See veebileht kasutab küpsiseid kasutaja sessiooni andmete hoidmiseks. Veebilehe kasutamisega nõustute ETISe kasutustingimustega. Loe rohkem
Olen nõus
11.08.1981
0046706070315
gemma.atkinson@gmail.com

Teenistuskäik

Töökohad ja ametid
05.09.2010–...   
Tartu Ülikool, Teadur (1,00)
01.01.2008–31.12.2010   
University of Uppsala, Sweden, Post doctoral researcher
 
 
Haridustee
2004–2008   
PhD, University of York, UK
2003–2004   
Masters of Research (MRes) Bioinformatics University of Leeds, UK (Distinction)
1999–2003   
BSc Honors Genetics, University of Newcastle Upon Tyne, UK
 
 
Teadusorganisatsiooniline ja -administratiivne tegevus
2005−2007   
Co-organisation of the University of York Bioinformatics seminar series
 
 
Lisainfo
September 2010-2014: Mobilitas funded post-doc in Tartu University.

This project with Professor Tanel Tenson concerns evolution of form and function of the RelA/SpoT (RSH) family of starvation response enzymes across the tree of life, searching for their distribution across complete genomes and retracing their evolutionary histories. RSH proteins produce and hydrolyze the alarmone ppGpp which is involved in cellular response to stress, metabolic regulation during the growth phases, as well as virulence in pathogens.
Previous Post-doctoral work:

September 2008-August 2010: Post-doctoral researcher in the Systematic Biology Department of the Evolutionary Biology Centre, Uppsala, Sweden.

The project, supervised by Professor Sandra Baldauf was on the functional evolution of the ancient family of translational GTPases (trGTPases). The trGTPases form a diverse protein superfamily involved in a wide variety of functions throughout the cell and across the tree of life. The core components of the superfamily originated before the last universal common ancestor (LUCA) and occur in some form in all living organisms. These core components have given rise to over 20 protein subfamilies with diverse functions, including major roles in all four stages of protein synthesis.


Kvalifikatsioon

 
 
Teadustöö põhisuunad
ETIS KLASSIFIKAATOR: 1. Bio- ja keskkonnateadused; 1.4. Ökoloogia, biosüstemaatika ja -füsioloogia; CERCS KLASSIFIKAATOR: B330 Paleozooloogia, fülogenees ; TÄPSUSTUS: protein molecular evolution
ETIS KLASSIFIKAATOR: 1. Bio- ja keskkonnateadused; 1.1. Biokeemia; CERCS KLASSIFIKAATOR: P310 Proteiinid, ensümoloogia; TÄPSUSTUS: enzyme form and function
ETIS KLASSIFIKAATOR: 1. Bio- ja keskkonnateadused; 1.12. Bio- ja keskkonnateadustega seotud uuringud, näiteks biotehnoloogia, molekulaarbioloogia, rakubioloogia, biofüüsika, majandus- ja tehnoloogiauuringud; CERCS KLASSIFIKAATOR: B220 Geneetika, tsütogeneetika ; TÄPSUSTUS: gene family distribution and evolution
 
 
Lisainfo

I have supervised the following projects at the University of York:

MRes Bioinformatics 3 month group project: “A database of protein synthesis GTPases” ,
MRes Bioinformatics 3 month student project “A database and functional classification of porcine ESTs”,
BSc Biology 2nd year Scientific Skills group project “Origin of Meiosis”,
BSc Biology 3rd year student final project “Phylogenetic analysis of the translation initiation factor IF2 family.”
Lecturing: 2015 Umeå University, “Introduction to bioinformatic methods for sequence analysis” on the course “Genetics and Genetic Techniques” (2 contact hours)
This is the students’ first introduction to bioinformatic methods for analysing nucleotide and amino acid sequence data. It is a practical guide to the use of online biological database and tools.

Lecturing: 2012 & 2013 University of Tartu, ”Translational GTPases” on the course “Protein synthesis” (1 contact hour per year; 2 contact hours total)
I introduce to the students to the essential translational GTPases that interact with the ribosome and tRNAs during protein synthesis. It is also the students’ first taste of phylogenetic inference and comparative genomics.

Demonstrating: 2004 to 2007 University of York: I have demonstrated computer programming, sequence analysis, phylogenetic and wet lab techniques in the following courses
- Structural Bioinformatics (MRes Bioinformatics)
- Programming in Python (MRes Bioinformatics)
- Biomolecular Analysis (MRes Functional Genomics and MRes Bioinformatics)
- Phylogenetic Analysis (MRes Functional Genomics and MRes Bioinformatics)
- Molecular Information on the Web (BSc Biology 1st year module)
Oral presentations at seminar series and national and international meetings (7)
2014 School of Science and Engineering, Saitama University, Japan (host: Yuzuru Tozawa)
“Using evolution to inform experimental molecular biology”
2014 Umeå Centre for Microbial Research (UCMR) Day, Umeå
“Functional evolution of the protein synthesis machinery”
2012 Biomedicinskt centrum (BMC), Uppsala University, Sweden (host: Måns Ehrenberg)
“Evolutionary and genetic analyses of mitochondrial translation initiation factors”
2011 Antibiotics and the ribosome meeting, Tartu, Estonia
“Evolution of form and function of translation factors”
2010 Engelhardt Institute of Molecular Biology, Moscow, Russia (host: Vladimir Mitkevich)
“Evolution of the translational GTPase superfamily ”
2009 Journal of Biomolecular Structure and Dynamics: Conversation 16, Albany, USA
“Evolution of the translational GTPase superfamily ”
2008 The Society for Molecular Biology & Evolution (SMBE) meeting, Nova Scotia, Canada
“Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms”
Research interests:

The focus of my research is the evolution of protein function and structure. I’m interested in how computational evolutionary analysis can be combined with experimental research to reconstruct functional evolution of proteins, and to generate testable hypotheses about unknown aspects of protein function.

I'm particularly interested in proteins associated with the ribosome and regulation of translation, as these molecules are often taxonomically widespread, essential in function and ancient, sometimes predating the ancestor of all life on earth.
Skills and techniques:

Programming (data handling and analysis): Python (including BioPython and mySQLdb modules) Programming (web development): PHP, HTML, CSS
Database development: MySQL (by command line and by Navicat Server)
Operating systems: Mac OS X, UNIX and LINUX command line, Windows XP
Sequence analysis software used regularly: PhyML, RaxML, MrBayes, PhyloBayes, T-Coffee, Mafft
Structural visualization and modification: MacPyMol with self written Python modules

I am currently learning methods in next generation sequence (NGS) analysis and have attended a course on RNA-Seq at Uppsala University (April 2015)

Publikatsioonid

Klass
Aasta
Publikatsioon
 
1.1.
2014
1.1.
2014
1.1.
2014
1.1.
2014
1.1.
2013
1.1.
2013
1.1.
2013
1.1.
2013
3.1.
2013
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2012
3.1.
2012
1.1.
2011
1.1.
2011
1.1.
2010
1.1.
2010
1.1.
2008
2.3.
2008
1.2.
2006
7.05.2019
11.08.1981
0046706070315
gemma.atkinson@gmail.com

Career

Institutions and positions
05.09.2010–...   
University of Tartu, Researcher (1,00)
01.01.2008–31.12.2010   
University of Uppsala, Sweden, Post doctoral researcher
 
 
Education
2004–2008   
PhD, University of York, UK
2003–2004   
Masters of Research (MRes) Bioinformatics University of Leeds, UK (Distinction)
1999–2003   
BSc Honors Genetics, University of Newcastle Upon Tyne, UK
 
 
R&D related managerial and administrative work
2005−2007   
Co-organisation of the University of York Bioinformatics seminar series
 
 
Additional information
September 2010-2014: Mobilitas funded post-doc in Tartu University.

This project with Professor Tanel Tenson concerns evolution of form and function of the RelA/SpoT (RSH) family of starvation response enzymes across the tree of life, searching for their distribution across complete genomes and retracing their evolutionary histories.RSH proteins produce and hydrolyze the alarmone ppGpp which is involved in cellular response to stress, metabolic regulation during the growth phases, as well as virulence in pathogens.
Previous Post-doctoral work:

September 2008-August 2010: Post-doctoral researcher in the Systematic Biology Department of the Evolutionary Biology Centre, Uppsala, Sweden.

The project, supervised by Professor Sandra Baldauf was on the functional evolution of the ancient family of translational GTPases (trGTPases). The trGTPases form a diverse protein superfamily involved in a wide variety of functions throughout the cell and across the tree of life. The core components of the superfamily originated before the last universal common ancestor (LUCA) and occur in some form in all living organisms. These core components have given rise to over 20 protein subfamilies with diverse functions, including major roles in all four stages of protein synthesis.

Qualifications

 
 
Fields of research
ETIS CLASSIFICATION: 1. Biosciences and Environment; 1.4. Ecology, Biosystematics and -physiology; CERCS CLASSIFICATION: B330 Palaeozoology, phylogeny ; SPECIFICATION: protein molecular evolution
ETIS CLASSIFICATION: 1. Biosciences and Environment; 1.1. Biochemistry; CERCS CLASSIFICATION: P310 Proteins, enzymology ; SPECIFICATION: enzyme form and function
ETIS CLASSIFICATION: 1. Biosciences and Environment; 1.12. Biotechnology, Molecular Biology, Cell Biology, Biophysics and Economic and Technological Research relating to Bio- and Environmental Sciences; CERCS CLASSIFICATION: B220 Genetics, cytogenetics ; SPECIFICATION: gene family distribution and evolution
 
 
Additional information

I have supervised the following projects at the University of York:

MRes Bioinformatics 3 month group project: “A database of protein synthesis GTPases” ,
MRes Bioinformatics 3 month student project “A database and functional classification of porcine ESTs”,
BSc Biology 2nd year Scientific Skills group project “Origin of Meiosis”,
BSc Biology 3rd year student final project “Phylogenetic analysis of the translation initiation factor IF2 family.”
Lecturing: 2015 Umeå University, “Introduction to bioinformatic methods for sequence analysis” on the course “Genetics and Genetic Techniques” (2 contact hours)
This is the students’ first introduction to bioinformatic methods for analysing nucleotide and amino acid sequence data. It is a practical guide to the use of online biological database and tools.

Lecturing: 2012 & 2013 University of Tartu, ”Translational GTPases” on the course “Protein synthesis” (1 contact hour per year; 2 contact hours total)
I introduce to the students to the essential translational GTPases that interact with the ribosome and tRNAs during protein synthesis. It is also the students’ first taste of phylogenetic inference and comparative genomics.

Demonstrating: 2004 to 2007 University of York: I have demonstrated computer programming, sequence analysis, phylogenetic and wet lab techniques in the following courses
- Structural Bioinformatics (MRes Bioinformatics)
- Programming in Python (MRes Bioinformatics)
- Biomolecular Analysis (MRes Functional Genomics and MRes Bioinformatics)
- Phylogenetic Analysis (MRes Functional Genomics and MRes Bioinformatics)
- Molecular Information on the Web (BSc Biology 1st year module)
Oral presentations at seminar series and national and international meetings (7)
2014 School of Science and Engineering, Saitama University, Japan (host: Yuzuru Tozawa)
“Using evolution to inform experimental molecular biology”
2014 Umeå Centre for Microbial Research (UCMR) Day, Umeå
“Functional evolution of the protein synthesis machinery”
2012 Biomedicinskt centrum (BMC), Uppsala University, Sweden (host: Måns Ehrenberg)
“Evolutionary and genetic analyses of mitochondrial translation initiation factors”
2011 Antibiotics and the ribosome meeting, Tartu, Estonia
“Evolution of form and function of translation factors”
2010 Engelhardt Institute of Molecular Biology, Moscow, Russia (host: Vladimir Mitkevich)
“Evolution of the translational GTPase superfamily ”
2009 Journal of Biomolecular Structure and Dynamics: Conversation 16, Albany, USA
“Evolution of the translational GTPase superfamily ”
2008 The Society for Molecular Biology & Evolution (SMBE) meeting, Nova Scotia, Canada
“Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms”
Research interests:

The focus of my research is the evolution of protein function and structure. I’m interested in how computational evolutionary analysis can be combined with experimental research to reconstruct functional evolution of proteins, and to generate testable hypotheses about unknown aspects of protein function.

I'm particularly interested in proteins associated with the ribosome and regulation of translation, as these molecules are often taxonomically widespread, essential in function and ancient, sometimes predating the ancestor of all life on earth.
Skills and techniques:

Programming (data handling and analysis): Python (including BioPython and mySQLdb modules) Programming (web development): PHP, HTML, CSS
Database development: MySQL (by command line and by Navicat Server)
Operating systems: Mac OS X, UNIX and LINUX command line, Windows XP
Sequence analysis software used regularly: PhyML, RaxML, MrBayes, PhyloBayes, T-Coffee, Mafft
Structural visualization and modification: MacPyMol with self written Python modules

I am currently learning methods in next generation sequence (NGS) analysis and have attended a course on RNA-Seq at Uppsala University (April 2015)

Completed projects

Publications

Category
Year
Publication
 
1.1.
2015
1.1.
2015
1.1.
2014
1.1.
2014
1.1.
2014
1.1.
2014
1.1.
2013
1.1.
2013
1.1.
2013
1.1.
2013
3.1.
2013
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2012
3.1.
2012
1.1.
2011
1.1.
2011
1.1.
2010
1.1.
2010
5.1.
2009
1.1.
2008
2.3.
2008
1.2.
2006
7.05.2019

Otsi projekti

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Asutus on projekti finantseerija   Asutus on projekti teostaja  
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Kõik   Tavaprojektid   Ülemprojektid   Alamprojektid  
Uus Frascati (2015)
Uus ja vana Frascati (otsing uue järgi väljastab ka seotud vanad)
Kõik
Käimasolevad
Lõppenud
Algus
Hajus
Täpne
  • Leitud 3 kirjet
ProgrammLiikNumberNimiProjekti algusProjekti lõppVastutav täitjaAsutusFinantseerijapoolne rahastamine
ETFETF9012Bakterite poomisvastuse uuringud kasutades biokeemia, fülogeneetilise analüüsi ja ühe molekuli mikroskoopia meetodeid01.01.201231.12.2015Vasili HauryliukTartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikooli Tehnoloogiainstituut57 600,00 EUR
ETFETF9020Mitokondri translatsiooni initsiatsioonifaktorite levik, funktsioon ja evolutsioon uurituna in silico, in vitro ja in vivo meetodite abil01.01.201231.12.2015Gemma AtkinsonTartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikooli Tehnoloogiainstituut69 600,00 EUR
MJDMJD99Ribosoomiga seotud stressivastuse ensüümide päritolu ja funktsionaalne evolutsioon.06.09.201011.04.2014Gemma AtkinsonTartu Ülikool; Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikooli Tehnoloogiainstituut100 341,29 EUR