Bilateral NSF/BIO-BBSRC - Translational landscape to link cell growth with proliferation in the root meristem
Lead Research Organisation:
Royal Holloway University of London
Department Name: Biological Sciences
Abstract
Our life depends on growing plants. Projected population increases together with anticipated disruptions to agricultural production by climate change create a pressing need to achieve step-change improvements in agricultural production to guarantee security of global food supplies. Increases in the application of nitrogen fertilizers underpinned the "green revolution" but are unsustainable. Work described in this proposal will contribute to an alternative route to increased agricultural production, which could be described as a "second green revolution". According to this strategy, agricultural productivity is increased through use of crops in which growth responses are optimized to sustain the increase in biomass in what would otherwise be limiting environments. Plant growth fundamentally depends on maintaining growth and proliferation of cells, which occurs in the meristems. The rate of cell production must be aligned with developmental cues, available energy, nutrient supplies and environmental conditions. Cytoplasmic growth in meristematic cells is largely constrained by protein synthesis and is coupled to cell division to maintain cell size homeostasis. There are evolutionarily conserved sensing and intracellular signalling mechanisms that inform cells on the available nutrient supply. Central to this is the so called TARGET OF RAPAMYCIN (TOR) protein, so named after an antifungal compound produced by a bacterium that was discovered in the Easter Island, Rapa Nui. TOR is central for cell growth mainly through the regulation of protein synthesis and connecting protein synthesis and cell proliferation, but these regulatory mechanisms are not well understood in plant cells. TOR is a master regulator and also functions through other output pathways. One main route of TOR function is through stimulating ribosomes to increase the translational capacity of cells for protein synthesis. Recent findings unexpectedly show that a canonical ribosomal protein target also functions as a transcriptional regulator (repressor). We found that this is in association with a key controller of the cell cycle, the RETINOBLASTOMA RELATED (RBR) protein, named after the cancer in the eye when mutated in humans. RBR and its partner proteins are thought to constitute a switch that controls cell proliferation and cell growth and can be flicked by environmental conditions. In this project we shall use root meristematic cells to systematically uncover transcriptionally and translationally regulated genes that function to connect cell growth and proliferation. We will then design experiments through which we can precisely observe the molecular behaviour of the components of the switch in time, as we alter the growth conditions, while at the same time following changes in growth through microscopic movies. These types of experiments will produce a wealth of data that allow building a comprehensive knowledge of the regulatory network. With additional help from carefully optimized computer models, we can learn the functioning of this cellular decision making circuitry and make predictions at different environmental and nutrient conditions what is the extent of cell proliferation and therefore root growth. Having achieved to construct such a predictive model we will test its performance in different real life situations, such as what happens to root growth in dark, or under limited nitrate or sucrose. We might also find that we missed some components, and this will prompt us for further experimentation. Having perfected the model we can start adapting it to other growth-altering conditions, such as stress, or to other parts of the plant important for crop yield, such as fruits or seeds.
Technical Summary
Cell growth and protein translation constrain cell proliferation. Emerging data indicate that growth signalling pathways (e.g. TOR and S6K) affect both translation and the commitment to cell proliferation through the RETINOBLASTOMA RELATED (RBR) pathway. The hypothesis is that translational control of specific mRNAs, for example through the untranslated regions, provides important regulatory links to couple cell growth and cell proliferation. Key pieces of evidence are that mutations of translation/ribosome associated proteins such as TOR, S6K, eIF3h and EBP1 deregulate the cell cycle.
This project aims to establish how growth-stimulating regulatory pathways (TOR, S6K) affect the Arabidopsis translatome as well as cell proliferation in the seedling root. Aim 1 will yield quantitative data on cell cycle parameters and translation over time while manipulating growth by environmental and genetic perturbation. In aim 2 the translation state of mRNAs will be measured in three ways, by ribosome immunopurification targeting root meristematic cells and cells in the elongation zone, by ribosome footprinting, and by density gradient fractionation of polysomes, followed by RNA sequencing. Together with mRNA transcript data, these techniques will reveal complementary aspects of translational control by the signalling pathways. In aim 3, we derive biochemical parameters of translation for all mRNAs. Aim 4 is to computationally identify cis-regulatory sequence motifs in mRNAs. Our final aim 5 is to condense the regulatory pathway to the principal components. We will collect time/spatially resolved data on the cell proliferation switch. Together with data from previous aims, we will use graph theoretical methods to generate a Bayesian network model of the cell proliferation switch.
Establishing the integration of protein translation and cell cycle control in the root tip model system will lay the groundwork for future modelling of cell proliferation in other plant organs.
This project aims to establish how growth-stimulating regulatory pathways (TOR, S6K) affect the Arabidopsis translatome as well as cell proliferation in the seedling root. Aim 1 will yield quantitative data on cell cycle parameters and translation over time while manipulating growth by environmental and genetic perturbation. In aim 2 the translation state of mRNAs will be measured in three ways, by ribosome immunopurification targeting root meristematic cells and cells in the elongation zone, by ribosome footprinting, and by density gradient fractionation of polysomes, followed by RNA sequencing. Together with mRNA transcript data, these techniques will reveal complementary aspects of translational control by the signalling pathways. In aim 3, we derive biochemical parameters of translation for all mRNAs. Aim 4 is to computationally identify cis-regulatory sequence motifs in mRNAs. Our final aim 5 is to condense the regulatory pathway to the principal components. We will collect time/spatially resolved data on the cell proliferation switch. Together with data from previous aims, we will use graph theoretical methods to generate a Bayesian network model of the cell proliferation switch.
Establishing the integration of protein translation and cell cycle control in the root tip model system will lay the groundwork for future modelling of cell proliferation in other plant organs.
Planned Impact
Our principal aim is to deliver excellent science that will provide profound novel insights into one of the most fundamental aspects of plant biology, namely how protein synthesis drives cell growth and proliferation, and how this impacts on biomass and plant yield. Uncovering the underlying regulatory machinery, and building predictive models that test our understanding of these processes, may improve our ability to optimize plant function by genetic improvement. While our model will necessarily focus on a tractable model system, the response of the Arabidopsis root tip to photosynthate, it is clear that aspects of the model will apply to other organs, such as fruits or seeds, to crop plants, where the same machinery is highly conserved, and to other signals, such as stress, or nitrogen status.
Besides disseminating the immediate intellectual merit of the work through publication, we also propose a strategy for translating the results for the benefit of agricultural biotechnology, through partnerships with industry, joint academic-industrial grant proposals, and exploring the protection of intellectual property. The public will benefit in the long term from economic activity, market forces on consumer prices, and sustainable agricultural production.
The immediate impact of this research will be enhanced knowledge and understanding of the fundamental process, which will be communicated to public in ways that enrich societal understanding of fundamental biological processes and scientific methods, such as genetic modifications. The PIs have skills and developed channels to disseminate this knowledge in schools and during University open days. An existing partnership with a local artist will be developed to produce documentation and to engage the public in creative ways.
Finally, the training and professional mentoring of the postdocs and PhD students employed in this multidisciplinary and collaborative project will develop the scientific workforce in academia or industry in a growth area that suffers from a shortage of skilled personnel.
Besides disseminating the immediate intellectual merit of the work through publication, we also propose a strategy for translating the results for the benefit of agricultural biotechnology, through partnerships with industry, joint academic-industrial grant proposals, and exploring the protection of intellectual property. The public will benefit in the long term from economic activity, market forces on consumer prices, and sustainable agricultural production.
The immediate impact of this research will be enhanced knowledge and understanding of the fundamental process, which will be communicated to public in ways that enrich societal understanding of fundamental biological processes and scientific methods, such as genetic modifications. The PIs have skills and developed channels to disseminate this knowledge in schools and during University open days. An existing partnership with a local artist will be developed to produce documentation and to engage the public in creative ways.
Finally, the training and professional mentoring of the postdocs and PhD students employed in this multidisciplinary and collaborative project will develop the scientific workforce in academia or industry in a growth area that suffers from a shortage of skilled personnel.
Organisations
- Royal Holloway University of London (Lead Research Organisation)
- University of Milan (Collaboration)
- Hungarian Academy of Sciences (MTA) (Collaboration)
- University of Paris-Saclay (Collaboration)
- Catalan Institution for Research and Advanced Studies (ICREA) (Collaboration)
- Royal Holloway, University of London (Collaboration)
- Nagoya University (Collaboration)
- University of Warwick (Collaboration)
- University of Tennessee (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- Academy of Sciences of the Czech Republic (Collaboration)
- Max Planck Society (Collaboration)
- Universität Hamburg (Collaboration)
- Cornell University (Collaboration)
- Universidad Nacional de Asunción (Collaboration)
- Yale University (Collaboration)
- Semmelweiss University (Collaboration)
- Utrecht University (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- BASF (Collaboration)
Publications
Kállai BM
(2020)
?-Tubulin interacts with E2F transcription factors to regulate proliferation and endocycling in Arabidopsis.
in Journal of experimental botany
Nomoto Y
(2022)
A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis.
in Nature communications
Casiraghi E
(2023)
A method for comparing multiple imputation techniques: A case study on the U.S. national COVID cohort collaborative.
in Journal of biomedical informatics
Caniza H
(2015)
A network medicine approach to quantify distance between hereditary disease modules on the interactome.
in Scientific reports
Jiang Y
(2016)
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
in Genome biology
Horvath BM
(2017)
Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control.
in The EMBO journal
Webster P
(2019)
Author Correction: Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates
in Nature Communications
Ahmad Z
(2019)
Cell cycle control by the target of rapamycin signalling pathway in plants.
in Journal of experimental botany
Loudya N
(2021)
Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf.
in Genome biology
Dory M
(2018)
Coevolving MAPK and PID phosphosites indicate an ancient environmental control of PIN auxin transporters in land plants.
in FEBS letters
Mohammed B
(2018)
Converging Light, Energy and Hormonal Signaling Control Meristem Activity, Leaf Initiation, and Growth.
in Plant physiology
Cáceres JJ
(2019)
Disease gene prediction for molecularly uncharacterized diseases.
in PLoS computational biology
Magyar Z
(2016)
DREAMs make plant cells to cycle or to become quiescent.
in Current opinion in plant biology
Galeano D
(2016)
Drug targets prediction using chemical similarity
Leviczky T
(2019)
E2FA and E2FB transcription factors coordinate cell proliferation with seed maturation.
in Development (Cambridge, England)
Oszi E
(2020)
E2FB Interacts with RETINOBLASTOMA RELATED and Regulates Cell Proliferation during Leaf Development.
in Plant physiology
Lokdarshi A
(2020)
ErbB-3 BINDING PROTEIN 1 Regulates Translation and Counteracts RETINOBLASTOMA RELATED to Maintain the Root Meristem.
in Plant physiology
Gliozzo J
(2022)
Heterogeneous data integration methods for patient similarity networks.
in Briefings in bioinformatics
Caniza H
(2024)
LanDis: the disease landscape explorer
in European Journal of Human Genetics
Santos SS
(2022)
Machine learning and network medicine approaches for drug repositioning for COVID-19.
in Patterns (New York, N.Y.)
Title | Artist in residence Kerry Lemon |
Description | Drawing of plants with increased understanding how development shapes growth |
Type Of Art | Artwork |
Year Produced | 2014 |
Impact | Stimulating discussions with students. Media release. Planned exhibition. |
URL | http://www.kerrylemon.co.uk/ |
Title | Exhibition Hidden/revealed |
Description | Hidden/Revealed exhibition accompanied by a series of short talks, 'Talking Triptychs,' |
Type Of Art | Artistic/Creative Exhibition |
Year Produced | 2017 |
Impact | Art work well recieved by the public visitors. Loads of comments in the visitors book. |
URL | https://www.royalholloway.ac.uk/staff/news-events/event-articles/hiddenrevealed-talking-triptychs.as... |
Description | 1. How photosynthates are utilised for plant growth is fundamental for crop productivity. We have discovered two novel pathways in this process involving the regulation of protein translation. On the top of both pathways is an evolutionary conserved signalling protein called TOR. We showed that TOR through the S6K regulates the phosphorylation of the RETINOBLASTOMA RELATED protein and cell proliferation. We have discovered together with our US collaborator a key translational regulator, the eIF3h which is targeted by the TOR-S6K pathway and regulates the translation initiation of mRNAs central for maintenance of cell proliferation in shoot and root meristems. We focussed on two of the most important targets that have translational control with detailed experimental work, the PLETHORA (PLT2) and TCP proteins (TCP8, TCP14, TCP15). We showed that PLT2 and TCP14 physically and genetically interact in the root to determine meristem maintenance and cell proliferation. 2. Plants and crops grow in a naturally fluctuating environment. Within this project we discovered how photosynthates and light through TOR signalling tune both shoot and root growth through the regulation of protein translation. Unexpectedly we found that photosynthates through TOR, RBR and E2F transcription factors provide an input to the circadian clock to determine the day-night rhythm of plants. We mapped two inputs, one in the morning and one in the evening with two opposing E2Fs that both negatively regulate each other and contribute to maintain the central oscillation mechanism of the clock. Our US collaborator focussed on the circadian control of protein translation, and found key translational targets that links with cell cycle control. 3. Understanding the diurnal cycle of Arabidopsis via network-based analysis of translatomics data (Paccanaro- Cheng Ye). Analysing the data came from our US collaborator, the Vonarnim Lab we constructed two time-varying networks for wildtype Arabidopsis and circadian-clock-interrupted Arabidopsis (CCA1-ox), respectively. The nodes in the networks are genes and remain the same across different time points. The weighted edges in the network represent the co-translation correlations between genes and are varying over time. A positive weight indicates that the translational states of two genes change in a similar manner, i.e., either both increase or both decrease, while a negative weight implies the opposite. We performed a well-developed network module detection technique, namely Louvain algorithm on both wildtype and CCA1-ox networks to find clusters of genes which are densely connected in the network and whose translational states peak at different times during the diurnal cycle. We found that the day cluster genes (peak at 12am) found in the wildtype network show significant overlap with night cluster genes (peak at 6pm) found in CCA1-ox network. This implies that there is an approximately 6-hour shift in the gene translational states between wildtype and CCA1-ox Arabidopsis, which can be supported by experimental results. We further performed Gene Set Enrichment Analysis (GSEA) on the clusters of genes we have detected and identified a list of GO terms which are statistically enriched in these clusters. 4. In collaboration with the US partner we have shown that TOR regulates the Erb3 binding protein (EBP1) and thereby ribosome biogenesis and translation initiation. EBP1 recently came to the forefront as a conserved central growth controller in yeast, human and plants. In this collaborative project we could show that EBP1 antagonising the RBR pathway to maintain cell proliferation in the meristem. Importantly, this genetic interaction is converging on the regulation of ribosome biogenesis. 5. Acceleration of cell cycle through TOR signalling poses a threat of frequent of DNA damage, and to prevent passage of damaged genome to the next generations, cell cycle must be halted. We found that the RBR-E2FA complex localise on damaged heterochromatin foci and together they act as transcriptional repressor of the orthologue of the human breast cancer susceptibility gene 1 as well as a chromatin modifier to non-transcriptionally facilitate DNA repair. Biologically, it makes sense that RBR, being a master cell cycle regulator, also has a role in safeguarding the genome and thus ensuring genome integrity during proliferation. 6. Studying how light activates the shoot meristem and how it relies on TOR and hormone signalling we uncovered the role of a MAPK pathway (MKK7-MPK6) that arrest meristem in the dark by direct phosphorylation of the PIN1 auxin transporter. 7. Detecting critical timings of Chlamydomonas cell growth using dynamic network analysis (Paccanaro- Cheng Ye). To identify the critical time points when the cell growth procedure changes fundamentally, we compared the proteomics data between two types of Chlamydomonas: control and rapamycin in which the TOR (target of rapamycin) gene is inhibited. We obtained a high time resolution dataset through a collaboration with the Giavalisco group in the Max Planck Institute for Molecular Plant Physiology, Golm. We built two dynamic networks from the proteomics data for control and rapamycin, respectively. The nodes in the network are genes, while the links between nodes represent the protein intensity correlation between genes and are varying through time. We used four robust network measurements to assess the structural complexity of the control and rapamycin networks, at each time point, which allows us to understand how the overall pattern of gene connections changes during cell growth. The four measurements are: 1) degree distribution, which shows the strength of connections in the network, e.g., how many genes are strongly connected to others and how many genes are weakly connected; 2) average shortest path length, which is the mean of the lengths of shortest paths between all possible pairs of genes in the network; 3) average clustering coefficient, which measures to which degree genes are forming tight groups in the network; 4) graph von Neumann entropy, which assesses to what degree a network deviates from the structures of randomized networks. One of the most important findings from the time series of the four measurements is that the control network undergoes a fundamental structural change around the 4th hour since the start of the experiment, while the rapamycin network changes around 2 or 3 hours later. This conforms to biological ground truth and these time points appear to be the commitment moments of the cell growth of control and rapamycin Chlamydomonas. 8. The Corrected Gene Proximity map for the analysis of the 3D genome organization (Paccanaro- Cheng Ye). The different types of cells in a tissue have an identical one-dimensional (1D) genome, i.e., a linear sequence of nucleotides, yet their genomes have different underlying 3D architectures. The spatial proximity between genomic elements plays a central role in gene regulation and cell fate determination, and its disruption might lead to dysregulation. RBR-E2Fs are centrally important for chromatin regulation, but how these regulation is happening in time and space is not understood. Over the last decade, genome-wide ligation-based assays such as Hi-C have provided an unprecedented opportunity to investigate the 3D organization of the genome, and thus the spatial proximity between any genomic elements of interest. We propose a novel graph-theoretical framework, the Corrected Gene Proximity (CGP) map, to study the effect of the 3D spatial organization of genes in regulation. The starting point of the CGP map is a weighted network, the gene proximity map, whose weights are based on the contact frequencies extracted from genome-wide Hi-C data. The CGP map is then obtained from the gene proximity map by reducing high contact frequencies that are due to small genomic distances between genes. Using Hi-C data and transcriptomics data from 12 human cancer cell lines, we show that the CGP map can detect and quantify to what degree co-expressed genes are tightly clustered more effectively than when using the raw contact frequencies. As a proof of concept for this methodology, we analyzed the expression pattern of 186 metabolic pathways of both normal and cancer cell lines, we further find that the relative positioning between genes, as captured and quantified by CGP, is highly correlated with their expression change. We also show that the CGP map can be renormalized to form an inter-chromosomal proximity map, allowing distinct chromosomal translocations in human leukemic cells to be identified. |
Exploitation Route | 1. Map the TOR-dependent phosphorylation sites on RBR and modify them for better growth characteristics. 2. EBP1 expression was correlated by hybrid vigour in the literature. Knowing the molecular mechanism how EBP1 controls growth will allow to investigate and exploit EBP1 regulation to attain better hybrids in crops. 3. The novel computational method for the analysis of time series molecular data is powerful to uncover biological transition points and drivers of these transitions. This method can be utilised wherever high resolution time series data are available. 4. Computational method to analyse Hi-C data to uncover the role of chromatin in bringing together genes for regulation in time and space. |
Sectors | Agriculture Food and Drink |
Description | 1. Hybrid vigour is outstandingly important for crop productivity in modern agriculture, but the molecular basis is purely understood. Previously we discovered that a gene called Erb3 binding protein (EBP1) dose-dependently regulates growth in potato. EBP1 was also linked as a major component behind hybrid vigour. Within this project in collaboration with our US partner we showed that the molecular function of EBP1 is to boost protein translation through two independent routes, regulating ribosome biogenesis in the nucleolus and regulating translation initiation in the cytoplasm. We also show that EBP1 antagonises the differentiation promoting function of the RETINOBLASTOMA RELATED and thereby maintain meristematic function to promote plant growth. We used Arabidopsis as a model for these mechanistic discoveries of EBP1 function. To realise this important discovery we are starting to collaborate with Prof Gerrit Beemster working on maize. Proposed collaboration on this topic with the seed company KWS. We have expanded the work on seed development, seed germination and how EBP1 amount effect this process. 2. A second lead developed from the project is the realisation that the E2F transcription factors and the S6K upstream regulator are repressors of organ growth in environmentally limiting conditions. Because it is feasible to genetically alter these genes to attain growth benefits of crop plants we are looking into ways to transfer this knowledge to crop plants, focusing on wheat, barley and maize. |
First Year Of Impact | 2019 |
Sector | Agriculture, Food and Drink |
Impact Types | Economic |
Description | Advisory Board of Agricultural Biotechnology Institute |
Geographic Reach | Europe |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | Influence the governance and funding and research evaluation of the Institute |
URL | http://www.abc.hu/en/ |
Description | Doctor Honoris Causa degree at the Semmelweis Medical University, Budapest |
Geographic Reach | Europe |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | Involvement in the governing bodies of the University |
URL | http://semmelweis.hu/english/ |
Description | ERC activities in Hungary |
Geographic Reach | Europe |
Policy Influence Type | Contribution to a national consultation/review |
Description | Evaluation of the Czech Academy of Sciences |
Geographic Reach | Europe |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | Evaluating the research of 59 research teams over the last 6 year period. |
Description | Hungarian Higher Education Accreditation Committee |
Geographic Reach | Europe |
Policy Influence Type | Membership of a guideline committee |
Impact | Giving advice on establishing and functioning of doctoral training programs, university professor appointments, higher education teaching programs |
URL | http://tir.mab.hu/ |
Description | Pilot project to support subsistence farming in sub-Saharan Africa |
Geographic Reach | Africa |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | A team of researchers, NGO organisation and stakeholder were brought together to design projects that enable to increase the efficiency and profitability of subsistence farming in sub Saharan Africa. This project combines basic science knowledge with available practices to improve farming and enable to develop water saving practices, focusing on vegetable farming. |
Description | REF Czech Republic |
Geographic Reach | National |
Policy Influence Type | Membership of a guideline committee |
Impact | Advice on Academic Institute structures, research directions |
Description | 11. Ara-MKK-D: A bioinformatics and systems biology approach for the functional analysis of a growth-regulating MAP kinase pathway in Arabidopsis. |
Amount | € 189,670 (EUR) |
Funding ID | 41909 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 09/2007 |
End | 10/2009 |
Description | ABI innovation |
Amount | $1,203,514 (USD) |
Organisation | National Science Foundation (NSF) |
Sector | Public |
Country | United States |
Start | 08/2017 |
End | 09/2020 |
Description | Inference of RBR network and dynamic RBR complexes during leaf development. |
Amount | € 319,888 (EUR) |
Funding ID | 330789 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 03/2013 |
End | 03/2015 |
Description | Molecular signatures: a systems biology tool to understand how leaf development is constrained by drought. |
Amount | € 121,869 (EUR) |
Funding ID | 255035 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 07/2010 |
End | 07/2011 |
Title | Identifying protein interactions for the E2F and RBR |
Description | Generating GFP-tagged lines for the RBR and E2F proteins and developed a pull down and mass spectrometry identification method for protein interactors |
Type Of Material | Technology assay or reagent |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Identification of the full components of the DREAM complex in plants. Identification of functional differences among the plant E2F transcription factors. Realising the involvement of E2Fs in DNA damage response |
Title | Purification of protein complexes |
Description | Use genomic tagged GFP lines for rapid purification of protein complexes and identification of protein complex components |
Type Of Material | Biological samples |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | Established collaborations and accepted manuscript in EMBO J in 2017 |
Title | Root cell type-specific tagging of RBR-E2F components |
Description | GFP and FLAG tagging of RBR, E2FA, E2FB, E2FC, S6K1, S6K2 under the root cell type specific promoters in stem cell progenitors and elongation zone to be able to analyse these proteins during root development |
Type Of Material | Cell line |
Provided To Others? | No |
Impact | Enable us to purify RBR, E2Fs cell type specifically |
Title | mutant lines, antibodies, GFP-tagged lines |
Description | Tools for lipid signalling kinases, MAPKs, E2F-RBR such as antibodies, mutant lines, GFP-tagged lines |
Type Of Material | Cell line |
Provided To Others? | Yes |
Impact | shared research material facilitate research in other groups |
Title | Disease Similarity |
Description | We introduce a MeSH-based method that accurately quantifies similarity between heritable diseases at molecular level. This method effectively brings together the existing information about diseases that is scattered across the vast corpus of biomedical literature. We prove that sets of MeSH terms provide a highly descriptive representation of heritable disease and that the structure of MeSH provides a natural way of combining individual MeSH vocabularies. We show that our measure can be used effectively in the prediction of candidate disease genes. |
Type Of Material | Computer model/algorithm |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | There are no impacts yet, this work appeared only about 3 months ago. |
Title | Landis |
Description | Disease similarity measures quantify the distance between disease modules on the interactome. These measures can provide a starting point for in-depth exploration of the diseases at molecular level, and are of particular relevance for orphan diseases. LanDis is an explorable database, containing the disease similarities of 28.5 million pairs of heritable diseases. These are calculated by summarising the existing phenotype information about diseases through large scale analysis of hand curated data. |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | The paper presenting this database/model is still under review, so most scientist are not aware of its existence yet. However, I have already presented to conferences and meetings, receiving an extremely good feedback from everyone who tried it, especially clinician scientists. |
URL | http://www.paccanarolab.org/landis/ |
Title | mutation3d |
Description | A new algorithm and Web server, mutation3D (http://mutation3d.org), proposes driver genes in cancer by identifying clusters of amino acid substitutions within tertiary protein structures. We demonstrated the feasibility of using a 3D clustering approach to implicate proteins in cancer based on explorations of single proteins using the mutation3D Web interface. |
Type Of Material | Computer model/algorithm |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | No notable impacts yet, the paper only appeared about a month ago. |
URL | http://mutation3d.org/ |
Description | Albrecht Von Arnim |
Organisation | University of Tennessee |
Department | Department of Geography |
Country | United States |
Sector | Academic/University |
PI Contribution | TOR and S6K signalling, EBP1 |
Collaborator Contribution | regulation of translation, making constructs for root meristem specific analysis of translatome and translational regulation |
Impact | project partner, manuscripts in preparation |
Start Year | 2015 |
Description | Cancer genomics -- Haiyuan Yu (Cornell University) |
Organisation | Cornell University |
Country | United States |
Sector | Academic/University |
PI Contribution | We recently started a collaboration with Yu lab in the field of cancer genomics, where we contributed to the development of a clustering method to predict cancer mutation hotspots in proteins. We used our expertise in clustering methods to provide an efficient solution an integrate it into a comprehensive analysis pipeline. |
Collaborator Contribution | Prof Yu and his lab have great expertise in the field of cancer genomics. They have contributed the biological question and the data. |
Impact | A journal paper describing the method is currently under review in BMC Biology. The collaboration is multi-disciplinary involving biologists and computational scientists. |
Start Year | 2013 |
Description | Csaba Koncz |
Organisation | Max Planck Society |
Department | Max Planck Institute for Plant Breeding Research |
Country | Germany |
Sector | Academic/University |
PI Contribution | Working on S6K |
Collaborator Contribution | Working on SnRK1, providing mutants and tool |
Impact | Joint projects, research papers |
Description | DREAM complex involvement in DNA damage |
Organisation | University of Hamburg |
Department | Institute of Plant Science and Microbiology |
Country | Germany |
Sector | Academic/University |
PI Contribution | Has identified novel components of the DREAM complex by label free mass spectrometry of E2F, RBR tagged lines. Identified the role of E2FB in the DNA damage checkpoint in G1/S and G2/M phase. |
Collaborator Contribution | Identified the involvement of DREAM in DNA damage response and made an interaction map among the components by Y2H |
Impact | The DREAM complex represses growth in response to DNA damage in Arabidopsis Lucas Lang1, Hasibe Tunçay1, Aladar Pettkó-Szandtner2, Maren Heese1, Geert de Jager3, Masaki Ito4, Zoltán Magyar2, László Bögre5 & Arp Schnittger1,* manuscript in preparation |
Start Year | 2020 |
Description | Development of a web resource for protein functional annotation -- Raj Sasidharan (BASF) |
Organisation | BASF |
Country | Germany |
Sector | Private |
PI Contribution | We developed ConSAT, a tool for protein functional annotation using protein consensus domain architectures. In this project a new algorithm was developed and a web resource (ConSAT) with precomputed results was created (available at http://paccanarolab.org/consat ). The method includes three different types of functional prediction methods, two assigning Gene Ontology terms from the protein architecture, and one assigning English weighted words. |
Collaborator Contribution | Rajkumar Sasidharan's help was very important for the development of this project, mainly in two different fields: first, he provided expert knowledge in structural biology; second, he helped giving feedback on the usability of the web server, leading to its improvement. |
Impact | The project main output is the above referenced website. Publications are currently being written. The collaboration is multi-disciplinary involving biologists and computational scientists. |
Start Year | 2012 |
Description | Disease gene prioritisation by the combination of gene networks -- Giorgio Valentini (Milan) |
Organisation | University of Milan |
Country | Italy |
Sector | Academic/University |
PI Contribution | We preprocessed, cleaned and provided a set of biological datasets to Giorgio Valentini to assist in the development of several methods of gene networks combination for disease-gene prioritisation (that is, finding new causative genes for diseases). We provided, among others, several semantic similarity networks among sets of human genes. We also suggested new evaluation measures for this task. |
Collaborator Contribution | Giorgio Valentini developed a set of algorithms for finding new disease-gene associations. In that context he proposed many different ways in which different gene networks (both weighted and unweighted) could be combined to produce a resulting network resembling a relation based on the fact that two linked genes are supposed to share an underlying disease. The new predictions are given as an output of the paper (available at http://homes.di.unimi.it/re/suppmat/genesmeshnetwpred/supmatTBL1.html ). |
Impact | Apart from the above mentioned URL, the collaboration led to the following publication: G Valentini, A Paccanaro, H Caniza, AE Romero, M Re An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods Artificial Intelligence in Medicine 61 (2), 63-78 |
Start Year | 2013 |
Description | Dr Tamas Meszaros |
Organisation | Semmelweiss University |
Country | Hungary |
Sector | Academic/University |
PI Contribution | In vitro translation of RBR and E2Fs and CDK kinases for protein-protein interaction and phosphorylation studies. In vitro translation of MAPKs and MKKs. Study protein-protein interaction and activation. |
Collaborator Contribution | In vitro protein interaction and phosphorylation screen |
Impact | Joined publications, projects |
Start Year | 2015 |
Description | Dr Zoltan Magyar |
Organisation | Hungarian Academy of Sciences (MTA) |
Department | Biological Research Centre (BRC) |
Country | Hungary |
Sector | Academic/University |
PI Contribution | Working on RBR-E2F, connecting translational regulation and cell cycle |
Collaborator Contribution | Providing antibodies and mutants in the RBR-E2F pathway |
Impact | research papers, collaboration with Bayern Crop Science |
Description | Dream complex roles and transcriptional targets |
Organisation | Nagoya University |
Country | Japan |
Sector | Academic/University |
PI Contribution | We made GFP-tagged lines for RBR, E2FA, E2FB, E2FC and characterised single and multiple KO lines for E2Fs. We performed GFP pull down mass spec experiments for RBR, E2Fs and MYB3Rs to identify DREAM complex components. Made ChIP experiments for E2Fs |
Collaborator Contribution | Made GFP-tagged lines for MYB3Rs, KO lines. Made RNAsec for e2f and myb3r KO lines. Made ChIPsec for MYB3Rs |
Impact | 5 publications, Visit and seminar of Dr Ito to RHUL. Planned joined grant application. |
Start Year | 2006 |
Description | Drug side effect prediction (with Mark Gerstein and Shantao Li, Yale University) |
Organisation | Yale University |
Country | United States |
Sector | Academic/University |
PI Contribution | We have developed a new method for predicting side effects of drugs. Our preliminary results show that our method represents a great improvement with respect to the existing state of the art in terns of side effect prediction. Moreover, it is the first method that can predict the expected frequency of side effects in the population. |
Collaborator Contribution | They are helping us to provide an explanation of some aspects of our models in terms of the biology/biochemistry/pharmacology. |
Impact | A journal article is in preparation.The collaboration is multi-disciplinary involving biologists and computer scientists. |
Start Year | 2017 |
Description | Enhancer prediction using epigenetic signals in different mouse tissues (with Mark Gerstein and Mengting Gu, Yale University) |
Organisation | Yale University |
Department | Department of Molecular Biophysics and Biochemistry |
Country | United States |
Sector | Academic/University |
PI Contribution | Apply machine learning, signal processing and pattern recognition methods for improving the performance of the enhancer prediction for different tissues in the mouse genome. Preliminary results indicate that ensemble methods perform better than other classifiers. More advanced methods for feature extraction such as deep learning are going to be tested on the data. |
Collaborator Contribution | Members of the Gerstein Lab developed a pattern recognition method called matched filters for enhancer prediction. However, our preliminary results show that advanced machine learning may improve prediction accuracy. The Gerstein Lab supplied the data and will interpret the results in the context of enhancer and promoters in the genome. |
Impact | The collaboration is multi-disciplinary involving biologists and computer scientists. |
Start Year | 2017 |
Description | Finding evolutionary relations between plant MAPKs -- Laszlo Bogre (Royal Holloway) |
Organisation | Royal Holloway, University of London |
Department | School of Biological Sciences |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We collaborated with the Bogre lab in the elucidation of the evolutionary relations between the different Mitogen-activated protein kinases (MAPKs) in different model plants. Using computational techniques we were able to depict some of this relations, ultimately leading to the construction of the 'Plant MAPK Network Resource', available at http://www.paccanarolab.org/static_content/MAPKevol/ . |
Collaborator Contribution | Prof Bogre and his team provided us with their MAPK dataset, their expert knowledge in the field and their biological questions. This lead to the improvement of our methods for ortholog detection. The collaboration is still ongoing and we are currently developing new computational methods to detect relations between MAPKs and substrates. |
Impact | The outputs of this project are two: one web resource (the plant MAPK network resource, see above) and one joint publication: R. Dóczi, L. Ökrész, A. E. Romero, A. Paccanaro, and L. Bögre Exploring the evolutionary path of plant MAPK networks Trends in Plant Science, vol. 17, iss. 9, pp. 518-525, 2012. The collaboration is multi-disciplinary involving biologists and computational scientists. |
Start Year | 2011 |
Description | Functional prediction for Macrophomina phaseolina -- Pablo Sotelo (Universidad Nacional de Asuncion) |
Organisation | National University of Asuncion |
Country | Paraguay |
Sector | Academic/University |
PI Contribution | We have provided the Sotelo lab with a complete functional annotation of the fungus Macrophomina phaseolina. This was done using both S2F and CONSAT, our systems for protein function prediction. Macrophomina phaseolina has been recently sequenced and is responsible for a plague affecting many crops and particularly soya, of which Paraguay is one of the largest producers in the world. Our contribution will help, in ultimate analysis, both the development of new pesticides to fight this fungus, and in the research of genetically modified varieties of soya, resistant to this plague. |
Collaborator Contribution | The Sotelo lab has been providing us with feedback to improve our system and on the accuracy of our predictions. This is very helpful for us in order to improve our system. |
Impact | This is a multidisciplinary collaboration, between computational scientists (Paccanaro lab) and life scientists (Sotelo lab). We expect to produce a joint publication in the near future as an output of this collaboration. The collaboration is multi-disciplinary involving biologists and computational scientists. |
Start Year | 2014 |
Description | Gene prioritisation for lymphoma growth on mutagenesis study |
Organisation | Medical Research Council (MRC) |
Department | MRC Clinical Sciences Centre (CSC) |
Country | United Kingdom |
Sector | Public |
PI Contribution | Prediction of lymphoma growth stage by analysis of gene clonality values from a sample. Prioritisation of genes selected from broad loci sources involved in lymphomagenesis. This process yielded a set of about 20 genes selected for further studies. |
Collaborator Contribution | Mutagenesis developed lymphoma studies on over 500 mice, with the corresponding sample clonality analysis. Ongoing gene relevance analysis. |
Impact | Studies are still ongoing on the relevance of the selected genes. We expect to obtain a publication about this work when the process finishes. The study is multi-disciplinary and it comprises the following disciplines: cancer genomics, molecular biotechnology, systems biology, computer science, big data analysis, bioinformatics. |
Start Year | 2015 |
Description | GoSSTo, a Tool for computing Gene Ontology Semantic Similarites -- Giorgio Valentini (University of Milan) |
Organisation | University of Milan |
Country | Italy |
Sector | Academic/University |
PI Contribution | We developed GoSSTo a command line based-tool to compute semantic similarities between gene products. The tool implemented an algorithm previously published in our group, trying to make it accessible to any possible researcher. We also implemented GoSSToWeb, a web server providing easier access to this tool for biological researchers. |
Collaborator Contribution | Giorgio Valentini and his lab provided help for the development of the web interface of our tool for computing semantic similarities which was recently published, and also provided user feedback on the command line tool. |
Impact | The output is constituted by our software tools (GoSSTo and GoSSToWeb). Our web tool, available at www.paccanarolab.org/gosstoweb has had over 50 registered users and 70 submitted jobs thus far. Moreover, the collaboration is manifested in the following publication: H. Caniza, A. E. Romero, S. Heron, H. Yang, A. Devoto, M. Frasca, M. Mesiti, G. Valentini, and A. Paccanaro, GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology Bioinformatics, vol. 30, iss. pp. 2235-2236, 2014. A preliminary version of this paper was submitted and accepted to the ISMB conference in 2013: H. Caniza, A. E. Romero, S. Heron, H. Yang, M. Frasca, M. Mesiti, G. Valentini, and A. Paccanaro. 'GOssTo and GOssToWeb: user-friendly tools for calculating semantic similarities on the Gene Ontology.' Bio-Ontologies SIG 2013-ISMB 2013 (2013). |
Start Year | 2012 |
Description | Learning disease-gene associations by exploiting disease similarities (with Mark Gerstein, Yale University) |
Organisation | Yale University |
Department | Department of Molecular Biophysics and Biochemistry |
Country | United States |
Sector | Academic/University |
PI Contribution | We recently developed a disease similarity measure and calculated all the disease-disease similarities between OMIM diseases. We established a prior disease-gene association probability and provided training and testing datasets for the learning. We fitted the model. |
Collaborator Contribution | Developed a Lipschitz diffusion model, that we used to spread the disease-gene association through the interactome, and a fully functional fast implementation of the algorithm. |
Impact | The collaboration is multi-disciplinary involving biologists and computer scientists. |
Start Year | 2017 |
Description | Network-based Genome Analysis Reveals Structural and Functional Properties of Genes (with Mark Gerstein and Koon-Kiu Yan, Yale University) |
Organisation | Yale University |
Country | United States |
Sector | Academic/University |
PI Contribution | We have analysed the spatial proximity of all pathway genes (KEGG Database) across various cancer cell lines. Our preliminary results provide strong evidence for a relationship between disease pathways and cancer. The study also helps identify candidate genes for a number of diseases. |
Collaborator Contribution | They have successfully applied network community detection techniques to Hi-C data (three-dimensional architecture of genomes) in order to identify topologically associating domains (TADs) of genomic regions. |
Impact | The collaboration is multi-disciplinary involving biologists and computer scientists. |
Start Year | 2017 |
Description | Objective of the project is to elucidate the mechanism of action of a drug for multiple sclerosis |
Organisation | Imperial College London |
Department | Faculty of Medicine |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | To analyse transcriptomics data obtained from a trial on human patients using network medicine approaches. |
Collaborator Contribution | They hosted a trial with human patients and extracted transcriptomics data at different times.. |
Impact | No outputs yet. This collaboration is multidisciplinary involving: computer science, network science, machine learning, medicine, biology and pharmacology. |
Start Year | 2015 |
Description | Patrick Giavalisco |
Organisation | Max Planck Society |
Department | Max Planck Institute of Molecular Plant Physiology |
Country | Germany |
Sector | Charity/Non Profit |
PI Contribution | Connecting TOR-S6K to RBR |
Collaborator Contribution | TOR silenced lines |
Impact | Joined project proposal |
Start Year | 2010 |
Description | Pavla Binarova |
Organisation | Academy of Sciences of the Czech Republic |
Country | Czech Republic |
Sector | Academic/University |
PI Contribution | Analysing RBR phosphorylation and interaction with microtubules. |
Collaborator Contribution | Microtubules, cell biology |
Impact | research papers, joined projects |
Start Year | 2010 |
Description | RBR phosphorylation mapping by mass spec |
Organisation | University of Warwick |
Department | Institute for Employment Research |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | providing phosphorylated RBR samples |
Collaborator Contribution | Start mapping RBR phosphosites by mass spec |
Impact | initial results of 7 new RBR phopsho-sites and 2 related kinases |
Start Year | 2015 |
Description | Role of chromatin in DNA damage |
Organisation | University of Paris-Saclay |
Country | France |
Sector | Academic/University |
PI Contribution | Knock out mutants in the DNA damage response pathway brca1, parp1, parp2, lifering. GFP fusions with these line. Discovery of the connection between BRCA1 and RBR. Direct role of RBR in DNA damage and repair |
Collaborator Contribution | Development of chromatin regulation experimental platform with NGS sequencing. ChIPsec and Hi-sec experiments. |
Impact | Exchange of materials and experimental protocols. Plan for joined grant applications |
Start Year | 2018 |
Description | Rossana Henriques |
Organisation | Catalan Institution for Research and Advanced Studies (ICREA) |
Department | ICREA Centre for Research in Agricultural Genomics (CRAG) |
Country | Spain |
Sector | Academic/University |
PI Contribution | Connect S6K to cell cycle |
Collaborator Contribution | S6K circadian regulation, providing tagged S6K1 and S6K2 constructs. The post doc on the award, Dr Csaba Papdi visited her lab in the frame of a 3 month short term EMBO fellowship to work on S6K connection to cell cycle and circadian rhythm. |
Impact | Manuscript in preparation |
Start Year | 2015 |
Description | Scheres |
Organisation | Utrecht University |
Department | Cancer, Stem Cells and Developmental Biology |
Country | Netherlands |
Sector | Academic/University |
PI Contribution | Functional characterisation of E2F transcription factors during root growth and development |
Collaborator Contribution | Methodologies and tools to study root development, collaboration on RBR phospho-mutants |
Impact | Modulating RBR-E2F levels to increase plant growth |
Title | Landis |
Description | Disease similarity measures quantify the distance between disease modules on the interactome. These measures can provide a starting point for in-depth exploration of the diseases at molecular level, and are of particular relevance for orphan diseases. LanDis is a freely available web-based interactive tool that allows domain experts, medical doctors and the larger community to graphically navigate the landscape of human disease similarities. LanDis is designed to explore the similarity landscape of over 28.5 million pairs of heritable diseases, introducing a fully interactive and navigable plot in which diseases are represented as nodes and their pairwise similarity as the links joining them. |
Type Of Technology | Webtool/Application |
Year Produced | 2016 |
Impact | The paper presenting this webtool is still under review, so most scientist are not aware of its existence yet. However, I have already presented to conferences and meetings, receiving an extremely good feedback from everyone who tried it, especially clinician scientists. |
URL | http://www.paccanarolab.org/landis |
Title | mutation3D |
Description | mutation3D is a functional prediction and visualization tool for studying the spatial arrangement of amino acid substitutions on protein models and structures. It is intended to be used to identify clusters of amino acid substitutions arising from somatic cancer mutations across many patients in order to identify functional hotspots and fuel downstream hypotheses. It is also useful for clustering other kinds of mutational data, or simply as a tool to quickly assess relative locations of amino acids in proteins. |
Type Of Technology | Webtool/Application |
Year Produced | 2016 |
Impact | It is still too early, the tool was released about a month ago. |
URL | http://mutation3d.org/ |
Description | Artist in Residence Kerry Lemon |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Stimulating discussions to bridge the gap between science and artistic thinking Artistic drawing with understanding of plant development |
Year(s) Of Engagement Activity | 2014,2015,2016,2017 |
URL | http://www.kerrylemon.co.uk/ |
Description | Biology Master Class Slough |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Organise the Biology Master Class at Slough. Purpose: Enthuse pupils in broad areas of biology and current research challenges Expose pupils to university-level teaching and learning Provide links between exciting, contemporary science and A-level syllabus Help pupils to be successful in the A-level exam, university entry and the transition to university. Talks from academics on big ideas in biology, linked to the A-level syllabus. Dissertation by the pupils supervised and marked by academics. Conference at RHUL where pupils present and discuss the best dissertations. |
Year(s) Of Engagement Activity | 2018 |
URL | http://www.uptoncourtgrammar.org.uk/ |
Description | Biology Masterclass |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | A lecture series of 10 was organised covering a broad range of topics complementing A-level biology on current research topics from climate change to sustainable agriculture and health. |
Year(s) Of Engagement Activity | 2019,2020 |
URL | https://sites.google.com/view/uc-rhul-master-class/home |
Description | Biology Masterclass at local schools and online |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | 11 topics covering broad base of biology relevant to A-level curriculum and brings current research to this audience on the topics. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.youtube.com/channel/UCq4EXlnha_5KKN1_6LzfWZA |
Description | Biology Masterclass online 2021 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Schools |
Results and Impact | Biology Masterclass, 13 talks on broad topics of recent research interests and connections to A-level curriculum. 27 UK schools joined and a school from Zambia |
Year(s) Of Engagement Activity | 2021 |
URL | https://sites.google.com/view/uc-rhul-master-class/home |
Description | Fascination of Plants Day 2017 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Organising the Fascination of Plants Day at RHUL, Introduce history, teaching, research on plants at RHUL. Organise 6 activities on 1. creative drawing of plants (Kerry Lemon), 2. Bees, 3. plant molecular biology, 4. seeds, 5. Botanic Garden, 6. herbarium |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.royalholloway.ac.uk/biologicalsciences/news-and-events/events/fascination-of-plants-day.... |
Description | Futures Day at Royal Holloway University of London for Upton Court Grammar School |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Organised a Career event for Upton Court Grammar School Slough to provide A-level students with an outlook to University studies at ~10 different Departments of RHUL and future careers associated with these studies. |
Year(s) Of Engagement Activity | 2022 |
Description | Invited participation in experts' roundtable at the The Bioinformatics Strategy Meeting in London |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | I participated in an Experts' roundtable together with other academics and members of Industry |
Year(s) Of Engagement Activity | 2016 |
Description | School visit (Upton Court Grammar School) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Biology Master Class for A level students, organised 10 talks |
Year(s) Of Engagement Activity | 2018,2019 |
URL | https://sites.google.com/view/uc-rhul-master-class/home |
Description | School visits |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | increase awareness in plant research Increased interest, motivation of school kids |
Year(s) Of Engagement Activity | Pre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014 |
Description | Science festival at Strodes College |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Delivering talks and taking part in the Science Festival organised by Strodes College. |
Year(s) Of Engagement Activity | 2022 |
Description | Talk at BenevolentAI, London |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | I gave a seminar presenting my latest results on drug side effects prediction at BenevolentAI |
Year(s) Of Engagement Activity | 2019 |
Description | Talks to the groups of Martin Wilkins and Paul Matthews -- summer 2015 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Other audiences |
Results and Impact | I presented our recent results in the area of Network Medicine to Prof Martin Wilkins and Prof Paul Matthews and their groups (I gave two separate talks) at the Department of Medicine, Imperial College, Hammersmith Hospital. The talk sparked interesting discussions and it was the beginning of a very interesting collaboration with the lab of Prof Matthews in the area of Multiple Sclerosis. |
Year(s) Of Engagement Activity | 2015 |
Description | talk at Galway -- May 2015 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | I presented my work at the School of Mathematics, Statistics and Applied Mathematics at Galway University, Ireland. The talk sparked discussions with other scientists. The feedback I obtained was useful for my current research. The talk was important to advertise my research and to make contacts for future collaborations. |
Year(s) Of Engagement Activity | 2015 |