http://www2.unil.ch/cbg/api.php?action=feedcontributions&user=Aurelien&feedformat=atomCBG - User contributions [en]2024-03-29T02:33:57ZUser contributionsMediaWiki 1.31.12http://www2.unil.ch/cbg/index.php?title=Journal_Club_(spring_2014)&diff=3916Journal Club (spring 2014)2014-04-16T17:02:26Z<p>Aurelien: </p>
<hr />
<div>The Journal Club is every other Thursday, from 12-13, in the Vulcano room. Feel free to bring your lunch.<br />
<br />
The schedule is indicated below. If it is your turn, please indicate the paper you are presenting by Monday and update the calendar accordingly. It can be any paper of scientific interest. Alternatively, you can also give tutorials on any scientific topic that may be of interest to other members of the group, organize a discussion on a scientific topic or invite an external speaker. Examples of past topics are given in the previous [[Journal Club (spring 2013)]]<br />
== January 9 ==<br />
David will talk about the nanopore sequencing technology<br />
<br />
== January 23 ==<br />
Micha has invited Gene Bunin for a discussion about his views on the current state of academia<br />
http://crypto.junod.info/2013/09/09/an-aspiring-scientists-frustration-with-modern-day-academia-a-resignation/<br />
<br />
== February 6 ==<br />
Sina on [http://www.ncbi.nlm.nih.gov/pubmed/23541341 The benefits of using genetic information to design prevention trials]<br />
<br />
== March 6 ==<br />
Rico on the new servers<br />
<br />
== March 13 ==<br />
Tanguy on the human population admixture history. http://www.sciencemag.org/content/343/6172/747.full<br />
<br />
== March 20 ==<br />
canceled<br />
<br />
== April 10 ==<br />
Aurélien on modeling 3D facial shape from DNA: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004224#pgen.1004224.s049<br />
<br />
== April 17 ==<br />
Rico<br />
== May 1 ==<br />
Daniel<br />
<br />
== May 15 ==<br />
Sina<br />
== May 29 ==<br />
David<br />
<br />
== June 12 ==<br />
Andrea<br />
== June 26 ==<br />
Micha<br />
== July 10 ==<br />
Daniel</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Journal_Club_(spring_2013)&diff=3614Journal Club (spring 2013)2013-05-02T12:07:03Z<p>Aurelien: </p>
<hr />
<div>The Journal Club is every other Thursday, from 12-13, in the small meeting room 219. Feel free to bring your lunch.<br />
<br />
The schedule is indicated below. If it is your turn, please indicate the paper you are presenting by Monday and update the calendar accordingly. It can be any paper of scientific interest. Alternatively, you can also give '''tutorials on any scientific topic''' that may be of interest to other members of the group or invite an external speaker.<br />
<br />
== January 24 ==<br />
Barbara will speak about "Google Effects on Memory: Cognitive Consequences of Having Information at Our Fingertips".<br />
<br />
http://www.sciencemag.org/content/333/6043/776.abstract<br />
<br />
== February 7 ==<br />
Canceled, there is a Seminar from B. Wollnik instead<br />
<br />
== February 21 ==<br />
Tim on the effect of synonymous snps<br />
<br />
== March 7 ==<br />
Micha will talk about Hans Jonas's book: The Phenomenon of Life<br />
<br />
==March 21 ==<br />
Andrea will discuss about a proposal for an Evolutionary Biology Experiment<br />
<br />
== April 4 ==<br />
Canceled<br />
<br />
== April 17 10 am (instead of April 18) ==<br />
Guest speaker Eyal Privman:<br />
Adaptive role of concerted evolution in the ant’s sex determination locus<br />
<br />
==May 2 ==<br />
Aurélien will talk about species' de-extinction:<br />
What If Extinction Is Not Forever, Jacob S. Sherkow and Henry T. Greely, Science, 2013<br />
http://www.sciencemag.org/content/340/6128/32.full.pdf<br />
<br />
== May 16 ==<br />
Sascha<br />
<br />
== May 30 ==<br />
Rico<br />
<br />
== June 13 ==<br />
David<br />
<br />
== June 27 ==<br />
Zoltan<br />
<br />
== July 11 ==<br />
Tanguy</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Journal_Club_(spring_2013)&diff=3613Journal Club (spring 2013)2013-05-02T12:06:16Z<p>Aurelien: </p>
<hr />
<div>The Journal Club is every other Thursday, from 12-13, in the small meeting room 219. Feel free to bring your lunch.<br />
<br />
The schedule is indicated below. If it is your turn, please indicate the paper you are presenting by Monday and update the calendar accordingly. It can be any paper of scientific interest. Alternatively, you can also give '''tutorials on any scientific topic''' that may be of interest to other members of the group or invite an external speaker.<br />
<br />
== January 24 ==<br />
Barbara will speak about "Google Effects on Memory: Cognitive Consequences of Having Information at Our Fingertips".<br />
<br />
http://www.sciencemag.org/content/333/6043/776.abstract<br />
<br />
== February 7 ==<br />
Canceled, there is a Seminar from B. Wollnik instead<br />
<br />
== February 21 ==<br />
Tim on the effect of synonymous snps<br />
<br />
== March 7 ==<br />
Micha will talk about Hans Jonas's book: The Phenomenon of Life<br />
<br />
==March 21 ==<br />
Andrea will discuss about a proposal for an Evolutionary Biology Experiment<br />
<br />
== April 4 ==<br />
Canceled<br />
<br />
== April 17 10 am (instead of April 18) ==<br />
Guest speaker Eyal Privman:<br />
Adaptive role of concerted evolution in the ant’s sex determination locus<br />
<br />
==May 2 ==<br />
Aurélien will talk about species' de-extinction<br />
What If Extinction Is Not Forever, Jacob S. Sherkow and Henry T. Greely, Science, 2013<br />
http://www.sciencemag.org/content/340/6128/32.full.pdf<br />
<br />
== May 16 ==<br />
Sascha<br />
<br />
== May 30 ==<br />
Rico<br />
<br />
== June 13 ==<br />
David<br />
<br />
== June 27 ==<br />
Zoltan<br />
<br />
== July 11 ==<br />
Tanguy</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Pathway_enrichment_in_DNAse1_footprinting_data&diff=3585Pathway enrichment in DNAse1 footprinting data2013-02-21T17:01:38Z<p>Aurelien: </p>
<hr />
<div>'''Background''': Unraveling the transcriptional network in human cells is of great interest in genetics. A new publicly available data source with genome wide coverage released by the ENCODE Project has the potential to really advance our understanding of transcription regulations<br />
<br />
'''Goal''': Using these data sources, we will try to rediscover well known functional knowledge about transcription factors by just using this data set. If this is successful, we will expand our analysis to make novel predictions about functional involvment of transcription factors.<br />
<br />
'''Mathematical tools''': Statistics. The students will learn about enrichment analysis and make contact with bias and variance issues in a practical setting. The students will learn about and perform large scale data analysis. Care is taken, that handling of the data is as simple as possible.<br />
<br />
'''Biological or Medical aspects''': <br />
<br />
'''Supervisors''': [[User:Aurelien | Aurelien Mace]] & [[User:David|David Lamparter]] <br />
<br />
'''Students''':<br />
<br />
'''Presentation''':[[Media:PresentationForStudents21_2_13.pdf]]<br />
<br />
Back to [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Pathway_enrichment_in_DNAse1_footprinting_data&diff=3584Pathway enrichment in DNAse1 footprinting data2013-02-21T17:01:11Z<p>Aurelien: </p>
<hr />
<div>'''Background''': Unraveling the transcriptional network in human cells is of great interest in genetics. A new publicly available data source with genome wide coverage released by the ENCODE Project has the potential to really advance our understanding of transcription regulations<br />
<br />
'''Goal''': Using these data sources, we will try to rediscover well known functional knowledge about transcription factors by just using this data set. If this is successful, we will expand our analysis to make novel predictions about functional involvment of transcription factors.<br />
<br />
'''Mathematical tools''': Statistics. The students will learn about enrichment analysis and make contact with bias and variance issues in a practical setting. The students will learn about and perform large scale data analysis. Care is taken, that handling of the data is as simple as possible.<br />
<br />
'''Biological or Medical aspects''': <br />
<br />
'''Supervisors''': [[User:Aurelien | Aurelien Mace]] & [[User:David|David Lamparter]] <br />
<br />
'''Students''':<br />
<br />
'''Presentation''':[[Media:PresentationForStudents21_2_13.pdf]]<br />
see [[Genome Wide Association Studies]], [[Media: McCarthy_review_GWAS.pdf ]], [[GIANT_height | GWAS papers]]<br />
<br />
Back to [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Pathway_enrichment_in_DNAse1_footprinting_data&diff=3583Pathway enrichment in DNAse1 footprinting data2013-02-21T16:59:33Z<p>Aurelien: </p>
<hr />
<div>'''Background''': Unraveling the transcriptional network in human cells is of great interest in genetics. A new publicly available data sources with genome wide coverage released by the ENCODE Project have the potential to really advance our understanding of transcription regulations<br />
<br />
'''Goal''': Using these data sources, we will try to rediscover well known functional knowledge about transcription factors by just using this data set. If this is successful, we will expand our analysis to make novel predictions about functional involvment of transcription factors.<br />
<br />
'''Mathematical tools''': Statistics. The students will learn about enrichment analysis and make contact with bias and variance issues in a practical setting. The students will learn about and perform large scale data analysis. Care is taken, that handling of the data is as simple as possible.<br />
<br />
'''Biological or Medical aspects''': <br />
<br />
'''Supervisors''': [[User:Aurelien | Aurelien Mace]] & [[User:David|David Lamparter]] <br />
<br />
'''Students''':<br />
<br />
'''Presentation''':[[Media:PresentationForStudents21_2_13.pdf]]<br />
see [[Genome Wide Association Studies]], [[Media: McCarthy_review_GWAS.pdf ]], [[GIANT_height | GWAS papers]]<br />
<br />
Back to [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=File:PresentationForStudents21_2_13.pdf&diff=3582File:PresentationForStudents21 2 13.pdf2013-02-21T16:58:29Z<p>Aurelien: </p>
<hr />
<div></div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Pathway_enrichment_in_DNAse1_footprinting_data&diff=3581Pathway enrichment in DNAse1 footprinting data2013-02-21T15:46:29Z<p>Aurelien: </p>
<hr />
<div>'''Background''': Unraveling the transcriptional network in human cells is of great interest in genetics. A new publicly available data sources with genome wide coverage released by the ENCODE Project have the potential to really advance our understanding of transcription regulations<br />
<br />
'''Goal''': Using these data sources, we will try to rediscover well known functional knowledge about transcription factors by just using this data set. If this is successful, we will expand our analysis to make novel predictions about functional involvment of transcription factors.<br />
<br />
'''Mathematical tools''': Statistics. The students will learn about enrichment analysis and make contact with bias and variance issues in a practical setting. The students will learn about and perform large scale data analysis. Care is taken, that handling of the data is as simple as possible.<br />
<br />
'''Biological or Medical aspects''': <br />
<br />
'''Supervisors''': [[User:Aurelien | Aurelien Mace]] & [[User:David|David Lamparter]] <br />
<br />
'''Students''':<br />
<br />
'''Presentation''':[[Media: Genetics of food behaviour.ppt]]<br />
see [[Genome Wide Association Studies]], [[Media: McCarthy_review_GWAS.pdf ]], [[GIANT_height | GWAS papers]]<br />
<br />
Back to [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Journal_Club_(spring_2013)&diff=3433Journal Club (spring 2013)2012-10-09T13:43:25Z<p>Aurelien: </p>
<hr />
<div>The Journal Club is every other Thursday, from 12-13, in the small meeting room. Feel free to bring your lunch.<br />
<br />
The schedule is indicated below. If it is your turn, please indicate the paper you are presenting by Monday and update the calendar accordingly. It can be any paper of scientific interest. Alternatively, you can also give '''tutorials on any scientific topic''' that may be of interest to other members of the group or invite an external speaker.<br />
<br />
== September 13 ==<br />
Sascha<br />
<br />
The biological impacts of the Fukushima nuclear accident on the pale grass blue butterfly<br />
<br />
[http://www.nature.com/srep/2012/120809/srep00570/full/srep00570.html http://www.nature.com/srep/2012/120809/srep00570/full/srep00570.html]<br />
<br />
== September 27 ==<br />
Micha will present an old but interesting account of the birth and development of academia by the father of sociology.<br />
<br />
Durkheim, ''L'évolution pédagogique en France'', 1938 [http://classiques.uqac.ca/classiques/Durkheim_emile/evolution_ped_france/evolution_ped_france.html full text]<br />
<br />
== October 11 ==<br />
Aurélien will present a new controversial idea to mitigate climate change.<br />
<br />
S. Matthew Liaoa, Anders Sandbergb & Rebecca Roacheb, "Human Engineering and Climate Change", Ethics, Policy and the Environment 15 (2) 2012: 206-221 [http://www.smatthewliao.com/2012/02/09/human-engineering-and-climate-change/ article]<br />
== October 25 ==<br />
Rico<br />
== November 8 ==<br />
Antony<br />
== November 22 ==<br />
David<br />
==December 6 ==<br />
Zoltán<br />
==December 20 (or January) ==<br />
Tanguy<br />
<br />
== And then... ==<br />
Barbara<br />
Nadya<br />
Diana<br />
Aurelien<br />
Tim</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Journal_Club_(spring_2012)&diff=3024Journal Club (spring 2012)2012-05-29T14:44:13Z<p>Aurelien: </p>
<hr />
<div>Journal Club is on Thursday, from 12-13, in the small meeting room. Feel free to bring your lunch.<br />
<br />
Ideally, someone from the group should volunteer to choose a paper for each meeting, and should update this page and email the paper around on the '''Friday the week before the meeting'''. Alternatively, people can also give '''tutorials on any scientific topic''' that may be of interest to other members of the group or invite an external speaker.<br />
<br />
<br />
== January 19 ==<br />
<br />
Sandra will present<br />
<br />
== February 2nd ==<br />
<br />
Sven: "Connecting points by Smooth Connection Functions defines shapes in the smoothest possible way" ([http://ceur-ws.org/Vol-812/paper2.pdf Paper])<br />
<br />
== March 2 (Friday at 2) ==<br />
<br />
David will present the following paper<br />
<br />
<biblio><br />
# yang2010 pmid=20562875 <br />
</biblio><br />
<br />
== March 15 ==<br />
Zoltán will present:<br />
<biblio><br />
#aa pmid=22391999<br />
</biblio><br />
<br />
== March 29 ==<br />
<br />
Micha will talk about statistical analysis of rnaseq data, with the following papers:<br />
<biblio><br />
#ab pmid=20167110<br />
#bb pmid=20979621<br />
</biblio><br />
<br />
== April 12 ==<br />
<br />
Tanguy will present <br />
<br />
<biblio><br />
#bc pmid=22065777<br />
</biblio><br />
<br />
== April 26 ==<br />
<br />
Nadya is going to discuss following paper:<br />
<biblio><br />
#Kolesov pmid=17709750<br />
</biblio><br />
<br />
== May 24 ==<br />
Diana will present the following paper:<br />
<biblio><br />
# Stephens pmid=19590391<br />
</biblio><br />
<br />
== May 31 ==<br />
<br />
Aurélien will present:<br />
<br />
8. The "impact factor" revisited<br />
Peng Dong, Marie Loh and Adrian Mondry*<br />
<br />
Link: http://www.bio-diglib.com/content/2/1/7<br />
<br />
== June 7 ==<br />
<br />
Sascha<br />
<br />
== June 21 ==<br />
<br />
Rico<br />
<br />
== July 5 ==<br />
<br />
Tim<br />
<br />
== July 19 ==<br />
(or possibly in september)<br />
<br />
Barbara</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Journal_Club_(spring_2012)&diff=3023Journal Club (spring 2012)2012-05-29T14:42:44Z<p>Aurelien: </p>
<hr />
<div>Journal Club is on Thursday, from 12-13, in the small meeting room. Feel free to bring your lunch.<br />
<br />
Ideally, someone from the group should volunteer to choose a paper for each meeting, and should update this page and email the paper around on the '''Friday the week before the meeting'''. Alternatively, people can also give '''tutorials on any scientific topic''' that may be of interest to other members of the group or invite an external speaker.<br />
<br />
<br />
== January 19 ==<br />
<br />
Sandra will present<br />
<br />
== February 2nd ==<br />
<br />
Sven: "Connecting points by Smooth Connection Functions defines shapes in the smoothest possible way" ([http://ceur-ws.org/Vol-812/paper2.pdf Paper])<br />
<br />
== March 2 (Friday at 2) ==<br />
<br />
David will present the following paper<br />
<br />
<biblio><br />
# yang2010 pmid=20562875 <br />
</biblio><br />
<br />
== March 15 ==<br />
Zoltán will present:<br />
<biblio><br />
#aa pmid=22391999<br />
</biblio><br />
<br />
== March 29 ==<br />
<br />
Micha will talk about statistical analysis of rnaseq data, with the following papers:<br />
<biblio><br />
#ab pmid=20167110<br />
#bb pmid=20979621<br />
</biblio><br />
<br />
== April 12 ==<br />
<br />
Tanguy will present <br />
<br />
<biblio><br />
#bc pmid=22065777<br />
</biblio><br />
<br />
== April 26 ==<br />
<br />
Nadya is going to discuss following paper:<br />
<biblio><br />
#Kolesov pmid=17709750<br />
</biblio><br />
<br />
== May 24 ==<br />
Diana will present the following paper:<br />
<biblio><br />
# Stephens pmid=19590391<br />
</biblio><br />
<br />
== May 31 ==<br />
<br />
Aurélien<br />
<br />
8. The "impact factor" revisited<br />
Peng Dong, Marie Loh and Adrian Mondry*<br />
<br />
Link: http://www.bio-diglib.com/content/2/1/7<br />
<br />
== June 7 ==<br />
<br />
Sascha<br />
<br />
== June 21 ==<br />
<br />
Rico<br />
<br />
== July 5 ==<br />
<br />
Tim<br />
<br />
== July 19 ==<br />
(or possibly in september)<br />
<br />
Barbara</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Journal_Club_(spring_2012)&diff=3022Journal Club (spring 2012)2012-05-29T14:41:59Z<p>Aurelien: </p>
<hr />
<div>Journal Club is on Thursday, from 12-13, in the small meeting room. Feel free to bring your lunch.<br />
<br />
Ideally, someone from the group should volunteer to choose a paper for each meeting, and should update this page and email the paper around on the '''Friday the week before the meeting'''. Alternatively, people can also give '''tutorials on any scientific topic''' that may be of interest to other members of the group or invite an external speaker.<br />
<br />
<br />
== January 19 ==<br />
<br />
Sandra will present<br />
<br />
== February 2nd ==<br />
<br />
Sven: "Connecting points by Smooth Connection Functions defines shapes in the smoothest possible way" ([http://ceur-ws.org/Vol-812/paper2.pdf Paper])<br />
<br />
== March 2 (Friday at 2) ==<br />
<br />
David will present the following paper<br />
<br />
<biblio><br />
# yang2010 pmid=20562875 <br />
</biblio><br />
<br />
== March 15 ==<br />
Zoltán will present:<br />
<biblio><br />
#aa pmid=22391999<br />
</biblio><br />
<br />
== March 29 ==<br />
<br />
Micha will talk about statistical analysis of rnaseq data, with the following papers:<br />
<biblio><br />
#ab pmid=20167110<br />
#bb pmid=20979621<br />
</biblio><br />
<br />
== April 12 ==<br />
<br />
Tanguy will present <br />
<br />
<biblio><br />
#bc pmid=22065777<br />
</biblio><br />
<br />
== April 26 ==<br />
<br />
Nadya is going to discuss following paper:<br />
<biblio><br />
#Kolesov pmid=17709750<br />
</biblio><br />
<br />
== May 24 ==<br />
Diana will present the following paper:<br />
<biblio><br />
# Stephens pmid=19590391<br />
</biblio><br />
<br />
== May 31 ==<br />
<br />
Aurélien<br />
<br />
The "impact factor" revisited<br />
Peng Dong, Marie Loh and Adrian Mondry*<br />
<br />
Link: http://www.bio-diglib.com/content/2/1/7<br />
<br />
== June 7 ==<br />
<br />
Sascha<br />
<br />
== June 21 ==<br />
<br />
Rico<br />
<br />
== July 5 ==<br />
<br />
Tim<br />
<br />
== July 19 ==<br />
(or possibly in september)<br />
<br />
Barbara</div>Aurelienhttp://www2.unil.ch/cbg/index.php?title=Journal_Club_(spring_2012)&diff=2941Journal Club (spring 2012)2012-05-09T10:47:55Z<p>Aurelien: </p>
<hr />
<div>Journal Club is on Thursday, from 12-13, in the small meeting room. Feel free to bring your lunch.<br />
<br />
Ideally, someone from the group should volunteer to choose a paper for each meeting, and should update this page and email the paper around on the '''Friday the week before the meeting'''. Alternatively, people can also give '''tutorials on any scientific topic''' that may be of interest to other members of the group or invite an external speaker.<br />
<br />
<br />
== January 19 ==<br />
<br />
Sandra will present<br />
<br />
== February 2nd ==<br />
<br />
Sven: "Connecting points by Smooth Connection Functions defines shapes in the smoothest possible way" ([http://ceur-ws.org/Vol-812/paper2.pdf Paper])<br />
<br />
== March 2 (Friday at 2) ==<br />
<br />
David will present the following paper<br />
<br />
<biblio><br />
# yang2010 pmid=20562875 <br />
</biblio><br />
<br />
== March 15 ==<br />
Zoltán will present:<br />
<biblio><br />
#aa pmid=22391999<br />
</biblio><br />
<br />
== March 29 ==<br />
<br />
Micha will talk about statistical analysis of rnaseq data, with the following papers:<br />
<biblio><br />
#ab pmid=20167110<br />
#bb pmid=20979621<br />
</biblio><br />
<br />
== April 12 ==<br />
<br />
Tanguy will present <br />
<br />
<biblio><br />
#bc pmid=22065777<br />
</biblio><br />
<br />
== April 26 ==<br />
<br />
Nadya is going to discuss following paper:<br />
<biblio><br />
#Kolesov pmid=17709750<br />
</biblio><br />
<br />
<br />
== May 31 ==<br />
<br />
Aurélien<br />
<br />
== May 24 ==<br />
<br />
Diana<br />
== June 7 ==<br />
<br />
Sascha<br />
<br />
== June 21 ==<br />
<br />
Rico<br />
<br />
== July 5 ==<br />
<br />
Tim<br />
<br />
== July 19 ==<br />
(or possibly in september)<br />
<br />
Barbara</div>Aurelien