mfutschik | Universidade do Algarve

Mattthias Erwin Futschik

Professor auxiliar convidado

Faculdade de Medicina e Ciências Biomédicas

Subsistema

Docentes Universitário

Regime

Parcial

Vínculo

CT em Funções Públicas a termo resolutivo certo

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 serves as Honorary Professor at the University of Plymouth (UK) and as invited professor at the University of Algarve (Portugal). Matthias has a strong interest in bioinformatics methods and resource development as well as in translational and interdisciplinary research. To date, he authored 60 papers in international peer review journals (including Nature, Science, Genome Biology, Genome Research, Nucleic Acids Research and Bioinformatics) and 6 book chapters that received 3826/2187 citations resulting in an h-factor of 30/25 (Google Scholar/Scopus on 25/2/2021). He co-holds 2 patents, developed 4 popular open-source R/Bioconductor software packages (>800 citations) and led the implementation of 9 publicly accessible databases and webservers. Moreover, he was PI in 5 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 7 Research assistants.

Atividades

2018. Entrevista (jornal / revista). Interview about my work on developing computational resources for stem cell biology. Website Algarve für Entdecker.

2016 - 2021. Orientação. Identification of key factors of heart regeneration using a systems biology approach .Biomedical Science (Doutoramento). Orientador de Rui Machado.

2021 - 2021. Outro júri / avaliação. External evaluator of NWO grant proposal . Dutch Research Council.

2016 - 2021. Membro de comissão. National delegate and work group leader in European COST action GREEKC (CA15205) . Membro. Norges teknisk-naturvitenskapelige universitet.

2021/02/23 - 2021/08/06. Orientação. The 3-dimensional genome in human health and disease.Molecular Medicine (Mestrado). Coorientador.

2016 - 2020. Membro de comissão. National delegate in European COST actions CHARME (CA15110) . Membro. Universität Potsdam.

2020 - 2020. Outro júri / avaliação. Rapporteur of evaluation panel for COST action proposal . European Cooperation in Science and Technology.

2020 - Presente. Membro de associação. Human Cell Atlas. Member.

2020/07/15. Apresentação oral de trabalho. Network biology: from databases to applications. MDR Bioinformatics meetings. Imperial College, Department of Metabolism, Digestion & Reproduction (London, Reino Unido).

2020/03/05. Apresentação oral de trabalho. Basis and applications of network biology . Molecular Epidemiology Seminars. Imperial College, Department of Epidemiology and Biostatistics (London, Reino Unido).

2018 - 2019. Tutoria. Personal tutor of first year students in Biomedicine at University of Plymouth . Rhiannon Wilton.

2018 - 2019. Orientação. Insights into Gene Expression and the Influence of Regulatory Mechanisms within Meningioma -
A Bioinformatic Approach
.Biomedical Science (Licenciatura/Bacharelato). Orientador de Louise Carr.

2019 - 2019. Orientação. Mitochondrial biogenesis and cellular bioenergetic function in uraemic myopathy.Postdoctoral Researcher (Outra). Orientador de Dr Jane Carre.

2019 - 2019. Orientação. The Role of Active L1 Retrotransposons in Alzheimer's Disease.Biomedical Sciences (Doutoramento). Orientador de Roxane Dunbar.

2019 - 2019. Orientação. LINE-1 elements: Genomic distribution and potential contribution to brain related disorders.Biomedical Sciences (Doutoramento). Orientador de Randa Ali.

2017 - 2019. Orientação. Research topics: Meta-analysis of meningioma expression data. Sequence data analysis to detect somatic mutations in Alzheimer's disease. Analysis of Nanopore sequence data. .Postdoctoral Researcher (Outra). Orientador de Dr Vasilis Lenis.

2018 - 2019. Orientação. Transcriptomic analysis of various WHO Grades of meningioma to establish the potential for targeted therapy based on prognosis following diagnosis of WHO Grade.Biomedical Sciences (Licenciatura/Bacharelato). Orientador de Bryant Lee.

2018 - 2019. Orientação. Neuroprotective Effects of NMNAT2, WIF-1, TIMP-1 and MYOC.Biomedical Sciences (Licenciatura/Bacharelato). Orientador de Jessica Woods.

2018 - 2019. Orientação. Evaluation of the axonal-regenerative role of Schwann cell differentiation by systematic review of gene expression data from Wt and WldS mutant mice.Biomedical Sciences (Licenciatura/Bacharelato). Orientador de Jonathan White.

2015 - 2019. Orientação. Cited2 in cardiac development: an inside and outside job.Mechanisms of Disease and Regenerative Medicine (Doutoramento). Coorientador de Joao Miguel Santos.

2019 - 2019. Outro júri / avaliação. External grant reviewer. Grantová agentura Ceské republiky.

2019 - 2019. Curso / Disciplina lecionado. Contemporary Applications of Cell Biology . Biomedical Sciences (Master). University of Plymouth.

2019 - 2019. Curso / Disciplina lecionado. Systems Biology workshop for MeInBio graduate school. Albert-Ludwigs-Universität Freiburg Fakultät für Biologie.

2019 - Presente. Membro de associação. Higher Education Academy (UK) . Fellow of the Higher Education Academy .

2019 - 2019. Curso / Disciplina lecionado. Study Skills and Personal Development . Biomedical Science (Bachelor). University of Plymouth.

2018 - 2019. Curso / Disciplina lecionado. Biomedical Investigation and Experimentation . Biomedical Sciences (Bachelor). University of Plymouth.

2018 - 2019. Curso / Disciplina lecionado. Current Developments in Biomedical Science: Applications of Bioinformatics and Systems Biology . Biomedical Sciences (Bachelor). University of Plymouth.

2018 - 2019. Tutoria. Personal tutor of first year students in Biomedicine at University of Plymouth . Vinay Bakshi.

2018 - 2019. Tutoria. Personal tutor of first year students in Biomedicine at University of Plymouth. Frances Ramshaw.

2018 - 2019. Tutoria. Personal tutor of first year students in Biomedicine at University of Plymouth . Elena Landregan.

2018 - 2019. Tutoria. Personal tutor of first year students in Biomedicine at University of Plymouth . Barachille Ortiz.

2019/11/05 - 2019/11/06. Participação em evento. Coordination of work package meeting . Oficina (workshop). Sarajevo workshop of COST Action CA15205. Internazionalni Univerzitet Sarajevo.

2017/05/01 - 2019/07/31. Membro de comissão. Coordination the research activities of Genomics and Genetics Group at University of Plymouth's Institute of Translational and Stratified Medicine (ITSMED), . Coordenador. University of Plymouth.

2019/03/26. Apresentação oral de trabalho. The long way from bench to bedside – an omics perspective. Dept of Cellular Pathology Seminar. University Hospitals Plymouth NHS Trust (Plymouth, Reino Unido).

2019/03/21 - Presente. Participação em evento. Facilitator of Artificial Intelligence & Machine Learning track . Conferência. 9th Bioinformatics Strategy Meeting Europe 2019. Proventa International .

2019/02 - Presente. Curso / Disciplina lecionado. Computational Biology Module - Network Biology. Master in Biomedical Science (Mestrado). Universidade do Algarve.

2017 - 2018. Orientação. Comparison and integration of meningioma expression profiles.Biomedical Science (Mestrado). Orientador de Alexander Walker.

2017 - 2018. Orientação. A bioinformatic meta-analysis identifying potential prognostic biomarkers for improved differential meningioma grade diagnosis.Biomedical Sciences (Licenciatura/Bacharelato). Orientador de Joshua Walker.

2013 - 2018. Orientação. 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).Postdoctoral Researcher (Outra). Orientador de Dr José Pinto.

2017 - 2018. Outro júri / avaliação. Reviewer of proposals to BBSRC. Biotechnology and Biological Sciences Research Council.

2018 - 2018. Outro júri / avaliação. External grant reviewer. Engineering and Physical Sciences Research Council.

2018/09/13. Apresentação oral de trabalho. Deciphering the gene regulatory networks of cyanobacteria. 3rd Early Career Researcher Symposium on Cyanobacteria. University of Freiburg (Freiburg, Alemanha).

2016 - 2017. Membro de associação. Sociedade Portuguesa de Células Estaminais e Terapia Celular (SPCE-TC) . Governing Board Member.

2017 - 2017. Outro júri / avaliação. External assessor of MPhil Transfer Report . University of Mauritius.

2017/10/23 - 2017/10/24. Organização de evento. Local co-organizer of COST action workshop (2017). Universidade de Lisboa Instituto Superior Técnico.

2017/08/20. Apresentação oral de trabalho. 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, Roménia).

2017/05/18. Apresentação oral de trabalho. 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, Alemanha).

2016 - 2016. Arbitragem científica em conferência. INFORM2016. Portuguese National Forum for Informatics .

2016 - Presente. Outro júri / avaliação. Scientific expert for the Governing Board of the International Doctoral Program. Institut Curie.

2016 - 2016. Outro júri / avaliação. External evaluator for grant proposal to Vidi scheme. Dutch Research Council.

2016 - 2016. Outro júri / avaliação. External evaluator of proposal to COST action. European Cooperation in Science and Technology.

2015 - 2016. Outro júri / avaliação. External evaluator for Austrian Science Fund . Fonds zur Förderung der wissenschaftlichen Forschung.

2016 - 2016. Outro júri / avaliação. Grant reviewer. Fonds National de la Recherche.

2016 - 2016. Outro júri / avaliação. Remote Referee for ERC grant . European Research Council.

2016 - 2016. Curso / Disciplina lecionado. Data analysis module in Marine Genomics summer school. Marine Genomics (Postgraduate Certificate). Centro de Ciências do Mar.

2016/09/09. Apresentação oral de trabalho. SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology. INFORUM 2016. Instituto Superior Tecnico (Lisbon, Portugal).

2015 - 2015. Orientação. Reseacher in FCT project: The regulation of photosynthesis in cyanobacteria: A systems biology approach. (PTDC/BIA-MIC/4418/2012) .Researcher (Outra). Orientador de Miquel Marco.

2014 - 2015. Orientação. Postdoctoral researcher in FCT project : The regulation of photosynthesis in cyanobacteria: A systems biology approach (FCT-PTDC/BIA-MIC/4418/2012).Postdoctoral Researcher (Outra). Orientador de Dr Joaquin Lamia.

2014 - 2015. Orientação. Researcher in FCT Project: Alternative splicing and its impact on molecular interaction networks (PTDC/BIA-GEN/116519/2010).Researcher (Outra). Orientador de MSc Isabel Duarte.

2015 - 2015. Orientação. Associated Researcher in FCT Project: Alternative splicing and its impact on molecular interaction networks (PTDC/BIA-GEN/116519/2010) .Researcher (Outra). Orientador de Susana Machado.

2015 - 2015. Tutoria. Host for research stay at University of Algarve . Tania Barata.

2010 - 2015. Orientação. 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..Postdoctoral Researcher (Outra). Orientador de Dr Ravi Kalathur.

2015 - 2015. Orientação. Associated Researcher in FCT project: Alternative splicing and its impact on molecular interaction networks (PTDC/BIA-GEN/116519/2010.Researcher (Outra). Orientador de Ivette Pacheco .

2013 - 2015. Curso / Disciplina lecionado. Invited lectures about Systems and Network biology. Biomedical Science (Mestrado). Universidade do Algarve.

2015/11/09 - 2015/11/11. Arbitragem científica em conferência. International Conference on Bioinformatics (GIW/InCoB2016) . APBioNET and the Japanese Society for Bioinformatics .

2015/10/15. Apresentação oral de trabalho. 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).

2015/03/17 - Presente. Participação em evento. 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.

2010 - 2014. Orientação. 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).Postdoctoral Researcher (Outra). Orientador de Dr Miguel Hernandez.

2014/05. Apresentação oral de trabalho. Systems Biology: Can it help in the study of neurodegeneration?. 1st Neuroimmunology Workshop. Institut du Cerveau (Paris, França).

2013 - 2013. Orientação. Analysis of the transcriptional regulatory network: underlying heart development.Biomedical Sciences (Mestrado). Orientador de Rui Machado.

2013. Apresentação oral de trabalho. 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, Polónia).

2013 - 2013. Orientação. Researcher in FCT project: The regulation of photosynthesis in cyanobacteria: A systems biology approach (FCT - PTDC/BIA-MIC/4418/2012).Researcher (Outra). Orientador de Dr. Shanmugam Hemaiswarya.

2012 - 2013. Orientação. Researcher in FCT project: The role and regulation of alpha-synuclein phosphorylation in both pathological and physiological conditions (PTDC/BIA-BCM/117975/2010.Researcher (Outra). Orientador de MSc Dulce Almeida.

2012 - 2013. Curso / Disciplina lecionado. Invited lectures on bioinformatics and neurodegenerative diseases. Neurosciences (Mestrado). Universidade do Algarve.

2013/11/19. Apresentação oral de trabalho. 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).

2013/08/01. Júri de grau académico. PhD thesis defense . Arguente principal. Filipe Pinto (Doutoramento). Universidade do Porto.

2012. Apresentação oral de trabalho. UniHI: Network biology goes to the bench. 3nd Meeting of the Institute for Biotechnology and Bioengineering,. Institute for Biotechnology and Bioengineering, (Lisbon, Portugal).

2012 - Presente. Arbitragem científica em revista. Scientifica. Hindawi.

2010 - 2011. Orientação. Postdoctoral researcher in Project: CHDI A2666 - Visualization and Analysis of HD-Related Molecular Interaction Networks..Postdoctoral researcher (Outra). Orientador de Dr. Kamesh Ayasolla.

2011 - 2011. Curso / Disciplina lecionado. Introduction to transcriptomics analysis . Biodiversity and Conservation (Mestrado). Universidade do Algarve.

2011/02. Apresentação oral de trabalho. Network biology, a key to understand the complexity of molecular systems. Departmental Seminar Biochemistry. University of Otago (Dunedin, Nova Zelândia).

2011/01. Apresentação oral de trabalho. Concepts and applications of network biology. KEDRI Seminar. Auckland University of Technology (Auckland, Nova Zelândia).

2010. Apresentação oral de trabalho. A Network Perspective on Signalling. 4th National Meeting on Signal Transduction, SINAL 2010. Universidade do Algarve (Faro, Portugal).

2010/10/24. Apresentação oral de trabalho. Chorea Huntington: A thousand changes due to a single mutation. 2nd Meeting of the Institute for Biotechnology and Bioengineering. Universidade do Minho (Minho, Portugal).

2005 - 2009. Orientação. Analysis of protein interaction networks in human health and disease.Bioinformatics (Doutoramento). Orientador de Gautam Chaurasia.

2009. Apresentação oral de trabalho. Disentangling molecular interaction networks for Huntington's Disease. Weizmann Institute (Rehovot, Israel).

2009. Apresentação oral de trabalho. Disentangling molecular interaction networks for Chorea Huntington. Institute for Systems Biology (Seattle, Estados Unidos).

2006 - 2009. Arbitragem científica em revista. Cancer Informatics. SAGE/Libertas Academica previously.

2009. Apresentação oral de trabalho. 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, Estados Unidos).

2004 - 2008. Orientação. Dysregulation of expression in Chorea Huntington.Theoretical Biology (Doutoramento). Coorientador de Branca Cajavec.

2008. Apresentação oral de trabalho. Disentangling molecular intaction networks for Chorea Huntington. European Huntington's Diesease Network Meeting. European Huntington's Diesease Network (Lisbon, Portugal).

2008. Apresentação oral de trabalho. Large-scale human protein-protein interacton maps: A tool for finding the magical bullets against complex diseases. Protein-Protein Interactions as Drug Targets Symposium.

2005 - 2008. Curso / Disciplina lecionado. Mathematical Fundamentals of Biology 1 . Biology (Bachelor). Humboldt-Universität zu Berlin.

2005 - 2008. Curso / Disciplina lecionado. Mathematical Fundamentals of Biology 2 . Biologie (Bachelor). Humboldt-Universität zu Berlin.

2005 - 2008. Curso / Disciplina lecionado. Time series analysis . Biology, Biophysics (Master). Humboldt Universität zu Berlin Institute for Theoretical Biology.

2006 - 2007. Orientação. Identification of periodically expressed genes in microarray data.Bioinformatics (Licenciatura/Bacharelato). Orientador de Mandy Fuchs.

2006 - 2007. Orientação. Comparison of microarray data sets for tissue expression.Bioinformatics (Licenciatura/Bacharelato). Orientador de Jenny Russ.

2007. Apresentação oral de trabalho. Are we overestimating the number of cell-cycling genes?. German Conference on Bioinformatics. University of Potsdam (Potsdam, Alemanha).

2007. Apresentação oral de trabalho. Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network. International workshop in Integrative Bioinformatics.

2007. Apresentação oral de trabalho. Concurrency between and coherency within human PPI maps . HUPO PSI, Spring Meeting,.

2007. Apresentação oral de trabalho. Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks. International Workshop on Bioinformatics and Systems Biology.

2007. Apresentação oral de trabalho. Network biology, a key to understand the complexity of molecular systems. University of Faro (Faro, Portugal).

2007. Apresentação oral de trabalho. 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. Apresentação oral de trabalho. Concurrency between and coherency within human PPI maps . HUPO PSI, Spring Meeting. HUPO Proteomics Standards Initiative (PSI) (Lyon , França).

2007/10/11. Apresentação oral de trabalho. Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Networks. 4th International workshop in Integrative Bioinformatics. University of Ghent (Ghent, Bélgica).

2006. Apresentação oral de trabalho. 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, Reino Unido).

2006. Apresentação oral de trabalho. Comparison of Human Protein-Protein Interaction Maps . German Conference on Bioinformatics. University of Tuebingen (Tübingen, Alemanha).

2006. Apresentação oral de trabalho. Comparison and integration of human protein interaction maps, Comparison of Human Protein-Protein Interaction Map. Interactome Networks. Wellcome Trust/Cold Spring Harbour Laboratory (Cambridge, Estados Unidos).

2005. Apresentação oral de trabalho. M. Futschik S. Legewie and H.Herzel (2005), Dynamics of Liver Regeneration- Microarrays, Arrays and Modelling, . BMBF-Initiative "Systembiologie", Platform Meeting "Modeling & Bioinformatics" .

2005. Apresentação oral de trabalho. 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, França).

2005. Apresentação oral de trabalho. Dynamics of Liver Regeneration- Microarrays, Arrays and Modelling. BMBF-Initiative "Systembiologie", Platform Meeting "Modeling & Bioinformatics" . University Heidelberg (Heidelberg, Alemanha).

2005. Apresentação oral de trabalho. Microarray data analysis - Gold-mining in a minefield. Mathematical Interdisciplinary Research Day: Genetic Network. Warwick Mathematical Instituts (Warwick, Reino Unido).

2004 - 2004. Curso / Disciplina lecionado. Microarray data analysis I-V, Summer school on cell biology and mathematical modelling . Humboldt Universität zu Berlin Institute for Theoretical Biology.

2004 - 2004. Curso / Disciplina lecionado. Microarrays & Expression Profiling, Bioinformatics summer school. Isik Üniversitesi.

2004. Apresentação oral de trabalho. Microarray data analysis - Gold-mining in a minefield. Warwick Mathematical Institute (Warwick, Reino Unido).

2004. Apresentação oral de trabalho. Prometheus under the microscope: Systems-Biological approaches to liver regeneration. Institutional Seminar. Freiburger Zentrum für Datenanalyse und Modellbildung (Freiburg, Alemanha).

2003. Apresentação oral de trabalho. Modular Decision System and Information Integration for Improved Disease Outcome prediction. ECCB 2003.

2003. Apresentação oral de trabalho. Prediction of clinical behaviours and treatment for cancers. New Zealand Bioinformatics Conference.

2000 - 2002. Membro de comissão. Representative for international postgraduate students in University council. Membro. University of Otago.

2001 - 2001. Curso / Disciplina lecionado. Biological Physics . Biology (Bachelor). University of Otago.

2001 - 2001. Curso / Disciplina lecionado. Foundations of Information Systems . Computer Science (Bachelor). University of Otago.

1999 - Presente. Membro de associação. International Society of Computational Biology . Member.

1997 - 1998. Curso / Disciplina lecionado. Physics for students of biology. Biologie (Bachelor). Humboldt-Universität zu Berlin Institut für Physik.

1997 - 1997. Curso / Disciplina lecionado. Physics practical for medical students . Medicine (Licence). Humboldt-Universität zu Berlin Institut für Physik.

Projetos

2022/01/01 - 2023/06/30. CARDIOMyogenisis In Silico: A computational framework for the study of stem cell differentiation towards cardiomyocytes. Investigador responsável. Universidade Nova de Lisboa.

2018/07/05 - 2021/07/04. Variant sequences Identification in human genomes and Their Assignment as true causative mutations for LVNC - VITAL, 9471 - RIDTI. Investigador. Universidade do Algarve.

2018/07/01 - 2021/06/30. Determining the Role of the Microenvironment in Shaping the Spectrum of Genetic Mutations Acquired During Cancer Development, 9471 - RIDTI. Investigador. Universidade do Porto Instituto de Patologia e Imunologia Molecular.

2016/05/01 - 2019/10/31. Regeneration in the African Spiny Mouse, 3599-PPCDT. Investigador. Universidade do Algarve; Universidade do Algarve Centro de Investigação em Biomedicina.

2014/02/17 - 2019/01/31. The regulation of photosynthesis in cyanobacteria: A systems biology approach, FCT Investigator. Investigador responsável. Centro de Ciências do Mar.

2014/01/01 - 2018/06/01. Development of software tools for the prediction of cellular fate in stem cell differentiation, Post-Doctoral fellowships. Orientador. Universidade do Algarve - Campus de Gambelas.

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, FCT/DAAD Transnational cooperation. Investigador responsável. Centro de Ciências do Mar.

2012/02/01 - 2015/01/31. Alternative splicing and its impact on molecular networks during stem cell differentiation, Scientific Research and Technological Development Projects. Investigador responsável. Universidade do Algarve.

2011/01/01 - 2015/01/31. Systems biology approach to unravel the molecular mechanisms involved in T-Cell Acute Lymphoblastic Leukaemia, Post-Doctoral fellowships. Orientador. Universidade do Algarve.

2012/01 - 2014/12. The role and regulation of alpha-synuclein phosphorylation in both pathological and physiological conditions, Scientific Research and Technological Development Projects in all Scientific Domains -. Investigador. Instituto de Medicina Molecular.

2010/01/01 - 2013/06/30. Regulation of iron homeostasis in cyanobacteria, Scientific Research and Technological Development Projects in all Scientific Domains. Investigador responsável. Universidade do Algarve.

2010 - 2011. Visualization and Analysis of HD-Related Molecular Interaction Networks. Investigador responsável. Universidade do Algarve.

2005/01/01 - 2009/02/01. Robustness, modularity and dynamics of protein-protein interaction networks, Sonderforschungsbereich. Investigador responsável. Humboldt Universität zu Berlin Institute for Theoretical Biology.

Produções

OLIN: R/Bioconductor package for optimized local intensity-dependent normalization of two colour microarrays: http://www.bioconductor.org/packages/release/bioc/html/OLIN.html. Investigador.

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. Investigador.

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. Investigador.

CyanoEXpress: a curated genome-wide expression database for the cyanobacterium Synechocystis . http://cyanoexpress.sysbiolab.eu/.

HeartEXpress: database for query and visualisation of integrated expression datasets associated with cardiomyogenesis. . http://heartexpress.sysbiolab.eu/.

HeartmiR: database and webserver for querying of relevant miRNA-mRNA interactions for late heart development in mouse. http://heartmir.sysbiolab.eu/.

Huntington's Disease Network Database (HDNetDB) for network-based analysis of Huntington's disease. . http://hdnetdb.sysbiolab.eu/.

StemChecker: database and web-based tool to examine stemness in gene sets. http://stemchecker.sysbiolab.eu/.

StemCellNet: interactive web server & database for network analysis and visualization in stem cell biology.. http://stemcellnet.sysbiolab.eu/.

StemMapper: manually curated database containing gene expression data for different lineages of Stem Cells (SCs) from human and mouse. http://stemmapper.sysbiolab.eu/.

UniHI: comprehensive database of human molecular interactions, functional annotation, disease assocation and drug target information. http://www.unihi.org/.

UPR-HD: dataset of expression of UPR-associated genes across various transcriptomic studies of Huntington's disease . http://uprhd.sysbiolab.eu/.

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 . Investigador.

Matthias Futschik; Catherine Francis; Futschik ME; Jian Huang; Wenjia Bai; Sargurupremraj M; Alexander Teumer; et al. 2022. "Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.". Nature communications. https://doi.org/10.1038/s41467-022-32219-x

Fernando Bonet; Sabrina Brito Añez; José Manuel Inácio; Matthias E. Futschik; José Antonio Belo. 2022. "CCBE1 Is Essential for Epicardial Function during Myocardium Development". International Journal of Molecular Sciences. https://doi.org/10.3390/ijms232012642

Inácio, José Manuel; Lopes,Joao; Silva, Ana M; Cristo, Fernando; Marques, Sara; Futschik, Matthias; Belo, José A.. 2021. "DAND5 inactivation promotes cardiac differentiation in mouse embryonic stem cells". Frontiers in Cell and Developmental Biology. https://www.frontiersin.org/articles/10.3389/fcell.2021.629430/abstract

Wallach, T; Mossmann, Z; Szczepek M; Wetzel, M.; Machado, Rui; Raden M; Miladi, M.; et al. 2021. "miR-100-5p and miR-298-5p released from apoptotic neurons act as Toll-like receptor 7/8 ligands, thereby contributing to brain inflammation and injury ". Molecular Neurodegeneration.

2021. "The gene regulation knowledge commons: the action area of GREEKC.". Biochimica et biophysica acta. Gene regulatory mechanisms. https://doi.org/10.1016/j.bbagrm.2021.194768

Jemma Dunn; Vasileios P. Lenis; David A. Hilton; Rolf Warta; Christel Herold-Mende; C. Oliver Hanemann; Futschik, Matthias. 2020. "Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma". Cancers, 12 (11). https://doi.org/10.3390/cancers12113270

Vendula Krynická; Jens Georg; Philip J. Jackson; Mark J. Dickman; C. Neil Hunter; Futschik, Matthias; Wolfgang R. Hess; Josef Komenda. 2019. "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): 2912-2928. https://doi.org/10.1105/tpc.19.00411

Santos, João; Mendes-Silva, Leonardo; Afonso, Vanessa; Martins, Gil; Machado, Rui; Lopes, Joao; Cancela, M. Leonor; et al. 2019. "Exogenous WNT5A and WNT11 proteins rescue CITED2 dysfunction in mouse embryonic stem cells and zebrafish morphants". Cell Death & Disease, 10. https://doi.org/10.1038/s41419-019-1816-6

Futschik, Matthias; Morkel, Markus; Schäfer, Reinhold; Sers, Christine. 2018. "The Human Transcriptome: Implications for Understanding, Diagnosing, and Treating Human Disease". Em Molecular Pathology, 135-164. Elsevier. https://doi.org/10.1016/b978-0-12-802761-5.00007-9

Dunn, J.; Ferluga, S.; Sharma, V.; Futschik, Matthias; Hilton, D.A.; Adams, C.L.; Lasonder, E.; Oliver Hanemann, C.. 2018. "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: 77-91. https://doi.org/10.1016/j.ebiom.2018.12.048

Pinto, J.P.; MacHado, R.S.R.; Magno, R.; Oliveira, D.V.; MacHado, S.; Andrade, R.P.; Braganca, J.; Duarte, I.; Futschik, Matthias. 2018. "StemMapper: A curated gene expression database for stem cell lineage analysis". Nucleic Acids Research, 46 (D1): D788-D793. https://doi.org/10.1093/nar/gkx921

Ho, P.-W.; Klein, M.; Futschik, Matthias; Nevoigt, E.. 2018. "Glycerol positive promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae". FEMS Yeast Research, 18 (3). https://doi.org/10.1093/femsyr/foy019

Ghezzo, M.N.; Fernandes, M.T.; Pacheco-Leyva, I.; Rodrigues, P.M.; Machado, R.S.; Araújo, M.A.S.; Kalathur, R.K.; et al. 2018. "FoxN1-dependent thymic epithelial cells promote T-cell leukemia development". Carcinogenesis, 39 (12): 1463-1476. https://doi.org/10.1093/carcin/bgy127

Sabour, D.; Machado, R.S.R.; Pinto, J.P.; Rohani, S.; Sahito, R.G.A.; Hescheler, J.; Futschik, Matthias; Sachinidis, A.. 2018. "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: 158-173. https://doi.org/10.1016/j.omtn.2018.04.018

Giner-Lamia, Joaquín; Hernández-Prieto, Miguel; Futschik, Matthias. 2018. "ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803". BIO-PROTOCOL, 8 (12). https://doi.org/10.21769/bioprotoc.2895

Hernandez-Prieto, Miguel A; Semeniuk, Trudi A.; Giner-Lamia, Joaquin; Futschik, Matthias. 2018. Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis - a comprehensive study based on CyanoEXpress. Em PHYCONET Annual Conference 2018.

Kalathur, R.K.R.; Pedro Pinto, J.; Sahoo, B.; Chaurasia, G.; Futschik, Matthias. 2017. "HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease". Scientific Reports, 7 (1). https://doi.org/10.1038/s41598-017-05224-0

Georg, J.; Kostova, G.; Vuorijoki, L.; Schön, V.; Kadowaki, T.; Huokko, T.; Baumgartner, D.; et al. 2017. "Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1". Current Biology, 27 (10): 1425-1436.e7. https://doi.org/10.1016/j.cub.2017.04.010

Macedo, J.A.; Schrama, D.; Duarte, I.; Tavares, E.; Renaut, J.; Futschik, Matthias; Rodrigues, P.M.; Melo, E.P.. 2017. "Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells". BMC Genomics, 18 (1). https://doi.org/10.1186/s12864-017-3694-6

Giner-Lamia, J.; Robles-Rengel, R.; Hernández-Prieto, M.A.; Isabel Muro-Pastor, M.; Florencio, F.J.; Futschik, Matthias. 2017. "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): 11800-11820. https://doi.org/10.1093/nar/gkx860

Giner-Lamia, Joaquin; Robles-Rengel, R.; Hernández-Prieto, M.A.; Isabel Muro-Pastor, M.; Florencio, F.J.; Futschik, Matthias. 2017. "Identification of the direct regulon of Ntc Aduring early acclimation to nitrogen starvation in the cyanobacterium Synechocystissp. PCC6803". Trabalho apresentado em 10th European Workshop on the Molecular Biology of Cyanobacteria, Cluj-Napoca, Roménia.

Machado, Rui; Sabour, D; Pinto, JP; Braganca, J; Sachinidis, Agapios; Futschik, Matthias. 2017. HEARTI ToolBox: An online platform for the analysis in silico of cardiogenesis. Em 9th International Meeting of the Stem Cell Network NRW.

Pinto, José Pedro; Kalathur, Ravi; Oliveira, DA; Barata, Tania; Machado, Rui S.R.; Machado, Susana; Pacheco-Leyva, Ivette; et al. 2017. SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology. Em 9th International Meeting of the Stem Cell Network NRW.

Giner-Lamia, Joaquín; Pereira, Sara B.; Bovea-Marco, Miquel; Futschik, Matthias; Tamagnini, Paula; Oliveira, Paulo. 2016. "Extracellular Proteins: Novel Key Components of Metal Resistance in Cyanobacteria?". Frontiers in Microbiology, 7. https://doi.org/10.3389/fmicb.2016.00878

Hernández-Prieto, Miguel A.; Semeniuk, Trudi Ann; Giner-Lamia, Joaquín; Futschik, Matthias. 2016. "The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803". Scientific Reports, 6 (1). https://doi.org/10.1038/srep22168

Kalathur, Ravi Kiran Reddy; Giner-Lamia, Joaquin; Machado, Susana; Barata, Tania; Ayasolla, Kameshwar R S; Futschik, Matthias; Kalathur RK; et al. 2016. "The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach". F1000Research, 4. https://doi.org/10.12688/f1000research.6358.2

Futschik, Matthias; Giner-Lamia, Joaquin; Hernández-Prieto, Miguel A. 2016. CyanoEXpress: An interactive web-tool for exploration and visualization of gene expression data from cyanobacteria. Em NorPlantBio 2016.

Hernandez-Prieto, Miguel A; Semeniuk, Trudi A.; Giner-Lamia, Joaquín; Futschik, Matthias. 2016. Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis. Em NorPlantBio 2016.

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 )". Concedida/Emitida.

Doron, Shany; Fedida, Ayalla; Hernández-Prieto, Miguel A; Sabehi, Gazalah; Karunker, Iris; Stazic, Damir; Feingersch, Roi; et al. 2015. "Transcriptome dynamics of a broad host-range cyanophage and its hosts". The ISME Journal, 10 (6): 1437-1455. https://doi.org/10.1038/ismej.2015.210

Bal, Gürkan; Futschik, Matthias; Hartl, Daniela; Ringel, Frauke; Kamhieh-Milz, Julian; Sterzer, Viktor; Hoheisel, Jörg D.; Alhamdani, Mohamed S. S.; Salama, Abdulgabar. 2015. "Identification of novel biomarkers in chronic immune thrombocytopenia (ITP) by microarray-based serum protein profiling". British Journal of Haematology, 172 (4): 602-615. https://doi.org/10.1111/bjh.13861

Stroedicke, Martin; Bounab, Yacine; Strempel, Nadine; Klockmeier, Konrad; Yigit, Sargon; Friedrich, Ralf P.; Chaurasia, Gautam; et al. 2015. "Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity". Genome Research, 25 (5): 701-713. https://doi.org/10.1101/gr.182444.114

Hill, Richard; Kalathur, Ravi Kiran Reddy; Colaço, Laura; Brandão, Ricardo; Ugurel, Selma; Futschik, Matthias; Link, Wolfgang. 2015. "TRIB2 as a biomarker for diagnosis and progression of melanoma". Carcinogenesis, 36 (4): 469-477. https://doi.org/10.1093/carcin/bgv002

Pinto, J; Kalathur, R.; Braganca, J.; Xavier, J.; Futschik, Matthias. 2015. "StemCellNet: an interactive platform for network-oriented investigations in stem cell biology. ". Trabalho apresentado em 9th International Meeting of the Portuguese society for Stem cells and Cell therapies, Oeiras, Portugal.

Oliveira, Daniel V.; Machado, Rui; Duarte, Isabel; Pacheco-Leyva, Ivette; Justo, T; Pinto, JP; Braganca, Jose; Futschik, Matthias. 2015. From Stem Cells 2 Heart: Finding novel candidate isoforms and genes for cardiomyogenesis.. Em 9th International Meeting of the Portuguese society for Stem cells and Cell therapies..

Machado, RS; Pinto, JP; Oliveira, DV; Duarte, I; Machado, S; Bragança, J.; Futschik, Matthias. 2015. A meta-analysis study of stem cell differentiation in the context of cardiogenesis. Em 9th International Meeting of the Portuguese society for Stem cells and Cell therapies..

Machado, S.; Kalathur, R.K.; Oliveira, DV; Barata, T.; Machado, RS; Pacheco-Leyva, Ivette; Duarte, Isabel; Futschik, Matthias; Pinto, JP. 2015. StemCellNet: an interactive platform for network-oriented investigations in stem cell biology.. Em 9th International Meeting of the Portuguese society for Stem cells and Cell therapies..

Futschik, Matthias; Giner-Lamia, Joaquin; Hernandez-Prieto, Miguel A. 2015. Transcriptional regulation and coordination of photosynthetic genes in Synechocystis: a comprehensive study based on CyanoEXpress. Em 15th International Symposium on Phototrophic Prokaryotes (ISPP 2015),.

Giner-Lamia, Joaquin; Bovea-Marco, Miquel; Hernandez-Prieto, Miguel A; Futschik, Matthias. 2015. CyanoEXpress: An enhanced tool for on-line analysis and visualization of gene expression data from cyanobacteria. Em 15th International Symposium on Phototrophic Prokaryotes (ISPP 2015).

Pinto JP; Kalathur RK; Oliveira DV; Barata T; Machado RS; Machado S; Pacheco-Leyva I; Duarte I; Futschik ME. 2015. "StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.". https://doi.org/10.1093/nar/gkv529

Pells, Steve; Koutsouraki, Eirini; Morfopoulou, Sofia; Valencia-Cadavid, Sara; Tomlinson, Simon R.; Kalathur, Ravi; Futschik, Matthias E.; De Sousa, Paul A.. 2015. "Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State". PLOS ONE, 10 (7). https://doi.org/10.1371/journal.pone.0131102

Julian Kamhieh-Milz; Reham Fadl Hassan Moftah; Gürkan Bal; Futschik, Matthias; Viktor Sterzer; Omid Khorramshahi; Martin Burow; et al. 2014. "Differentially Expressed MicroRNAs in Maternal Plasma for the Noninvasive Prenatal Diagnosis of Down Syndrome (Trisomy 21)". BioMed Research International, 2014: 1-9. https://doi.org/10.1155/2014/402475

Hill, Richard; Kalathur, Ravi Kiran Reddy; Callejas, Sergio; Colaço, Laura; Brandão, Ricardo; Serelde, Beatriz; Cebriá, Antonio; et al. 2014. "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). https://doi.org/10.1186/s13058-014-0482-y

Hernandez-Prieto, Miguel A.; Kalathur, Ravi K.R.; Futschik, Matthias E.; Futschik, Matthias. 2014. "Molecular Networks - Representation and Analysis". Em Springer Handbook of Bio-/Neuroinformatics, 399-418. Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-30574-0_24

Pinto, J; Kalathur, R.K.; Machado, R.; Xavier, J.; Braganca, J.; Futschik, Matthias. 2014. StemCellNet: an interactive platform for network-oriented investigations in stem cell biolog. Em Heart without Boarders International Conference.

Duarte, I.; Justo, T; Pinto, J.; Oliveira, D.; Braganca, J.; Belo, J.; Futschik, Matthias. 2014. From Stem Cells 2 heart: Elucidating the role of alternative splicing in cardiomyogenesis. Em Heart without Boarders, International Conference.

Oliveira, D.; Machdo, R.; Pacheco-Leyva, I.; Duarte, I.; Justo, T; Pinto, J.; Belo, J.; Futschik, Matthias. 2014. From Stem Cells 2 heart: Finding novel candidate genes for cardiomyogenesis. Em Heart without Boarders, International Conference.

Kalathur, R.K.R.; Pinto, J.P.; Hernández-Prieto, M.A.; MacHado, R.S.R.; Almeida, D.; Chaurasia, G.; Futschik, M.E.. 2014. "UniHI 7: An enhanced database for retrieval and interactive analysis of human molecular interaction networks". Nucleic Acids Research, 42 (D1). https://doi.org/10.1093/nar/gkt1100

Hernández-Prieto, M.A.; Semeniuk, T.A.; Futschik, M.E.. 2014. "Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria". Frontiers in Genetics, 5 (JUL). https://doi.org/10.3389/fgene.2014.00191

Pinto, J.P.; Reddy Kalathur, R.K.; Machado, R.S.R.; Xavier, J.M.; Bragança, J.; Futschik, M.E.. 2014. "StemCellNet: An interactive platform for network-oriented investigations in stem cell biology". Nucleic Acids Research, 42 (W1). https://doi.org/10.1093/nar/gku455

Pinto, J.P.; Machado, R.S.R.; Xavier, J.M.; Futschik, M.E.. 2014. "Targeting molecular networks for drug research". Frontiers in Genetics, 5 (JUN). https://doi.org/10.3389/fgene.2014.00160

Machado, R.; Pinto, JP.; Braganca, J.; Futschik, Matthias. 2013. What a heart makes or breaks: A meta-analysis of gene expression profiles. Em 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies.

Pinto, JP.; Machado, RSR; Kalathur, R.; Futschik, Matthias. 2013. StemCellNet: A web-based Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells. Em 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies.

Futschik, Matthias. 2013. "How the internal world of Synechocystis adapts to the ever-changing world outside: A comprehensive meta-analysis of its transcriptional responses". Trabalho apresentado em ESF-EMBO Symposium Molecular Bioenergetics Of Cyanobacteria: Shaping The Environment,, Pultusk, Polónia.

Futschik, Matthias; Hernández-Prieto, M.A.. 2013. 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. Em ESF-EMBO Symposium Molecular Bioenergetics Of Cyanobacteria: Shaping The Environment,.

Wallach, T.; Schellenberg, K.; Maier, B.; Kalathur, R.K.R.; Porras, P.; Wanker, E.E.; Futschik, M.E.; Kramer, A.. 2013. "Dynamic Circadian Protein-Protein Interaction Networks Predict Temporal Organization of Cellular Functions". PLoS Genetics, 9 (3). https://doi.org/10.1371/journal.pgen.1003398

Bal, Gürkan; Kamhieh-Milz, Julian; Futschik, Matthias; Häupl, Thomas; Salama, Abdulgabar; Moldenhauer, Anja. 2012. "Transcriptional Profiling of the Hematopoietic Support of Interleukin-Stimulated Human Umbilical Vein Endothelial Cells (HUVECs)". Cell Transplantation, 21 (1): 251-267. https://doi.org/10.3727/096368911x580581

Kalathur, Ravi Kiran Reddy; Hernández-Prieto, Miguel A; Futschik, Matthias E. 2012. "Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database". BMC Neurology, 12 (1). https://doi.org/10.1186/1471-2377-12-47

Hernández-Prieto, Miguel A.; Schön, Verena; Georg, Jens; Barreira, Luísa; Varela, João; Hess, Wolfgang R.; Futschik, Matthias E.. 2012. "Iron Deprivation in Synechocystis: Inference of Pathways, Non-coding RNAs, and Regulatory Elements from Comprehensive Expression Profiling". G3 Genes|Genomes|Genetics, 2 (12): 1475-1495. https://doi.org/10.1534/g3.112.003863

Ayasolla, Kameshwar; Kalathur, Ravi; Futschik, Matthias. 2012. "A Systems Biology Approach towards Deciphering the Unfolded Protein Response in Huntington's Disease". Nature Precedings. https://doi.org/10.1038/npre.2012.7078.1

Kalathur, Ravi; Ayasolla, Kamesh; Futschik, Matthias. 2012. "The Unfolded Protein Response and its potential role in Huntington's disease". Nature Precedings. https://doi.org/10.1038/npre.2012.7145.1

Futschik, Matthias; Hernández-Prieto, M.A.. 2012. CyanoExpress: A Comprehensive Database for Evaluating the Transcriptional Response in Synechocystis. Em International Symposium on Phototrophic Prokaryotes 2012.

Hernandez-Prieto, Miguel A; Schön, Verena; Steglich, Claudia; Hess, Wolfgang R.; Futschik, Matthias. 2012. Simultaneous profiling of coding and non-coding RNAs from Synechocystis under iron-limiting conditions. Em International Symposium on Phototrophic Prokaryotes 2012.

Hernandez-Prieto, Miguel A; Futschik, Matthias. 2012. "CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803". Bioinformation, 8 (13): 634-638. https://doi.org/10.6026/97320630008634

Bal, G.; Kamhieh-Milz, J.; Futschik, M.; Häupl, T.; Salama, A.; Moldenhauer, A.. 2012. "Transcriptional profiling of the hematopoietic support of interleukin-stimulated human umbilical vein endothelial cells (HUVECs)". Cell Transplantation, 21 (1): 251-267. https://doi.org/10.3727/096368911X580581

Moldenhauer, Anja; Futschik, Matthias; Lu, Huili; Helmig, Melanie; Götze, Patricc; Bal, Gürkan; Zenke, Martin; Han, Wei; Salama, Abdulgabar. 2011. "Interleukin 32 promotes hematopoietic progenitor expansion and attenuates bone marrow cytotoxicity". European Journal of Immunology, 41 (6): 1774-1786. https://doi.org/10.1002/eji.201040986

Duong, C.T.; Strack, L.; Futschik, M.; Katou, Y.; Nakao, Y.; Fujimura, T.; Shirahige, K.; Kodama, Y.; Nevoigt, E.. 2011. "Identification of Sc-type ILV6 as a target to reduce diacetyl formation in lager brewers' yeast". Metabolic Engineering, 13 (6): 638-647. https://doi.org/10.1016/j.ymben.2011.07.005

Chaurasia, Gautam; Futschik, Matthias. 2011. "The Integration and Annotation of the Human Interactome in the UniHI Database". Em Methods in Molecular Biology, 175-188. Humana Press. https://doi.org/10.1007/978-1-61779-455-1_10

Kalathur, R.K.; Futschik, Matthias. 2011. The UniHI Database: A Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells. Em Cell Symposia: Stem Cell Programming & Reprogramming 2011.

Futschik, Matthias; Hernandez-Prieto, Miguel A. 2011. The Transcriptional Landscape of the Cyanobacterium Synechocystis. Em 8th European Workshop on Molecular Biology of Cyanobacteri.

Marras, Elisabetta; Travaglione, Antonella; Chaurasia, Gautam; Futschik, Matthias; Capobianco, Enrico. 2010. "Inferring modules from human protein interactome classes". BMC Systems Biology, 4 (1). https://doi.org/10.1186/1752-0509-4-102

Russ, Jenny; Futschik, Matthias E. 2010. "Comparison and consolidation of microarray data sets of human tissue expression". BMC Genomics, 11 (1). https://doi.org/10.1186/1471-2164-11-305

Allen, Michael J.; Tiwari, Bela; Futschik, Matthias E.; Lindell, Debbie. 2010. "Construction of microarrays and their application to virus analysis". Em Manual of Aquatic Viral Ecology, 34-56. American Society of Limnology and Oceanography. https://doi.org/10.4319/mave.2010.978-0-9845591-0-7.34

Kalathur, Ravi; Futschik, Matthias. 2010. Network-based analyses of Huntington's Disease. Em EHDN 2010. https://doi.org/10.1038/npre.2012.7090.1

Hernández-Prietoa, Miguel A; Barreira, Luísa; Varela, João; Futschik, Matthias. 2010. Concerted responses to iron availability in cyanobacteria. Em 4th National Meeting on Signal Transduction, SINAL 2010.

Steglich, Claudia; Lindell, Debbie; Futschik, Matthias; Rector, Trent; Steen, Robert; Chisholm, Sallie W. 2010. "Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus". Genome Biology, 11 (5). https://doi.org/10.1186/gb-2010-11-5-r54

Chaurasia, Gautam; Futschik, Matthias E.. 2009. "Interactomics and Cancer". Em An Omics Perspective on Cancer Research, 167-182. Springer Netherlands. https://doi.org/10.1007/978-90-481-2675-0_9

Futschik, Matthias E.; Kemmner, Wolfgang; Schäfer, Reinhold; Sers, Christine. 2009. "The Human Transcriptome: Implications for the Understanding of Human Disease". Em Molecular Pathology, 123-149. Elsevier. https://doi.org/10.1016/b978-0-12-374419-7.00007-x

Chaurasia, G.; Malhotra, S.; Russ, J.; Schnoegl, S.; Hänig, C.; Wanker, E.E.; Futschik, M.E.. 2009. "UniHI 4: New tools for query, analysis and visualization of the human protein-protein interactome". Nucleic Acids Research, 37 (SUPPL. 1). https://doi.org/10.1093/nar/gkn841

Zinser, E.R.; Lindell, D.; Johnson, Z.I.; Futschik, M.E.; Steglich, C.; Coleman, M.L.; Wright, M.A.; et al. 2009. "Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus". PLoS ONE, 4 (4). https://doi.org/10.1371/journal.pone.0005135

Gsponer, J.; Futschik, M. E.; Teichmann, S. A.; Babu, M. M.. 2008. "Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation". Science, 322 (5906): 1365-1368. https://doi.org/10.1126/science.1163581

Futschik, Matthias; Chaurasia, Gautam; Wanker, Erich E.. 2008. " DISENTANGLING MOLECULAR INTERACTION NETWORKS FOR CHOREA HUNTINGTON". Trabalho apresentado em European Huntington Disease Network Annual Meeting , Lisabon, Portugal, 79 (1), A1-A1.

2008. "Medical Applications Of Adaptive Learning Systems And Diagnostic Kits (NZ547894A)". Divulgado.

Reeve, A; Futschik, Matthias; Sullivan, M.; Kasabov, N; Guilford, P. 2008. "Medical applications of adaptive learning systems using gene expression data (US7370021B2)". Estados Unidos. Concedida/Emitida.

Steglich, C.; Futschik, M.E.; Lindell, D.; Voss, B.; Chisholm, S.W.; Hess, W.R.. 2008. "The challenge of regulation in a minimal photoautotroph: Non-coding RNAs in Prochlorococcus". PLoS Genetics, 4 (8). https://doi.org/10.1371/journal.pgen.1000173

Futschik, M.E.; Herzel, H.. 2008. "Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis". Bioinformatics, 24 (8): 1063-1069. https://doi.org/10.1093/bioinformatics/btn072

Futschik, M.E.; Herzel, H.. 2007. "Are we overestimating the number of cell-cycling genes? The impact of background models for time series data.". Em Lecture Notes in Informatics (LNI) - Proceedings, Volume P-115, 2-14.

Lindell, Debbie; Jaffe, Jacob D.; Coleman, Maureen L.; Futschik, Matthias E.; Axmann, Ilka M.; Rector, Trent; Kettler, Gregory; et al. 2007. "Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution". Nature, 449 (7158): 83-86. https://doi.org/10.1038/nature06130

FUTSCHIK, MATTHIAS E.; TSCHAUT, ANNA; CHAURASIA, GAUTAM; HERZEL, HANSPETER. 2007. "GRAPH-THEORETICAL COMPARISON REVEALS STRUCTURAL DIVERGENCE OF HUMAN PROTEIN INTERACTION NETWORKS". Em Genome Informatics Series Vol. 18, 141-151. https://doi.org/10.1142/9781860949920_0014

Futschik, Matthias E.; Chaurasia, Gautam; Tschaut, Anna; Russ, Jenny; Babu, M. Madan; Herzel, Hanspeter. 2007. "Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network". Journal of Integrative Bioinformatics, 4 (3): 198-207. https://doi.org/10.1515/jib-2007-76

Chaurasia, Gautam; Iqbal, Yasir; Hänig, Christian; Herzel, Hanspeter; Wanker, Erich E.; Futschik, Matthias E.. 2007. "Flexible web-based integration of distributed large-scale human protein interaction maps". Journal of Integrative Bioinformatics, 4 (1): 40-50. https://doi.org/10.1515/jib-2007-51

Umbach, P; Futschik, Matthias; Stelzl, U; Wanker, E.E.. "Funktion durch Netzwerke von Proteinen und ihren Wechselwirkungen". Laborwelt, 2 (fevereiro, 2007): 9-11. http://193.136.227.175/sysbiolab/publications/laborwelt.ps

Futschik, Matthias; Suillivan, M; Reeve, Anthony; Kasabov, Nikola. 2007. "Modular Decision System and Information Integration for Improved Disease Outcome prediction,". Em Proceedings of the ECCB'2003,, 13-15.

Chaurasia, G.; Iqbal, Y.; Hänig, C.; Herzel, H.; Wanker, E.E.; Futschik, M.E.. 2007. "UniHI: An entry gate to the human protein interactome". Nucleic Acids Research, 35 (SUPPL. 1). https://doi.org/10.1093/nar/gkl817

Futschik, M.E.; Chaurasia, G.; Herzel, H.. 2007. "Comparison of human protein-protein interaction maps". Bioinformatics, 23 (5): 605-611. https://doi.org/10.1093/bioinformatics/btl683

Futschik ME; Tschaut A; Chaurasia G; Herzel H. 2007. "Graph-theoretical comparison reveals structural divergence of human protein interaction networks.". http://europepmc.org/abstract/med/18546482

Steglich, Claudia; Futschik, Matthias; Rector, Trent; Steen, Robert; Chisholm, Sallie W.; Steglich C; Futschik M; et al. 2006. "Genome-Wide Analysis of Light Sensing in Prochlorococcus". Journal of Bacteriology, 188 (22): 7796-7806. https://doi.org/10.1128/jb.01097-06

Kumar L; Futschik M; Herzel H. 2006. "DNA motifs and sequence periodicities.". In Silico Biology, 6 (1-2): 71-78. https://pubmed.ncbi.nlm.nih.gov/16789915/

Chaurasia, G.; Herzel, H.; Wanker, E.E.; Futschik, M.E.. 2006. "Systematic functional assessment of human protein-protein interaction maps.". Em Genome Informatics Vol. 17, No. 1, 36-45.

Futschik, Matthias; Chaurasia, Gautam; Herzel, Hanspeter. 2006. "Comparison of human protein-protein interaction maps". Em Lecture Notes in Informatics (LNI) - Proceedings, Volume P-83, 21-32.

Futschik, Matthias; Haenig, Christian; Chaurasia, Gautam; Wanker, Erich E.; Herzel, Hanspeter. 2006. UniHI: Unifying Large-Scale Maps of the Human Protein Interactome. Em International Conference on Intelligent Systems for Molecular Biology (ISMB) 2006.

Futschik, Matthias; Legewie, Stefan; Herzel, Hanspeter. 2006. "Prometheus under the microscope: Modelling the complex dynamics of liver regeneration". Trabalho apresentado em 6th European Conference on Mathematical and Theoretical Biolog, Dresden, Alemanha.

2006. "Medical Applications Of Adaptive Learning Systems (NZ 537160A)". Divulgado.

FUTSCHIK, MATTHIAS E.; CARLISLE, BRONWYN. 2005. "NOISE-ROBUST SOFT CLUSTERING OF GENE EXPRESSION TIME-COURSE DATA". Journal of Bioinformatics and Computational Biology, 03 (04): 965-988. https://doi.org/10.1142/s0219720005001375

Futschik, M.E.; Crompton, T.. 2005. "OLIN: Optimized normalization, visualization and quality testing of two-channel microarray data". Bioinformatics, 21 (8): 1724-1726. https://doi.org/10.1093/bioinformatics/bti199

Futschik, Matthias; Suillivan, M; Reeve, Anthony; Kasabov, Nikola. 2004. Modular decision system and information integration for cancer outcome prediction. Em RECOMB 2003.

Futschik, M.; Crompton, T.. 2004. "Model selection and efficiency testing for normalization of cDNA microarray data.". Genome biology, 5 (8). https://doi.org/10.1186/gb-2004-5-8-r60

Futschik, Matthias E; Reeve, Anthony; Kasabov, Nikola; Futschik, M.E.; Reeve, A.; Kasabov, N.. 2003. "Evolving connectionist systems for knowledge discovery from gene expression data of cancer tissue". Artificial Intelligence in Medicine, 28 (2): 165-189. https://doi.org/10.1016/s0933-3657(03)00063-0

Futschik ME; Sullivan M; Reeve A; Kasabov N. 2003. "Prediction of clinical behaviour and treatment for cancers.". OMJ Applied Bioinformatics , 2 (3): S53-58. http://europepmc.org/abstract/med/15130817

Futschik, Matthias. 2003. "Methods for knowledge discovery in microarray data.". Doutoramento. http://www.sysbiolab.eu/PhD/index.htm

Futschik, M.E.; Kasabov, N.K.. 2002. "Fuzzy clustering of gene expression data". Em 2002 IEEE World Congress on Computational Intelligence. 2002 IEEE International Conference on Fuzzy Systems. FUZZ-IEEE'02. Proceedings (Cat. No.02CH37291). https://doi.org/10.1109/fuzz.2002.1005026

Humar, Bostjan; Graziano, Francesco; Cascinu, Stefano; Catalano, Vincenzo; Ruzzo, Anna M; Magnani, Mauro; Toro, Tumi; et al. 2002. "Association of CDH1 haplotypes with susceptibility to sporadic diffuse gastric cancer". Oncogene, 21 (53): 8192-8195. https://doi.org/10.1038/sj.onc.1205921

Futschik, Matthias; Jeffs, Aaron; Pattison, Sharon; Kasabov, Nikola; Sullivan, Michael; Merrie, Arend; Reeve, Anthony. 2002. "Gene Expression Profiling of Metastatic and Nonmetastatic Colorectal Cancer Cell Lines". Genome Letters, 1 (1): 26-34. https://doi.org/10.1166/gl.2002.005

Kasabov, N.; Middlemiss, M.; Futschik, M.. 2001. "Knowledge based neural networks for on-line and off-line modeling and rule extraction in bioinformatics". Em Proceedings of the CGBI'2001 , 240-244.

Futschik, Matthias; Kasabov, N.K.. 2001. "Revealing the Fine-Structures: Wavelet-based fuzzy clustering of gene expression data". Trabalho apresentado em Ninth International Conference on Intelligent Systems for Molecular Biology, Kopenhagen, Dinamarca.

Kasabov, N.; Futschik, Matthias. 2001. Evolving Fuzzy Neural Networks for Knowledge Discovery from Gene Expression Data - A Case Study. Em Research in Computational Molecular Biology (RECOMB) 2001.

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".

Futschik, Matthias; Brown, Chris; Kasabov, Nikola. 2000. Clustering of gene expression data by evolving self-organising maps. Em The 10th annual Queenstown Molecular Biology Meeting.

Futschik, Matthias; Schreiber, M; Brown, C; Kasabov, Nikola. 1999. "Comparative studies of neural network models for ribosome binding site recognition". Em Proceedings of the ICONIP/ANZIIS/ANNES'99 International Workshop "Future Directions for Intelligent Systems and Information Sciences", 141-146.

Futschik, Matthias; Schreiber, M; Brown, Chris; Kasabov, Nikola. 1999. Comparative Studies of Neural Network Models for mRNA Analysis. Em Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB-99).

Futschik, Matthias. 1998. "Experimentelle Charakterisierung und theoretische Modellierung von Dendrimer-Tetrapyrrol Komplexen (Experimental characterisation and theoretical modelling of dendrimer-tetrapyrrol complexes).". Mestrado.

Mattthias Erwin Futschik

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