Projekt

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Population Genomics

Titel Englisch Population Genomics
Gesuchsteller/in Sanders Ian
Nummer 126393
Förderungsinstrument ProDoc
Forschungseinrichtung Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Hochschule Universität Lausanne - LA
Hauptdisziplin Oekologie
Beginn/Ende 01.02.2010 - 28.02.2014
Bewilligter Betrag 482'396.00
Alle Daten anzeigen

Alle Disziplinen (2)

Disziplin
Oekologie
Genetik

Keywords (10)

population biology; population genetics; evolutionary genomics; deep genome sequencing; bioinformatics; animals; plants; microorganisms; transcriptomics; ecological genomics

Lay Summary (Englisch)

Lead
Lay summary
Recent advances in sequencing technology (such as 454 titanium, Solexa, SOLiD, Helicos and Complete Genomics) allow the deep coverage of genomes and transcriptomes in a large number of individuals. These advances pave the way for the emerging field of population genomics, which combines the principles of population biology and genetics with deep genome and transcriptome sequencing, as well as the latest bioinformatics tools necessary to process the massive amount of data involved. This approach will allow us to understand, at an unprecedented level, the key micro-evolutionary processes of mutation, genetic drift, gene flow and natural selection,. It is these within-population processes that are ultimately responsible for the origin of new species and divergence of their genomic and phenotypic traits. The fundamentals of population genomics allow researchers to cross disciplinary boundaries because it is applicable to a wide variety of questions in biology and medicine. The technological developments also mean that genomics, including functional genomics, are no longer limited to a handful of model organisms. This technology now allows the observation of large-scale patterns of gene expression. For the first time, ecologists and evolutionary biologists have the possibly to understand the influence of the environment on which parts of the genome are expressed. The development of deep genome sequencing, coupled with major advances in quantitative DNA amplification technologies also add new possibilities in population genetics for looking at genome-wide gene expression differences within and among populations that will ultimately lead to identification of adaptive molecular variation.
The training program is focussed on activities enabling PhD students to integrate the fields of population genetics, deep genome and transcriptome sequencing, bioinformatics and ecological and evolutionary genomics.
It is clear that researchers of the future will be able to use population genomics approaches to solve a variety of scientific and practical problems in biology and medicine. As a leading country in technology and biotechnology it is essential that Switzerland develops a solid research base in population genomics. It is expected that doctoral students trained in this program will be widely sought after on the job market in fundamental research in biology and medicine, in biotechnology and in the biomedical and pharmaceutical industry.
Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
A Y-like social chromosome causes alternative colony organization in fire ants.
Wang John, Wurm Yannick, Nipitwattanaphon Mingkwan, Riba-Grognuz Oksana, Huang Yu-Ching, Shoemaker Dewayne, Keller Laurent (2013), A Y-like social chromosome causes alternative colony organization in fire ants., in Nature, 493, 664-668.
Effects of interspecific recombination on functional traits in trees revealed by metabolomics and genotyping-by-resequencing
Caseys Celine, Glauser G, Stölting KN, Christe C, Albrectsen BR, Lexer Christian (2012), Effects of interspecific recombination on functional traits in trees revealed by metabolomics and genotyping-by-resequencing, in Plant Ecology and Diversity , 1-45.
PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs.
Lischer H E L, Excoffier L (2012), PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs., in Bioinformatics (Oxford, England), 28(2), 298-9.
Visualization and quality assessment of de novo genome assemblies.
Riba-Grognuz Oksana, Keller Laurent, Falquet Laurent, Xenarios Ioannis, Wurm Yannick (2011), Visualization and quality assessment of de novo genome assemblies., in Bioinformatics (Oxford, England), 27(24), 3425-6.
When orthologs diverge between human and mouse.
Gharib Walid H, Robinson-Rechavi Marc (2011), When orthologs diverge between human and mouse., in Briefings in bioinformatics, 12(5), 436-41.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Swiss Insitute of Bioinformatics Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten

Wissenschaftliche Veranstaltungen



Selber organisiert

Titel Datum Ort
Research Seminar - Prof. Ary A. Hoffmann 29.01.2014 Lausanne, Schweiz
Research Seminar - Prof. Sergey Gavrilets 09.01.2014 Basel & Bern, Schweiz
Research Seminars - Dr. Peter Thrall 18.11.2013 Basel & Lausanne, Schweiz
Students' Retreat 2013 22.03.2013 Charmey, FR, Schweiz
Research Seminar - Professor Timothy Y. James 30.11.2012 Universities Lausanne and Basel, Schweiz
Workshop: Host-associated Microbiota 2012 11.09.2012 Basel, Schweiz
Bayesian Statistics for Population Genomics 21.05.2012 Lausanne, Schweiz
Students' Retreat 2012 16.03.2012 Churwalden, Schweiz
Introduction to R 17.10.2011 Lausanne, Schweiz
Introduction to Coalescent Theory 05.09.2011 Bern, Schweiz
Model selection and statistical inference 03.05.2011 Lausanne, Schweiz
An Introduction to Bayesian Statistics in Ecology 07.02.2011 Bern, Schweiz
How to give a scientific presentation: talks and posters 05.11.2010 Lausanne, Schweiz

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
130313 Population genomic survey of genes influencing fitness in a hybrid zone of fire ants 01.10.2010 ProDoc
130309 Detection of adaptive genomic interactions at different evolutionary time scales 01.09.2010 ProDoc
135129 Microbial biogeography and global change: Linking pyrosequencing, phy-logenetics and habitat modelling to study the ecogeography of soil fungal and bacterial communities along a wide elevation gradient in the Alps 01.10.2011 ProDoc
127371 Evolutionary genetics of arbuscular mycorrhizal fungi and its effect on the mycorrhizal symbiosis: from genomics and transcriptomics to its application 01.10.2009 Projektförderung (Abt. I-III)
130479 Loss of heterozygosity during asexual reproduction 01.09.2010 ProDoc
135116 Population genomics of evolutionary response to nutritional stress in Drosophila 01.09.2011 ProDoc
134660 High density admixture mapping for assessing the impact of interspecific recombination in ecologically important species 01.12.2011 ProDoc
134979 A pedigree of structural variants 01.02.2012 ProDoc
130309 Detection of adaptive genomic interactions at different evolutionary time scales 01.09.2010 ProDoc

Abstract

Recent advances in sequencing technology (such as 454 titanium, Solexa, SOLiD, Helicos and Complete Genomics) allow the deep coverage of genomes and transcriptomes in a large number of individuals. These advances pave the way for the emerging field of population genomics, which combines the principles of population biology and genetics with deep genome and transcriptome sequencing, as well as the latest bioinformatics tools necessary to process the massive amount of data involved. This approach will allow us to understand, at an unprecedented level, the key micro-evolutionary processes of mutation, genetic drift, gene flow and natural selection,. It is these within-population processes that are ultimately responsible for the origin of new species and divergence of their genomic and phenotypic traits. The fundamentals of population genomics allow researchers to cross disciplinary boundaries because it is applicable to a wide variety of questions in biology and medicine. The technological developments also mean that genomics, including functional genomics, are no longer limited to a handful of model organisms. This technology now allows the observation of large-scale patterns of gene expression. For the first time, ecologists and evolutionary biologists have the possibly to understand the influence of the environment on which parts of the genome are expressed. The development of deep genome sequencing, coupled with major advances in quantitative DNA amplification technologies also add new possibilities in population genetics for looking at genome-wide gene expression differences within and among populations that will ultimately lead to identification of adaptive molecular variation.Switzerland’s future experts in population genomics need across-discipline training in population genetics, hands-on experience with up-to-date genomics and bioinformatics tools, for acquiring, organizing and analyzing large-scale population genomic data. We need to offer this training to our PhD students. The cross-disciplinary nature means it cannot be offered by one Swiss University. The training module in Population Genomics brings together applicants with experience in deep genome and transcriptome sequencing (Sanders, Ebert and Keller) with population genetics and bioinformatics (Goudet and Excoffier). It brings together leaders in ecology, evolution, includes bioinformatics expertise from 3 group leaders of the Swiss Institute of Bioinformatics (SIB: Excoffier, Robinson-Rechavi, Salamin) and state-of-the-art bioinformatics support from the SIB VitalIT platform (Xenarios). The combined expertise in these fields afforded by the universities of Lausanne, Bern and Basel would provide a perfect opportunity for PhD students to obtain the necessary training in population genomics that could not be obtained outside such a program.The training program is focussed on activities enabling PhD students to integrate the fields of population genetics, deep genome and transcriptome sequencing, bioinformatics and ecological and evolutionary genomics. Additional goals are:•To offer a coherent set of activities to improve the quality of the students research and develop additional scientific skills such as scientific communication and presentation•To enhance the sharing of ideas among Swiss research institutions and PhD students and increase the ability of these institutions to develop in the new field of population genomics•To attract and select top level PhD students through the international visibility of the school•To foster links with top international researchers and research institutes in these disciplines in order to maximize the doctoral students chance of subsequent employmentThe training program for the ProDoc in Population Genomics comprises activities for developing scientific skills, learning new techniques and methods and exchange of ideas among groups and disciplines. The activities comprise scientific seminars, workshops, methods courses in population genomics and scientific exchanges.It is clear that researchers of the future will be able to use population genomics approaches to solve a variety of scientific and practical problems in biology and medicine. As a leading country in technology and biotechnology it is essential that Switzerland develops a solid research base in population genomics. It is expected that doctoral students trained in this program will be widely sought after on the job market in fundamental research in biology and medicine, in biotechnology and in the biomedical and pharmaceutical industry.
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