Director

Detlef Weigel

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Detlef Weigel

I started out as a developmental biologist, but over the past two decades years, my lab has come to focus more and more on questions of evolution. We investigate these both from a genomic perspective and starting from phenotypes, primarily, but not exclusively in Arabidopsis thaliana. The most recent addition is a strong investment in plant-microbe interactions, including natural microbiomes; see our Pathopdopsis project! I am an elected member of the US National Academy of Sciences, the Royal Society, the German National Academy of Sciences and EMBO. I have served or am serving on many advisory and editorial boards and have co-founded three biotech start-ups. Download a recent CV here.

Bio

- 2002 to present / Director / Max Planck Institute for Developmental Biology
- 1993 to 2002 / Assistant and Associate Professor / Salk Institute for Biological Studies, USA
- 1989 to 1993 / Postdoc / California Institute of Technology, USA
- 1988 to 1989 / Research Associate / Ludwig Maximilian University Munich, Germany
- 1986 to 1988 / PhD student / Max Planck Institute for Developmental Biology
- 1981 to 1986 / Diploma student / University of Cologne

Selected References

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales

Karasov, T. L., Almario, J., Friedemann, C., Ding, W., Giolai, M., Heavens, D., Kersten, S., Lundberg, D., Neumann, M., Regalado, J., Neher, R. A., Kemen, E., Weigel D.
Cell Host Microbe (2018), 24(1) 168-179.

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

1001 Genomes Consortium
Cell (2016), 166(2) 481-491.

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis

Chae E., Bomblies K., Kim S. T., Karelina D., Zaidem M., Ossowski S., Martin-Pizarro C., Laitinen R. A., Rowan B. A., Tenenboim H., Lechner S., Demar M., Habring-Müller A., Lanz C., Rätsch G. and Weigel D.
Cell (2014), 159(6) 1341-51.

Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

Todesco M., Balasubramanian S., Hu T. T., Traw M. B., Horton M., Epple P., Kuhns C., Sureshkumar S., Schwartz C., Lanz C., Laitinen R. A., Huang Y., Chory J., Lipka V., Borevitz J. O., Dangl J. L., Bergelson J., Nordborg M. and Weigel D.
Nature (2010), 465(7298) 632-6.

Integration of spatial and temporal information during floral induction in Arabidopsis

Wigge P. A., Kim M. C., Jaeger K. E., Busch W., Schmid M., Lohmann J. U. and Weigel D.
Science (2005), 309(5737) 1056-9.

Control of leaf morphogenesis by microRNAs

Palatnik J. F., Allen E., Wu X., Schommer C., Schwab R., Carrington J. C. and Weigel D.
Nature (2003), 425(6955) 257-63.

A molecular link between stem cell regulation and floral patterning in Arabidopsis

Lohmann J. U., Hong R. L., Hobe M., Busch M. A., Parcy F., Simon R. and Weigel D.
Cell (2001), 105(6) 793-803.

A developmental switch sufficient for flower initiation in diverse plants

Weigel D. and Nilsson O.
Nature (1995), 377(6549) 495-500.

The homeotic gene fork head encodes a nuclear protein and is expressed in the terminal regions of the Drosophila embryo

Weigel D., Jürgens G., Küttner F., Seifert E. and Jäckle H.
Cell (1989), 57(4) 645-58.

Contact

detlef.weigel@tuebingen.mpg.de

Evolutionary Genetics

Max Collenberg

Gene expression in hybrid plants.

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Max Collenberg

Phenotypic variation within species is often observed both at the morphological and the physiological level. While genetic variation contributes to structural alterations in proteins, differences in gene expression can provide an additional means of varying cellular composition and cell responses. I am using next generation sequencing to study the transcriptomes of several natural Arabidopsis thaliana accessions with full genome information, and also manually generated F1 hybrids. My main focus is on detecting cis and trans factors that contribute to differences in spatial and temporal expression, particularly those with roles in local adaptation such as to respond to pathogen pressures.

Research Topics

- Gene expression in hybrid plants

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013-2016 / MSc in Agricultural Biotechnology / University of Hohenheim, Germany
- 2010-2013 / BSc in Agricultural Biology / University of Hohenheim, Germany

Contact

max.collenberg@tuebingen.mpg.de

Adrian Contreras

small RNAs. Epigenetics.

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Adrian Contreras

I'm part of the Epidiverse training network, which investigates epigenetic variation in plants, focusing on adaptive processes in wild plant populations as well as ecologically relevant challenges. My focus is on small RNAs, thereby linking the molecular and computational aspects of the team.
I also look at GxG interactions by testing the effect of genetic background on the loss of epigenetic factors in Arabidopsis thaliana, using CRISPR/Cas9 technology.

Research Topics

- small RNAs
- Epigenetics

Bio

- 2018 to present / PhD student / Max Planck Institute for Developmental Biology
- 2017 / Research assistant / University of Valencia, Spain
- 2015 to 2017 / MSc in Plant Molecular & Cellular Biotechnology / Polytechnic University of Valencia, Spain
- 2010 to 2015 / BSc in Biological Sciences / Universidad de Valencia, Spain

Contact

adrian.contreras@tuebingen.mpg.de

Alba Gonzalez

Co-evolution of Arabidopsis and its oomycete pathogen Hyaloperonospora.

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Alba Gonzalez

Co-evolution of pathogens and their host shape the diversity of both partners. In contrast to many well-studied crops, wild plant populations usually provide extensive genetic diversity to counteract pathogen pressure. My work focusses on the other side of the coin: using Arabidopsis thaliana and its natural pathogen Hyaloperonospora arabidopsidis (Hpa), I use genetic, genomic, and molecular tools to characterize how plant diversity shapes that of its pathogen. In combination with directed infection assays, association of phenotype and genotype will help me pinpoint genomic regions involved in pathogen adaptation.

Research Topics

- Co-evolution of Arabidopsis and its oomycete pathogen Hyaloperonospora

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2016 / Research internship / Max Planck Institute for Developmental Biology
- 2015 to 2016 / Research Assistant / University of Utah, USA
- 2009 to 2015 / BSc in Biology / University of Malaga, Spain

Contact

alba.gonzalez@tuebingen.mpg.de

Christa Lanz

DNA sequencing and all associated challenges.

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Christa Lanz

I’m heading the Genome Center at the institute. Apart from making sure all our instruments run smoothly and continuously, establishing and advancing protocols for Next Generation Sequencing libraries is my prime focus. Over the last years, I have experienced the tremendous advancement in sequencing technologies, and moved from classical Sanger sequencing to highly parallelized short-read sequencing on a series of Illumina instruments. Our latest acquisition, the Pacbio Sequel, adds single-molecule long-read sequencing to our repertoire and, as the other instruments before, gives us the possibility to master numerous exciting challenges.

Research Topics

- DNA sequencing and all associated challenges

Bio

- 2000 to present / Technical Staff / Genome Center, Max Planck Institute for Developmental Biology
- 1990 to 2000 / Technician / Max Planck Institute for Biology
- 1986 to 1989 / PhD in Biology / University of Tübingen , Germany
- 1979 to 1986 / Diploma in Biology / University of Tübingen, Germany
- 1977 to 1979 / MTA education / Hygiene Institute, Tübingen, Germany

Selected References

The genome of the stress-tolerant wild tomato species Solanum pennellii

Bolger, A., Scossa, F., Bolger, M. E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sorensen, I., Lichtenstein, G., Fich, E. A., Conte, M., Keller, H., Schneeberger, K., Schwacke, R., Ofner, I., Vrebalov, J., Xu, Y., Osorio, S., Aflitos, S. A., Schijlen, E., Jimenez-Gomez, J. M., Ryngajllo, M., Kimura, S., Kumar, R., Koenig, D., Headland, L. R., Maloof, J. N., Sinha, N., van Ham, R. C., Lankhorst, R. K., Mao, L., Vogel, A., Arsova, B., Panstruga, R., Fei, Z., Rose, J. K., Zamir, D., Carrari, F., Giovannoni, J. J., Weigel, D., Usadel, B., Fernie A. R.
Nat Genet (2014), 46(9), 1034-8

Species-wide genetic incompatibility analysis identifies immune genes as hotspots of deleterious epistasis

Chae, E., Bomblies, K., Kim, S.-T., Karelina, D., Zaidem, M., Ossowski, S., Martin Pizarro, C., Laitinen, R. A. E., Rowan, B. A., Tenenboim, H., Lechner, S., Demar, M., Habring-Müller, A., Lanz, C., Rätsch, G., Weigel, D.
Cell (2014), 159(6), 1341-51

Whole-genome sequencing of multiple Arabidopsis thaliana population

Cao, J., Schneeberger, K., Ossowski, S., Gunther, T., Bender, S., Fitz, J., Koenig, D., Lanz, C., Stegle, O., Lippert, C., Wang, X., Ott, F., Muller, J., Alonso-Blanco, C., Borgwardt, K., Schmid, K. J., Weigel, D.
Nat Gen (2011), 43(10), 956-63

Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

Hanikenne, M., Talke, I. N., Haydon, M. J., Lanz, C., Nolte, A., Motte, P., Kroymann, J., Weigel, D., Krämer, U.
Nature (2008), 453(7193), 391-5

A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective

Rendulic, S., Jagtap, P., Rosinus, A., Eppinger, M., Baar, C., Lanz, C., Keller, H., Lambert, C., Evans, K. J., Goesmann, A., Meyer, F., Sockett, R. E., Schuster, S. C.
Science (2004), 303(5658), 689-92

Contact

christa.lanz@tuebingen.mpg.de

Ulrich Lutz

GxG interactions. Flowering time variation. Herbicide resistance.

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Ulrich Lutz

I am interested in deciphering the genetic basis of adaptation and phenotypic plasticity of flowering time of plants, especially in response to changing environmental conditions. I use natural variation as a resource of genetic diversity to identify new alleles of known genes to better understand gene function, regulation, and interaction. Employing CRISPR/Cas9 technology, I investigate GxG interaction by testing a deleterious genetic deletion in a large set of natural Arabidopsis genetic backgrounds. I also work on herbicide resistance of Alopecurus myosuroides (black-grass), a plant species classified as a weed. Several next generation sequencing technologies and methods are applied to study the dynamics of resistance dispersion and the population structure of local and nationwide samples.

Research Topics

- GxG interactions. Flowering time variation. Herbicide resistance

Bio

- 2017 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2011 to 2016 / PhD student / Plant Systems Biology / Technical University of Munich (TUM), Germany
- 2010 to 2011 / Diploma thesis / Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
- 2005 to 2011 / Studies of Agricultural Biotechnology, University of Hohenheim, Germany

Selected References

Natural haplotypes of FLM non-coding sequences fine-tune flowering time in ambient spring temperatures in Arabidopsis.

Lutz, U., Nussbaumer, T., Spannagl, M., Dienter, J., Mayer, K. F., Schwechheimer C.
eLIFE (2017), e22114

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M.

Lutz, U., Posé, D., Pfeifer, M., Gundlach, H., Hagmann, J., Wang, C., Weigel, D., Mayer, K. F., Schmid, M., Schwechheimer C.
PLoS Genet. (2015), 11(10):e1005588

A set of Columbia-0-specific single nucleotide polymorphism markers for the genetic analysis of natural variation in Arabidopsis thaliana.

Lutz, U., Schwechheimer C.
bioRxiv preprint (2017), doi: 10.1101/153197

Contact

ulrich.lutz@tuebingen.mpg.de

Fernando Rabanal

Evolution and regulation of ribosomal RNA genes. Herbicide resistance.

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Fernando Rabanal

Research Topics

- Evolution and regulation of ribosomal RNA genes
- Herbicide resistance

Bio

- 2017 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2010 to 2017 / PhD in Molecular Biology / Gregor Mendel Institute (GMI), Austria
- 2005 to 2009 / BSc in Genomic Sciences / National Autonomous University of Mexico (UNAM)

Selected References

Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana.

Rabanal, F. A., Mandáková, T., Soto-Jiménez, L. M., Greenhalgh, R., Parrott, D. L., Lutzmayer S., Steffen, J. G., Nizhynska, V., Mott, R., Lysak, M. A., Clark, R. M. and Nordborg, M.
Genome Biol. (2017), 18(1):75

Unstable Inheritance of 45S rRNA Genes in Arabidopsis thaliana.

Rabanal, F. A., Nizhynska, V., Mandáková, T., Novikova, P. Y., Lysak, M. A., Mott, R. and Nordborg, M.
G3 (Bethesda) (2017), 7(4): 1201-1209

1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana.

1001 Genomes Consortium
Cell (2016), 166(2): 481-91

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden.

Long, Q., Rabanal, F. A., Meng, D., Huber, C. D., Farlow, A., Platzer, A., Zhang, Q., Vilhjálmsson, B. J., Korte, A., Nizhynska, V., Vronin, V., Korte, P., Sedman, L., Mandáková, T., Lysak, M. A., Seren, Ü., Hellmann, I. and Nordborg, M.
Nat Genet (2013), 45(8): 884-90

Contact

fernando.rabanal@tuebingen.mpg.de

Gautam Shirsekar

Co-evolution in natural A. thaliana – oomycete pathosystems.

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Gautam Shirsekar

I am a plant pathologist interested in understanding co-evolutionary patterns in host-pathogen interactions. In the long-term I intend to apply the knowledge I acquire for development of durable and sustainable crop disease management strategies. In the Weigel lab, I am studying phenotypic and molecular evolution in North American A. thaliana and co-existing oomycete pathogens H. arabidopsidis (downy mildew) and A. candida (white rust) populations. Important questions are whether new pathogen recognition capabilities in the host more often evolve through mutation or introgression from divergent lineages, and whether virulence factors in the pathogens are co-evolving in response.

Research Topics

- Co-evolution in natural A. thaliana – oomycete pathosystems

Bio

- 2013 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2013 / PhD in Plant Pathology / The Ohio State University, USA
- 2002 to 2006 / Senior Research Fellow / Regional Station, Indian Agricultural Research Institute, India
- 2002 / MSc in Plant Pathology / Konkan Agricultural University, India
- 2000 / BSc in Agriculture / Konkan Agricultural University, India

Selected References

Identification and characterization of suppressor mutants of spl11- mediated cell death in rice

Shirsekar G. S., Vega-Sanchez M. E., Bordeos A., Baraoidan M., Swisshelm A., Fan J., Park C. H., Leung H. and Wang G. L.
Mol Plant Microbe Interact (2014), 27(6) 528-36.

The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice

Park C. H*., Chen S*., Shirsekar G*., Zhou B*., Khang C. H., Songkumarn P., Afzal A. J., Ning Y., Wang R., Bellizzi M., Valent B. and Wang G. L.
Plant Cell (2012), 24(11) 4748-62. (*equal contribution)

The U-Box E3 ligase SPL11/PUB13 is a convergence point of defense and flowering signaling in plants

Liu J., Li W., Ning Y., Shirsekar G., Cai Y., Wang X., Dai L., Wang Z., Liu W. and Wang G. L.
Plant Physiol (2012), 160(1) 28-37.

Contact

gautam.shirsekar@tuebingen.mpg.de

Thanvi Srikant

DNA methylation. Epigenetics.

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Thanvi Srikant

My project is focused on understanding how epigenetic modifications can impact gene expression at the molecular level. I am employing transgene-induced epi-mutations as well as natural epigenetic variants in Arabidopsis thaliana, and primarily focus on alterations in DNA methylation. Monitoring genome-wide changes in chromatin architecture and gene expression in varying methylation backgrounds helps me distinguish the processes at play and their temporal roles.

Research Topics

- DNA methylation
- Epigenetics

Bio

- 2017 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2017 / B.Tech Industrial Biotechnology / Anna University, Chennai, India
- 2017 / Intern / Max Planck Institute for Plant Breeding Research, Cologne
- 2016 / Intern / Max Planck Institute for Developmental Biology

Contact

thanvi.srikant@tuebingen.mpg.de

Bridgit Waithaka

Evolutionary genomics of herbicide-resistant weeds.

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Bridgit Waithaka

The evolution of herbicide-resistant weeds is a predictable consequence of natural selection. Although resistance alleles bestow a fitness advantage in the presence of herbicide, resistance may come at a fitness cost in the absence of herbicide selection. This would influence the spread of herbicide-resistance-conferring alleles in natural populations.
I am evaluating the costs associated with a prominent herbicide-resistant mutation in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), the target enzyme of glyphosate, by modelling herbicide resistance in A. thaliana using CRISPR-Cas9 technology. High resolution phenotyping and competition experiments are employed to assess fitness and changes in allele frequency.
In addition, I am conducting a genome-wide association study investigating the alleles underlying the differential response of A. thaliana accessions to varying glyphosate doses.

Research Topics

- Evolutionary genomics of herbicide-resistant weeds

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2015 / MSc in Forensic Science / Universidad de Córdoba, Spain; Instituto Superior de Ciências da Saúde Egas Moniz, Portugal; University of Lincoln, UK; John Jay College of Criminal Justice, USA
- 2011 to 2013 / Research technician / International Maize and Wheat Improvement Centre, CIMMYT, Nairobi, Kenya
- 2007 to 2010 / BSc in Biochemistry / University of Nairobi, Kenya

Contact

bridgit.waithaka@tuebingen.mpg.de

Frank Weiss

Plant Breeding.

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Frank Weiss

I am a trained gardener and help with plant care in various projects. Apart from the standard lab pet Arabidopsis thaliana, I am also in charge of other plant species that require more specialized growth conditions.

Research Topics

- Plant Breeding

Bio

- 2013 to present / Gardener / Max Planck Institute for Developmental Biology

Contact

frank.weiss@tuebingen.mpg.de

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Genome Informatics

Haim Ashkenazy

Plant evolutionary genomics. Evolutionary dynamics of gene content in bacterial and plant genomes. Co-evolution of plant-microbe interactions.

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Haim Ashkenazy

Exposure to bacterial pathogens and symbionts plays a major role in shaping plant genomes through the course of evolution. My research focuses on identifying genomic signatures of plant-bacterial interactions in order to discover and understand plant adaptations to biotic stress. As a bioinformatician, I address these questions by developing computational methods, which take advantage of rich sequence data, such as population-level genomics. Specifically, I employ a comparative-genomics approach, which frames the analysis of sequence information in the context of the underlying evolutionary process. Homepage: http://haimashkenazy.wixsite.com/home

Research Topics

- Plant evolutionary genomics
- Evolutionary dynamics of gene content in bacterial and plant genomes
- Co-evolution of plant-microbe interactions

Bio

- 2018 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2016 to 2018 / Postdoc / Tel Aviv University, Israel
- 2010 to 2015 / PhD in Bioinformatics / Tel Aviv University, Israel
- 2006 to 2009 / M.Sc. in Computational Biology / Bar Ilan University, Israel
- 2003 to 2005 / B.Sc. in Computational Biology / Bar Ilan University, Israel

Selected References

Multiple sequence alignment averaging improves phylogeny reconstruction

Ashkenazy, H., Sela, I., Levy Karin, E., Landan, G., Pupko, T. Systematic Biology (2018).

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

Ashkenazy, H. Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., Ben-Tal, N. Nucleic Acids Res (2016), 44: W344-350.

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

Sela, I.*, Ashkenazy, H.*, Katoh, K., Pupko, T. Nucleic Acids Res, (2015), 43: W7-14 (* Equal contribution).

Indel reliability in indel-based phlyogenetic inference

Ashkenazy, H., Cohen, O., Pupko, T., Huchon, D. Genome Biol Evol, (2014), 6(12): 3199-3209.

Contact

haim.ashkenazy@tuebingen.mpg.de

Ilja Bezrukov

Automated Phenotyping. Pipelines for processing of short and long read sequencing data.

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Ilja Bezrukov

Research Topics

- Automated Phenotyping
- Pipelines for processing of short and long read sequencing data

Bio

- 2016 to present / Staff scientist / Max Planck Institute for Developmental Biology
- 2014 to 2015 / Researcher / Werner Siemens Imaging Center, Tübingen, Germany
- 2008 to 2014 / PhD student / Werner Siemens Imaging Center and Max Planck Institute for Intelligent Systems, Tübingen, Germany
- 2007 / Research assistant / Department of Medical Informatics, Aachen, Germany
- 2006 / Diploma in Computer Science / RWTH Aachen University, Germany

Selected References

Quantitative Evaluation of Segmentation- and Atlas-Based Attenuation Correction for PET/MR on Pediatric Patients

Bezrukov, I., Schmidt, H., Gatidis, S., Mantlik, F., Schafer, J. F., Schwenzer, N. and Pichler, B. J.
J Nucl Med (2015), 56(7):1067-74

MR-based attenuation correction methods for improved PET quantification in lesions within bone and susceptibility artifact regions

Bezrukov, I., Schmidt, H., Mantlik, F., Schwenzer, N., Brendle, C., Schölkopf, B. and Pichler, B.
J Nucl Med (2013), 54(10):1768-74

MRI-based attenuation correction for whole-body PET/MRI: quantitative evaluation of segmentation- and atlas-based methods

Hofmann, M., Bezrukov, I., Mantlik, F., Aschoff, P., Steinke, F., Beyer, T., Pichler, B. J. and Schölkopf, B.
J Nucl Med (2011), 52(9):1392-9 (*equal contribution)

Contact

ilja.bezrukov@tuebingen.mpg.de

Pablo Carbonell

Long-read sequencing and genome assembly. Grapevine somatic variation.

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Pablo Carbonell

I am interested in somatic variation as a source of cultivar innovation in grapevine. Vegetative propagation is used by viticulturists to keep the varietal attributes of highly heterozygous grape cultivars. Paradoxically, somatic mutations accumulate during long periods of vegetative propagation, eventually giving rise to new phenotypes of agronomic interest. To map the causal mutations in selected somatic variants of traditional wine cultivars, I produce haplotype-aware genome assemblies and use them in comparative genomics and genetic studies. Target traits range from grape color variation to adaptation of production to climate change.

Research Topics

- Long-read sequencing and genome assembly
- Grapevine somatic variation

Bio

- 2018 to present / Postdoctoral fellow / Max Planck Institute for Developmental Biology
- 2012 to 2018 / Research Associate / Institute for Grape and Wine Sciences, La Rioja, Spain
- 2009 to 2011 / Postdoc / Spanish National Center for Biotechnology (CNB), Madrid, Spain
- 2003 to 2008 / PhD in Biotechnology / Plant Molecular and Cell Biology Institute (IBMCP), Valencia, Spain
- 1998 to 2002 / BSc in Biology / University of Alicante, Spain

Selected References

The Major Origin of Seedless Grapes Is Associated with a Missense Mutation in the MADS-Box Gene VviAGL11.

Royo, C., Torres-Pérez, R., Mauri, N., Diestro, N., Cabezas, J. A., Marchal, C. Lacombe, T., Ibanez, J., Tornel, M., Carreno, J., Martínez-Zapater, J. M., Carbonell-Bejerano, P.
Plant Physiol (2018), 177(3): 1234-1253.

Catastrophic Unbalanced Genome Rearrangements Cause Somatic Loss of Berry Color in Grapevine.

Carbonell-Bejerano, P., Royo, C., Torres-Pérez, R., Grimplet, J., Fernandez, L., Franco-Zorilla, J. M., Lijavetzky, D., Baroja, E., Martinez, J., Garcia-Escudero, E., Ibanez, J., Martínez-Zapater, J. M.
Plant Physiol (2017), 175(2): 786-801.

A fertilization-independent developmental program triggers partial fruit development and senescence processes in pistils of Arabidopsis.

Carbonell-Bejerano, P., Urbez, C., Carbonell, J., Granell, A., Perez-Amador, M. A.
Plant Physiol (2010), 154(1): 163-172.

Contact

pablo.carbonell@tuebingen.mpg.de

Oliver Deusch

Plant-microbiome-interaction. Comparative genomics of phyllosphere bacteria.

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Oliver Deusch

I am a bioinformatician with a wide range of interests, having worked in areas such as plant and organelle evolution, bacterial genomics, genome and transcriptome assembly and companion animal microbiome.

Research Topics

- Plant-microbiome-interaction
- Comparative genomics of phyllosphere bacteria

Bio

- 2018 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2018 to present / Scientific Head of Bioinformatics / CeMeT GmbH, Tübingen
- 2011 to 2017 / Bioinformatician / Mars Petcare, Melton Mowbray, UK
- 2010 to 2011 / Postdoc / Massey University, Palmerston North, New Zealand
- 2005 to 2009 / PhD in Biology / Düsseldorf University, Germany
- 1998 to 2005 / Diplom in Biology / Düsseldorf University, Germany

Selected References

Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens

Deusch, O., O'Flynn, C., Colyer, A., Morris, P., Allaway, D., Jones, P. G., Swanson, K. S.
PLoS One (2014), 9(7):e101021

A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis

Davis, I. J., Wallis, C., Deusch, O., Colyer, A., Milella, L., Loman, N., Harris, S.
PLoS One (2013), 8(12):e83158

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

Gruenheit, N., Deusch, O., Esser, C., Becker, M., Voelckel, C., Lockhart, P.
BMC Genomics (2012), 13:92

Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor

Deusch, O., Landan, G., Roettger, M., Gruenheit, N., Kowallik, K. V., Allen, J. F., Martin, W., Dagan, T.
Mol Biol Evol (2008), 25(4):748-61

Contact

oliver.deusch@tuebingen.mpg.de

Christian Kubica

Patterns of structural variation in genomes.

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Christian Kubica

My main goal is to describe structural variation in plant genomes, and understand its contribution to natural selection and adaptation. To do so, I use Next Generation Sequencing data, importantly sequencing reads obtained with long-read technology, as well as comparative genomics.

Research Topics

- Patterns of structural variation in genomes

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2012 to 2016 / MSc in Genome-Based Systems Biology / Bielefeld University
- 2009 to 2012 / BSc in Biosciences / Münster University

Contact

christian.kubica@tuebingen.mpg.de

Grey Monroe

Plant genomics. Climate adaptation.

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Grey Monroe

Our research aims to connect genomic diversity with plant traits and the climate components that drive their evolution. We use functional annotation of genomic diversity and gene-editing to identify causal loci at genomic scales and functional molecular resolutions. We also use remote sensing and function-valued trait approaches to study the environmental drivers, physiology, and ecosystem consequences of genome-environment interactions. I believe the key to a mechanistic understanding of climate adaptation lies in multidisciplinary syntheses connecting genomes, traits, and environments.

Research Topics

- Plant genomics
- Climate adaptation

Bio

- 2019 - present / Post Doctoral Fellow / Max Planck Institute for Developmental Biology
- 2014-2019 / PhD student / Colorado State University

Selected References

Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function.

Monroe, J. G., Powell, T., Price, N., Mullen, J. L., Howard, A., Evans, K., Lovell, J.T., McKay, J. K.
eLife. (2018), e41038

Contact

grey.monroe@tuebingen.mpg.de

Yoav Voichek

Evolution of transcriptional networks. Transcriptional regulation. Plant evolutionary genomics.

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Yoav Voichek

Plants adapting to distinct ecological niches need to cope with variable antagonistic factors, such as limited nutritional resources, competitors, pathogens, and adverse climate. Gene expression is expected to change accordingly, hence, plants adapted to separate environments will transcribe their genome differently even when grown under the same controlled conditions. I am interested in how transcription regulation is moulded by the environment and how the regulatory genome facilitates these changes, focusing on natural strains of A. thaliana.

Research Topics

- Evolution of transcriptional networks
- Transcriptional regulation
- Plant evolutionary genomics

Bio

- 2018 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2010 to 2016 / PhD in Bioinformatics / Weizmann Institute of Science, Israel
- 2001 to 2008 / BSc in Mathematics / Open University, Israel

Selected References

Epigenetic Control of Expression Homeostasis during Replication is Stabilized by the Replication Checkpoint

Voichek, Y.*, Mittelman, K.*, Gordon, Y., Bar-Ziv, R., Lifshitz Smit, D., Shenhav R., Barkai, N.
Mol Cell. (2018), S1097-2765(18): 30389-7

Expression homeostasis during DNA replication

Voichek, Y.*, Bar-Ziv, R.*, Barkai, N.
Science. (2016), 351(6277): 1087-90

Chromatin dynamics during DNA replication

Bar-Ziv, R.*, Voichek, Y.*, Barkai, N.
Genome Res. (2016), 26(9):1245-56

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencing within cells

Fuchs, G.*, Voichek, Y.*, Benjamin, S., Gilad, S., Amit, I., Oren, M.
Genome Biol. (2014), 15(5):R69

Contact

Yoav.Voichek@tuebingen.mpg.de

Sebastian Vorbrugg

Application of genome graphs.

‹ ›

Sebastian Vorbrugg

Due to local adaptation and population structure, genomes of different individuals can vary to a great extent. To represent this variation, we utilize the concept of variation graphs, which provide a powerful toolkit. I am working to combine these genome graphs with genome-wide-association (GWA) approaches to connect complex genomic variation with organism traits. Beginning with multiple whole-genome assemblies, I will first tackle the problem of graph construction, providing an accurate representation of genomic variation and the basis of the analysis.

Research Topics

- Application of genome graphs

Bio

- 2019 to present / PhD student / Max Planck Institute for Developmental Biology
- 2015 to 2019 / MSc in Molecular Biology and Bioinformatics / University of Tübingen
- 2012 to 2015 / BSc Biochemistry / University of Ulm

Contact

sebastian.vorbrugg@tuebingen.mpg.de

Hua Wang

The pre-historica human activity impact on the genetic diversity and genetic structure of endanger tree populations.

‹ ›

Hua Wang

The health of forest resources in the Amazon have been severely damaged in recent years. To identify human impacts in Amazonian forests important for forest conservation and sustainable management, we are comparing Brazil nut (Bertholletia excelsa) genetics and dendrochronology at different distances from archaeological sites. With these analyses we seek to uncover the effects of deliberate human management and selection. We are also comparing mahogany (Swietenia macrophylla) genetics and dendrochronology at different distances from archaeological sites to investigate how human intervention and abandonment affect non-selected tree species.

Research Topics

- The pre-historica human activity impact on the genetic diversity and genetic structure of endanger tree populations

Bio

- 2019 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2010 to 2018 / Associate professor / Hua Zhong Agricultural University, China
- 2004 to 2018 / PhD in Tree genetics and breeding / Chinese Academy of Forestry, China
- 2000 to 2004 / Majored in Forestry / College of Forestry, Sichuan Agricultural University, China

Selected References

The genetic diversity and introgression of Juglans regia and Juglans sigillata in Tibet as revealed by SSR markers.

Wang, H., Pan, G., Ma, Q., Zhang, J., Pei, D.
Tree Genetics & Genomes (2015), 11(1)

Contact

hua.wang@tuebingen.mpg.de

To Top

Plant Microbe Co-Evolution

Alejandra Duque

Plant - microbe interactions. Genetic determinats of pathogenicity. Infection genetics.

‹ ›

Alejandra Duque

Pseudomonas is one of the most common plant pathogens, and can infect a wide range of species. However, infection potential varies greatly between individual Pseudomonas isolates, in part due to their specific repertoire of effectors. I am interested in how genetic variation of both host and pathogen impacts the outcome of infection. To address this question, I use a natural Arabidopsis – Pseudomonas pathosystem, as Arabidopsis thaliana is a host to different strains of Pseudomonas species in the wild.

Research Topics

- Plant - microbe interactions
- Genetic determinats of pathogenicity
- Infection genetics

Bio

- 2018 to present / PhD student / Max Planck Institute for Developmental Biology
- 2016-2018 / International Master in Innovative Medicine / University of Groningen, The Netherlands and Uppsala University, Sweden
- 2015-2016 / Young Researcher / Universidad de Antioquia, Colombia
- 2010-2014 / Bachelor degree in Biology / Universidad CES, Colombia

Contact

alejandra.duque@tuebingen.mpg.de

Talia Karasov

Microbial evolution. Plant evolutionary genomics. Plant pathogen interactions.

‹ ›

Talia Karasov

Successful pathogen colonization of a host requires not only that the pathogen successfully surpass the host immune system, but also that it survive and proliferate in the presence of other microbes. My research focuses on the evolution of pathogen and plant in the context of a larger microbial community.

Research Topics

- Microbial evolution
- Plant evolutionary genomics
- Plant pathogen interactions

Bio

- 2015 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2015 / PhD in Genetics, Genomics & Systems Biology / University of Chicago, USA
- 2008 / BSc in Biological Sciences / Stanford University, USA

Selected References

The long-term maintenance of a resistance polymorphism through diffuse interactions

Karasov T. L., Kniskern J. M., Gao L., DeYoung B. J., Ding J., Dubiella U., Lastra R. O., Nallu S., Roux F., Innes R. W., Barrett L. G., Hudson R. R.and Bergelson J. Nature (2014), 512(7515) 436-40.

Genomic variability as a driver of plant-pathogen coevolution?

Karasov T. L., Horton M. W. and Bergelson J.
Curr Opin Plant Biol (2014), 18 24-30.

Evidence that adaptation in Drosophila is not limited by mutation at single sites

Karasov T., Messer P. W. and Petrov D. A.
PLoS Genet (2010), 6(6) e1000924.

Contact

talia.karasov@tuebingen.mpg.de

Derek Lundberg

Map distribution of microbial genotypes onto that of plant genotypes in a wild field. Associate plant and microbial genotypes in nature while tracking plant growth and transcriptional output. Test predictions about the microbial community and fitness using targeted genome engineering of locally adapted plants.

‹ ›

Derek Lundberg

Nature exposes plants to large communities of microbes that are also interacting amongst themselves. Because maintaining an immune system is costly, successful plants must streamline their defense capabilities. I am investigating the influence of locally-adapted plant genetic variation on the colonization of wild microbes in the field. This will help understand the pressures that drive the evolution of the plant immune system, and to identify plant genes and key microbes that significantly contribute to microbial colonization patterns.

Research Topics

- Map distribution of microbial genotypes onto that of plant genotypes in a wild field
- Associate plant and microbial genotypes in nature while tracking plant growth and transcriptional output
- Test predictions about the microbial community and fitness using targeted genome engineering of locally adapted plants

Bio

- 2014 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2007 to 2014 / PhD in Genetics and Molecular Biology / University of North Carolina, Chapel Hill, USA
- 2002 to 2006 / BSc in Biology / University of North Carolina, Chapel Hill, USA

Selected References

Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

Wagner M. R., Lundberg D. S., Coleman-Derr D., Tringe S. G., Dangl J. L. and Mitchell-Olds T.
Ecol Lett (2014), 17(6) 717-26.

Practical innovations for high-throughput amplicon sequencing

Lundberg D. S., Yourstone S., Mieczkowski P., Jones C. D. and Dangl J. L.
Nat Methods (2013), 10(10) 999-1002.

Defining the core Arabidopsis thaliana root microbiome

Lundberg D. S., Lebeis S. L., Paredes S. H., Yourstone S., Gehring J., Malfatti S., Tremblay J., Engelbrektson A., Kunin V., del Rio T. G., Edgar R. C., Eickhorst T., Ley R. E., Hugenholtz P., Tringe S. G. and Dangl J. L.
Nature (2012), 488(7409) 86-90.

Contact

derek.lundberg@tuebingen.mpg.de

Manuela Neumann

Flowering time regulation in Arabidopsis. INTACT technology.

‹ ›

Manuela Neumann

I am currently on maternity leave - back at the bench in 2017.

Research Topics

- Flowering time regulation in Arabidopsis
- INTACT technology

Bio

- 2010 to present / Technician / Max Planck Institute for Developmental Biology
- 2010 / Lab Assistant / Helmholtz Centre for Infection Research, Brunswick, Germany
- 2007 to 2010 / Vocational education / Helmholtz Centre for Infection Research, Brunswick, Germany

Contact

manuela.neumann@tuebingen.mpg.de

Or Shalev

Genetic factors determining the specificity of plant-microbe interactions.

‹ ›

Or Shalev

Plants serve as a rich habitat for microbes. Numerous macro and micro niches, both inside the plant and on its surface, allow a diverse set of microbes to thrive and propagate.
Using Arabidopsis thaliana and the wide-spread gram-negative bacterium Pseudomonas syringae as a model system, I aim to understand the interaction of host and microbe genotypes, and thus the selectivity of colonization. I am investigating both pathogenic and mutualistic Pseudomonas strains, and use genomic tools to decipher the dynamics of gene repertoires enabling or preventing plant colonization - both from a plant and a microbe perspective.

Research Topics

- Genetic factors determining the specificity of plant-microbe interactions

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2016 / MSc in Plant Science / Hebrew University, Israel
- 2013 to 2014 / Student exchange semester / Göttingen University, Germany
- 2010 to 2013 / BSc in Agroecology and Biotechnology / Hebrew University, Israel

Selected References

Pseudozyma aphidis Induces Salicylic-Acid-Independent Resistance to Clavibacter michiganensis in Tomato Plants

Barda, O., Shalev, O., Alster, S., Buxdorf, K., Gafni, A. and Levy, M.
Plant Disease (2015), 99(5): 621-626

Contact

or.shalev@tuebingen.mpg.de

To Top

Hybrid performance and fitness tradeoffs

Ana-Cristina Barragan Lopez

Hybrid incompatibility. Evolution of immune receptors. Arabidopsis arenosa.

‹ ›

Ana-Cristina Barragan Lopez

The combination of two genomes in hybrid plants can lead to detrimental effects, often caused by interaction of incompatible immune genes. NLR-type immune receptors play major roles in this interaction, and to gain a better understanding of the molecular mechanisms involved in their activation, I am investigating the complexity and variability of NLR-type immune receptor gene clusters in Arabidopsis thaliana. I also study the Arabidopsis arenosa to find out whether hybrid incompatibility is more or less prevalent in this naturally outcrossing species, compared to the closely related selfer Arabidopsis thaliana.

Research Topics

- Hybrid incompatibility
- Evolution of immune receptors
- Arabidopsis arenosa

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2016 / MSc in Plant Molecular Biology / University of Tübingen, Germany
- 2010 to 2013 / BSc in Biology / University of Tübingen, Germany

Contact

cristina.barragan@tuebingen.mpg.de

Monika Demar

I'm a research technician in the department.

Contact

monika.demar@tuebingen.mpg.de

Anette Habring

Hybrid incompatibility. Evolution of disease resistance.

‹ ›

Anette Habring

My work as a technician in the group focuses on molecular and plant projects aimed at identifying hybrid incompatibilities and characterizing the underlying causal genes. I have been coordinating the generation and maintenance of the 80x80 diallel of Arabiodopsis thalinana accessions. Furthermore, I am generating molecular tools for the analysis of RPW8, and RPP8, two of the genes we are analyzing more closely now. Aside from research, I am lab safety person and have several organizational tasks that help the department run smoothly.

Research Topics

- Hybrid incompatibility
- Evolution of disease resistance

Bio

- 2002 to present / Technician / Dept. of Molecular Biology, Max Planck Institute for Developmental Biology
- 2001 to 2002 / Technichan / Dept. of Cell Biology, Max Planck Institute for Developmental Biology
- 1991 to 2001 / Technichan / Dept. of Biochemistry, Max Planck Institute for Developmental Biology
- 1986 to 1991 / Technician / Friedrich Miescher Laboratory, Tübingen, Germamy

Selected References

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis

Chae E., Bomblies K., Kim S. T., Karelina D., Zaidem M., Ossowski S., Martin-Pizarro C., Laitinen R. A., Rowan B. A., Tenenboim H., Lechner S.,Demar M., Habring-Muller A., Lanz C., Ratsch G. and Weigel D.
Cell (2014), 159(6) 1341-51.

Contact

anette.habring@tuebingen.mpg.de

Lei Li

Biochemical characterization of immune protein complexes. Plant-pathogen interaction. Hybrid incompatibility.

‹ ›

Lei Li

Plants have evolved sophisticated mechanisms to recognize non-self molecules, allowing them to deploy effective immune reactions against a myriad of pathogens. Resistance protein plays an important role in the process of pathogen defense, autoimmunity, and hybrid incompatibility. My research focuses on the activation mechanism of plant resistance proteins.

Research Topics

- Biochemical characterization of immune protein complexes
- Plant-pathogen interaction
- Hybrid incompatibility

Bio

- 2016 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2010 to 2015 / PhD in Genetics / Chinese Academy of Sciences, Beijing, China
- 2006 to 2010 / BSc in Biotechnology / Northwest A&F University, Yangling, China

Selected References

Activation-Dependent Destruction of a Co-receptor by a Pseudomonas syringae Effector Dampens Plant Immunity

Li, L.*, Kim, P.*, Yu, L.*, Cai, G., Chen, S., Alfano, J. R., Zhou, J. M.
Cell Host Microbe. (2014), 20(4):504-14.

The FLS2-associated kinase BIK1 directly phosphorylates the NADPH oxidase RbohD to control plant immunity

Li, L.*, Li, M.*, Zhou, Z., Liang, X., Liu, Z., Cai, G., Gao, L., Zhang, X., Wang, Y., Chen, S., Zhou, J. M.
Cell Host Microbe. (2014), 15(3):329-38.

Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex

Sun, Y.*, Li, L.*, Macho, A. P., Han, Z., Hu, Z., Zipfel, C., Zhou, J. M., Chai, J.
Science. (2013), 342(6158):624-8.

Contact

lei.li@tuebingen.mpg.de

Wei Yuan

The molecular mechanism of heterosis.

‹ ›

Wei Yuan

I am a plant population geneticist being trained to exploit state-of-the-art molecular, genomics, and statistical tools to address evolutionary questions. My current research focus is on hybrid plants, and I use systematically acquired growth trajectories and transcriptome profiles from Arabidopsis thaliana hybrids and their parents to apply GWAS, TWAS, and eQTL analyses that will allow me uncover the relationship between genetic variation (available from the 1001 Genomes resource) and hybrid phenotype. My research will systematically evaluate whether heterosis is mainly dictated by overall heterozygosity in hybrid genomes, or rather by the expression/interactions of a core set of genes.

Research Topics

- The molecular mechanism of heterosis

Bio

- 2016 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2016 / PhD in Biology / New York University, USA
- 2009 / BSc in Plant Biology/ China Agricultural University, China

Selected References

Extreme QTL mapping of germination speed in Arabidopsis thaliana

Yuan, W., Flowers, J. M., Sahraie, D. J., Ehrenreich, I. M., Purugganan, M. D.
Molecluar Ecology (2016), 25(17):4177-96.

Cryptic genetic variation for Arabidopsis thaliana seed germination speed in a novel salt stress environment

Yuan, W., Flowers, J. M., Sahraie, D. J., Ehrenreich, I. M., Purugganan, M. D.
G3 (2016), 6(10):3129-38.

Contact

wei.yuan@tuebingen.mpg.de

To Top

Ecological Genetics

Marie Klein

Genetics of disease resistance.

‹ ›

Marie Klein

Plants fend off pathogens with an arsenal of molecular weapons. Prominent players are NLR genes, which are numerous and very diverse, even within a single species. It is believed that drawing from this diversity allows plant populations to survive rapid changes in pathogen pressure. I study Arabidopsis thaliana and its oomycete pathogen Hyaloperonospora arabidopsidis to uncover genes conferring resistance. Looking at host and pathogen from local as well as global collections, I aim to uncover at which spatial scales resistance strategies change, vary, or co-occur. At the same time, I interrogate the pathogen genomes to study associated changes in virulence genes.

Research Topics

- Genetics of disease resistance

Bio

- 2019 to present / Research Assistant / Max Planck Institute for Developmental Biology
- 2015-2018 / MSc in Crop Science / University of Bonn, Germany
- 2012-2015 / BSc in Agriculture / University of Bonn, Germany

Contact

marie.klein@tuebingen.mpg.de

Sabine Schaefer

Disease resistance genes.

‹ ›

Sabine Schaefer

Disease resistance is often conferred by Nucleotide-binding Leucine-rich-Repeat (NLR) proteins. Many copies, often highly similar, are encoded in plant genomes, and small changes may alter the plant defense response. My work focusses on the molecular identification and functional characterization of Arabidopsis thaliana NLR genes conferring resistance to diverse isolates of the oomycete Hyaloperonospora arabidopsidis. Furthermore, I develop enrichment protocols for the characterization of NLR loci from different A. thaliana collections.

Research Topics

- Disease resistance genes

Bio

- 2019 to present / Technician / Max Planck Institute for Developmental Biology
- 2016-2019 / Technician / University of Tübingen, Germany
- 2004-2008, 2013-2014 / Technician / Helmholtz Zentrum and LMU Munich, Germany
- 1997-2004, 2008-2013, 2015 / Technician / University hospital Tübingen, Germany

Contact

sabine.schaefer@tuebingen.mpg.de

Rebecca Schwab

Spatial genetics. Molecular evolution of disease resistance genes. Oomycete biology.

‹ ›

Rebecca Schwab

Trained as a molecular geneticist, I have always been curious about molecular mechanisms, and spent many years investigating small RNAs and their impact on Arabidopsis development. A game-changer was our Pathodopsis adventure, where the bind-blowing experience of finding and studying plants ‘in the wild’ taught me that molecular biology is often like watching an elephant in a zoo – a small part of reality. Extending the ‘safari’ feeling, I am now combining ecology and genetics. Drawing from the naturally occurring variation in Arabidopsis populations, we study disease resistance to a wide-spread oomycete pathogen. Our goal is to understand the spatio-temporal dynamics of resistance and virulence, as well as the molecular (and functional) evolution of resistance loci at various spatial scales.

Research Topics

- Spatial genetics
- Molecular evolution of disease resistance genes
- Oomycete biology

Bio

- 2020 to present / Project leader / Max Planck Institute for Developmental Biology
- 2012-2019 / Research coordinator / Max Planck Institute for Developmental Biology
- 2009-2012 / Postdoc / IMBP, Strasbourg, France; ETH Zürich, Switzerland
- 2006-2008 / Postdoc / Cold Spring Harbor Laboratory, USA
- 2006 / PhD in Biology / Max Planck Institute for Developmental Biology
- 2002 / Diploma in Biology / University of Tübingen, Germany, and Salk Institute for Biological Studies, USA

Selected References

Enhanced microRNA accumulation through stemloop-adjacent introns

Schwab R., Speth C., Laubinger S. and Voinnet O.
EMBO Rep (2013), 14(7) 615-21.

Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana

Schwab R., Maizel A., Ruiz-Ferrer V., Garcia D., Bayer M., Crespi M., Voinnet O. and Martienssen R. A.
PLoS One (2009), 4(6) e5980.

Highly specific gene silencing by artificial microRNAs in Arabidopsis

Schwab R., Ossowski S., Riester M., Warthmann N. and Weigel D.
Plant Cell (2006), 18(5) 1121-33.

Contact

rebecca.schwab@tuebingen.mpg.de

To Top

Ancient Genomics and Evolution

Katrin Fritschi

DNA sequencing and associated challenges.

‹ ›

Katrin Fritschi

My work focuses on challenges associated with Next Generation Sequencing. Apart from operating the instruments, I am involved in various research projects.

Research Topics

- DNA sequencing and associated challenges

Bio

- 2014 to present / Technical and Scientific Assistant / Max Planck Institute for Developmental Biology
- 2012 to 2014 / Technician / Max Planck Institute for Developmental Biology
- 2010 to 2012 / Research Technician / Philips
- 2010 / MSc in Biotechnology / RWTH Aachen University, Germany

Selected References

SPECT/CT imaging of temperature-sensitive liposomes for MR-image guided drug delivery with high intensity focused ultrasound.

de Smet, M., Langereis, S. van den Bosch, S., Bitter, K., Hijnen, N. M., Heijman, E., Grüll, H.
J Control Release (2013), 169(1-2): 82-90.

Treatment planning based on polypeptide radiotoxicity serum markers.

Bitter, K., Ribbing, C.
WIPO Patentscope (2013), WO2013001507

Clinical Decision Support (CDS) for Radiotherapy in prostate cancer.

Ribbing, C., Bitter, Katrin
WIPO Patentscope (2014), WO2014147509

Contact

katrin.fritschi@tuebingen.mpg.de

Sergio Latorre

Ancient genomics. Evolution of methylation in key plant species. Dynamics of host - pathogen interactions through history.

‹ ›

Sergio Latorre

Historical and ancient samples, such as dried plants in herbaria, can tell us about the genetic makeup of a species at the time of collection and allow us to directly study, rather than infer, changes in DNA sequences over historical time spans. Advances in sequencing technologies and extraction methods have allowed us to interrogate not only very small amounts of material, but also epigenetic modifications on the DNA, such as cytosine methylation. I am analyzing those methylation patterns in ancient and modern plant samples to study changes across recent history, which will allow us to investigate the evolution of epigenetically controlled traits.

Research Topics

- Ancient genomics
- Evolution of methylation in key plant species
- Dynamics of host - pathogen interactions through history

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2014 / MSc in Microbiology / Universidad Nacional de Colombia
- 2010 / Agronomic Engineer / Universidad Nacional de Colombia

Selected References

Environmental occurrence of arsenic in Colombia: a review.

Alonso, D. L*., Latorre, S*., Castillo, E., Brandão, P.F.
Environmental Pollution (2014). 186: 272-281. (*equal contribution)

Contact

sergio.latorre@tuebingen.mpg.de

To Top

Alumni

Filippo Abbondanza (former Intern, 2016)

MSc student,

University of Edinburgh, UK

Ji Hoon Ahn (former Postdoc, 1998-2001)

Professor,

Korea University, Korea

Florian Aldehoff (former MS student, 2006-2007)

Bioinformatics Staff Scientist,

CeGAT, Tübingen, Germany

Stig Andersen (former Postdoc, 2006-2007)

Assistant Professor,

University of Aarhus, Denmark

Chloé-Agathe Azencott (former Postdoc, 2011-2013)

Researcher,

CBIO, Fontainbleau, France

Sureshkumar Balasubramanian (former Postdoc, 2002-2007)

Associate Professor,

Monash University, Melbourne, Australia

Claude Becker (former Postdoc, 2010 to 2016)

Group Leader,

Gregor Mendel Institute, Vienna, Austria

Felix Bemm

Staff Scientist,

KWS Saat SE, Einbeck, Germany

Daniela Bezdan (former PhD student, 2005-2009)

Chief Scientific Officer,

at Bumrungrad International Hospital, New York

Paul Bilinski (former Postdoc, 2016-2017)

Associate professor,

West Shore Community College, MI, USA

Miguel Blázquez (former Postdoc, 1996-2000)

Professor,

IBMCP, Valencia, Spain

Helena Boldt (former MS student, 2008-2009)

Research Technician,

Boston Children's Hospital, Boston, MA, USA

Kirsten Bomblies (former Postdoc, 2004-2009)

Professor,

ETH Zürich Switzerland

Karsten Borgwardt (former Group Leader)

Professor,

ETH Zürich, Switzerland

Marie Bouteillé (visiting PhD student, 2009-2010)

Postdoc,

INRA, Montpellier, France

Felix Breden (Sabbatical visitor, 2003)

Professor,

Simon Fraser University, Burnaby, Canada

Hernán Burbano (former Postdoc, 2012-2014)

Associate Professor,

UCL, London, UK

Maximilian A. Busch (former Postdoc, 1996-2000)

Sales Representative,

Tecniplast, Germany

Wolfgang Busch (former PhD student, 2004-2008)

Associate Professor,

Salk Institute, La Jolla, USA

Jun Cao (former Postdoc, 2007-2012)

Staff Scientist,

Dow Agrosciences, Indianapolis, IN, USA

Giovanna Capovilla (former PhD student, 2013-2017)

Postdoc,

Massachusetts Institute of Technology, USA

Jim Carrington (Sabbatical visitor, 2008)

Professor,

Donald Danforth Plant Science Center, St. Louis, MO, USA

Eunyoung Chae (former Postdoc, 2007-2017)

Assistant Professor,

National University of Singapore

Susan K. Christensen (former Postdoc, 1996-2000)

Michael Christie (former Postdoc, 2012-2014)

Patent Attorney,

Sydney, Australia

Richard Clark (former Postdoc, 2004-2008)

Associate Professor,

University of Utah, Salt Lake City, UT, USA

Silvio Collani (former Postdoc, 2012-2015)

Postdoc,

Umeå Plant Science Centre, Sweden

Vinicius Costa Galvão (former PhD student, 2008-2013)

Postdoc,

University of Lausanne, Switzerland

Sandip Das (former Postdoc, 2002-2004)

Associate Professor,

University of Delhi, New Delhi, India

Timothy Davison (former Postdoc, 2004-2005)

Vice President,

Almac Diagnostics, Craigavon, UK

Jane Devos (former PhD student, 2013-2016)

Staff scientist,

Symrise, Madagascar

José Dinenny (former PhD student, 2001-2005)

Staff Member,

Carnegie Institution, Stanford, USA

Ezgi Dogan (former MS student, 2015-2016)

PhD student,

Center for Plant Molecular Biology, Tübingen, Germany

Christian Dreischer (former MS student, 2011-2012)

Scientific Analyst, Computomics GmbH, Tübingen, Germany

Christine Dreyer (former Group leader, 2003-2013)

retired

Marion Dubarry (former MS Student, 2015)

Bioinformatics Engineer,

Genoscope, Evry, France

Moisés Expósito Alonso (former PhD student, 2014-2018)

Staff Associate and Assistant Professor by courtesy,

Carnegie Institution of Science and Stanford University, USA

WeigelWorld scientists

Director

Detlef Weigel

Detlef Weigel

Bio

Selected References

Contact

Evolutionary Genetics

Max Collenberg Gene expression in hybrid plants.

Max Collenberg

Research Topics

Bio

Contact

Adrian Contreras small RNAs. Epigenetics.

Adrian Contreras

Research Topics

Bio

Contact

Alba Gonzalez Co-evolution of Arabidopsis and its oomycete pathogen Hyaloperonospora.

Alba Gonzalez

Research Topics

Bio

Contact

Christa Lanz DNA sequencing and all associated challenges.

Christa Lanz

Research Topics

Bio

Selected References

Contact

Ulrich Lutz GxG interactions. Flowering time variation. Herbicide resistance.

Ulrich Lutz

Research Topics

Bio

Selected References

Contact

Fernando Rabanal Evolution and regulation of ribosomal RNA genes. Herbicide resistance.

Fernando Rabanal

Research Topics

Bio

Selected References

Contact

Gautam Shirsekar Co-evolution in natural A. thaliana – oomycete pathosystems.

Gautam Shirsekar

Research Topics

Bio

Selected References

Identification and characterization of suppressor mutants of spl11- mediated cell death in rice

The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice

The U-Box E3 ligase SPL11/PUB13 is a convergence point of defense and flowering signaling in plants

Contact

Thanvi Srikant DNA methylation. Epigenetics.

Thanvi Srikant

Research Topics

Bio

Contact

Bridgit Waithaka Evolutionary genomics of herbicide-resistant weeds.

Bridgit Waithaka

Research Topics

Bio

Contact

Frank Weiss Plant Breeding.

Frank Weiss

Research Topics

Bio

Contact

Genome Informatics

Haim Ashkenazy Plant evolutionary genomics. Evolutionary dynamics of gene content in bacterial and plant genomes. Co-evolution of plant-microbe interactions.

Haim Ashkenazy

Research Topics

Bio

Selected References

Contact

Ilja Bezrukov Automated Phenotyping. Pipelines for processing of short and long read sequencing data.

Ilja Bezrukov

Research Topics

Bio

Selected References

Contact

Pablo Carbonell Long-read sequencing and genome assembly. Grapevine somatic variation.

Pablo Carbonell

Max Collenberg

Gene expression in hybrid plants.

Adrian Contreras

small RNAs. Epigenetics.

Alba Gonzalez

Co-evolution of Arabidopsis and its oomycete pathogen Hyaloperonospora.

Christa Lanz

DNA sequencing and all associated challenges.

Ulrich Lutz

GxG interactions. Flowering time variation. Herbicide resistance.

Fernando Rabanal

Evolution and regulation of ribosomal RNA genes. Herbicide resistance.

Gautam Shirsekar

Co-evolution in natural A. thaliana – oomycete pathosystems.

Thanvi Srikant

DNA methylation. Epigenetics.

Bridgit Waithaka

Evolutionary genomics of herbicide-resistant weeds.

Frank Weiss

Plant Breeding.

Haim Ashkenazy

Plant evolutionary genomics. Evolutionary dynamics of gene content in bacterial and plant genomes. Co-evolution of plant-microbe interactions.

Ilja Bezrukov

Automated Phenotyping. Pipelines for processing of short and long read sequencing data.

Pablo Carbonell

Long-read sequencing and genome assembly. Grapevine somatic variation.

Oliver Deusch

Plant-microbiome-interaction. Comparative genomics of phyllosphere bacteria.

Christian Kubica

Patterns of structural variation in genomes.

Grey Monroe

Plant genomics. Climate adaptation.

Yoav Voichek

Evolution of transcriptional networks. Transcriptional regulation. Plant evolutionary genomics.