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Matthias Erwin Futschik is a leading bioinformatician and systems biologists with over 20 years of international research experience. He obtained a PhD in Information Science at University of Otago in Dunedin (New Zealand) and has worked in senior positions for over 15 years in the academic and entrepreneurial sector in New Zealand, Germany, Portugal and UK. Currently, he works as Principal investigator at the Centre for Innovative Biomedicine and Biotechnology of the University of Coimbra (Portugal). and serves as Honorary Professor at the University of Plymouth (UK). Matthias has a strong interest in bioinformatics methods and resource development as well as in translational and interdisciplinary research. To date, he authored over 80 papers in international peer review journals (including Nature, Science, Lancet Infectious Diseases, Genome Biology, Genome Research, Nucleic Acids Research and Bioinformatics) and 6 book chapters that received over 5800/3000 citations resulting in an h-factor of 36/29 (Google Scholar/Scopus in Feb 24). He co-holds 2 patents, developed 4 popular open-source R/Bioconductor software packages (>1000 citations) and led the implementation of 9 publicly accessible databases and webservers. Moreover, he was PI in 6 projects and successfully secured more than 1.3 M Euro in external funding. Finally, Matthias is a very passionate teacher and instructor in bioinformatics and computational biology. He has taught at various universities and guided 7 Post-doctoral researchers, 6 PhD theses, 13 Masters & Bachelor dissertations and 8 Research assistants.
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Identification

Personal identification

Full name
Matthias Erwin Futschik
Gender
Male

Citation names

  • Futschik, Matthias
  • Futschik, Matthias Erwin

Author identifiers

Ciência ID
A71B-AD01-3501
ORCID iD
0000-0002-6245-8071
Google Scholar ID
zHC1yBQAAAAJ
Scopus Author Id
14017989400

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences - Molecular Biology
  • Medical and Health Sciences - Basic Medicine - Human Genetics
Education
Degree Classification
2018 - 2019
Concluded
 Postgraduate Certificate in Academic Practice (Postgraduate Certificate)
University of Plymouth, United Kingdom
 Distinction
2003/08/08
Concluded
 PhD in Information Science (Doutoramento)
University of Otago, New Zealand
"Knowledge Discovery in Microarray Data" (THESIS/DISSERTATION)
 A
1998/02/23
Concluded
 Physics (Mestrado)
Humboldt-Universität zu Berlin, Germany
"Experimental characterisation and theoretical modelling of dendrimer-tetrapyrrol complexes" (THESIS/DISSERTATION)
 A
Affiliation

Science

Category
Host institution 		Employer
2023/05/29 - Current Principal Investigator (Research) Universidade de Coimbra, Portugal
Universidade de Coimbra Centro de Inovação em Biomedicina e Biotecnologia, Portugal
2022/01/11 - 2024/03/31 Researcher (Research) Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2021/04/04 - 2021/07/26 Researcher (Research) MRC London Institute of Medical Sciences, United Kingdom
MRC London Institute of Medical Sciences, United Kingdom
2020/01/08 - 2021/03/15 Coordinating Researcher (Research) Imperial College London Faculty of Medicine, United Kingdom
Imperial College London School of Public Health, United Kingdom
2017/05/01 - 2019/07/31 Coordinating Researcher (Research) University of Plymouth, United Kingdom
University of Plymouth Faculty of Health and Human Sciences, United Kingdom
2014/02/18 - 2016/11/30 Principal Investigator (Research) Centro de Ciências do Mar, Portugal
2008/09/01 - 2013/08/31 Principal Investigator (Research) Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
2003/11/01 - 2004/06/30 Auxiliary Researcher (Research) Humboldt Universität zu Berlin Institute for Theoretical Biology, Germany

Teaching in Higher Education

Category
Host institution 		Employer
2019/02/04 - 2023/06/30 Invited Assistant Professor (University Teacher) Universidade do Algarve, Portugal
Universidade do Algarve Departamento de Ciências Biomédicas e Medicina, Portugal
2016/11/14 - 2019/06/30 Full Professor (University Teacher) University of Plymouth, United Kingdom
University of Plymouth Faculty of Health and Human Sciences, United Kingdom
2004/07/01 - 2008/08/31 Assistant Professor (University Teacher) Charité Universitätsmedizin Berlin, Germany
2000/10/01 - 2001/07/31 Assistant (University Teacher) University of Otago Department of Information Science, New Zealand
1996/02/01 - 1998/06/30 Tutor (University Teacher) Humboldt-Universität zu Berlin Institut für Physik, Germany

Other Careers

Category
Host institution 		Employer
2021/07/26 - 2024/03/31 Carreiras / Categorias Subsistentes United Kingdom Department of Health and Social Care, United Kingdom
United Kingdom Department of Health and Social Care, United Kingdom

Others

Category
Host institution 		Employer
2019/08/01 - Current Honorary Professor University of Plymouth, United Kingdom
University of Plymouth, United Kingdom
2003/02/01 - 2003/10/30 Bioinformatics consultant Pacific Edge Ltd, New Zealand
2002/01/01 - 2003/01/31 Senior bioinformatician Pacific Edge Ltd, New Zealand
Projects

Grant

Designation Funders
2023/07/01 - 2023/12/31 Reverse engineering of genetic regulatory networks underlying stem cell differentiation and cardiogenesis
2022.75275.CPCA.A0
Principal investigator
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
Concluded
2022/01/01 - 2023/06/30 CARDIOMyogenisis In Silico: A computational framework for the study of stem cell differentiation towards cardiomyocytes
EXPL/CCI-BIO/1650/2021
Principal investigator
Universidade Nova de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
2022/01/01 - 2022/12/31 Mechanisms of central nervous system infiltration in Philadelphia chromosome-like B-cell precursor acute leukemia
None
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Amgen Biofarmaceutica Lda

Associação Portuguesa Contra a Leucemia

Sociedade Portuguesa de Hematologia
Ongoing
2018/07/05 - 2021/07/04 Variant sequences Identification in human genomes and Their Assignment as true causative mutations for LVNC - VITAL
PTDC/BTM-TEC/28044/2017
Researcher
Universidade do Algarve, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/01 - 2021/06/30 Determining the Role of the Microenvironment in Shaping the Spectrum of Genetic Mutations Acquired During Cancer Development
PTDC/MED-ONC/32592/2017
Researcher
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2016/05/01 - 2019/10/31 Regeneration in the African Spiny Mouse
PTDC/BIA-ANM/0697/2014
Researcher
Universidade do Algarve, Portugal

Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2014/02/17 - 2019/01/31 The regulation of photosynthesis in cyanobacteria: A systems biology approach
Provided by PTCRIS: 131253
131253
Principal investigator
Centro de Ciências do Mar, Portugal
 Ministério da Ciência Tecnologia e Ensino Superior
Concluded
2016/01/01 - 2017/12/31 From Petri Dish to the living heart: A systems biology approach to identify and validate key genes and processes driving cardiogenesis
NA
Principal investigator
Centro de Ciências do Mar, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2012/02/01 - 2015/01/31 Alternative splicing and its impact on molecular networks during stem cell differentiation
Provided by PTCRIS: 116519
116519
Principal investigator
Universidade do Algarve, Portugal
 Ministério da Ciência Tecnologia e Ensino Superior
Concluded
2012/01 - 2014/12 The role and regulation of alpha-synuclein phosphorylation in both pathological and physiological conditions
117975
Provided by PTCRIS: 117975
Researcher
Instituto de Medicina Molecular, Portugal
 Ministério da Ciência Tecnologia e Ensino Superior
Concluded
2010/01/01 - 2013/06/30 Regulation of iron homeostasis in cyanobacteria
101036
Provided by PTCRIS: 101036
Principal investigator
Universidade do Algarve, Portugal
 Ministério da Ciência Tecnologia e Ensino Superior
2005/01/01 - 2009/02/01 Robustness, modularity and dynamics of protein-protein interaction networks
SFB 618 - A5
Principal investigator
Humboldt Universität zu Berlin Institute for Theoretical Biology, Germany
 Deutsche Forschungsgemeinschaft
Concluded

Contract

Designation Funders
2019/01/01 - 2020/03/31 Centre for Biomedical Research
UID/BIM/04773/2019
Universidade do Algarve, Portugal

Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2019/01/01 - 2019/12/31 Centre of Marine Sciences
UID/Multi/04326/2019
Centro de Ciências do Mar, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2010 - 2011 Visualization and Analysis of HD-Related Molecular Interaction Networks
A-2666
Principal investigator
Universidade do Algarve, Portugal
 CHDI Foundation Inc Los Angeles

Other

Designation Funders
2014/01/01 - 2018/06/01 Development of software tools for the prediction of cellular fate in stem cell differentiation
SFRH/BPD/96890/2013
Supervisor
Universidade do Algarve - Campus de Gambelas, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2015/01/31 Systems biology approach to unravel the molecular mechanisms involved in T-Cell Acute Lymphoblastic Leukaemia
SFRH/BPD/70718/2010
Supervisor
Universidade do Algarve, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Futschik, M.E.; Morkel, M.; Sers, C.; Schäfer, R.. "The human transcriptome: implications for understanding, diagnosing, and treating human disease". 113-138. 2020.
  2. Futschik, Matthias; Morkel, Markus; Schäfer, Reinhold; Sers, Christine. "The Human Transcriptome: Implications for Understanding, Diagnosing, and Treating Human Disease". In Molecular Pathology, 135-164. Elsevier, 2018.
    Published • 10.1016/b978-0-12-802761-5.00007-9
  3. Hernandez-Prieto, Miguel A.; Kalathur, Ravi K.R.; Futschik, Matthias E.; Futschik, Matthias. "Molecular Networks - Representation and Analysis". In Springer Handbook of Bio-/Neuroinformatics, 399-418. Springer Berlin Heidelberg, 2014.
    Published • 10.1007/978-3-642-30574-0_24
  4. Chaurasia, Gautam; Futschik, Matthias. "The Integration and Annotation of the Human Interactome in the UniHI Database". In Methods in Molecular Biology, 175-188. Humana Press, 2011.
    Published • 10.1007/978-1-61779-455-1_10
  5. Allen, Michael J.; Tiwari, Bela; Futschik, Matthias E.; Lindell, Debbie. "Construction of microarrays and their application to virus analysis". In Manual of Aquatic Viral Ecology, 34-56. American Society of Limnology and Oceanography, 2010.
    Published • 10.4319/mave.2010.978-0-9845591-0-7.34
  6. Chaurasia, Gautam; Futschik, Matthias E.. "Interactomics and Cancer". In An Omics Perspective on Cancer Research, 167-182. Springer Netherlands, 2009.
    Published • 10.1007/978-90-481-2675-0_9
  7. Futschik, Matthias E.; Kemmner, Wolfgang; Schäfer, Reinhold; Sers, Christine. "The Human Transcriptome: Implications for the Understanding of Human Disease". In Molecular Pathology, 123-149. Elsevier, 2009.
    Published • 10.1016/b978-0-12-374419-7.00007-x
Conference abstract
  1. Pinto, J; Kalathur, R.; Braganca, J.; Xavier, J.; Futschik, Matthias. "StemCellNet: an interactive platform for network-oriented investigations in stem cell biology.". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies, Oeiras, 2015.
    Published
  2. Futschik, Matthias. "How the internal world of Synechocystis adapts to the ever-changing world outside: A comprehensive meta-analysis of its transcriptional responses". Paper presented in ESF-EMBO Symposium Molecular Bioenergetics Of Cyanobacteria: Shaping The Environment,, Pultusk, 2013.
    Published
  3. Futschik, Matthias; Chaurasia, Gautam; Wanker, Erich E.. "DISENTANGLING MOLECULAR INTERACTION NETWORKS FOR CHOREA HUNTINGTON". Paper presented in European Huntington Disease Network Annual Meeting, Lisabon, 2008.
    Published
  4. Futschik, Matthias; Legewie, Stefan; Herzel, Hanspeter. "Prometheus under the microscope: Modelling the complex dynamics of liver regeneration". Paper presented in 6th European Conference on Mathematical and Theoretical Biolog, Dresden, 2006.
    Published
  5. Futschik, Matthias; Kasabov, N.K.. "Revealing the Fine-Structures: Wavelet-based fuzzy clustering of gene expression data". Paper presented in Ninth International Conference on Intelligent Systems for Molecular Biology, Kopenhagen, 2001.
    Published
Conference paper
  1. Futschik, Matthias; Suillivan, M; Reeve, Anthony; Kasabov, Nikola. "Modular Decision System and Information Integration for Improved Disease Outcome prediction,". Paper presented in European Conference on Computational Biology (ECCB 2003), Paris, 2007.
  2. Futschik, M.E.; Herzel, H.. "Are we overestimating the number of cell-cycling genes? The impact of background models for time series data.". Paper presented in German Conference on Bioinformatics, Potsdam, 2007.
    Published
  3. FUTSCHIK, MATTHIAS E.; TSCHAUT, ANNA; CHAURASIA, GAUTAM; HERZEL, HANSPETER. "GRAPH-THEORETICAL COMPARISON REVEALS STRUCTURAL DIVERGENCE OF HUMAN PROTEIN INTERACTION NETWORKS". Paper presented in 7th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2007), Tokyo, 2007.
    Published • 10.1142/9781860949920_0014
  4. Futschik, Matthias; Chaurasia, Gautam; Herzel, Hanspeter. "Comparison of human protein-protein interaction maps". Paper presented in German Conference on Bioinformatics 2006, Tuebingen, 2006.
    Published
  5. Chaurasia, G.; Herzel, H.; Wanker, E.E.; Futschik, M.E.. "Systematic functional assessment of human protein-protein interaction maps.". Paper presented in Sixth International Workshop on Bioinformatics and Systems Biology, Boston, 2006.
    Published
  6. Futschik, M.E.; Kasabov, N.K.. "Fuzzy clustering of gene expression data". Paper presented in 2002 IEEE World Congress on Computational Intelligence. 2002 IEEE International Conference on Fuzzy Systems. FUZZ-IEEE'02, Honolulu, 2002.
    Published • 10.1109/fuzz.2002.1005026
  7. Kasabov, N.; Middlemiss, M.; Futschik, M.. "Knowledge based neural networks for on-line and off-line modeling and rule extraction in bioinformatics". Paper presented in CGBI'2001 Atlantic Symposium on Computational Biology, Durham, 2001.
    Published
  8. Futschik, Matthias; Schreiber, M; Brown, C; Kasabov, Nikola. "Comparative studies of neural network models for ribosome binding site recognition". Paper presented in ICONIP/ANZIIS/ANNES'99 Workshop, Dunedin, 1999.
    Published
Conference poster
  1. Sofia Torres; Belo, José A.; Futschik, Matthias. Corresponding author: Sofia Torres. "Comparison of methods for inference of gene regulatory networks underlying cardiac cell differentiation". Paper presented in ETRS & SPCE-TS Annual Meeting, 2023.
  2. Hernandez-Prieto, Miguel A; Semeniuk, Trudi A.; Giner-Lamia, Joaquin; Futschik, Matthias. "Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis - a comprehensive study based on CyanoEXpress". Paper presented in PHYCONET Annual Conference 2018, 2018.
  3. Machado, Rui; Sabour, D; Pinto, JP; Braganca, J; Sachinidis, Agapios; Futschik, Matthias. "HEARTI ToolBox: An online platform for the analysis in silico of cardiogenesis". Paper presented in 9th International Meeting of the Stem Cell Network NRW, 2017.
  4. Pinto, José Pedro; Kalathur, Ravi; Oliveira, DA; Barata, Tania; Machado, Rui S.R.; Machado, Susana; Pacheco-Leyva, Ivette; et al. "SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology". Paper presented in 9th International Meeting of the Stem Cell Network NRW, 2017.
  5. Futschik, Matthias; Giner-Lamia, Joaquin; Hernández-Prieto, Miguel A. "CyanoEXpress: An interactive web-tool for exploration and visualization of gene expression data from cyanobacteria". Paper presented in NorPlantBio 2016, 2016.
  6. Hernandez-Prieto, Miguel A; Semeniuk, Trudi A.; Giner-Lamia, Joaquín; Futschik, Matthias. "Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis". Paper presented in NorPlantBio 2016, 2016.
  7. Oliveira, Daniel V.; Machado, Rui; Duarte, Isabel; Pacheco-Leyva, Ivette; Justo, T; Pinto, JP; Braganca, Jose; Futschik, Matthias. "From Stem Cells 2 Heart: Finding novel candidate isoforms and genes for cardiomyogenesis.". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies., 2015.
  8. Machado, RS; Pinto, JP; Oliveira, DV; Duarte, I; Machado, S; Bragança, J.; Futschik, Matthias. "A meta-analysis study of stem cell differentiation in the context of cardiogenesis". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies., 2015.
  9. Machado, S.; Kalathur, R.K.; Oliveira, DV; Barata, T.; Machado, RS; Pacheco-Leyva, Ivette; Duarte, Isabel; Futschik, Matthias; Pinto, JP. "StemCellNet: an interactive platform for network-oriented investigations in stem cell biology.". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies., 2015.
  10. Futschik, Matthias; Giner-Lamia, Joaquin; Hernandez-Prieto, Miguel A. "Transcriptional regulation and coordination of photosynthetic genes in Synechocystis: a comprehensive study based on CyanoEXpress". Paper presented in 15th International Symposium on Phototrophic Prokaryotes (ISPP 2015),, 2015.
  11. Giner-Lamia, Joaquin; Bovea-Marco, Miquel; Hernandez-Prieto, Miguel A; Futschik, Matthias. "CyanoEXpress: An enhanced tool for on-line analysis and visualization of gene expression data from cyanobacteria". Paper presented in 15th International Symposium on Phototrophic Prokaryotes (ISPP 2015), 2015.
  12. Pinto, J; Kalathur, R.K.; Machado, R.; Xavier, J.; Braganca, J.; Futschik, Matthias. "StemCellNet: an interactive platform for network-oriented investigations in stem cell biolog". Paper presented in Heart without Boarders International Conference, 2014.
  13. Duarte, I.; Justo, T; Pinto, J.; Oliveira, D.; Braganca, J.; Belo, J.; Futschik, Matthias. "From Stem Cells 2 heart: Elucidating the role of alternative splicing in cardiomyogenesis". Paper presented in Heart without Boarders, International Conference, 2014.
  14. Oliveira, D.; Machdo, R.; Pacheco-Leyva, I.; Duarte, I.; Justo, T; Pinto, J.; Belo, J.; Futschik, Matthias. "From Stem Cells 2 heart: Finding novel candidate genes for cardiomyogenesis". Paper presented in Heart without Boarders, International Conference, 2014.
  15. Machado, R.; Pinto, JP.; Braganca, J.; Futschik, Matthias. "What a heart makes or breaks: A meta-analysis of gene expression profiles". Paper presented in 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, 2013.
  16. Pinto, JP.; Machado, RSR; Kalathur, R.; Futschik, Matthias. "StemCellNet: A web-based Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells". Paper presented in 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, 2013.
  17. Futschik, Matthias; Hernández-Prieto, M.A.. "Combined analysis under iron limiting conditions of microarray and RNA-seq data reveals novel transcriptional units and facilitates the prediction of a Fur-box in Synechocystis". Paper presented in ESF-EMBO Symposium Molecular Bioenergetics Of Cyanobacteria: Shaping The Environment,, 2013.
  18. Futschik, Matthias; Hernández-Prieto, M.A.. "CyanoExpress: A Comprehensive Database for Evaluating the Transcriptional Response in Synechocystis". Paper presented in International Symposium on Phototrophic Prokaryotes 2012, 2012.
  19. Hernandez-Prieto, Miguel A; Schön, Verena; Steglich, Claudia; Hess, Wolfgang R.; Futschik, Matthias. "Simultaneous profiling of coding and non-coding RNAs from Synechocystis under iron-limiting conditions". Paper presented in International Symposium on Phototrophic Prokaryotes 2012, 2012.
  20. Kalathur, R.K.; Futschik, Matthias. "The UniHI Database: A Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells". Paper presented in Cell Symposia: Stem Cell Programming & Reprogramming 2011, 2011.
  21. Futschik, Matthias; Hernandez-Prieto, Miguel A. "The Transcriptional Landscape of the Cyanobacterium Synechocystis". Paper presented in 8th European Workshop on Molecular Biology of Cyanobacteri, 2011.
  22. Hernández-Prietoa, Miguel A; Barreira, Luísa; Varela, João; Futschik, Matthias. "Concerted responses to iron availability in cyanobacteria". Paper presented in 4th National Meeting on Signal Transduction, SINAL 2010, 2010.
  23. Kalathur, Ravi; Futschik, Matthias. "Network-based analyses of Huntington's Disease". Paper presented in EHDN 2010, 2010.
    10.1038/npre.2012.7090.1
  24. Futschik, Matthias; Haenig, Christian; Chaurasia, Gautam; Wanker, Erich E.; Herzel, Hanspeter. "UniHI: Unifying Large-Scale Maps of the Human Protein Interactome". Paper presented in International Conference on Intelligent Systems for Molecular Biology (ISMB) 2006, 2006.
  25. Futschik, Matthias; Suillivan, M; Reeve, Anthony; Kasabov, Nikola. "Modular decision system and information integration for cancer outcome prediction". Paper presented in RECOMB 2003, 2004.
  26. Kasabov, N.; Futschik, Matthias. "Evolving Fuzzy Neural Networks for Knowledge Discovery from Gene Expression Data - A Case Study". Paper presented in Research in Computational Molecular Biology (RECOMB) 2001, 2001.
  27. Futschik, Matthias; Brown, Chris; Kasabov, Nikola. "Clustering of gene expression data by evolving self-organising maps". Paper presented in The 10th annual Queenstown Molecular Biology Meeting, 2000.
  28. Futschik, Matthias; Schreiber, M; Brown, Chris; Kasabov, Nikola. "Comparative Studies of Neural Network Models for mRNA Analysis". Paper presented in Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB-99), 1999.
Journal article
  1. Laura R Diaz; Dr Jon Gil-Ranedo; Karolina Jaworek; Nsikan Nsek; João Pinheiro Marques; Eleni Costa; David A Hilton; et al. "Ribogenesis boosts controlled by HEATR1-MYC interplay promote transition into brain tumour growth". EMBO Reports (2024): http://dx.doi.org/10.1038/s44319-023-00017-1.
    10.1038/s44319-023-00017-1
  2. Fowler, T.; Chapman, D.; Futschik, M.E.; Tunkel, S.A.; Blandford, E.; Turek, E.; Kolade, O.; et al. "Self-swabbing versus assisted swabbing for viral detection by qRT-PCR: the experience from SARS-CoV-2 based on a meta-analysis of six prospectively designed evaluations conducted in a UK setting". European Journal of Clinical Microbiology and Infectious Diseases 43 8 (2024): 1621-1630. http://www.scopus.com/inward/record.url?eid=2-s2.0-85195512797&partnerID=MN8TOARS.
    10.1007/s10096-024-04866-z
  3. Ryan, F.; Cole-Hamilton, J.; Dandamudi, N.; Futschik, M.E.; Needham, A.; Saquib, R.; Kulasegaran-Shylini, R.; et al. "Faster detection of asymptomatic COVID-19 cases among care home staff in England through the combination of SARS-CoV-2 testing technologies". Scientific Reports 14 1 (2024): http://www.scopus.com/inward/record.url?eid=2-s2.0-85188908441&partnerID=MN8TOARS.
    10.1038/s41598-024-57817-1
  4. Futschik, M.E.; Tunkel, S.A.; Turek, E.; Chapman, D.; Thorlu-Bangura, Z.; Kulasegaran-Shylini, R.; Blandford, E.; et al. "Double testing with lateral flow antigen test devices for COVID-19: does a second test in quick succession add value?". Journal of Virological Methods 329 (2024): http://www.scopus.com/inward/record.url?eid=2-s2.0-85199136366&partnerID=MN8TOARS.
    10.1016/j.jviromet.2024.115000
  5. Futschik, M.E.; Johnson, S.; Turek, E.; Chapman, D.; Carr, S.; Thorlu-Bangura, Z.; Klapper, P.E.; et al. "Rapid antigen testing for SARS-CoV-2 by lateral flow assay: A field evaluation of self- and professional testing at UK community testing sites". Journal of Clinical Virology 171 (2024): http://www.scopus.com/inward/record.url?eid=2-s2.0-85185932639&partnerID=MN8TOARS.
    10.1016/j.jcv.2024.105654
  6. Toby Nonnenmacher; Niharika Dandamudi; Futschik, Matthias; Sarah A Tunkel; Raghavendran Kulasegaran-Shylini; Nick Germanacos; Joanna Cole-Hamilton; et al. "PCR testing of traced contacts for SARS-CoV-2 in England, January to July 2021". Eurosurveillance (2023): https://doi.org/10.2807/1560-7917.ES.2023.28.44.2300019.
    10.2807/1560-7917.ES.2023.28.44.2300019
  7. Fagg, Jamie; Beale, Rupert; Futschik, Matthias E.; Turek, Elena; Chapman, David; Halstead, Susan; Jones, Marc; et al. "Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing". Journal of Clinical Virology 167 (2023): 105574. http://dx.doi.org/10.1016/j.jcv.2023.105574.
    10.1016/j.jcv.2023.105574
  8. Lucy Reeve; Elise Tessier; Amy Trindall; Nurin Iwani Binti Abdul Aziz; Nick Andrews; Matthias Futschik; Jessica Rayner; et al. "High attack rate in a large care home outbreak of SARS-CoV-2 BA.2.86, East of England, August 2023". Eurosurveillance (2023): http://dx.doi.org/10.2807/1560-7917.es.2023.28.39.2300489.
    10.2807/1560-7917.es.2023.28.39.2300489
  9. Kay, Olivia; Futschik, Matthias; Turek, Elena; Chapman, David; Carr, Simon; Sudhanva, Malur; Klapper, Paul E.; et al. "Performance of self-collected saliva samples for SARS-CoV-2 mass testing in community settings". Journal of Clinical Virology Plus 3 3 (2023): 100161. http://dx.doi.org/10.1016/j.jcvp.2023.100161.
    10.1016/j.jcvp.2023.100161
  10. Dounia Djeghloul; Andrew Dimond; Sherry Cheriyamkunnel; Holger Kramer; Bhavik Patel; Karen Brown; Alex Montoya; et al. "Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis". Nature Structural & Molecular Biology 30 4 (2023): 489-501. http://dx.doi.org/10.1038/s41594-023-00943-7.
    10.1038/s41594-023-00943-7
  11. Tânia Barata; Isabel Duarte; Matthias E. Futschik. "Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes". Genes 14 3 (2023): 745-745. http://dx.doi.org/10.3390/genes14030745.
    10.3390/genes14030745
  12. David W Eyre; Matthias Futschik; Sarah Tunkel; Jia Wei; Joanna Cole-Hamilton; Rida Saquib; Nick Germanacos; et al. "Performance of antigen lateral flow devices in the UK during the alpha, delta, and omicron waves of the SARS-CoV-2 pandemic: a diagnostic and observational study". The Lancet Infectious Diseases (2023): http://dx.doi.org/10.1016/s1473-3099(23)00129-9.
    10.1016/s1473-3099(23)00129-9
  13. Fernando Bonet; Sabrina Brito Añez; José Manuel Inácio; Matthias E. Futschik; José Antonio Belo. "CCBE1 Is Essential for Epicardial Function during Myocardium Development". International Journal of Molecular Sciences (2022): https://doi.org/10.3390/ijms232012642.
    10.3390/ijms232012642
  14. Matthias Futschik; Catherine Francis; Futschik ME; Jian Huang; Wenjia Bai; Sargurupremraj M; Alexander Teumer; et al. "Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.". Nature communications (2022): https://europepmc.org/articles/PMC9349177.
    10.1038/s41467-022-32219-x
  15. "The gene regulation knowledge commons: the action area of GREEKC.". Biochimica et biophysica acta. Gene regulatory mechanisms (2021): https://doi.org/10.1016/j.bbagrm.2021.194768.
    10.1016/j.bbagrm.2021.194768
  16. Machado, R.; Sachinidis, A.; Futschik, M.E.. "Detection of novel potential regulators of stem cell differentiation and cardiogenesis through combined genome-wide profiling of protein-coding transcripts and microRNAs". Cells 10 9 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85115889476&partnerID=MN8TOARS.
    10.3390/cells10092477
  17. Wallach, T.; Mossmann, Z.J.; Szczepek, M.; Wetzel, M.; Machado, R.; Raden, M.; Miladi, M.; et al. "MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration". Molecular Neurodegeneration 16 1 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85120033204&partnerID=MN8TOARS.
    10.1186/s13024-021-00498-5
  18. Riediger, M.; Hernández-Prieto, M.A.; Song, K.; Hess, W.R.; Futschik, M.E.. "Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714". DNA Research 28 6 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85121277695&partnerID=MN8TOARS.
    10.1093/dnares/dsab023
  19. Inácio, J.M.; von Gilsa Lopes, J.; Silva, A.M.; Cristo, F.; Marques, S.; Futschik, M.E.; Belo, J.A.. "DAND5 Inactivation Enhances Cardiac Differentiation in Mouse Embryonic Stem Cells". Frontiers in Cell and Developmental Biology 9 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85104990479&partnerID=MN8TOARS.
    10.3389/fcell.2021.629430
  20. Jemma Dunn; Vasileios P. Lenis; David A. Hilton; Rolf Warta; Christel Herold-Mende; C. Oliver Hanemann; Futschik, Matthias. "Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma". Cancers 12 11 (2020): 3270. https://doi.org/10.3390/cancers12113270.
    Open access • Published • 10.3390/cancers12113270
  21. Vendula Krynická; Jens Georg; Philip J. Jackson; Mark J. Dickman; C. Neil Hunter; Futschik, Matthias; Wolfgang R. Hess; Josef Komenda. "Depletion of the FtsH1/3 Proteolytic Complex Suppresses the Nutrient Stress Response in the Cyanobacterium Synechocystis sp strain PCC 6803". The Plant Cell 31 12 (2019): 2912-2928. https://doi.org/10.1105/tpc.19.00411.
    Published • 10.1105/tpc.19.00411
  22. Santos, João; Mendes-Silva, Leonardo; Afonso, Vanessa; Martins, Gil; Machado, Rui; Lopes, Joao; Cancela, M. Leonor; et al. "Exogenous WNT5A and WNT11 proteins rescue CITED2 dysfunction in mouse embryonic stem cells and zebrafish morphants". Cell Death & Disease 10 (2019): 582. https://www.nature.com/articles/s41419-019-1816-6.
    Open access • Published • 10.1038/s41419-019-1816-6
  23. Dunn, J.; Ferluga, S.; Sharma, V.; Futschik, Matthias; Hilton, D.A.; Adams, C.L.; Lasonder, E.; Oliver Hanemann, C.. "Proteomic analysis discovers the differential expression of novel proteins and phosphoproteins in meningioma including NEK9, HK2 and SET and deregulation of RNA metabolism". EBioMedicine 40 (2018): 77-91. https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(18)30625-X/fulltext.
    Open access • Published • 10.1016/j.ebiom.2018.12.048
  24. Pinto, J.P.; MacHado, R.S.R.; Magno, R.; Oliveira, D.V.; MacHado, S.; Andrade, R.P.; Braganca, J.; Duarte, I.; Futschik, Matthias. "StemMapper: A curated gene expression database for stem cell lineage analysis". Nucleic Acids Research 46 D1 (2018): D788-D793. https://doi.org/10.1093/nar/gkx921.
    Published • 10.1093/nar/gkx921
  25. Ho, P.-W.; Klein, M.; Futschik, Matthias; Nevoigt, E.. "Glycerol positive promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae". FEMS Yeast Research 18 3 (2018): https://doi.org/10.1093/femsyr/foy019.
    Published • 10.1093/femsyr/foy019
  26. Ghezzo, M.N.; Fernandes, M.T.; Pacheco-Leyva, I.; Rodrigues, P.M.; Machado, R.S.; Araújo, M.A.S.; Kalathur, R.K.; et al. "FoxN1-dependent thymic epithelial cells promote T-cell leukemia development". Carcinogenesis 39 12 (2018): 1463-1476. https://doi.org/10.1093/carcin/bgy127.
    Published • 10.1093/carcin/bgy127
  27. Sabour, D.; Machado, R.S.R.; Pinto, J.P.; Rohani, S.; Sahito, R.G.A.; Hescheler, J.; Futschik, Matthias; Sachinidis, A.. "Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart". Molecular Therapy - Nucleic Acids 12 (2018): 158-173. https://doi.org/10.1016/j.omtn.2018.04.018.
    Open access • Published • 10.1016/j.omtn.2018.04.018
  28. Giner-Lamia, Joaquín; Hernández-Prieto, Miguel; Futschik, Matthias. "ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803". BIO-PROTOCOL 8 12 (2018): http://dx.doi.org/10.21769/bioprotoc.2895.
    Open access • Published • 10.21769/bioprotoc.2895
  29. Giner-Lamia, J.; Robles-Rengel, R.; Hernández-Prieto, M.A.; Isabel Muro-Pastor, M.; Florencio, F.J.; Futschik, Matthias. "Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803". Nucleic Acids Research 45 20 (2017): 11800-11820. https://doi.org/10.1093/nar/gkx860.
    Open access • Published • 10.1093/nar/gkx860
  30. Georg, J.; Kostova, G.; Vuorijoki, L.; Schön, V.; Kadowaki, T.; Huokko, T.; Baumgartner, D.; et al. "Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1". Current Biology 27 10 (2017): 1425-1436.e7. https://doi.org/10.1016/j.cub.2017.04.010.
    Open access • Published • 10.1016/j.cub.2017.04.010
  31. Kalathur, R.K.R.; Pedro Pinto, J.; Sahoo, B.; Chaurasia, G.; Futschik, Matthias. "HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease". Scientific Reports 7 1 (2017): 5216. https://doi.org/10.1038/s41598-017-05224-0.
    Open access • Published • 10.1038/s41598-017-05224-0
  32. Macedo, J.A.; Schrama, D.; Duarte, I.; Tavares, E.; Renaut, J.; Futschik, Matthias; Rodrigues, P.M.; Melo, E.P.. "Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells". BMC Genomics 18 1 (2017): 319. https://doi.org/10.1186/s12864-017-3694-6.
    Open access • Published • 10.1186/s12864-017-3694-6
  33. Giner-Lamia, Joaquín; Pereira, Sara B.; Bovea-Marco, Miquel; Futschik, Matthias; Tamagnini, Paula; Oliveira, Paulo. "Extracellular Proteins: Novel Key Components of Metal Resistance in Cyanobacteria?". Frontiers in Microbiology 7 (2016): 878. http://dx.doi.org/10.3389/fmicb.2016.00878.
    Open access • Published • 10.3389/fmicb.2016.00878
  34. Kalathur, Ravi Kiran Reddy; Giner-Lamia, Joaquin; Machado, Susana; Barata, Tania; Ayasolla, Kameshwar R S; Futschik, Matthias; Kalathur RK; et al. "The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach". F1000Research 4 (2016): 103. http://dx.doi.org/10.12688/f1000research.6358.2.
    Open access • Published • 10.12688/f1000research.6358.2
  35. Hernández-Prieto, Miguel A.; Semeniuk, Trudi Ann; Giner-Lamia, Joaquín; Futschik, Matthias. "The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803". Scientific Reports 6 1 (2016): 22168. http://dx.doi.org/10.1038/srep22168.
    Open access • Published • 10.1038/srep22168
  36. Bal, Gürkan; Futschik, Matthias; Hartl, Daniela; Ringel, Frauke; Kamhieh-Milz, Julian; Sterzer, Viktor; Hoheisel, Jörg D.; Alhamdani, Mohamed S. S.; Salama, Abdulgabar. "Identification of novel biomarkers in chronic immune thrombocytopenia (ITP) by microarray-based serum protein profiling". British Journal of Haematology 172 4 (2015): 602-615. http://dx.doi.org/10.1111/bjh.13861.
    Published • 10.1111/bjh.13861
  37. Doron, Shany; Fedida, Ayalla; Hernández-Prieto, Miguel A; Sabehi, Gazalah; Karunker, Iris; Stazic, Damir; Feingersch, Roi; et al. "Transcriptome dynamics of a broad host-range cyanophage and its hosts". The ISME Journal 10 6 (2015): 1437-1455. http://dx.doi.org/10.1038/ismej.2015.210.
    Published • 10.1038/ismej.2015.210
  38. Pells, Steve; Koutsouraki, Eirini; Morfopoulou, Sofia; Valencia-Cadavid, Sara; Tomlinson, Simon R.; Kalathur, Ravi; Futschik, Matthias E.; De Sousa, Paul A.. "Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State". PLOS ONE 10 7 (2015): e0131102. http://dx.doi.org/10.1371/journal.pone.0131102.
    Open access • 10.1371/journal.pone.0131102
  39. Pinto JP; Kalathur RK; Oliveira DV; Barata T; Machado RS; Machado S; Pacheco-Leyva I; Duarte I; Futschik ME. "StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.". (2015): http://europepmc.org/abstract/med/26007653.
    10.1093/nar/gkv529
  40. Stroedicke, Martin; Bounab, Yacine; Strempel, Nadine; Klockmeier, Konrad; Yigit, Sargon; Friedrich, Ralf P.; Chaurasia, Gautam; et al. "Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity". Genome Research 25 5 (2015): 701-713. http://dx.doi.org/10.1101/gr.182444.114.
    Published • 10.1101/gr.182444.114
  41. Hill, Richard; Kalathur, Ravi Kiran Reddy; Colaço, Laura; Brandão, Ricardo; Ugurel, Selma; Futschik, Matthias; Link, Wolfgang. "TRIB2 as a biomarker for diagnosis and progression of melanoma". Carcinogenesis 36 4 (2015): 469-477. http://dx.doi.org/10.1093/carcin/bgv002.
    Published • 10.1093/carcin/bgv002
  42. Hill, Richard; Kalathur, Ravi Kiran Reddy; Callejas, Sergio; Colaço, Laura; Brandão, Ricardo; Serelde, Beatriz; Cebriá, Antonio; et al. "A novel phosphatidylinositol 3-kinase (PI3K) inhibitor directs a potent FOXO-dependent, p53-independent cell cycle arrest phenotype characterized by the differential induction of a subset of FOXO-regulated genes". Breast Cancer Research 16 6 (2014): http://dx.doi.org/10.1186/s13058-014-0482-y.
    Open access • Published • 10.1186/s13058-014-0482-y
  43. Julian Kamhieh-Milz; Reham Fadl Hassan Moftah; Gürkan Bal; Futschik, Matthias; Viktor Sterzer; Omid Khorramshahi; Martin Burow; et al. "Differentially Expressed MicroRNAs in Maternal Plasma for the Noninvasive Prenatal Diagnosis of Down Syndrome (Trisomy 21)". BioMed Research International 2014 (2014): 1-9. http://dx.doi.org/10.1155/2014/402475.
    Open access • Published • 10.1155/2014/402475
  44. Kalathur, R.K.R.; Pinto, J.P.; Hernández-Prieto, M.A.; MacHado, R.S.R.; Almeida, D.; Chaurasia, G.; Futschik, M.E.. "UniHI 7: An enhanced database for retrieval and interactive analysis of human molecular interaction networks". Nucleic Acids Research 42 D1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84891763323&partnerID=MN8TOARS.
    10.1093/nar/gkt1100
  45. Hernández-Prieto, M.A.; Semeniuk, T.A.; Futschik, M.E.. "Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria". Frontiers in Genetics 5 JUL (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84906266629&partnerID=MN8TOARS.
    10.3389/fgene.2014.00191
  46. Pinto, J.P.; Reddy Kalathur, R.K.; Machado, R.S.R.; Xavier, J.M.; Bragança, J.; Futschik, M.E.. "StemCellNet: An interactive platform for network-oriented investigations in stem cell biology". Nucleic Acids Research 42 W1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84904816435&partnerID=MN8TOARS.
    10.1093/nar/gku455
  47. Pinto, J.P.; Machado, R.S.R.; Xavier, J.M.; Futschik, M.E.. "Targeting molecular networks for drug research". Frontiers in Genetics 5 JUN (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84906249332&partnerID=MN8TOARS.
    10.3389/fgene.2014.00160
  48. Wallach, T.; Schellenberg, K.; Maier, B.; Kalathur, R.K.R.; Porras, P.; Wanker, E.E.; Futschik, M.E.; Kramer, A.. "Dynamic Circadian Protein-Protein Interaction Networks Predict Temporal Organization of Cellular Functions". PLoS Genetics 9 3 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875967429&partnerID=MN8TOARS.
    10.1371/journal.pgen.1003398
  49. Hernández-Prieto, Miguel A.; Schön, Verena; Georg, Jens; Barreira, Luísa; Varela, João; Hess, Wolfgang R.; Futschik, Matthias E.. "Iron Deprivation in Synechocystis: Inference of Pathways, Non-coding RNAs, and Regulatory Elements from Comprehensive Expression Profiling". G3 Genes|Genomes|Genetics 2 12 (2012): 1475-1495. http://dx.doi.org/10.1534/g3.112.003863.
    Open access • Published • 10.1534/g3.112.003863
  50. Hernandez-Prieto, Miguel A; Futschik, Matthias. "CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803". Bioinformation 8 13 (2012): 634-638. http://dx.doi.org/10.6026/97320630008634.
    Open access • 10.6026/97320630008634
  51. Kalathur, Ravi Kiran Reddy; Hernández-Prieto, Miguel A; Futschik, Matthias E. "Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database". BMC Neurology 12 1 (2012): 47. http://dx.doi.org/10.1186/1471-2377-12-47.
    Open access • Published • 10.1186/1471-2377-12-47
  52. Kalathur, Ravi; Ayasolla, Kamesh; Futschik, Matthias. "The Unfolded Protein Response and its potential role in Huntington's disease". Nature Precedings (2012): http://dx.doi.org/10.1038/npre.2012.7145.1.
    Open access • Published • 10.1038/npre.2012.7145.1
  53. Ayasolla, Kameshwar; Kalathur, Ravi; Futschik, Matthias. "A Systems Biology Approach towards Deciphering the Unfolded Protein Response in Huntington's Disease". Nature Precedings (2012): http://dx.doi.org/10.1038/npre.2012.7078.1.
    Open access • Published • 10.1038/npre.2012.7078.1
  54. Bal, Gürkan; Kamhieh-Milz, Julian; Futschik, Matthias; Häupl, Thomas; Salama, Abdulgabar; Moldenhauer, Anja. "Transcriptional Profiling of the Hematopoietic Support of Interleukin-Stimulated Human Umbilical Vein Endothelial Cells (HUVECs)". Cell Transplantation 21 1 (2012): 251-267. http://dx.doi.org/10.3727/096368911x580581.
    Published • 10.3727/096368911x580581
  55. Bal, G.; Kamhieh-Milz, J.; Futschik, M.; Häupl, T.; Salama, A.; Moldenhauer, A.. "Transcriptional profiling of the hematopoietic support of interleukin-stimulated human umbilical vein endothelial cells (HUVECs)". Cell Transplantation 21 1 (2012): 251-267. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858143659&partnerID=MN8TOARS.
    10.3727/096368911X580581
  56. Duong, C.T.; Strack, L.; Futschik, M.; Katou, Y.; Nakao, Y.; Fujimura, T.; Shirahige, K.; Kodama, Y.; Nevoigt, E.. "Identification of Sc-type ILV6 as a target to reduce diacetyl formation in lager brewers' yeast". Metabolic Engineering 13 6 (2011): 638-647. http://dx.doi.org/10.1016/j.ymben.2011.07.005.
    Published • 10.1016/j.ymben.2011.07.005
  57. Moldenhauer, Anja; Futschik, Matthias; Lu, Huili; Helmig, Melanie; Götze, Patricc; Bal, Gürkan; Zenke, Martin; Han, Wei; Salama, Abdulgabar. "Interleukin 32 promotes hematopoietic progenitor expansion and attenuates bone marrow cytotoxicity". European Journal of Immunology 41 6 (2011): 1774-1786. http://dx.doi.org/10.1002/eji.201040986.
    Open access • Published • 10.1002/eji.201040986
  58. Russ, Jenny; Futschik, Matthias E. "Comparison and consolidation of microarray data sets of human tissue expression". BMC Genomics 11 1 (2010): 305. http://dx.doi.org/10.1186/1471-2164-11-305.
    Open access • Published • 10.1186/1471-2164-11-305
  59. Marras, Elisabetta; Travaglione, Antonella; Chaurasia, Gautam; Futschik, Matthias; Capobianco, Enrico. "Inferring modules from human protein interactome classes". BMC Systems Biology 4 1 (2010): 102. http://dx.doi.org/10.1186/1752-0509-4-102.
    Open access • Published • 10.1186/1752-0509-4-102
  60. Steglich, Claudia; Lindell, Debbie; Futschik, Matthias; Rector, Trent; Steen, Robert; Chisholm, Sallie W. "Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus". Genome Biology 11 5 (2010): R54. http://dx.doi.org/10.1186/gb-2010-11-5-r54.
    Open access • Published • 10.1186/gb-2010-11-5-r54
  61. Chaurasia, G.; Malhotra, S.; Russ, J.; Schnoegl, S.; Hänig, C.; Wanker, E.E.; Futschik, M.E.. "UniHI 4: New tools for query, analysis and visualization of the human protein-protein interactome". Nucleic Acids Research 37 SUPPL. 1 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-58149183692&partnerID=MN8TOARS.
    10.1093/nar/gkn841
  62. Zinser, E.R.; Lindell, D.; Johnson, Z.I.; Futschik, M.E.; Steglich, C.; Coleman, M.L.; Wright, M.A.; et al. "Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus". PLoS ONE 4 4 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-65249154859&partnerID=MN8TOARS.
    10.1371/journal.pone.0005135
  63. Gsponer, J.; Futschik, M. E.; Teichmann, S. A.; Babu, M. M.. "Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation". Science 322 5906 (2008): 1365-1368. http://dx.doi.org/10.1126/science.1163581.
    Published • 10.1126/science.1163581
  64. Steglich, C.; Futschik, M.E.; Lindell, D.; Voss, B.; Chisholm, S.W.; Hess, W.R.. "The challenge of regulation in a minimal photoautotroph: Non-coding RNAs in Prochlorococcus". PLoS Genetics 4 8 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-50849096398&partnerID=MN8TOARS.
    10.1371/journal.pgen.1000173
  65. Futschik, M.E.; Herzel, H.. "Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis". Bioinformatics 24 8 (2008): 1063-1069. http://www.scopus.com/inward/record.url?eid=2-s2.0-41949124936&partnerID=MN8TOARS.
    10.1093/bioinformatics/btn072
  66. Futschik, Matthias E.; Chaurasia, Gautam; Tschaut, Anna; Russ, Jenny; Babu, M. Madan; Herzel, Hanspeter. "Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network". Journal of Integrative Bioinformatics 4 3 (2007): 198-207. http://dx.doi.org/10.1515/jib-2007-76.
    Open access • Accepted • 10.1515/jib-2007-76
  67. Lindell, Debbie; Jaffe, Jacob D.; Coleman, Maureen L.; Futschik, Matthias E.; Axmann, Ilka M.; Rector, Trent; Kettler, Gregory; et al. "Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution". Nature 449 7158 (2007): 83-86. http://dx.doi.org/10.1038/nature06130.
    Published • 10.1038/nature06130
  68. Chaurasia, Gautam; Iqbal, Yasir; Hänig, Christian; Herzel, Hanspeter; Wanker, Erich E.; Futschik, Matthias E.. "Flexible web-based integration of distributed large-scale human protein interaction maps". Journal of Integrative Bioinformatics 4 1 (2007): 40-50. http://dx.doi.org/10.1515/jib-2007-51.
    Open access • Published • 10.1515/jib-2007-51
  69. Chaurasia, G.; Iqbal, Y.; Hänig, C.; Herzel, H.; Wanker, E.E.; Futschik, M.E.. "UniHI: An entry gate to the human protein interactome". Nucleic Acids Research 35 SUPPL. 1 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-33846048729&partnerID=MN8TOARS.
    10.1093/nar/gkl817
  70. Futschik, M.E.; Chaurasia, G.; Herzel, H.. "Comparison of human protein-protein interaction maps". Bioinformatics 23 5 (2007): 605-611. http://www.scopus.com/inward/record.url?eid=2-s2.0-34047168855&partnerID=MN8TOARS.
    10.1093/bioinformatics/btl683
  71. Futschik ME; Tschaut A; Chaurasia G; Herzel H. "Graph-theoretical comparison reveals structural divergence of human protein interaction networks.". (2007): http://europepmc.org/abstract/med/18546482.
  72. Steglich, Claudia; Futschik, Matthias; Rector, Trent; Steen, Robert; Chisholm, Sallie W.; Steglich C; Futschik M; et al. "Genome-Wide Analysis of Light Sensing in Prochlorococcus". Journal of Bacteriology 188 22 (2006): 7796-7806. http://dx.doi.org/10.1128/jb.01097-06.
    Open access • Published • 10.1128/jb.01097-06
  73. Kumar L; Futschik M; Herzel H. "DNA motifs and sequence periodicities.". In Silico Biology 6 1-2 (2006): 71-78. https://pubmed.ncbi.nlm.nih.gov/16789915/.
    Published
  74. FUTSCHIK, MATTHIAS E.; CARLISLE, BRONWYN. "NOISE-ROBUST SOFT CLUSTERING OF GENE EXPRESSION TIME-COURSE DATA". Journal of Bioinformatics and Computational Biology 03 04 (2005): 965-988. http://dx.doi.org/10.1142/s0219720005001375.
    Published • 10.1142/s0219720005001375
  75. Futschik, M.E.; Crompton, T.. "OLIN: Optimized normalization, visualization and quality testing of two-channel microarray data". Bioinformatics 21 8 (2005): 1724-1726. http://www.scopus.com/inward/record.url?eid=2-s2.0-17444399363&partnerID=MN8TOARS.
    10.1093/bioinformatics/bti199
  76. Futschik, M.; Crompton, T.. "Model selection and efficiency testing for normalization of cDNA microarray data.". Genome biology 5 8 (2004): http://www.scopus.com/inward/record.url?eid=2-s2.0-16644384356&partnerID=MN8TOARS.
    10.1186/gb-2004-5-8-r60
  77. Futschik, Matthias E; Reeve, Anthony; Kasabov, Nikola; Futschik, M.E.; Reeve, A.; Kasabov, N.. "Evolving connectionist systems for knowledge discovery from gene expression data of cancer tissue". Artificial Intelligence in Medicine 28 2 (2003): 165-189. http://dx.doi.org/10.1016/s0933-3657(03)00063-0.
    Published • 10.1016/s0933-3657(03)00063-0
  78. Futschik ME; Sullivan M; Reeve A; Kasabov N. "Prediction of clinical behaviour and treatment for cancers.". OMJ Applied Bioinformatics 2 3 (2003): S53-58. http://europepmc.org/abstract/med/15130817.
    Open access • Published
  79. Humar, Bostjan; Graziano, Francesco; Cascinu, Stefano; Catalano, Vincenzo; Ruzzo, Anna M; Magnani, Mauro; Toro, Tumi; et al. "Association of CDH1 haplotypes with susceptibility to sporadic diffuse gastric cancer". Oncogene 21 53 (2002): 8192-8195. http://dx.doi.org/10.1038/sj.onc.1205921.
    Open access • Published • 10.1038/sj.onc.1205921
  80. Futschik, Matthias; Jeffs, Aaron; Pattison, Sharon; Kasabov, Nikola; Sullivan, Michael; Merrie, Arend; Reeve, Anthony. "Gene Expression Profiling of Metastatic and Nonmetastatic Colorectal Cancer Cell Lines". Genome Letters 1 1 (2002): 26-34. http://dx.doi.org/10.1166/gl.2002.005.
    Published • 10.1166/gl.2002.005
Magazine article
  1. Umbach, P; Futschik, Matthias; Stelzl, U; Wanker, E.E.. "Funktion durch Netzwerke von Proteinen und ihren Wechselwirkungen", Laborwelt, 2007, http://193.136.227.175/sysbiolab/publications/laborwelt.ps.
  2. Brown, C; Jacobs, G; Schreiber, M; Magnum, J; McNaughton, J; M. Cambray,; Futschik, Matthias; et al. "Using bioinformatics to investigate post-transcriptional control of gene expression", 2000
Thesis / Dissertation
  1. Futschik, Matthias. "Methods for knowledge discovery in microarray data.". PhD, University of Otago, 2003. http://www.sysbiolab.eu/PhD/index.htm.
  2. Futschik, Matthias. "Experimentelle Charakterisierung und theoretische Modellierung von Dendrimer-Tetrapyrrol Komplexen (Experimental characterisation and theoretical modelling of dendrimer-tetrapyrrol complexes).". Master, Humboldt-Universität zu Berlin, 1998.

Intellectual property

Patent
  1. Kasabov, N; Futschik, Matthias; Suillivan, M; Reeve, A. 2016. "Medical Decision Support Systems Utilizing Gene Expression And Clinical Information And Method For Use ( EP 1534122 A4 )".
    Granted/Issued
  2. Reeve, A; Futschik, Matthias; Sullivan, M.; Kasabov, N; Guilford, P. 2008. "Medical applications of adaptive learning systems using gene expression data (US7370021B2)". United States.
    Granted/Issued
Provisional application for patent
  1. 2008. "Medical Applications Of Adaptive Learning Systems And Diagnostic Kits (NZ547894A)".
    Disclosed
  2. 2006. "Medical Applications Of Adaptive Learning Systems (NZ 537160A)".
    Disclosed

Other

Dataset
  1. Futschik, Matthias. CyanoEXpress: a curated genome-wide expression database for the cyanobacterium Synechocystis. http://cyanoexpress.sysbiolab.eu/.
  2. Futschik, Matthias. HeartEXpress: database for query and visualisation of integrated expression datasets associated with cardiomyogenesis.. http://heartexpress.sysbiolab.eu/.
  3. Futschik, Matthias. HeartmiR: database and webserver for querying of relevant miRNA-mRNA interactions for late heart development in mouse. http://heartmir.sysbiolab.eu/.
  4. Futschik, Matthias. Huntington's Disease Network Database (HDNetDB) for network-based analysis of Huntington's disease.. http://hdnetdb.sysbiolab.eu/.
  5. Futschik, Matthias. StemChecker: database and web-based tool to examine stemness in gene sets. http://stemchecker.sysbiolab.eu/.
  6. Futschik, Matthias. StemCellNet: interactive web server & database for network analysis and visualization in stem cell biology.. http://stemcellnet.sysbiolab.eu/.
  7. Futschik, Matthias. StemMapper: manually curated database containing gene expression data for different lineages of Stem Cells (SCs) from human and mouse. http://stemmapper.sysbiolab.eu/.
  8. Futschik, Matthias. UniHI: comprehensive database of human molecular interactions, functional annotation, disease assocation and drug target information. http://www.unihi.org/.
  9. Futschik, Matthias. UPR-HD: dataset of expression of UPR-associated genes across various transcriptomic studies of Huntington's disease. http://uprhd.sysbiolab.eu/.
Research technique
  1. OLIN: R/Bioconductor package for optimized local intensity-dependent normalization of two colour microarrays: http://www.bioconductor.org/packages/release/bioc/html/OLIN.html. Researcher. Futschik, Matthias.
    Researcher
  2. Mfuzz: R/Bioconductor package for soft clustering of time series gene expression data based on fuzzy c-means clustering algorithm http://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html. Researcher. Futschik, Matthias.
    Researcher
  3. Cycle: R/Bioconductor package for determining the significance of periodic expression pattern in time-series data: http://www.bioconductor.org/packages/release/bioc/html/cycle.html. Researcher. Futschik, Matthias.
    Researcher
  4. OLINGui: R/Bioconductor package implementing a graphical user interface for optimized local intensity-dependent normalization (OLIN). http://www.bioconductor.org/packages/release/bioc/html/OLINgui.html. Researcher. Futschik, Matthias.
    Researcher
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2020/07/15 Network biology: from databases to applications MDR Bioinformatics meetings
Imperial College, Department of Metabolism, Digestion & Reproduction (London, United Kingdom)
2020/03/05 Basis and applications of network biology Molecular Epidemiology Seminars
Imperial College, Department of Epidemiology and Biostatistics (London, United Kingdom)
2019/03/26 The long way from bench to bedside – an omics perspective Dept of Cellular Pathology Seminar
University Hospitals Plymouth NHS Trust (Plymouth, United Kingdom)
2018/09/13 Deciphering the gene regulatory networks of cyanobacteria 3rd Early Career Researcher Symposium on Cyanobacteria
University of Freiburg (Freiburg, Germany)
2017/08/20 Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC6803 10th European Workshop on the Molecular Biology of Cyanobacteria
Federation of European Microbiological Societies/Biological Research Centre Jibou ( Cluj-Napoca, Romania)
2017/05/18 The many faces of stem cells: Meta-analysis of stemness signatures, 7th Bioinformatics and Stem Cells Satellite Meeting (NRW SC BioINF 2017)
Institute for Biostatistics and Informatics in Medicine and Ageing Research (Muenster, Germany)
2016/09/09 SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology INFORUM 2016
Instituto Superior Tecnico (Lisbon, Portugal)
2015/10/15 StemCellNet: an interactive platform for network-oriented investigations in stem cell biology. 9th International Meeting of the Portuguese society for Stem cells and Cell therapies
Portuguese society for Stem cells and Cell therapies (Oeiras, Portugal)
2014/05 Systems Biology: Can it help in the study of neurodegeneration? 1st Neuroimmunology Workshop
Institut du Cerveau (Paris, France)
2013/11/19 How Synechocystis adapts to changes in environment: A meta-analysis of its transcriptional responses CyanoFactory Meeting
CyanoFactory (EU project, FP7-ENERGY-2012-1-2STAGE) (Porto, Portugal)
2013 How the internal world of Synechocystis adapts to the ever-changing world outside: A comprehensive meta-analysis of its transcriptional responses ESF-EMBO Symposium
European Science Foundation (Pultusk, Poland)
2012 UniHI: Network biology goes to the bench 3nd Meeting of the Institute for Biotechnology and Bioengineering,
Institute for Biotechnology and Bioengineering, (Lisbon, Portugal)
2011/02 Network biology, a key to understand the complexity of molecular systems Departmental Seminar Biochemistry
University of Otago (Dunedin, New Zealand)
2011/01 Concepts and applications of network biology KEDRI Seminar
Auckland University of Technology (Auckland, New Zealand)
2010/10/24 Chorea Huntington: A thousand changes due to a single mutation 2nd Meeting of the Institute for Biotechnology and Bioengineering
Universidade do Minho (Minho, Portugal)
2010 A Network Perspective on Signalling 4th National Meeting on Signal Transduction, SINAL 2010
Universidade do Algarve (Faro, Portugal)
2009 Disentangling molecular interaction networks for Huntington's Disease
Weizmann Institute (Rehovot, Israel)
2009 Disentangling molecular interaction networks for Chorea Huntington
Institute for Systems Biology (Seattle, United States)
2009 Revealing the molecular Complexity of Human Diseases 15th Annual German-American Kavli Frontiers of Science Symposium
Alexander von Humboldt-Stiftung - U.S. National Academy of Science (Irvine, United States)
2008 Disentangling molecular intaction networks for Chorea Huntington European Huntington's Diesease Network Meeting
European Huntington's Diesease Network (Lisbon, Portugal)
2008 Large-scale human protein-protein interacton maps: A tool for finding the magical bullets against complex diseases Protein-Protein Interactions as Drug Targets Symposium
(Berlin)
2008 Large-scale human protein-protein interacton maps: A tool for finding the magical bullets against complex diseases Protein-Protein Interactions as Drug Targets Symposium
(Berlin, Germany)
2007/10/11 Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Networks 4th International workshop in Integrative Bioinformatics
University of Ghent (Ghent, Belgium)
2007 Are we overestimating the number of cell-cycling genes? German Conference on Bioinformatics
University of Potsdam (Potsdam, Germany)
2007 Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network International workshop in Integrative Bioinformatics
(Ghent, Belgium)
2007 Concurrency between and coherency within human PPI maps HUPO PSI, Spring Meeting,
(Lyon, France)
2007 Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks International Workshop on Bioinformatics and Systems Biology
(Tokyo, Japan)
2007 Network biology, a key to understand the complexity of molecular systems
University of Faro (Faro, Portugal)
2007 Network biology, a key to understand the complexity of molecular systems Invited Seminar
Universidade do Algarve, Centre for Molecular and Structural Biomedicine (Faro, Portugal)
2007 Concurrency between and coherency within human PPI maps HUPO PSI, Spring Meeting
HUPO Proteomics Standards Initiative (PSI) (Lyon , France)
2006 Comparison and integration of human protein interaction maps, Comparison of Human Protein-Protein Interaction Maps, Interactome Networks,
Wellcome Trust/Cold Spring Harbour Laboratory Conference, (Hinxton, United Kingdom)
2006 Comparison of Human Protein-Protein Interaction Maps German Conference on Bioinformatics
University of Tuebingen (Tübingen, Germany)
2006 Comparison and integration of human protein interaction maps, Comparison of Human Protein-Protein Interaction Map Interactome Networks
Wellcome Trust/Cold Spring Harbour Laboratory (Cambridge, United States)
2005 M. Futschik S. Legewie and H.Herzel (2005), Dynamics of Liver Regeneration- Microarrays, Arrays and Modelling, BMBF-Initiative "Systembiologie", Platform Meeting "Modeling & Bioinformatics"
(Heidelberg, Germany)
2005 Whole genome screening for non-coding RNAs in Prochlorococcus MED4 using a high-density oligonucleotide probe microarray International Symposium on the Genomics of Marine Phytoplankton
Station Biologique de Roscoff, Sorbonne University (Roscoff, France)
2005 Dynamics of Liver Regeneration- Microarrays, Arrays and Modelling BMBF-Initiative "Systembiologie", Platform Meeting "Modeling & Bioinformatics"
University Heidelberg (Heidelberg, Germany)
2005 Microarray data analysis - Gold-mining in a minefield Mathematical Interdisciplinary Research Day: Genetic Network
Warwick Mathematical Instituts (Warwick, United Kingdom)
2004 Microarray data analysis - Gold-mining in a minefield
Warwick Mathematical Institute (Warwick, United Kingdom)
2004 Prometheus under the microscope: Systems-Biological approaches to liver regeneration Institutional Seminar
Freiburger Zentrum für Datenanalyse und Modellbildung (Freiburg, Germany)
2003 Modular Decision System and Information Integration for Improved Disease Outcome prediction ECCB 2003
(Paris, France)
2003 Prediction of clinical behaviours and treatment for cancers New Zealand Bioinformatics Conference
(Wellington, New Zealand)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021/02/23 - 2021/08/06 The 3-dimensional genome in human health and disease
Co-supervisor
 Molecular Medicine (Master)
Imperial College London, United Kingdom
2016 - 2021 Identification of key factors of heart regeneration using a systems biology approach
Supervisor of Rui Machado
 Biomedical Science (PhD)
Universidade do Algarve - Campus de Gambelas, Portugal
2019 - 2019 Mitochondrial biogenesis and cellular bioenergetic function in uraemic myopathy
Supervisor of Dr Jane Carre
 Postdoctoral Researcher (Other)
University of Plymouth, United Kingdom
2019 - 2019 The Role of Active L1 Retrotransposons in Alzheimer's Disease
Supervisor of Roxane Dunbar
 Biomedical Sciences (PhD)
University of Plymouth, United Kingdom
2019 - 2019 LINE-1 elements: Genomic distribution and potential contribution to brain related disorders
Supervisor of Randa Ali
 Biomedical Sciences (PhD)
University of Plymouth, United Kingdom
2018 - 2019 Insights into Gene Expression and the Influence of Regulatory Mechanisms within Meningioma - A Bioinformatic Approach
Supervisor of Louise Carr
 Biomedical Science (Degree)
University of Plymouth, United Kingdom
2018 - 2019 Transcriptomic analysis of various WHO Grades of meningioma to establish the potential for targeted therapy based on prognosis following diagnosis of WHO Grade
Supervisor of Bryant Lee
 Biomedical Sciences (Degree)
University of Plymouth, United Kingdom
2018 - 2019 Neuroprotective Effects of NMNAT2, WIF-1, TIMP-1 and MYOC
Supervisor of Jessica Woods
 Biomedical Sciences (Degree)
University of Plymouth, United Kingdom
2018 - 2019 Evaluation of the axonal-regenerative role of Schwann cell differentiation by systematic review of gene expression data from Wt and WldS mutant mice
Supervisor of Jonathan White
 Biomedical Sciences (Degree)
University of Plymouth, United Kingdom
2017 - 2019 Research topics: Meta-analysis of meningioma expression data. Sequence data analysis to detect somatic mutations in Alzheimer's disease. Analysis of Nanopore sequence data.
Supervisor of Dr Vasilis Lenis
 Postdoctoral Researcher (Other)
University of Plymouth, United Kingdom
2015 - 2019 Cited2 in cardiac development: an inside and outside job
Co-supervisor of Joao Miguel Santos
 Mechanisms of Disease and Regenerative Medicine (PhD)
Universidade do Algarve, Portugal
2017 - 2018 Comparison and integration of meningioma expression profiles
Supervisor of Alexander Walker
 Biomedical Science (Master)
University of Plymouth, United Kingdom
2017 - 2018 A bioinformatic meta-analysis identifying potential prognostic biomarkers for improved differential meningioma grade diagnosis
Supervisor of Joshua Walker
 Biomedical Sciences (Degree)
University of Plymouth, United Kingdom
2013 - 2018 Postdoctoral research fellow (FCT - SFRH/BPD/96890/2013 ): Development of software tools for the prediction of cellular fate in stem cell differentiation. Postdoctoral researcher in FCT project: Alternative splicing and its impact on molecular interaction networks (PTDC/BIA-GEN/116519/2010)
Supervisor of Dr José Pinto
 Postdoctoral Researcher (Other)
Universidade do Algarve, Portugal
2015 - 2015 Reseacher in FCT project: The regulation of photosynthesis in cyanobacteria: A systems biology approach. (PTDC/BIA-MIC/4418/2012)
Supervisor of Miquel Marco
 Researcher (Other)
Universidade do Algarve, Portugal
2015 - 2015 Associated Researcher in FCT Project: Alternative splicing and its impact on molecular interaction networks (PTDC/BIA-GEN/116519/2010)
Supervisor of Susana Machado
 Researcher (Other)
Universidade do Algarve, Portugal
2015 - 2015 Associated Researcher in FCT project: Alternative splicing and its impact on molecular interaction networks (PTDC/BIA-GEN/116519/2010
Supervisor of Ivette Pacheco
Researcher (Other)
Universidade do Algarve, Portugal
2014 - 2015 Postdoctoral researcher in FCT project : The regulation of photosynthesis in cyanobacteria: A systems biology approach (FCT-PTDC/BIA-MIC/4418/2012)
Supervisor of Dr Joaquin Lamia
 Postdoctoral Researcher (Other)
Universidade do Algarve, Portugal
2014 - 2015 Researcher in FCT Project: Alternative splicing and its impact on molecular interaction networks (PTDC/BIA-GEN/116519/2010)
Supervisor of MSc Isabel Duarte
 Researcher (Other)
Universidade do Algarve, Portugal
2014 - 2015 Researcher in FCT Project: Alternative splicing and its impact on molecular interaction networks (PTDC/BIA-GEN/116519/2010)
Supervisor of MSc Daniel Oliveira
 Researcher (Other)
Universidade do Algarve, Portugal
2010 - 2015 Postdoctoral research fellow (SFRH/BPD/70718/2010): Systems Biology approach to unravel the molecular mechanisms involved in T-Cell Acute Lymphoblastic Leukaemia. Postdoctoral researcher in Project: CHDI A2666: Visualization and Analysis of HD-Related Molecular Interaction Network.
Supervisor of Dr Ravi Kalathur
 Postdoctoral Researcher (Other)
Universidade do Algarve, Portugal
2010 - 2014 Postdoctoral researcher in FCT projects: 'Regulation of iron homeostasis in cyanobacteria' (PTDC/BIA-MIC/101036/2008) and 'The regulation of photosynthesis in cyanobacteria: A systems biology approach' (PTDC/BIA-MIC/4418/2012)
Supervisor of Dr Miguel Hernandez
 Postdoctoral Researcher (Other)
Universidade do Algarve, Portugal
2013 - 2013 Analysis of the transcriptional regulatory network: underlying heart development
Supervisor of Rui Machado
 Biomedical Sciences (Master)
Universidade do Algarve, Portugal
2013 - 2013 Researcher in FCT project: The regulation of photosynthesis in cyanobacteria: A systems biology approach (FCT - PTDC/BIA-MIC/4418/2012)
Supervisor of Dr. Shanmugam Hemaiswarya
 Researcher (Other)
Universidade do Algarve, Portugal
2012 - 2013 Researcher in FCT project: The role and regulation of alpha-synuclein phosphorylation in both pathological and physiological conditions (PTDC/BIA-BCM/117975/2010
Supervisor of MSc Dulce Almeida
 Researcher (Other)
Universidade do Algarve, Portugal
2010 - 2011 Postdoctoral researcher in Project: CHDI A2666 - Visualization and Analysis of HD-Related Molecular Interaction Networks.
Supervisor of Dr. Kamesh Ayasolla
 Postdoctoral researcher (Other)
Universidade do Algarve, Portugal
2005 - 2009 Analysis of protein interaction networks in human health and disease
Supervisor of Gautam Chaurasia
 Bioinformatics (PhD)
Humboldt Universität zu Berlin Institute for Theoretical Biology, Germany
2004 - 2008 Dysregulation of expression in Chorea Huntington
Co-supervisor of Branca Cajavec
 Theoretical Biology (PhD)
Humboldt Universität zu Berlin Institute for Theoretical Biology, Germany
2006 - 2007 Identification of periodically expressed genes in microarray data
Supervisor of Mandy Fuchs
 Bioinformatics (Degree)
Freie Universität Berlin, Germany
2006 - 2007 Comparison of microarray data sets for tissue expression
Supervisor of Jenny Russ
 Bioinformatics (Degree)
Freie Universität Berlin, Germany

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2017/10/23 - 2017/10/24 Local co-organizer of COST action workshop (2017/06 - 2017/10)
Workshop (Co-organisor)
 Universidade de Lisboa Instituto Superior Técnico, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2019/03/21 - Current Facilitator of Artificial Intelligence & Machine Learning track
Conference
 9th Bioinformatics Strategy Meeting Europe 2019
Proventa International , United Kingdom
2015/03/17 - Current Talk to local high school pupils about the possibility of computational biology to help to find a cure for neurodegenerative diseases
Festival
 Brain Awareness Week
Universidade do Algarve, Portugal
2019/11/05 - 2019/11/06 Coordination of work package meeting
Workshop
 Sarajevo workshop of COST Action CA15205
Internazionalni Univerzitet Sarajevo, Bosnia and Herzegovina

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2013/08/01 PhD thesis defense
(Thesis) Main arguer
 Filipe Pinto (PhD)
Universidade do Porto, Portugal

Association member

Society Organization name Role
2020 - Current Human Cell Atlas Member
2019 - Current Higher Education Academy (UK) Fellow of the Higher Education Academy
1999 - Current International Society of Computational Biology Member
2016 - 2017 Sociedade Portuguesa de Células Estaminais e Terapia Celular (SPCE-TC) Governing Board Member

Committee member

Activity description
Role 		Institution / Organization
2016 - 2021 National delegate and work group leader in European COST action GREEKC (CA15205)
Member
 Norges teknisk-naturvitenskapelige universitet, Norway
2016 - 2020 National delegate in European COST actions CHARME (CA15110)
Member
 Universität Potsdam, Germany
2017/05/01 - 2019/07/31 Coordination the research activities of Genomics and Genetics Group at University of Plymouth's Institute of Translational and Stratified Medicine (ITSMED),
Coordinator
 University of Plymouth, United Kingdom
2000 - 2002 Representative for international postgraduate students in University council
Member
 University of Otago, New Zealand

Conference scientific committee

Conference name Conference host
2016 - 2016 INFORM2016 Portuguese National Forum for Informatics
2015/11/09 - 2015/11/11 International Conference on Bioinformatics (GIW/InCoB2016) APBioNET and the Japanese Society for Bioinformatics

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2019/02 - Current Computational Biology Module - Network Biology Master in Biomedical Science (Mestrado) Universidade do Algarve, Portugal
2019 - 2019 Contemporary Applications of Cell Biology Biomedical Sciences (Master) University of Plymouth, United Kingdom
2019 - 2019 Systems Biology workshop for MeInBio graduate school (Doktor (PhD)) Albert-Ludwigs-Universität Freiburg Fakultät für Biologie, Germany
2019 - 2019 Study Skills and Personal Development Biomedical Science (Bachelor) University of Plymouth, United Kingdom
2018 - 2019 Biomedical Investigation and Experimentation Biomedical Sciences (Bachelor) University of Plymouth, United Kingdom
2018 - 2019 Current Developments in Biomedical Science: Applications of Bioinformatics and Systems Biology Biomedical Sciences (Bachelor) University of Plymouth, United Kingdom
2016 - 2016 Data analysis module in Marine Genomics summer school Marine Genomics (Postgraduate Certificate) Centro de Ciências do Mar, Portugal
2013 - 2015 Invited lectures about Systems and Network biology Biomedical Science (Mestrado) Universidade do Algarve, Portugal
2012 - 2013 Invited lectures on bioinformatics and neurodegenerative diseases Neurosciences (Mestrado) Universidade do Algarve, Portugal
2011 - 2011 Introduction to transcriptomics analysis Biodiversity and Conservation (Mestrado) Universidade do Algarve, Portugal
2005 - 2008 Mathematical Fundamentals of Biology 1 Biology (Bachelor) Humboldt-Universität zu Berlin, Germany
2005 - 2008 Mathematical Fundamentals of Biology 2 Biologie (Bachelor) Humboldt-Universität zu Berlin, Germany
2005 - 2008 Time series analysis Biology, Biophysics (Master) Humboldt Universität zu Berlin Institute for Theoretical Biology, Germany
2004 - 2004 Microarray data analysis I-V, Summer school on cell biology and mathematical modelling (Graduado) Humboldt Universität zu Berlin Institute for Theoretical Biology, Germany
2004 - 2004 Microarrays & Expression Profiling, Bioinformatics summer school (Postgraduate Certificate) Isik Üniversitesi, Turkey
2001 - 2001 Biological Physics Biology (Bachelor) University of Otago, New Zealand
2001 - 2001 Foundations of Information Systems Computer Science (Bachelor) University of Otago, New Zealand
1997 - 1998 Physics for students of biology Biologie (Bachelor) Humboldt-Universität zu Berlin Institut für Physik, Germany
1997 - 1997 Physics practical for medical students Medicine (Licence) Humboldt-Universität zu Berlin Institut für Physik, Germany

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2018 Interview about my work on developing computational resources for stem cell biology Website Algarve für Entdecker

Journal scientific committee

Journal title (ISSN) Publisher
2012 - Current Scientifica Hindawi
2006 - 2009 Cancer Informatics SAGE/Libertas Academica previously

Mentoring / Tutoring

Topic Student name
2018 - 2019 Personal tutor of first year students in Biomedicine at University of Plymouth Rhiannon Wilton
2018 - 2019 Personal tutor of first year students in Biomedicine at University of Plymouth Vinay Bakshi
2018 - 2019 Personal tutor of first year students in Biomedicine at University of Plymouth Frances Ramshaw
2018 - 2019 Personal tutor of first year students in Biomedicine at University of Plymouth Elena Landregan
2018 - 2019 Personal tutor of first year students in Biomedicine at University of Plymouth Barachille Ortiz
2015 - 2015 Host for research stay at University of Algarve Tania Barata

Other jury / evaluation

Activity description Institution / Organization
2016 - Current Scientific expert for the Governing Board of the International Doctoral Program Institut Curie, France
2021 - 2021 External evaluator of NWO grant proposal Dutch Research Council, Netherlands
2020 - 2020 Rapporteur of evaluation panel for COST action proposal European Cooperation in Science and Technology, Belgium
2019 - 2019 External grant reviewer Grantová agentura Ceské republiky, Czech Republic
2018 - 2018 External grant reviewer Engineering and Physical Sciences Research Council, United Kingdom
2017 - 2018 Reviewer of proposals to BBSRC Biotechnology and Biological Sciences Research Council, United Kingdom
2017 - 2017 External assessor of MPhil Transfer Report University of Mauritius, Mauritius
2016 - 2016 External evaluator for grant proposal to Vidi scheme Dutch Research Council, Netherlands
2016 - 2016 External evaluator of proposal to COST action European Cooperation in Science and Technology, Belgium
2016 - 2016 Grant reviewer Fonds National de la Recherche, Luxembourg
2016 - 2016 Remote Referee for ERC grant European Research Council, Belgium
2015 - 2016 External evaluator for Austrian Science Fund Fonds zur Förderung der wissenschaftlichen Forschung, Austria
Distinctions

Award

2013 FCT Investigador (Developmental Grant)
Fundação para a Ciência e a Tecnologia, Portugal
2008 Erwin-Schrödinger-Prize
Helmholtz-Gemeinschaft, Germany
2007 Royal Society visiting fellow
The Royal Society, United Kingdom

Title

2019 Honorary Professor
University of Plymouth, United Kingdom
2019 Fellow of the Higher Education Academy
Higher Education Academy, United Kingdom
2009 Kavli Fellow
Kavli Foundation, United States