirement for those studying towards a mention in bioinformatics. By dissecting (rather than reviewing) papers they will really understand how the analyses were done, preparing them for their own future projects.<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Course_idea_and_teaching_goals_of_Forensics_in_BioinformaticsCourse idea and teaching goals of Forensics in Bioinformatics2015-02-25T10:55:19Z<p>Sven: </p>
<hr />
<div>The general idea of the "Forensics in Bioinformatics" is to expose the students to published bioinformatics analyses that will be re-examined critically in a hands-on fashion. Specifically, we will consider four individual cases, corresponding to four teaching modules. The teacher of each module will introduce a paper and its context, and then guide the students to study in detail one or several of its bioinformatics analysis with the goal to reproduce their results. This will typically involve some programming, where the students can apply and develop their skills in using Python and/or R programming. <br />
<br />
The rationale of our “Forensics in Bioinformatics” an integral part of the “mention Bioinformatics” in the life science Master is three fold:<br />
<br />
* It is quite common that Master or PhD projects build on existing work and it is usually a good start to critically examine some of the key results. This course will train students on how to validate bioinformatics analyses. <br />
<br />
* Focusing on published analyses provides a good focus, because usually the analysis pipelines are well described and the data are readily available.<br />
<br />
* On some occasions students might find minor or even major mistakes in published analyses. The bioinformatics community would profit from revealing such issues and we will motivate our students to think about how they can share their “question marks” (e.g. on this wiki). <br />
<br />
The course aims to teach also key concepts of bioinformatics, including:<br />
<br />
* data normalization<br />
* similarity measures<br />
* clustering<br />
* data (over-)fitting<br />
* cross validation<br />
<br />
Students will be asked to provide a written report for one of the modules, detailing their code and explaining their results. This grade will be based on this report.<br />
<br />
In summary this course puts emphasis on developing the analysis and programming skills of UNIL Master students and is a requirement for those studying towards a mention in bioinformatics. By dissecting (rather than reviewing) papers they will really understand how the analyses were done, preparing them for their own future projects.<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Course_idea_and_teaching_goals_of_Forensics_in_BioinformaticsCourse idea and teaching goals of Forensics in Bioinformatics2015-02-25T10:54:14Z<p>Sven: </p>
<hr />
<div>The general idea of the "Forensics in Bioinformatics" is to expose the students to published bioinformatics analyses that will be re-examined critically in a hands-on fashion. Specifically, we will consider four individual cases, corresponding to four teaching modules. The teacher of each module will introduce a paper and its context, and then guide the students to study in detail one or several of its bioinformatics analysis with the goal to reproduce their results. This will typically involve some programming, where the students can apply their skills in using Python and/or R programming. <br />
<br />
The rationale of our “Forensics in Bioinformatics” an integral part of the “mention Bioinformatics” in the life science Master is three fold:<br />
<br />
* It is quite common that Master or PhD projects build on existing work and it is usually a good start to critically examine some of the key results. This course will train students on how to validate bioinformatics analyses. <br />
<br />
* Focusing on published analyses provides a good focus, because usually the analysis pipelines are well described and the data are readily available.<br />
<br />
* On some occasions students might find minor or even major mistakes in published analyses. The bioinformatics community would profit from revealing such issues and we will motivate our students to think about how they can share their “question marks” (e.g. on this wiki). <br />
<br />
The course aims to teach also key concepts of bioinformatics, including:<br />
<br />
* data normalization<br />
* similarity measures<br />
* clustering<br />
* data (over-)fitting<br />
* cross validation<br />
<br />
Students will be asked to provide a written report for one of the modules, detailing their code and explaining their results. This grade will be based on this report.<br />
<br />
In summary this course puts emphasis on developing the analysis and programming skills of UNIL Master students and is a requirement for those studying towards a mention in bioinformatics. By dissecting (rather than reviewing) papers they will really understand how the analyses were done, preparing them for their own future projects.<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Schedule_for_Forensics_in_Bioinformatics_2015Schedule for Forensics in Bioinformatics 20152015-02-25T10:48:26Z<p>Sven: </p>
<hr />
<div>* Module 1<br />
** Monday, 26 Oct 2015 13:00-16:00<br />
** Tuesday, 3 Nov 9:00-12:00 <br />
** Tuesday, 3 Nov 13:00-16:00<br />
<br />
* Module 2<br />
** Monday 9 Nov 2015, 9:00-12:00 <br />
** Tuesday 10 Nov 2015, 14:00-17:00<br />
** Monday 16 Nov 2015, 9:00-12:00 <br />
<br />
* Module 3<br />
** Monday 23 Nov 2015, 9:00-12:00 <br />
** Tuesday 24 Nov 2015 14:00-17:00<br />
** Monday 30 Nov 2015, 9:00-12:00 <br />
<br />
* Module 4<br />
** Monday 7 Dec 2015, 9:00-12:00 <br />
** Tuesday 8 Dec 2015 14:00-17:00<br />
** Monday 14 Dec 2015, 9:00-12:00 <br />
<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Schedule_for_Forensics_in_Bioinformatics_2015Schedule for Forensics in Bioinformatics 20152015-02-25T10:47:56Z<p>Sven: Created page with "* Module 1 ** Monday, 26 Oct 2015 13:00-16:00 ** Tuesday, 3 Nov 9:00-12:00 ** Tuesday, 3 Nov 13:00-16:00 * Module 2 ** Monday 9 Nov 2015, 9:00-12:00 ** Tuesday 10 Nov 2015..."</p>
<hr />
<div>* Module 1<br />
** Monday, 26 Oct 2015 13:00-16:00<br />
** Tuesday, 3 Nov 9:00-12:00 <br />
** Tuesday, 3 Nov 13:00-16:00<br />
<br />
* Module 2<br />
** Monday 9 Nov 2015, 9:00-12:00 <br />
** Tuesday 10 Nov 2015, 14:00-17:00<br />
** Monday 16 Nov 2015, 9:00-12:00 <br />
<br />
* Module 3<br />
** Monday 23 Nov 2015, 9:00-12:00 <br />
** Tuesday 24 Nov 2015 14:00-17:00<br />
** Monday 30 Nov 2015, 9:00-12:00 <br />
<br />
* Module 4<br />
** Monday 7 Dec 2015, 9:00-12:00 <br />
** Tuesday 8 Dec 2015 14:00-17:00<br />
** Monday 14 Dec 2015, 9:00-12:00 <br />
<br />
<br />
<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Course_idea_and_teaching_goals_of_Forensics_in_BioinformaticsCourse idea and teaching goals of Forensics in Bioinformatics2015-02-25T10:40:43Z<p>Sven: </p>
<hr />
<div>The general idea of the "Forensics in Bioinformatics" is to expose the students to published bioinformatics analyses that will be re-examined critically in a hands-on fashion. Specifically, we will consider four individual cases, corresponding to four teaching modules. The teacher of each module will introduce a paper and its context, and then guide the students to study in detail one or several of its bioinformatics analysis with the goal to reproduce their results. This will typically involve some programming, where the students can apply their skills in using Python and/or R programming. <br />
<br />
The rationale of our “Forensics in Bioinformatics” an integral part of the “mention Bioinformatics” in the life science Master is three fold:<br />
<br />
* It is quite common that Master or PhD projects build on existing work and it is usually a good start to critically examine some of the key results. This course will train students on how to validate bioinformatics analyses. <br />
<br />
* Focusing on published analyses provides a good focus, because usually the analysis pipelines are well described and the data are readily available.<br />
<br />
* On some occasions students might find minor or even major mistakes in published analyses. The bioinformatics community would profit from revealing such issues and we will motivate our students to think about how they can share their “question marks” (e.g. on this wiki). <br />
<br />
In summary this course puts emphasis on developing the analysis and programming skills of UNIL Master students and is a requirement for those studying towards a mention in bioinformatics. By dissecting (rather than reviewing) papers they will really understand how the analyses were done, preparing them for their own future projects.<br />
<br />
* back to [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Course_idea_and_teaching_goals_of_Forensics_in_BioinformaticsCourse idea and teaching goals of Forensics in Bioinformatics2015-02-25T10:38:42Z<p>Sven: </p>
<hr />
<div>The general idea of the "Forensics in Bioinformatics" is to expose the students to published bioinformatics analyses that will be re-examined critically in a hands-on fashion. Specifically, we will consider four individual cases, corresponding to four teaching modules. The teacher of each module will introduce a paper and its context, and then guide the students to study in detail one or several of its bioinformatics analysis with the goal to reproduce their results. This will typically involve some programming, where the students can apply their skills in using Python and/or R programming. <br />
<br />
The rationale of our “Forensics in Bioinformatics” an integral part of the “mention Bioinformatics” in the life science Master is three fold:<br />
<br />
* It is quite common that Master or PhD projects build on existing work and it is usually a good start to critically examine some of the key results. This course will train students on how to validate bioinformatics analyses. <br />
<br />
* Focusing on published analyses provides a good focus, because usually the analysis pipelines are well described and the data are readily available.<br />
<br />
* On some occasions students might find minor or even major mistakes in published analyses. The bioinformatics community would profit from revealing such issues and we will motivate our students to think about how they can share their “question marks” (e.g. on this wiki). <br />
<br />
In summary this course puts emphasis on developing the analysis and programming skills of UNIL Master students and is a requirement for those studying towards a mention in bioinformatics. By dissecting (rather than reviewing) papers they will really understand how the analyses were done, preparing them for their own future projects.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Course_idea_and_teaching_goals_of_Forensics_in_BioinformaticsCourse idea and teaching goals of Forensics in Bioinformatics2015-02-25T10:36:57Z<p>Sven: Created page with "The general idea of the "Forensics in Bioinformatics" is to expose the students to published bioinformatics analyses that will be re-examined critically in a hand-on fashion. ..."</p>
<hr />
<div>The general idea of the "Forensics in Bioinformatics" is to expose the students to published bioinformatics analyses that will be re-examined critically in a hand-on fashion. Specifically, we will consider four individual cases, corresponding to four teaching modules. The teacher of each module will introduce a paper and its context, and then guide the students to study in detail one or several of its bioinformatics analysis with the goal to reproduce their results. This will typically involve some programming, where the students can apply their skills in using Python and/or R programming. <br />
<br />
The rationale of our “Forensics in Bioinformatics” an integral part of the “mention Bioinformatics” in the life science Master is three fold:<br />
<br />
* It is quite common that Master or PhD projects build on existing work and it is usually a good start to critically examine some of the key results. This course will train students on how to validate bioinformatics analyses. <br />
<br />
* Focusing on published analyses provides a good focus because usually the analysis pipelines are well described and the data are readily available.<br />
<br />
* On some occasions students might find minor or even major mistakes in published analyses. The bioinformatics community would profit from revealing such issues and we will motivate our students to think about how they can share their “question marks” (e.g. on this wiki). <br />
<br />
In summary this course puts emphasis on developing the analysis and programming skills of UNIL Master students and is a requirement for those studying towards a mention in bioinformatics. By dissecting (rather than reviewing) papers they will really understand how the analyses were done, preparing them for their own future projects.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-02-25T10:12:01Z<p>Sven: </p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals of Forensics in Bioinformatics]]<br />
* [[Schedule for Forensics in Bioinformatics 2015]]<br />
* Modules<br />
** [[Is the hourglass model for gene expression really supported by the data?]]<br />
** [[David's project]]<br />
** [[Mauro's project]]<br />
** [[Ana or Giovanni's project]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello (to be confirmed)]]<br />
* Students<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-02-25T10:11:25Z<p>Sven: </p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals]]<br />
* [[Schedule for Forensics in Bioinformatics 2015]]<br />
* Modules<br />
** [[Is the hourglass model for gene expression really supported by the data?]]<br />
** [[David's project]]<br />
** [[Mauro's project]]<br />
** [[Ana or Giovanni's project]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello (to be confirmed)]]<br />
* Students<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-02-25T10:10:43Z<p>Sven: </p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals]]<br />
* [[Forensics schedule 2015]]<br />
* Modules<br />
** [[Is the hourglass model for gene expression really supported by the data?]]<br />
** [[David's project]]<br />
** [[Mauro's project]]<br />
** [[Ana or Giovanni's project]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello (to be confirmed)]]<br />
* Students<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-02-25T10:08:18Z<p>Sven: </p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals]]<br />
* [[Dates & Deadlines 2015]]<br />
* Modules<br />
** [[Is the hourglass model for gene expression really supported by the data?]]<br />
** [[David's project]]<br />
** [[Mauro's project]]<br />
** [[Ana or Giovanni's project]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello (to be confirmed)]]<br />
* Students<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_%22Forensics_in_Bioinformatics_2015%22UNIL MSc course: "Forensics in Bioinformatics 2015"2015-02-25T10:07:13Z<p>Sven: Created page with "* Coordinator: Sven Bergmann * Course idea and teaching goals * Dates & Deadlines 2015 * Modules ** [[Is the hourglass model for gene expression really supported b..."</p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Course idea and teaching goals]]<br />
* [[Dates & Deadlines 2015]]<br />
* Modules<br />
** [[Is the hourglass model for gene expression really supported by the data?]]<br />
** [[David's project]]<br />
** [[Mauro's project]]<br />
** [[Ana or Giovanni's project]]<br />
* Teachers<br />
** [[User:Sven|Sven Bergmann]]<br />
** [[User:David|David Gfeller]]<br />
** [[User:Mauro|Mauro Delorenzi]]<br />
** [[User: Giovanni|Giovanni Ciriello (to be confirmed)]]<br />
<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=TeachingTeaching2015-02-25T09:59:22Z<p>Sven: </p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2015 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2015"]]<br />
* [[UNIL MSc course: "Forensics in Bioinformatics 2015"]]<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
* [[EPFL doctoral course: "Functional Genomics 2012"]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2011"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design 2010"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2010"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design 2009"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Metabolomics%E2%80%94_Linking_Genotype_and_PhenotypeMetabolomics— Linking Genotype and Phenotype2015-02-20T07:46:00Z<p>Sven: </p>
<hr />
<div>'''Background''': It has been well established that genetic variants strongly affect diseases and other heritable traits. In a basic Genome-Wide Association Study (GWAS), individuals are genotyped with a dense SNP array to identify their genotypes across common genetic variations. Eventually GWAS aims to explore these genetic variations that can have a role in diseases or quantitative traits that are risk factors for the diseases.<br />
<br />
'''Goal''': Students will learn the key concepts of the design and analysis of GWAS for common diseases and complex traits. With the help of statistical tools they will observe the links between Genotype - Metabotype - Phenotype and relate their findings with the published research.<br />
<br />
'''Mathematical tools''': Students will use Matlab to do the association analysis with main emphasis on linear regression. Various visual data representation techniques like correlation plots, qq-plots and Manhattan plots will also be studied.<br />
<br />
'''Biological or Medical aspects''': The students will get insight of this new groundbreaking discipline to explore the relationship between sequence variations and disease susceptibility.<br />
<br />
'''Supervisor''': [[User:Reyhan|Reyhan Sonmez Flitman]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_%22Solving_Biological_Problems_that_require_Math_2015%22UNIL BSc course: "Solving Biological Problems that require Math 2015"2015-01-21T22:01:00Z<p>Sven: </p>
<hr />
<div>* Coordinators: [[Sven Bergmann]] and [[User:Micha|Micha Hersch]]<br />
* [[Concept]]<br />
* [[Useful tools]]<br />
* [[Dates & Deadlines 2015]]<br />
* Projects<br />
** to be announced (please enter your project here)<br />
* Supervisors<br />
** [[User:Micha|Micha Hersch]]<br />
** [[User:Tanguy|Tanguy Corre]]<br />
** [[User:Daniel|Daniel Marbach]]<br />
** [[User:Rico|Rico Rueedi]]<br />
** [[User:David|David Lamparter]]<br />
** [[User:Reyhan|Reyhan Sönmez]]<br />
** [[User: Ana|Ana Claudia Machado Rebelo Marques (to be confirmed)]]<br />
** [[User: Giovanni|Giovanni Ciriello (to be confirmed)]]<br />
<br />
* see also [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_%22Solving_Biological_Problems_that_require_Math_2015%22UNIL BSc course: "Solving Biological Problems that require Math 2015"2015-01-21T21:59:36Z<p>Sven: </p>
<hr />
<div>* Coordinators: [[Sven Bergmann]] and [[User:Micha|Micha Hersch]]<br />
* [[Concept]]<br />
* [[Useful tools]]<br />
* [[Dates & Deadlines 2015]]<br />
* Projects<br />
** to be announced (please enter your project here)<br />
* Supervisors<br />
** [[User:Micha|Micha Hersch]]<br />
** [[User:Tanguy|Tanguy Corre]]<br />
** [[User:Daniel|Daniel Marbach]]<br />
** [[User:Rico|Rico Rueedi]]<br />
** [[User:David|David Lamparter]]<br />
** [[User:Reyhan|Reyhan Sönmez]]<br />
** [[User: Ana|Ana Claudia Machado Rebelo Marques]]<br />
<br />
* see also [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_%22Solving_Biological_Problems_that_require_Math%22UNIL BSc course: "Solving Biological Problems that require Math"2015-01-21T21:59:14Z<p>Sven: Redirected page to UNIL BSc course: "Solving Biological Problems that require Math 2015"</p>
<hr />
<div>#REDIRECT [[UNIL BSc course: "Solving Biological Problems that require Math 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=PeoplePeople2015-01-21T21:58:35Z<p>Sven: </p>
<hr />
<div>[[Category:Homepage]]<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
!Name<br />
!Telephone<br />
!Current Projects<br />
!Present<br />
|-<br />
|'''[[User:Sven|Sven Bergmann]]''' (Principal Investigator) <br />
|54 52<br />
| Computational analyses of biological systems <br />
|04/05-<br />
<br />
|-<br />
|'''[[User:Micha|Micha Hersch]]''' (Postdoc)<br />
|52 46<br />
|Plant Growth in a Changing Environment<br />
|10/08-<br />
|-<br />
|'''[[User:Rico|Rico Rueedi]]''' (Postdoc)<br />
|54 02<br />
|Metabolomics<br />
|05/10-<br />
|-<br />
|'''[[User:Andrea|Andrea Prunotto]]''' (Postdoc)<br />
|53 91<br />
|Analysis of large-scale biomedical data<br />
|04/11-<br />
|-<br />
|'''[[User:Tanguy|Tanguy Corre]]''' (Postdoc)<br />
|54 02<br />
|Genome-wide Association Analyses<br />
|05/11-<br />
|-<br />
|'''[[User:David|David Lamparter]]''' (PhD student)<br />
|53 79<br />
|Data integration for Genome-wide Association Analyses<br />
|05/11-<br />
|-<br />
|'''[[User:Daniel|Daniel Marbach]]''' (Postdoc)<br />
|53 78<br />
|Network-based interpretation of genetic variants<br />
|08/13-<br />
|-<br />
|'''[[User:Charlotte|Charlotte Hor]]''' (Visiting postdoc)<br />
|53 78<br />
|<br />
|05/14-<br />
|-<br />
|'''[[User:Reyhan|Reyhan Sönmez]]''' (PhD student)<br />
|54 56<br />
|Gene expression using RNA-Seq data<br />
|08/14-<br />
|}<br />
<br />
<br />
from outside dial +41 (0) 21 692 [extension]<br><br />
e-mail addresses: [first name].[last name without spaces]@unil.ch<br />
<br />
== Former Group Members ==<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
!Name<br />
!Projects<br />
!Present<br />
|-<br />
|'''[[User:Sascha.Dalessi|Sascha Dalessi]]''' (Postdoc)<br />
|Modeling of patterning processes in Drosophila development<br />
|01/09-12/13<br />
|-<br />
|'''Tania Ngo''' (intern)<br />
|Trhr and blood pressure drug response in mice<br />
|08/13-11/13<br />
|-<br />
|'''[[User:Tim|Tim Hohm]]''' (Postdoc)<br />
|Modeling gene regulative networks responsible for light-responses in plants<br />
|01/10-06/13<br />
|-<br />
|'''[[User:Nadya|Nadya Monina]]''' (Postdoc)<br />
|Laboratory evolution of E coli and Staphylococcus aureus<br />
|04/11-06/13<br />
|-<br />
|'''[[User:Diana|Diana Marek]]''' (Postdoc) <br />
|Pharmacogenetics study of Swiss HIV cohort data<br />
Analysis of large-scale clinical and genetic data <br />
|10/05-03/13<br />
|-<br />
|'''[[User:Barbara|Barbara Piasecka]]''' (Candoc, joint with Prof. Marc Robinson-Rechavi)<br />
|Comparative modular analysis of gene expression in vertebrate development<br />
|10/08-03/13<br />
|-<br />
|'''[[User:Aitana|Aitana Morton de Lachapelle]]''' (Candoc) <br />
|Modeling of patterning processes in Drosophila development<br />
|02/07-9/11<br />
|-<br />
|'''[[User:Bastian|Bastian Peter]]''' (Postdoc) <br />
<br />
|Modular analysis of clinical microarray data <br />
|03/06-03/11<br />
|-<br />
|'''[[User:Gabor|Gábor Csárdi]]''' (Postdoc)<br />
|Analysis of EuroDia data<br />
|01/08-03/11<br />
|-<br />
|'''[http://www3.unil.ch/wpmu/sgg/zoltan/ Zoltán Kutalik]''' (Postdoc) <br />
|Genome-wide association studies <br />
|05/06-2/11<br />
|-<br />
|'''[[User:Armand|Armand Valsesia]]''' (Candoc, joint with Prof. Victor Jongeneel)<br />
|CNV analysis<br />
|07/07-02/11<br />
|-<br />
|'''[[User:Karen|Karen Kapur]]''' (Postdoc)<br />
|Integrative Analysis of Genetic Interactions<br />
|10/08-02/11<br />
|-<br />
|'''[[User:Andreas|Andreas Lüscher]]''' (Postdoc/Programmer)<br />
|Development of module visualization and analysis tools<br />
|09/09-12/09<br />
|-<br />
|'''[[User:Toby|Toby Johnson]]''' (Postdoc, joint with Prof. Murielle Bochud) <br />
|Analysis of CoLaus data <br />
|05/07-04/09<br />
|-<br />
|'''Alain Sewer''' (Postdoc) <br />
|Human microRNA analysis using microarray data <br />
|07/06-12/08<br />
|-<br />
|}</div>Svenhttp://www2.unil.ch/cbg/index.php?title=PeoplePeople2015-01-21T21:58:04Z<p>Sven: </p>
<hr />
<div>[[Category:Homepage]]<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
!Name<br />
!Telephone<br />
!Current Projects<br />
!Present<br />
|-<br />
|'''[[User:Sven|Sven Bergmann]]''' (Principal Investigator) <br />
|54 52<br />
| Computational analyses of biological systems <br />
|04/05-<br />
<br />
|-<br />
|'''[[User:Micha|Micha Hersch]]''' (Postdoc)<br />
|52 46<br />
|Plant Growth in a Changing Environment<br />
|10/08-<br />
|-<br />
|'''[[User:Rico|Rico Rueedi]]''' (Postdoc)<br />
|54 02<br />
|Metabolomics<br />
|05/10-<br />
|-<br />
|'''[[User:Andrea|Andrea Prunotto]]''' (Postdoc)<br />
|53 91<br />
|Analysis of large-scale biomedical data<br />
|04/11-<br />
|-<br />
|'''[[User:Tanguy|Tanguy Corre]]''' (Postdoc)<br />
|54 02<br />
|Genome-wide Association Analyses<br />
|05/11-<br />
|-<br />
|'''[[User:David|David Lamparter]]''' (PhD student)<br />
|53 79<br />
|Data integration for Genome-wide Association Analyses<br />
|05/11-<br />
|-<br />
|'''[[User:Daniel|Daniel Marbach]]''' (Postdoc)<br />
|53 78<br />
|Network-based interpretation of genetic variants<br />
|08/13-<br />
|-<br />
|'''[[User:Charlotte|Charlotte Hor]]''' (Visiting postdoc)<br />
|53 78<br />
|<br />
|05/14-<br />
|-<br />
|'''[[User:Reyhan|Rehan Sönmez]]''' (PhD student)<br />
|54 56<br />
|Gene expression using RNA-Seq data<br />
|08/14-<br />
|}<br />
<br />
<br />
from outside dial +41 (0) 21 692 [extension]<br><br />
e-mail addresses: [first name].[last name without spaces]@unil.ch<br />
<br />
== Former Group Members ==<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
!Name<br />
!Projects<br />
!Present<br />
|-<br />
|'''[[User:Sascha.Dalessi|Sascha Dalessi]]''' (Postdoc)<br />
|Modeling of patterning processes in Drosophila development<br />
|01/09-12/13<br />
|-<br />
|'''Tania Ngo''' (intern)<br />
|Trhr and blood pressure drug response in mice<br />
|08/13-11/13<br />
|-<br />
|'''[[User:Tim|Tim Hohm]]''' (Postdoc)<br />
|Modeling gene regulative networks responsible for light-responses in plants<br />
|01/10-06/13<br />
|-<br />
|'''[[User:Nadya|Nadya Monina]]''' (Postdoc)<br />
|Laboratory evolution of E coli and Staphylococcus aureus<br />
|04/11-06/13<br />
|-<br />
|'''[[User:Diana|Diana Marek]]''' (Postdoc) <br />
|Pharmacogenetics study of Swiss HIV cohort data<br />
Analysis of large-scale clinical and genetic data <br />
|10/05-03/13<br />
|-<br />
|'''[[User:Barbara|Barbara Piasecka]]''' (Candoc, joint with Prof. Marc Robinson-Rechavi)<br />
|Comparative modular analysis of gene expression in vertebrate development<br />
|10/08-03/13<br />
|-<br />
|'''[[User:Aitana|Aitana Morton de Lachapelle]]''' (Candoc) <br />
|Modeling of patterning processes in Drosophila development<br />
|02/07-9/11<br />
|-<br />
|'''[[User:Bastian|Bastian Peter]]''' (Postdoc) <br />
<br />
|Modular analysis of clinical microarray data <br />
|03/06-03/11<br />
|-<br />
|'''[[User:Gabor|Gábor Csárdi]]''' (Postdoc)<br />
|Analysis of EuroDia data<br />
|01/08-03/11<br />
|-<br />
|'''[http://www3.unil.ch/wpmu/sgg/zoltan/ Zoltán Kutalik]''' (Postdoc) <br />
|Genome-wide association studies <br />
|05/06-2/11<br />
|-<br />
|'''[[User:Armand|Armand Valsesia]]''' (Candoc, joint with Prof. Victor Jongeneel)<br />
|CNV analysis<br />
|07/07-02/11<br />
|-<br />
|'''[[User:Karen|Karen Kapur]]''' (Postdoc)<br />
|Integrative Analysis of Genetic Interactions<br />
|10/08-02/11<br />
|-<br />
|'''[[User:Andreas|Andreas Lüscher]]''' (Postdoc/Programmer)<br />
|Development of module visualization and analysis tools<br />
|09/09-12/09<br />
|-<br />
|'''[[User:Toby|Toby Johnson]]''' (Postdoc, joint with Prof. Murielle Bochud) <br />
|Analysis of CoLaus data <br />
|05/07-04/09<br />
|-<br />
|'''Alain Sewer''' (Postdoc) <br />
|Human microRNA analysis using microarray data <br />
|07/06-12/08<br />
|-<br />
|}</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Dates_%26_Deadlines_2015Dates & Deadlines 20152015-01-21T21:56:27Z<p>Sven: Created page with "* '''First ''kick-off'' meeting''': Friday, 20. February 2015 at 9:00 (Bugnon 27, room to be announced) ** The concept of the course will be explained (~15 min, [[User:Micha|M..."</p>
<hr />
<div>* '''First ''kick-off'' meeting''': Friday, 20. February 2015 at 9:00 (Bugnon 27, room to be announced)<br />
** The concept of the course will be explained (~15 min, [[User:Micha|Micha Hersch]])<br />
** The projects will be briefly presented by the respective supervisors (~10 min for each supervisor)<br />
** The course wiki will be explained (~15 min, [[User:Micha|Micha Hersch]])<br />
<br />
* Students need <br />
** to '''confirm their participation''' in this course by: Tuesday, 24. February 2015 (midnight),<br />
** to '''form study groups''' of 3 students and <br />
** to announce by e-mail the '''three projects they are most interested in working on'''<br />
<br />
* Projects will be assigned no later than: Thursday, 26. February 2015<br />
<br />
* The first session with the supervisors will arranged per e-mail<br />
<br />
* ''free working & weekly meetings with supervisors'': until the intermediate meeting<br />
<br />
* '''[[Intermediate report meeting 2015]]''': Friday 17 April 2015 at 9:00<br />
* Students will present their projects highlighting<br />
** the goals they want to achieve<br />
** the analysis tools they will use<br />
** potential challenges <br />
** preliminary results (if any) <br />
<br />
* ''free working & weekly meetings with supervisors'': until end of May 2015<br />
<br />
* '''[[Final report meeting 2015]]''': Wednesday 27 May 2015 or Friday 29 May 2015 at 9:00<br />
** Each study group presents their results (Presentations should take no longer than 15 minutes and are the basis for the student evaluation)<br />
** Feedback on the course in general<br />
<br />
(Meetings will be arranged freely between students and supervisors.)<br />
<br />
* back to [[UNIL BSc course: "Solving Biological Problems that require Math 2015"]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_%22Solving_Biological_Problems_that_require_Math_2015%22UNIL BSc course: "Solving Biological Problems that require Math 2015"2015-01-21T21:50:36Z<p>Sven: Created page with "* Coordinators: Sven Bergmann and Micha Hersch * Concept * Useful tools * Dates & Deadlines 2015 * Projects ** to be announced (please enter you..."</p>
<hr />
<div>* Coordinators: [[Sven Bergmann]] and [[User:Micha|Micha Hersch]]<br />
* [[Concept]]<br />
* [[Useful tools]]<br />
* [[Dates & Deadlines 2015]]<br />
* Projects<br />
** to be announced (please enter your project here)<br />
* Supervisors<br />
** [[User:Micha|Micha Hersch]]<br />
** [[User:Tanguy|Tanguy Corre]]<br />
** [[User:Daniel|Daniel Marbach]]<br />
** [[User:Rico|Rico Rueedi]]<br />
** [[User:David|David Lamparter]]<br />
** [[User:Reyhan|Reyhan Sonmez]]<br />
** [[User: Ana|Ana Claudia Machado Rebelo Marques]]<br />
<br />
* see also [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=TeachingTeaching2015-01-21T21:44:47Z<p>Sven: </p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2015 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2015"]]<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
* [[EPFL doctoral course: "Functional Genomics 2012"]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2011"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design 2010"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2010"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design 2009"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=TeachingTeaching2014-11-11T16:54:29Z<p>Sven: /* 2012 */</p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
* [[EPFL doctoral course: "Functional Genomics 2012"]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2011"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design 2010"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2010"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design 2009"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=EPFL_doctoral_course:_%22Functional_Genomics_2012%22EPFL doctoral course: "Functional Genomics 2012"2014-11-11T16:53:52Z<p>Sven: Created page with "'''Organizer''': Prof. Bart Deplancke '''Venue''': EPFL, AI1153 '''Time''': 3/2/12 - 13-16:00 '''My contribution''': Lecture on Genome Wide Association Studies (GWAS)"</p>
<hr />
<div>'''Organizer''': Prof. Bart Deplancke<br />
<br />
'''Venue''': EPFL, AI1153<br />
<br />
'''Time''': 3/2/12 - 13-16:00<br />
<br />
'''My contribution''': Lecture on [[Genome Wide Association Studies]] (GWAS)</div>Svenhttp://www2.unil.ch/cbg/index.php?title=EPFL_doctoral_course:_%22Functional_Genomics_2011%22EPFL doctoral course: "Functional Genomics 2011"2014-11-11T16:51:37Z<p>Sven: </p>
<hr />
<div>'''Organizer''': Prof. Bart Deplancke<br />
<br />
'''Venue''': EPFL, AI1153<br />
<br />
'''Time''': 4/2/11 - 13-16:00<br />
<br />
'''My contribution''': Lecture on [[Genome Wide Association Studies]] (GWAS)</div>Svenhttp://www2.unil.ch/cbg/index.php?title=EPFL_doctoral_course:_%22Functional_Genomics_2009%22EPFL doctoral course: "Functional Genomics 2009"2014-11-11T16:51:16Z<p>Sven: </p>
<hr />
<div>'''Organizer''': Prof. Bart Deplancke<br />
<br />
'''Venue''': EPFL, AI1153<br />
<br />
'''Time''': 5/3/09 - 13:00-16:00<br />
<br />
'''My contribution''': Lecture on [[Genome Wide Association Studies]] (GWAS)</div>Svenhttp://www2.unil.ch/cbg/index.php?title=EPFL_doctoral_course:_%22Functional_Genomics_2009%22EPFL doctoral course: "Functional Genomics 2009"2014-11-11T16:50:55Z<p>Sven: Created page with "'''Organizer''': Prof. Bart Deplancke '''Venue''': EPFL, AI1153 '''Time''': 5/3/10 - 13:00-16:00 '''My contribution''': Lecture on Genome Wide Association Studies (GWAS)"</p>
<hr />
<div>'''Organizer''': Prof. Bart Deplancke<br />
<br />
'''Venue''': EPFL, AI1153<br />
<br />
'''Time''': 5/3/10 - 13:00-16:00<br />
<br />
'''My contribution''': Lecture on [[Genome Wide Association Studies]] (GWAS)</div>Svenhttp://www2.unil.ch/cbg/index.php?title=TeachingTeaching2014-11-11T16:49:52Z<p>Sven: /* 2009 */</p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2011"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design 2010"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2010"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design 2009"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=EPFL_doctoral_course:_%22Functional_Genomics_2010%22EPFL doctoral course: "Functional Genomics 2010"2014-11-11T16:48:52Z<p>Sven: Created page with "'''Organizer''': Prof. Bart Deplancke '''Venue''': EPFL, AI1153 '''Time''': 26/2/10 - 13:00-16:00 '''My contribution''': Lecture on Genome Wide Association Studies (GWAS)"</p>
<hr />
<div>'''Organizer''': Prof. Bart Deplancke<br />
<br />
'''Venue''': EPFL, AI1153<br />
<br />
'''Time''': 26/2/10 - 13:00-16:00<br />
<br />
'''My contribution''': Lecture on [[Genome Wide Association Studies]] (GWAS)</div>Svenhttp://www2.unil.ch/cbg/index.php?title=EPFL_doctoral_course:_%22Functional_Genomics_2011%22EPFL doctoral course: "Functional Genomics 2011"2014-11-11T16:46:11Z<p>Sven: Created page with "'''Organizer''': Prof. Bart Deplancke '''Venue''': EPFL, AI1153 '''Time''': 4/2/11 - 13-16:00 '''My contribution''': Lecture on Genome Wide Association Studies (GWAS) ..."</p>
<hr />
<div>'''Organizer''': Prof. Bart Deplancke<br />
<br />
'''Venue''': EPFL, AI1153<br />
<br />
'''Time''': 4/2/11 - 13-16:00<br />
<br />
'''My contribution''': Lecture on [[Genome Wide Association Studies]] (GWAS) <br />
<br />
(see also [[EPFL doctoral course: "Functional Genomics 2010"]])</div>Svenhttp://www2.unil.ch/cbg/index.php?title=TeachingTeaching2014-11-11T16:43:00Z<p>Sven: /* 2011 */</p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2011"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design 2010"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2010"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design 2009"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=TeachingTeaching2014-11-11T16:41:55Z<p>Sven: /* 2010 */</p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design 2010"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2010"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design 2009"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=TeachingTeaching2014-11-11T16:41:27Z<p>Sven: /* 2009 */</p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design 2009"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=TeachingTeaching2014-11-11T16:40:22Z<p>Sven: /* 2011 */</p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Sven