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People: Network Partners

There are nine partners involved in the SYSFLO network, and each group has a Early Stage Research Fellow training with them. Groups details can be found below, while fellow details are on their individual pages (links to left).

Prof Brendan Davies, University of Leeds

Prof Brendan Davies

Prof Davies' research group focuses on two related aspects of plant development; regulation by transcription and post-transcriptional regulation. The group has investigates the processes of nonsense-mediated mRNA decay in plants, as a means to ensure co-ordinated regulation of a suite of genes. There is also a long-standing interest in the transcription factors that regulate plant development, particularly flower development and their role in specification of floral organ identity and floral evolution. Prof Davies is coordinator of the SYSFLO project. More

The Davies' group is part of the Centre for Plant Sciences (CPS), in the Faculty of Biological Sciences at the University of Leeds. The CPS is one of the University's top performing research groups and its research spans the full range of plant science from basic molecular mechanisms to crops. CPS benefits from excellent research facilities, including a transgenic plant growth suite and University farm, as well as having access to the full range of expertise, equipment and facilities that a faculty with more than 150 academic groups can provide. More

Sandra Biewers is the SYSFLO research fellow at Leeds, click to find out more about her and her project.

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Prof Gerco Angenent, Plant Research International, Wageningen

Prof Gerco Angenent

Prof Angenent’s research group focuses on unravelling the molecular mechanisms underlying flower, floral organs and fruit development. Key regulators (mainly transcription factors) involved in these processes have been identified and the position of these regulators in the various pathways is being studied. The research group is also interested in the molecular action of transcription factors, in general by studying how these proteins form complexes, how they recognize specific DNA sequences and bind DNA and how they control transcription of target genes. Angenent is coordinator of the ERA-PG funded project CISCODE , which aims at the understanding of transcription factor-DNA interactions and how these interactions are conserved among different plant species. More

The Angenent group is part of Plant Research International (PRI), which is the largest plant research institute in The Netherlands (about 400 employees) and conducts multidisciplinary research in the fields of breeding, agronomy, genomics, bioinformatics and plant-environment interactions. From early 2009, PRI will be housed together with all the University’s Plant Sciences groups in a new building, with state-of-the-art facilities, equipment, techniques and expertise needed to carry out the proposed research. More

Alice Pajoro is the SYSFLO research fellow with the Angenent group, click to find out more about her and her project.

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Prof Lucia Colombo, University of Milan

Prof Lucia Colombo

Prof Lucia Colombo’s research group focuses on the unravelling of the molecular mechanisms underlying flower and ovule development. Key-regulators and target genes (mainly transcription factors) involved in these processes have been identified and the position of these regulators in the various pathways is being studied. The group is involved in a number projects including Marie Curie RTN TRANSISTOR focusing on transcriptional regulation, which is coordinated by Prof. Colombo. More

Prof. Colombo’s group is in the Biology department of the University of Milan. The University of Milan is one of the leading centres in Italy for plant molecular biology and houses more than 60 research groups working in fields of biology ranging from human genetics to plant biodiversity. This allows the researchers to exchange techniques and ideas with people working in different fields. A substantial number of groups are working on transcriptional regulation, abiotic and biotic stress response, and photosynthesis in Arabidopsis. More

Marta Mendes is the SYSFLO research fellow at Milan, click to find out more about her and her project.

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Prof George Coupland, Max Planck Institute for Plant Breeding

Prof George Coupland

The Coupland group was founded in Cologne during 2001, having spent the period between 1989 and 2001 at the John Innes Centre in the UK. The main research focus has been in the mechanisms underlying the control of flowering time, particularly to seasonal changes in day length and temperature. Papers defining several key regulatory mechanisms in flowering-time control have been published by the group, and are widely cited in the field. The lab has been involved in many national and international research projects, including the current EC Integrated Project AGRON-OMICS. More

The Max Planck Institute for Plant Breeding in Cologne is a leading European centre in plant science. It aims to utilize a wide range of genetic, genomic, cell biology, biochemical and chemical approaches to study fundamental regulatory processes in plants, and to propose how these could be exploited in plant breeding programmes. The institute employs around 350 people organised into four scientific departments as well as service groups and independent research groups. There are 28 research groups working on different aspects of plant biology in the institute. More

Aimone Porri is the SYSFLO research fellow with Prof Coupland, click to find out more about him and his project.

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Prof Robert Sablowski, John Innes Centre

Prof Robert Sablowski

The Sablowski team was initiated ten years ago and contains complementary expertise in plant molecular genetics, cell biology and biochemistry. The main focus of the research group has been on how regulatory genes control the different cellular activities required for meristem maintenance and floral organ initiation in Arabidopsis. Prof Sablowski currently co-ordinates a project that aims to model how regulatory genes control growth parameters of floral organs in Arabidopsis (ERASysBio BB/F005571/1). More

The John Innes Centre (JIC) is a leading European centre of excellence in plant and microbial science. Its mission is to carry out fundamental and strategic research, to train scientists and to make its findings available to society. The JIC employs approximately 800 scientists, support staff, visitors and students and is sponsored by nearly 50 organisations, including UK research councils, the EU, industry and charities. These resources facilitate exceptional research activities including significant investment to provide state-of-the-art platform technologies such as transcriptomics, proteomics and metabolomics with underpinning bioinformatics support. More

Katharina Schiessl is the SYSFLO research fellow at the JIC, click to find out more about her and her project.

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Dr Birgit Lewicki-Potapov, BIOBASE

Since its creation in 1997, BIOBASE's core business is to maintain and distribute databases on gene regulation and signal transduction. The original databases were developed as part of publicly funded projects at the Bioinformatics Research group in the GBF (now called HZI), in Germany. The main product is TRANSFAC®, a database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles (PWMs), which is extended by TRANSCompel™, a collection of experimentally proven composite regulatory elements, and TRANSPATH®, a signal transduction database which provides the possibility to compose signalling chains, pathways and networks, as well as to visualize them. The new ExPlain™ tool is devoted to the analysis of high-throughput gene expression data, such as the one generated by microarray, ChIP-on-CHIP or tiling array experiments.

BIOBASE has proven expertise in the study of promoter structure and prediction of binding sites for transcription factors. DNA sequence analysis has been performed for several groups of functionally related genes, such as cell cycle genes, genes induced upon immune response and genes expressed in cancer tissue among others. After acquisition of the Proteome databases from Incyte in January 2005, BIOBASE also owns one of the most comprehensive data resources on mammalian, plant, yeast and Caenorhabditis proteomes. More

Miguel Godinho is the SYSFLO research fellow at BIOBASE, click to find out more about him and his project.

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Prof Pawel Krajewski, Polish Academy of Sciences

Dr hab. Paweł Krajewski has more than 20 years experience in research on mathematical, statistical and computational methods applicable in genetics, genomics and plant breeding. His group focuses on estimation and hypotheses testing in mixed linear and semiparametric models and problems in simultaneous testing of many statistical hypotheses. Applications of the obtained solutions are considered in the analysis of phenotypic data, analysis of microarray data, analysis of high-throughput sequencing data, and analysis of protein structure data. Group members have experience in development of statistical and bioinformatic software tools for plant scientists. The team is equipped with statistical software and general computing tools run both in the PC and supercomputer environments. More

The Krajewski group is part of the Institute of Plant Genetics, Polish Academy of Sciences (IPG-PAS). The Institute is an important centre of agrobiology and molecular genetics in Poland, with the staff of 100 scientific and technical workers. It is located in the outskirts of Poznań and uses its laboratory, greenhouse and field facilities for conducting multidisciplinary research in genetics, genomics, cytogenetics, biotechnology, in vitro cultures, plant resistance and biometry, on crop and model plants. More

Pedro Madrigal is the SYSFLO research fellow with Prof Krajewski's group, click to find out more about him and his project.

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Prof Yves Van de Peer, VIB

Prof Yves van de Peer

Prof Van de Peer’s research group studies the evolution of entire biological processes and networks through gene duplication and divergence of transcriptional regulation. It takes a system biology perspective, by linking the genome models with experimental genomics information as well as in silico functional predictions, miRNAs and cis-acting transcriptional modules. The group is involved in the development of novel gene prediction and modelling tools, making a wider use of machine learning algorithms but also of comparative approaches using sequence information from other genomes. More

Yves Van de Peer leads the Bioinformatics and Systems Biology Division in the Department of Plant Systems Biology (PSB) at Ghent University, Belgium. The division is a centre of excellence in the field of gene and genome annotation, comparative and evolutionary genomics and (top-down) Systems Biology. The PSB Department forms part of the Vlaams Instituut voor Biotechnologie (VIB), which combines 70 research groups, belonging to eight different Departments at four Flemish universities: Ghent University, K.U.Leuven, the University of Antwerp and the Vrije Universiteit Brussel. Through close cooperation with these universities and a solid funding program for strategic basic research, VIB joins the forces of 1100 scientists and technologists in one single institute. More

Evangelia Dougali is the SYSFLO research fellow at the VIB, click to find out more about her and her project.

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Dr Aalt-Jan van Dijk, Plant Research International, Wageningen

Dr Aalt-Jan van Dijk

The Applied Bioinformatics group develops standardized and generic systems for the management, analysis and integration of plant omics data, in support of the technology platforms of the Wageningen Genomics Facility ((next generation) sequencing, proteomics and metabolomics). The group’s research interest focuses on genome analysis (genome assembly and annotation, gene function prediction, analysis of small RNA and alternative splicing) and plant metabolome analysis (in particular development of computational methods for metabolite identification).

In the Applied Bioinformatics group, Dr. Aalt-Jan van Dijk, together with the Angenent group, has initiated a research line on the computational analysis of regulatory protein-interaction networks and is expanding this to “systems biology” studies of such regulatory networks underlying floral developmental processes. More

The Applied Bioinformatics group is part of Plant Research International (PRI), which is the largest plant research institute in The Netherlands (about 400 employees) and conducts multidisciplinary research in the fields of breeding, agronomy, genomics, bioinformatics and plant-environment interactions. PRI is be housed together with all the University’s Plant Sciences groups in one building, with state-of-the-art facilities, equipment, techniques and expertise needed to carry out the proposed research. More

Felipe Leal Valentim is the SYSFLO research fellow with the Applied Bioinformatics group, click to find out more about him and his project.

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