User:Kristian Ullrich: Difference between revisions
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==Contact Info== | ==Contact Info== | ||
*Kristian Ullrich | *Kristian Ullrich | ||
*[http://www. | *[http://www.labutils.de www.labutils.de] | ||
*[[Special:Emailuser/Kristian Ullrich|Email me through OpenWetWare]] or through ullrich@evolbio.mpg.de | |||
*[http://orcid.org/0000-0003-4308-9626 orcid.org/0000-0003-4308-9626] | |||
*[[Special:Emailuser/Kristian Ullrich|Email me through OpenWetWare]] or through | |||
==Education== | ==Education== | ||
* | *2016 - Scientific coworker (Postdoc) in the group of Diethard Tautz [http://www.evolbio.mpg.de/2719/evolutionarygenetics MPI-Ploen Evolutionary Genetics] | ||
*2013-2016 Scientific coworker (Postdoc) in the group of Stefan Rensing [http://www.plantco.de plantco.de] | |||
*2012-2012 Short visit in the group of Dirk Inzé (VIB - UGent - PSB) as a scientific coworker [http://www.psb.ugent.be/the-ipb-division/systems-biology-of-yield System biology of yield] | |||
*2009-2012 PhD in the group of Marcel Quint [https://quintlab.landw.uni-halle.de/ Quint Lab] | |||
*2008 Diplom (~MSc), Christian-Albrechts-University Kiel, Institue of Molecular Phytopathology ([http://www.uni-kiel.de/phytomed/ D. Cai Lab]) | *2008 Diplom (~MSc), Christian-Albrechts-University Kiel, Institue of Molecular Phytopathology ([http://www.uni-kiel.de/phytomed/ D. Cai Lab]) | ||
*2001-2008 study of Biology at the [http://www.uni-kiel.de Christian-Albrechts-University Kiel] | *2001-2008 study of Biology at the [http://www.uni-kiel.de Christian-Albrechts-University Kiel] | ||
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==Research interests== | ==Research interests== | ||
<!-- Feel free to add brief descriptions to your research interests as well --> | <!-- Feel free to add brief descriptions to your research interests as well --> | ||
[[Image:Cover_nature_the_green_hourglass.jpg|thumb|right|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11394.html Nature 2012 Oct 04.]]] | |||
plant genetics | plant genetics | ||
*phytohormone signaling | *phytohormone signaling | ||
*natural variation | *natural variation | ||
*population genomics | |||
molecular evolution | |||
*gene family expansion/contraction | |||
*protein domain composition | |||
*phylostratigraphy | |||
software development | |||
*Image processing | |||
== | ==Publications== | ||
'''Books''' | |||
[1] The Genome of the Model Moss Physcomitrella patens (Lang D, vanGessel N, <u>Ullrich KK</u>, Reski R) [http://www.sciencedirect.com/science/article/pii/S0065229616300040 Advances in Botanical Research] | |||
'''International peer-reviewed papers''' | |||
[16] The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project (Weston D, Turetsky M, Johnson M, Granath G, Lindo Z, Belyea L, Rice S, Hanson D, Engelhardt K, Schmutz J, Dorrepaal E, Euskirchen E, Stenoien H, Szoevenyi P, Jackson M, Piatkowski B, Muchero W, Norby R, Kostka J, Glass J, Rydin H, Limpens J, Tuittila ES, <u>Ullrich KK</u>, Carrell A, Benscoter B, Chen J, Oke T, Nilsson M, Ranjan P, Jacobsen D, Lilleskov E, Shaw AJ) New Phytologist under review | |||
[15] Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. (Richards C, Alonso C, Becker C, Bossdorf O, Bucher E, Colome-Tatche M, Durka W, Engelhardt J, Gaspar B, Gogol-Doering A, Grosse I, van Gurp T, Heer K, Kronholm I, Lampei C, Latzel V, Milrouze M, Opgenoorth L, Paun O, Prohaska S, Rensing AS, Stadler P, Trucchi E, <u>Ullrich KK</u>, Verhoeven K) Ecology Letters accepted | |||
[14] Protoplast expansion and hypocotyl growth of Arabidopsis depend on different auxin signaling pathways. (Dahlke RI, Fraas S, <u>Ullrich KK</u>, Heinemann K, Romeiks M, Rickmeyer T, Klebe G, Palme K, Luethen H, Steffens B) [http://www.plantphysiol.org/content/early/2017/08/31/pp.17.00733 Plant Physiology early access] | |||
[13] Selfing in haploid plants and efficacy of selection: codon usage bias in the model moss Physcomitrella patens. (Szövénzi P, <u>Ullrich KK</u>, Rensing SA, Lang D, vanGessel N, Stenoien HK, Conti E, Reski R) [https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evx098 Genome Bioloy Evolution 2017 May 26] | |||
[12] Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens: introducing the ecotype Reute. (Hiss M, Meyberg R, Westermann J, Haas F, Schneider L, Schallenberg-Rüdinger M, <u>Ullrich KK</u>, Rensing SA) [http://onlinelibrary.wiley.com/doi/10.1111/tpj.13501/abstract The Plant Journal 2017 Mar 25] | |||
[11] Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst. (Heer K, <u>Ullrich KK</u>, Liepelt S, Rensing SA, Zhou J, Ziegenhagen B, Opgenoorth L) [http://link.springer.com/article/10.1007/s12686-016-0520-4?wt_mc=internal.event.1.SEM.ArticleAuthorOnlineFirst Conservation Genetics Resources 2016 Jan 22] | |||
[10] Evidence of divergent selection for drought and cold tolerance at landscape and local scales in Abies alba Mill. in the French Mediterranean Alps. (Roschanski A, Csillery K, Liepelt S, Oddou-Muratori S, Ziegenhagen B, Huard F, <u>Ullrich K</u>, Posolache D, Vendramin, G, Fady B) [http://onlinelibrary.wiley.com/doi/10.1111/mec.13516/abstract Molecular Ecology 2016 Feb 01.] | |||
[9] Localization and evolution of putative triose phosphate translocators in the diatom Phaeodactylum tricornutum. (Moog D, Rensing SA, Archibald JM, Maier UG, <u>Ullrich KK</u>) [http://gbe.oxfordjournals.org/content/7/11/2955.long GBE 2015 Sep 29.] | |||
[8] Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4-dependent auxin response genes. (Raschke A, Ibanez C, <u>Ullrich KK</u>, Anwer MU, Becker S, Glöckner A, Trenner J, Denk K, Saal B, Sun X, Ni M, Davis SJ, Delker C and Quint M) [http://www.biomedcentral.com/1471-2229/15/197 BMC Plant Biology 2015 Jul 02.] | |||
[7] Means to optimize protein expression in transgenic plants. (<u>Ullrich KK</u>, Hiss M, Rensing SA) [http://www.sciencedirect.com/science/article/pii/S0958166914001980 Current Opinion in Biotechnology 2014 Nov 25.] | |||
[6] Functional analysis of COP1 and SPA orthologs from Physcomitrella and rice during photomorphogenesis of transgenic Arabidopsis reveals distinct evolutionary conservation. (Ranjan A, Dickopf S, <u>Ullrich KK</u>, Rensing SA, Höcker U) [http://www.biomedcentral.com/1471-2229/14/178/abstract BMC Plant Biology 2014 Jul 01.] | |||
[5] Optimized probe masking for comparative transcriptomics of closely related species. (Pöschl Y, Delker C, Trenner J, <u>Ullrich KK</u>, Quint M, Grosse I) [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0078497 Plos ONE 2013 Nov 08.] | |||
[4] Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom. (Janitza P, <u>Ullrich KK</u>, Quint M) [http://www.frontiersin.org/Plant_Proteomics/10.3389/fpls.2012.00271/abstract frontiers in PLANT SCIENCE 2012 Dec 06.] | |||
[3] A transcriptomic hourglass in plant embryogenesis. (Quint M, Drost H-G, Gabel A, <u>Ullrich KK</u>, Boenn M, Grosse I) [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11394.html Nature 2012 Oct 04.] | |||
[2] Molecular Evolution and Selection Patterns of Plant F-box Proteins with C-terminal Kelch Repeats. (Schumann N, Navarro-Quezada AR, <u>Ullrich K</u>, Kuhl C and Quint M) [http://www.plantphysiol.org/content/155/2/835 Plant Physiology 2010 Nov 30] | |||
[1] Natural Variation of Transcriptional Auxin Response Networks in Arabidopsis thaliana. (Delker C, Pöschl Y, Raschke A, <u>Ullrich K</u>, Ettingshausen S, Hauptmann V, Grosse I, Quint M) [http://www.plantcell.org/content/22/7/2184.long Plant Cell. 2010 Jul 09.] | |||
'''Theses''' | |||
<u>Ullrich KK</u> 2013. Population and quantitative genetic analysis of auxin response pathways in Arabidopsis thaliana. PhD Thesis, University of Halle-Wittenberg, Germany. 174pp. [http://digital.bibliothek.uni-halle.de/hs/content/titleinfo/1691867 PDF] | |||
<u>Ullrich KK</u> 2009. Klonierung Organ-spezifischer Gene aus der Kartoffel und Untersuchung ihres Potentials zur Erzeugung gentechniser Pathogen-Resistenz. Diploma (~MSc) Thesis, Christian-Albrechts University of Kiel, Germany. 115pp. | |||
==Editorial Work== | |||
*reviewing editor for BMC Plant Biology (since 2014) | |||
*reviewing editor for BMC Biology (since 2015) | |||
*member of the editorial board: Frontiers in Plant Science Section: Plant Evolution and Development (since 2015) | |||
*reviewing editor for Plant Physiology (since 2016) | |||
==Conference/Workshop Participation== | |||
2015 Botanikertagung, Freising, Germany (Poster) | |||
2015 sEpiDiv Towards understanding the causes and consequences of epigenetic diversity, Leipzig, Germany (Talk) | |||
2014 NESCent Catalysis Meeting: Scaling Evoluiton from genomes to ecosystems in peatmosses - Sphagnum (Participant) | |||
2014 MOSS: The 17th Annual Moss International Conference, Bejing, China (Talk) | |||
2014 PAG: Plant and Animal Genome XXII Conference, San Diego, CA, USA (Talk) | |||
2013 MOSS: The 16th Annual Moss International Conference, Praha, Czech Republic (Talk) | |||
2013 PAG: Plant and Animal Genome XXI Conference, San Diego, CA, USA (Paticipant) | |||
2012 Meeting on Advances and Challenges of RNA-Seq Analysis, Halle (Saale), Germany (Paticipant) | |||
2012 Workshop of Molecular Evolution, Cesky Krumlov, Czech Republic (Paticipant) | |||
2011 Botanikertagung, Berlin, Germany (Poster) | |||
2011 Plant Science Student Conference, Halle (Saale), Germany (Poster) | |||
== | 2011 Molekularbiologie der Pflanzen, Dabringhausen, Germany (Poster) | ||
2010 Plant Science Student Conference, Gatersleben, Germany (Poster) | |||
==Conference/Workshop Organization== | |||
2015 Black Forest Summer School | |||
2015 Imaging-Workshop: Modern high throughput phenotyping of Arabidopsis and other species | |||
2014 Imaging-Workshop: Modern high throughput phenotyping of Arabidopsis | |||
2014 XVI. Annual Meeting of the International Society of Endocytobiology - German Section (ISE-G) | |||
2013 Black Forest Summer School on Bioinformatics | |||
==Teaching Experience== | |||
'''(Co-)Supervision''' of Masters and Bachelor theses as well as student projects | |||
'''Participation in courses on teaching methods''' | |||
'''Courses (co-)taught''' | |||
Botanisches Anfängerpraktikum | |||
Funktionelle und vergleichende Genomik der Pflanzen und Algen | |||
Pflanzliche Zellbiologie | |||
Einführung in die Bioinformatik und Statistik | |||
Bioinformatik: Genomevolution, Sequenzanalyse, Genomik, Phylogenie | |||
==external links== | |||
*[http://www.labutils.de RootDetection - Software to measure root length full automatically] | |||
*[https://github.com/kullrich personal github] | |||
==Useful links== | ==Useful links== | ||
*[[OpenWetWare:Welcome|Introductory tutorial]] | *[[OpenWetWare:Welcome|Introductory tutorial]] | ||
*[[Help|OpenWetWare help pages]] | *[[Help|OpenWetWare help pages]] |
Revision as of 23:05, 5 September 2017
Contact Info
- Kristian Ullrich
- www.labutils.de
- Email me through OpenWetWare or through ullrich@evolbio.mpg.de
- orcid.org/0000-0003-4308-9626
Education
- 2016 - Scientific coworker (Postdoc) in the group of Diethard Tautz MPI-Ploen Evolutionary Genetics
- 2013-2016 Scientific coworker (Postdoc) in the group of Stefan Rensing plantco.de
- 2012-2012 Short visit in the group of Dirk Inzé (VIB - UGent - PSB) as a scientific coworker System biology of yield
- 2009-2012 PhD in the group of Marcel Quint Quint Lab
- 2008 Diplom (~MSc), Christian-Albrechts-University Kiel, Institue of Molecular Phytopathology (D. Cai Lab)
- 2001-2008 study of Biology at the Christian-Albrechts-University Kiel
Research interests
plant genetics
- phytohormone signaling
- natural variation
- population genomics
molecular evolution
- gene family expansion/contraction
- protein domain composition
- phylostratigraphy
software development
- Image processing
Publications
Books
[1] The Genome of the Model Moss Physcomitrella patens (Lang D, vanGessel N, Ullrich KK, Reski R) Advances in Botanical Research
International peer-reviewed papers
[16] The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project (Weston D, Turetsky M, Johnson M, Granath G, Lindo Z, Belyea L, Rice S, Hanson D, Engelhardt K, Schmutz J, Dorrepaal E, Euskirchen E, Stenoien H, Szoevenyi P, Jackson M, Piatkowski B, Muchero W, Norby R, Kostka J, Glass J, Rydin H, Limpens J, Tuittila ES, Ullrich KK, Carrell A, Benscoter B, Chen J, Oke T, Nilsson M, Ranjan P, Jacobsen D, Lilleskov E, Shaw AJ) New Phytologist under review
[15] Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. (Richards C, Alonso C, Becker C, Bossdorf O, Bucher E, Colome-Tatche M, Durka W, Engelhardt J, Gaspar B, Gogol-Doering A, Grosse I, van Gurp T, Heer K, Kronholm I, Lampei C, Latzel V, Milrouze M, Opgenoorth L, Paun O, Prohaska S, Rensing AS, Stadler P, Trucchi E, Ullrich KK, Verhoeven K) Ecology Letters accepted
[14] Protoplast expansion and hypocotyl growth of Arabidopsis depend on different auxin signaling pathways. (Dahlke RI, Fraas S, Ullrich KK, Heinemann K, Romeiks M, Rickmeyer T, Klebe G, Palme K, Luethen H, Steffens B) Plant Physiology early access
[13] Selfing in haploid plants and efficacy of selection: codon usage bias in the model moss Physcomitrella patens. (Szövénzi P, Ullrich KK, Rensing SA, Lang D, vanGessel N, Stenoien HK, Conti E, Reski R) Genome Bioloy Evolution 2017 May 26
[12] Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens: introducing the ecotype Reute. (Hiss M, Meyberg R, Westermann J, Haas F, Schneider L, Schallenberg-Rüdinger M, Ullrich KK, Rensing SA) The Plant Journal 2017 Mar 25
[11] Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst. (Heer K, Ullrich KK, Liepelt S, Rensing SA, Zhou J, Ziegenhagen B, Opgenoorth L) Conservation Genetics Resources 2016 Jan 22
[10] Evidence of divergent selection for drought and cold tolerance at landscape and local scales in Abies alba Mill. in the French Mediterranean Alps. (Roschanski A, Csillery K, Liepelt S, Oddou-Muratori S, Ziegenhagen B, Huard F, Ullrich K, Posolache D, Vendramin, G, Fady B) Molecular Ecology 2016 Feb 01.
[9] Localization and evolution of putative triose phosphate translocators in the diatom Phaeodactylum tricornutum. (Moog D, Rensing SA, Archibald JM, Maier UG, Ullrich KK) GBE 2015 Sep 29.
[8] Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4-dependent auxin response genes. (Raschke A, Ibanez C, Ullrich KK, Anwer MU, Becker S, Glöckner A, Trenner J, Denk K, Saal B, Sun X, Ni M, Davis SJ, Delker C and Quint M) BMC Plant Biology 2015 Jul 02.
[7] Means to optimize protein expression in transgenic plants. (Ullrich KK, Hiss M, Rensing SA) Current Opinion in Biotechnology 2014 Nov 25.
[6] Functional analysis of COP1 and SPA orthologs from Physcomitrella and rice during photomorphogenesis of transgenic Arabidopsis reveals distinct evolutionary conservation. (Ranjan A, Dickopf S, Ullrich KK, Rensing SA, Höcker U) BMC Plant Biology 2014 Jul 01.
[5] Optimized probe masking for comparative transcriptomics of closely related species. (Pöschl Y, Delker C, Trenner J, Ullrich KK, Quint M, Grosse I) Plos ONE 2013 Nov 08.
[4] Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom. (Janitza P, Ullrich KK, Quint M) frontiers in PLANT SCIENCE 2012 Dec 06.
[3] A transcriptomic hourglass in plant embryogenesis. (Quint M, Drost H-G, Gabel A, Ullrich KK, Boenn M, Grosse I) Nature 2012 Oct 04.
[2] Molecular Evolution and Selection Patterns of Plant F-box Proteins with C-terminal Kelch Repeats. (Schumann N, Navarro-Quezada AR, Ullrich K, Kuhl C and Quint M) Plant Physiology 2010 Nov 30
[1] Natural Variation of Transcriptional Auxin Response Networks in Arabidopsis thaliana. (Delker C, Pöschl Y, Raschke A, Ullrich K, Ettingshausen S, Hauptmann V, Grosse I, Quint M) Plant Cell. 2010 Jul 09.
Theses
Ullrich KK 2013. Population and quantitative genetic analysis of auxin response pathways in Arabidopsis thaliana. PhD Thesis, University of Halle-Wittenberg, Germany. 174pp. PDF
Ullrich KK 2009. Klonierung Organ-spezifischer Gene aus der Kartoffel und Untersuchung ihres Potentials zur Erzeugung gentechniser Pathogen-Resistenz. Diploma (~MSc) Thesis, Christian-Albrechts University of Kiel, Germany. 115pp.
Editorial Work
- reviewing editor for BMC Plant Biology (since 2014)
- reviewing editor for BMC Biology (since 2015)
- member of the editorial board: Frontiers in Plant Science Section: Plant Evolution and Development (since 2015)
- reviewing editor for Plant Physiology (since 2016)
Conference/Workshop Participation
2015 Botanikertagung, Freising, Germany (Poster)
2015 sEpiDiv Towards understanding the causes and consequences of epigenetic diversity, Leipzig, Germany (Talk)
2014 NESCent Catalysis Meeting: Scaling Evoluiton from genomes to ecosystems in peatmosses - Sphagnum (Participant)
2014 MOSS: The 17th Annual Moss International Conference, Bejing, China (Talk)
2014 PAG: Plant and Animal Genome XXII Conference, San Diego, CA, USA (Talk)
2013 MOSS: The 16th Annual Moss International Conference, Praha, Czech Republic (Talk)
2013 PAG: Plant and Animal Genome XXI Conference, San Diego, CA, USA (Paticipant)
2012 Meeting on Advances and Challenges of RNA-Seq Analysis, Halle (Saale), Germany (Paticipant)
2012 Workshop of Molecular Evolution, Cesky Krumlov, Czech Republic (Paticipant)
2011 Botanikertagung, Berlin, Germany (Poster)
2011 Plant Science Student Conference, Halle (Saale), Germany (Poster)
2011 Molekularbiologie der Pflanzen, Dabringhausen, Germany (Poster)
2010 Plant Science Student Conference, Gatersleben, Germany (Poster)
Conference/Workshop Organization
2015 Black Forest Summer School
2015 Imaging-Workshop: Modern high throughput phenotyping of Arabidopsis and other species
2014 Imaging-Workshop: Modern high throughput phenotyping of Arabidopsis
2014 XVI. Annual Meeting of the International Society of Endocytobiology - German Section (ISE-G)
2013 Black Forest Summer School on Bioinformatics
Teaching Experience
(Co-)Supervision of Masters and Bachelor theses as well as student projects
Participation in courses on teaching methods
Courses (co-)taught
Botanisches Anfängerpraktikum
Funktionelle und vergleichende Genomik der Pflanzen und Algen
Pflanzliche Zellbiologie
Einführung in die Bioinformatik und Statistik
Bioinformatik: Genomevolution, Sequenzanalyse, Genomik, Phylogenie