There is always a way up

Matthias E. Futschik (PhD)

Principal Investigator, Centre for Innovative Biomedicine and Biotechnology (CiBB), University of Coimbra, Portugal

Honorary Professor, Faculty of Health, University of Plymouth, UK



Academic Degrees


Positions


Links


Publications

Matthias E Futschik, Sarah A Tunkel, Elena Turek, David Chapman, Zareen Thorlu-Bangura, Raghavendran Kulasegaran-Shylini, Edward Blandford, Andrew Dodgson, Paul E Klapper, Malur Sudhanva, Derrick Crook, John Bell, Susan Hopkins, Tim Peto, and Tom Fowler (2024) Double testing with lateral flow antigen test devices for COVID-19: does a second test in quick succession add value? Journal of Virological Methods 329:115000. (html+pdf)

Tom Fowler, David Chapman, Matthias E Futschik, Sarah A Tunkel, Edward Blandford , Elena Turek, Olumide Kolade, Sergio Souza da Cunha, Andrew Dodgson, Paul Klapper, Malur Sudhanva, Lindsey Davies, Sue Hill, Susan Hopkins, and Tim Peto (2024) 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 & Infectious Diseases 43(8):1621-1630.(html+pdf)

Finola Ryan, Joanna Cole-Hamilton, Niharika Dandamudi, Matthias E Futschik , Alexander Needham, Rida Saquib, Raghavendran Kulasegaran-Shylini, Edward Blandford, Michael Kidd, Eamonn O'Moore, Ian Hall, Malur Sudhanva, Paul Klapper, Andrew Dodgson, Adam Moore, Madeleine Duke, Sarah Tunkel, Chris Kenny, and Tom Fowler (2024) 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):7475. (html+pdf)

Matthias E Futschik, Samuel Johnson, Elena Turek, David Chapman, Simon Carr, Zareen Thorlu-Bangura, Paul E Klapper, Malur Sudhanva, Andrew Dodgson, Joanna R Cole-Hamilton, Nick Germanacos, Raghavendran Kulasegaran-Shylini, Edward Blandford, Sarah Tunkel, Timothy Peto, Susan Hopkins, and Tom Fowler (2024) Rapid antigen testing for SARS-CoV-2 by lateral flow assay: A field evaluation of self- and professional testing at UK community testing sites. Journl of Clincal Virolology, 171:105654 (html+pdf)

Laura R Diaz, Jon Gil-Ranedo, Karolina J Jaworek, Nsikan Nsek, Joao Pinheiro Marques, Eleni Costa, David A Hilton, Hubert Bieluczyk, Oliver Warrington, C Oliver Hanemann, Matthias E Futschik, Torsten Bossing, and Claudia S Barros (2024) Ribogenesis boosts controlled by HEATR1-MYC interplay promote transition into brain tumour growth. EMBO Reports, 25(1):168-197.(html+pdf)

Lucy Reeve, Elise Tessier, Amy Trindall1, Nurin Iwani Binti Abdul Aziz, Nick Andrews, Matthias Futschik, Jessica Rayner, Alexis Didier’Serre, Rebecca Hams1, Natalie Groves, Eileen Gallagher, Rachael Graham, Beatrix Kele, Katja Hoschler, Tom Fowler, Edward Blandford, Hamid Mahgoub, Jorg Hoffmann, Mary Ramsay, Gavin Dabrera, Meera Chand, Maria Zambon, Ashley Sharp, Ellen Heinsbroek, and Jamie Lopez Bernal (2023) High attack rate in a large care home outbreak of SARS-CoV-2 BA.2.86, East of England, August 2023. Eurosurveillance 28(44):2300019 (html+pdf)

Toby Nonnenmacher*, Niharika Dandamudi*, Matthias Futschik*, Sarah Tunkel*, Nick Germanacos, Raghavendran Kulasegaran-Shylini, Joanna Cole-Hamilton, Ashley Goddard, Joe Hillier, Stephen Finer, Susan Hopkins, and Tom Fowler (2023) PCR testing of close contacts for COVID-19 in England, January to July 2021. Eurosurveillance 28(44):2300019 (html+pdf) (* Shared first author)

Jamie Fagg*, Rupert Beale*, Matthias E. Futschik*, Elena Turek, David Chapman, Susan Halstead, Marc Jones, Joanna Cole-Hamilton, Rory Gunson, Malur Sudhanva, Paul E. Klapper, Harper Vansteenhouse, Sarah Tunkel, Anna Dominiczak, Timothy EA Peto, and Tom Fowler (2023) Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing. Journal of Clinical Virology 167:105574 (html+pdf) (* Shared first author)

Olivia Kay*, Matthias E Futschik*, Elena Turek, David Chapman, Simon Carr, Malur Sudhanva, Paul E. Klapper, Tony Cox, Michael Hill, Joanna Cole-Hamilton, Peter Marks, Sarah A Tunkel, Timothy Peto, Lindsey Davies and Tom Fowler (2023) Performance of self-collected saliva samples for SARS-CoV-2 mass testing in community settings,Journal of Clinical Virology Plus, 3:3, 100161 (pdf+html) (* Shared first authors)

Dounia Djeghloul, Andrew Dimond, Sherry Cheriyamkunnel, Holger Kramer, Bhavik Patel, Karen Brown, Alex Montoya, Chad Whilding, Yi-Fang Wang, Matthias E Futschik, Nicolas Veland, Thomas Montavon, Thomas Jenuwein, Matthias Merkenschlager and Amanda G Fisher (2023) Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis. Nature Structural & Molecular Biology 30 4: 489-501. (html+pdf)

Tânia Barata, Isabel Duarte and Matthias E. Futschik (2023) Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes. Genes 14 3: 745-745. (html+pdf)

David W Eyre*, Matthias Futschik*, Sarah Tunkel, Jia Wei, Joanna Cole-Hamilton, Rida Saquib, Nick Germanacos, Andrew R Dodgson, Paul E Klapper, Malur Sudhanva, Chris Kenny, Peter Marks, Edward Blandford, Susan Hopkins, Tim E A Peto and Tom Fowler (2023) 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 (html+pdf) (*Shared first authors)

Fernando Bonet, Sabrina Brito Añez, José Manuel Inácio, Matthias E. Futschik and José Antonio Belo (2022) CCBE1 Is Essential for Epicardial Function during Myocardium Development. International Journal of Molecular Sciences , 23(20), 12642 (html+pdf)

Catherine Francis*, Matthias Futschik*, Jian Huang*, Wenjia Bai, Murali Sargurupremraj, Alexander Teumer, Monique Breteler, Enrico Petretto, Amanda Ho, Philippe Amouyel, Stefan Engelter, Robin Bülow, Uwe Völker, Henry Völzke, Marcus Dörr, Mohammed-Aslam Imtiaz, N. Ahmad Aziz, Valerie Lohner, James Ware, Stéphanie Debette, Paul Elliott, Abbas Dehghan, and Paul Matthews (2022) Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities. Nature Communications, 13, Article number: 4505 (html+pdf) (* Shared first author)

Kuiper M, Bonello J, Fernández-Breis JT, Bucher P, Futschik ME, Gaudet P, Kulakovskiy IV, Licata L, Logie C, Lovering RC, Makeev VJ, Orchard S, Panni S, Perfetto L, Sant D, Schulz S, Vercruysse S, Zerbino DR, Lægreid A; GRECO Consortium (2022) The gene regulation knowledge commons: the action area of GREEKC. Biochim Biophys Acta Gene Regul Mech.;1865(1):194768 (pdf+html)

Thomas Wallach, Zoé J. Mossmann, Michal Szczepek, Max Wetzel, Rui Machado, Martin Raden, Milad Miladi, Gunnar Kleinau, Christina Krüger, Paul Dembny, Drew Adler, Yuanyuan Zhai, Victor Kumbol, Omar Dzaye, Jutta Schüler, Matthias Futschik, Rolf Backofen, Patrick Scheerer, Seija Lehnardt (2021) 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 27;16(1):80 (pdf+html)

Matthias Riediger, Miguel A. Hernández-Prieto, Kuo Song, Wolfgang R. Hess and Matthias E. Futschik (2021) Genome-wide identification and characterization of Fur binding sites in the cyanobacterium Synechocystis sp. PCC 6803. DNA Research, 28, (6): dsab023 (pdf+html)

Rui Machado, Agapios Sachinidis and Matthias E. Futschik (2021) 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), 2477 (pdf+html)

José M Inácio, João Lopes, Ana M. Silva, Fernando Cristo, Sara Marques, Matthias E. Futschik and José A. Belo (2021) DAND5 inactivation promotes cardiac differentiation in mouse embryonic stem cells, Frontiers in Cell and Developmental Biology 9:846 (pdf+html)

Jemma Dunn, Vasileios P Lenis, David A Hilton, Rolf Warta, Christel Herold-Mende, C Oliver Hanemann and Matthias E Futschik (2020) Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma, Cancers 12(11), 3270 (pdf+html)

Vendula Krynicksá, Jens Georg, Philip J. Jackson, Mark J. Dickman, C. Neil Hunter, Matthias E. Futschik, Wolfgang R. Hess and Josef Komenda (2019) Depletion of the FtsH1/3 proteolytic complex suppresses the nutrient stress response in the cyanobacterium Synechocystis PCC6803, Plant Cell 31:2912-2928 (pdf+html)

João Santos, Leonardo Mendes-Silva, Vanessa Afonso, Gil Martins, Rui Machado, João Lopes, Leonor Cancela, Matthias Futschik, Agapios Sachinidis, Paulo Gavaia, and José Bragança (2019) Exogenous Wnt5a and Wnt11 proteins rescue Cited2 dysfunction in mouse embryonic stem cells and zebrafish morphants, Cell Death & Disease volume 10, Article number: 582 (pdf + html )

Jemma Dunn, Sara Ferluga, Vikram Sharma, Matthias Futschik, David A. Hilton, Claire L. Adams, Edwin Lasonder and C. Oliver Hanemann (2019) 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 (pdf + html )

Marinella N Ghezzo, Mónica T Fernandes, Ivette Pacheco-Leyva, Pedro M Rodrigues, Rui S Machado, Marta A S Araújo, Ravi K Kalathur, Matthias E Futschik, Nuno L Alves and Nuno R dos Santos (2018) FoxN1-dependent thymic epithelial cells promote T-cell leukemia development, Carcinogenesis 39, 12, 1463 - 1476 (pdf+html)

Davood Sabour, Rui S.R. Machado, José P. Pinto, Susan Rohani, Raja G.A. Sahito, Jürgen Hescheler, Matthias E. Futschik and Agapios Sachinidis (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 (pdf+html)

Joaquín Giner-Lamia, Miguel A. Hernández-Prieto, and Matthias E. Futschik (2018) ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803. Bio-protocol 8(12): e2895 (pdf+html)

Ping-Wei Ho, Mathias Klein, Matthias Futschik & Elke Nevoigt (2018) Glycerol positive promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae. FEMS Yeast Research, 18, 3 foy019 (pdf+html)

José Pinto, Rui Machado, Ramiro Magno, Daniel Oliveira, Susana Machado, Raquel Andrade, José Bragança, Isabel Duarte & Matthias Futschik (2018) StemMapper: A Curated Gene Expression Database for Stem Cell Lineage Analysis, Nucleic Acids Research D1: D788 - D793 (pdf+html)

Joaquín Giner-Lamia, Rocio Robles-Rengel, Miguel A. Hernández-Prieto, M. Isabel Muro-Pastor, Francisco J. Florencio, and Matthias E. Futschik (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: 11800 - 11820 (pdf+html)

Matthias Futschik, Markus Morkel, Reinhold Schäfer and Christine Sers (2017) The Human Transcriptome: Implications for the Understanding, Diagnosing and Treating of Human Disease. In: Molecular Pathology, 2nd edition. W.B. Coleman and G. Tsongalis, Academic Press, Elsevier, Chapter 7 :136-164

Ravi Kiran Reddy Kalathur, José Pedro Pinto, Biswanath Sahoo, Gautam Chaurasia & Matthias E. Futschik (2017) HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease, Scientific Reports 7: 5216 (pdf+html)

Jens Georg, Gergana Kostova , Linda Vuorijoki, Verena Schön, Taro Kadowaki, Tuomas Huokko, Desirée Baumgartner, Maximilian Müller, Stephan Klähn, Yagut Allahverdiyeva , Yukako Hihara, Matthias E. Futschik, Eva-Mari Aro, Wolfgang R. Hess (2017) Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1, Current Biology 27(10): 1425-1436 (pdf+html)

JA Macedo, D Schrama, I Duarte, E Tavares, J Renaut, ME Futschik, PM Rodrigues , EP Melo (2017) Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells BMC Genomics 18: 319 (pdf+html)

Joaquín Giner-Lamia, Sara B. Pereira, Miquel Bovea-Marco, Matthias E. Futschik, Paula Tamagnini, and Paulo Oliveira (2016) Extracellular proteins: Novel key components of metal homeostasis in cyanobacteria? Frontiers in Microbiology 7:878 (pdf+html)

Miguel Hernández-Prieto , Trudi Semeniuk , Joaquín Giner-Lamia and Matthias Futschik (2016) The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803, Scientific Reports 6:22168 (pdf + html)

Shany Doron, Ayalla Fedida, Miguel A Hernández-Prieto, Gazalah Sabehi, Iris Karunker, Damir Stazic, Roi Feingersch, Claudia Steglich, Matthias Futschik, Debbie Lindell and Rotem Sorek (2016) Transcriptome dynamics of a broad host-range cyanophage and its hosts. The ISME Journal 10, 1437-1455 (pdf + html)

Gürkan Bal, Matthias E. Futschik, Daniela Hartl, Frauke Ringel, Julian Kamhieh-Milz, Viktor Sterzer, Jörg D. Hoheisel, Mohamed S. S. Alhamdani, and Abdulgabar Salama (2016) Identification of novel biomarkers in chronic immune thrombocytopenia (ITP) by microarray-based serum protein profiling, British Journal of Haematology, 172(4):602-15. (pdf + html)

Ravi Kiran Reddy Kalathur, Joaquín Giner-Lamia, Susana Machado, Tânia Barata, Kameshwar R S Ayasolla, and Matthias E. Futschik (2015) The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach, F1000Research 4:103 (pdf + html)

Stephen Pells, Eirini Koutsouraki, Sofia Morfopoulou, Sara Valencia-Cadavid, Simon Tomlinson, Ravi Kalathur, Matthias Futschik and Paul De Sousa (2015) Novel human embryonic stem cell regulators identified by conserved and distinct CpG island methylation state, PLoS ONE 10(7): e0131102. (pdf + html)

José P. Pinto, Ravi K. Kalathur, Daniel V. Oliveira, Tânia Barata, Rui S. R. Machado, Susana Machado, Ivette Pacheco-Leyva, Isabel Duarte and Matthias E. Futschik (2015). StemChecker: a web-based tool to discover and explore stemness signatures in gene sets, Nucleic Acids Research 43 (W1): W72-W77 (pdf + html)

M. Stroedicke, Y. Bounab, N. Strempel, K. Klockmeier, S. Yigit, RP Friedrich, G. Chaurasia, S. Li, F. Hesse, SP Riechers, J. Russ, C. Nicoletti, A. Boeddrich, T. Wiglenda, C. Haenig, S. Schnoegl, D. Fournier, RK Graham, MR Hayden, S. Sigrist, GP Bates, J. Priller, Ma Andrade-Navarro, Matthias E. Futschik and EE Wanker (2015) Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity. Genome Research 25: 701-713 (pdf + html)

Richard Hill, Ravi K Kalathur, L. Colaço, R. Brandão, S. Ugurel, Matthias Futschik and Wolfgang Link (2015) TRIB2 as a biomarker for diagnosis and progression of melanoma. Carcinogenesis 36(4):469-77 (pdf + html)

Richard Hill, Ravi Kalathur, S. Callejas, L. Colaço, R. Brandão, Beatriz Serelde, A. Cebriá, C. Blanco-Aparicio, J. Pastor, Matthias Futschik, A. Dopazo and W. Link (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):482 (pdf + html)

Julian Kamhieh-Milz, Reham Moftah, Gürkan Bal, Matthias Futschik, Viktor Sterzer, Omid Khorramshahi, Martin Burow, Gundula Thiel, Annegret Stuke-Sontheimer, Rabih Chaoui, Sundrela Kamhieh-Milz, and Abdulgabar Salama (2014) Differentially Expressed MicroRNAs in Maternal Plasma for the Noninvasive Prenatal Diagnosis of Down Syndrome (Trisomy 21), BioMed Research International, Volume 2014, Article ID 402475 (pdf + html)

Miguel A. Hernández-Prieto, Trudi A. Semeniuk and Matthias E. Futschik (2014) Towards a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. Frontiers in Genetics 5:191 (pdf + html)

José P. Pinto, Ravi K.R. Kalathur, Rui S. R. Machado, Joana M. Xavier, José Bragança, and Matthias E. Futschik, José Bragança, and Matthias E. Futschik (2014) StemCellNet: an interactive platform for network-oriented investigations in stem cell biology. Nucleic Acids Research 42:W154-W160. (pdf+html)

José P. Pinto, Rui Machado, Xavier and Matthias E. Futschik (2014) Targeting molecular networks for drug research. Frontiers in Genetics 5: 160 (pdf + html )

Miguel Hernandez-Prieto, Ravi Kalathur and Matthias E. Futschik (2014) Molecular networks, their analysis and representation, Chapter 24, 399-418, , Springer Handbook of Bio- and Neuroinformatics, ed. Nik Kasabov, Springer (preprint-pdf, Book's web-page)

Ravi K. Kalathur, José P. Pinto, Miguel Hernandez, Rui Machado, Dulce Almeida, Gautam Chaurasia and Matthias Futschik (2014) UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks, Nucleic Acids Research, Database issue, 42 (D1): D408-D414. (html, pdf)

Thomas Wallach, Katja Schellenberg, Bert Maier, Ravi Kalathur , Pablo Porras, Erich E. Wanker, Matthias E. Futschik and Achim Kramer (2013) Dynamic Circadian Protein-Protein Interaction Networks Predict Temporal Organization of Cellular Functions, PloS Genetics , 9(3): e1003398. doi:10.1371/journal.pgen.1003398 (html, pdf)

Miguel A. Hernández-Prieto, Verena Schön, Jens Georg, Luísa Barreira, João Varela, Wolfgang R. Hess and Matthias E. Futschik (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 (html, pdf)

Miguel Hernandez-Prieto and Matthias E. Futschik (2012) CyanoEXpress: a web database for interactive exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803, Bioinformation 8:13,634-638 (Html/Pdf)

Ravi Kalathur, Miguel Hernandez-Prieto and Matthias E. Futschik (2012) Huntington's Disease and its target genes: A global functional profile based on the HD Research Crossroads database, BMC Neurology , 12:47 (html+pdf)

Gürkan Bal, Julian Kamhieh-Milz, Tayseer Zaid, Matthias Futschik, Thomas Häupl, Abdulgabar Salama and Anja Moldenhauer (2012) Transcriptional profiling of the haematopoietic support of interleukin-stimulated human umbilical vein endothelial cells (HUVEC), Cell Transplantation 21(1):251-67 (html + pdf)

Gautam Chaurasia and Matthias E. Futschik (2012) The Integration and Annotation of the Human Interactome in the UniHI Database Methods in Molecular Biology 812: 175-188 (PubMed, pdf)

C. T. Duong, L. Strack, M. Futschik, Y. Katou, Y. Nakao, T. Fujimura, K. Shirahige, Y. Kodama, E. Nevoigt (2011) Identification of Sc-type ILV6 as a target to reduce diacetyl formation in lager brewers' yeast, Metabolic Engineering, 13(6):638-47 (PubMed, pdf)

Anja Moldenhauer, Matthias Futschik, Huili Lu, Melanie Helmig, Patric Götze, Gürkan Bal, Martin Zenke,Wei Han an Abdulgabar Salama (2011) Interleukin 32 promotes hematopoietic progenitor expansion and attenuates bone marrow cytotoxicity, European Journal of Immunology, 41(6):1774-86 (html + pdf)

Elisabetta Marras, Antonella Travaglione, Gautam Chaurasia, Matthias Futschik and Enrico Capobianco (2010) Inferring modules from human protein interactome classes, BMC Systems Biology, 4:102 (pdf, html)

Jenny Russ and Matthias E. Futschik (2010) Comparison and consolidation of microarray data sets of human tissue expression, BMC Genomics (pdf,html)

Claudia Steglich, Debbie Lindell, Matthias Futschik, Trent Rector, Robert Steen and Sallie W. Chisholm (2010) Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus, Genome Biology (pdf,html)

Gautam Chaurasia and Matthias E. Futschik (2009) Interactomics and Cancer, An Omics Perspective of Cancer, eds. W. Cho, Springer, Chapter 5: 167- 182 (pdf)

Michael J. Allen, Bela Tiwari, Matthias E. Futschik and Debbie Lindell (2009) Methods in aquatic virus ecology: Construction of microarrays and their application to virus analysis, Manual of Aquatic Viral Ecology, American Society of Limnology and Oceanography, Chapter 5: 34 - 56 (pdf)

E.R. Zinser, D. Lindell, Z.I.Johnson, M.E. Futschik, C. Steglich, M.L. Coleman, M.A. Wright, T. Rector, R. Steen, N, McNulty, L.R. Thompson and S.W. Chisholm (2009) Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus, PlosONE, 4(4): e5135. doi:10.1371/journal.pone.0005135 (pdf)

Matthias Futschik, Wolfgang Kemmner, Reinhold Schäfer and Christine Sers (2009) The Human Transcriptome: Implications for the Understanding of Human Diseases, Molecular Pathology, eds. W.B. Coleman and G. Tsongalis, Academic Press, Elsevier, Chapter 7 :123-150 (pdf)

Gautam Chaurasia, Soniya Malhotra, Jenny Russ, Sigrid Schnoegl, Christian Hänig, Erich. E. Wanker and Matthias. E. Futschik. (2009) UniHI 4: New tools for query, analysis and visualization of the human protein-protein interactome, Nucleic Acids Research, 37, Database issue: D657-D660 (pdf)

Jörg Gsponer, Matthias E. Futschik, Sarah A. Teichmann and M. Madan Babu (2008) Tight regulation of intrinsically unstructured proteins: from transcript synthesis to protein degradation, Science, 322, 1365-1368 (pdf)

Claudia Steglich, Matthias E. Futschik, Debbie Lindell, Bjoern Voss, Sallie W. Chisholm and Wolfgang R. Hess (2008) The challenge of regulation in a minimal photoautotroph: Non-coding RNAs in Prochlorococcus, Plos Genetics 4(8): e1000173 (pdf)

Matthias E. Futschik and Hanspeter Herzel (2008) Are we overestimating the number of cell-cycling genes? The impact of background models on time series analysis, Bioinformatics, 24(8):1063-1069 (pdf)

Matthias E. Futschik, Gautam Chaurasia, Anna Tschaut, Jenny Russ, M. Madan Babu and Hanspeter Herzel (2007) Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network, Journal of Integrative Bioinformatics, 4(3):76 (pdf)

Matthias Futschik, Anna Tschaut, Gautam Chaurasia, and Hanspeter Herzel (2007) Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks, Genome Informatics, 18, 141-15 (pdf)

D. Lindell, J. Jaffe, M. Coleman, M. Futschik, I. Axmann, T. Rector, G. Kettler, M. Sullivan, R. Steen, W. Hess, G. Church and S. Chisholm (2007) Genome-Wide Expression Dynamics of a Marine Virus and its Host Reveal Features of Co-evolution, Nature, 449, 83 - 86 (pdf)

P. Umbach, M. Futschik, U.Stelzl and E.Wanker (2007) Funktion durch Netzwerke von Proteinen und ihren Wechselwirkungen, Laborwelt, 8(2):9-11 (ps)

L. Kumar and M.E. Futschik (2007) Mfuzz: a software package for soft clustering of microarray data, Bioinformation, 2(1) 5-7 (pdf)

Matthias Futschik, Gautam Chaurasia, and Hanspeter Herzel (2007) Comparison of human protein-protein interaction maps, Bioinformatics, 23(5):605-611 (pdf)

G. Chaurasia, C. Hänig, Y. Iqbal, H. Herzel, E.Wanker and M. E. Futschik (2007) Flexible web-based integration of distributed large-scale interaction data sets, Journal of Integrative Bioinformatics, 4(1) (pdf)

G. Chaurasia, Y. Iqbal, C. Hänig, H. Herzel, E. E. Wanker and M. E. Futschik (2007) UniHI: An Entry Gate to the Human Protein Interactome, Nucleic Acids Research Database issue, 35, D590-4 (pdf)

C. Steglich, M. Futschik, T. Rector and S.W. Chisholm (2006) Genome-wide analysis of light sensing in Prochlorococcus, Journal of Bacteriology, 188(22):7796-806 (pdf)

Gautam Chaurasia, Hanspeter Herzel, Erich Wanker and Matthias E. Futschik (2006) Systematic functional assessment of human protein interaction maps, Genome Informatics, 17(1), 36-45. (pdf)

L. Kumar, M. Futschik and H. Herzel (2006) DNA motifs and sequence periodicities, In Silico Biology, 6, 0008 (pdf)

M.E. Futschik and B. Charlisle (2005) Noise robust soft clustering of gene expression time-course data, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 4, 965-98 (pdf)

M.E. Futschik and T. Crompton (2005) OLIN: optimized normalization, visualization and quality testing of two-channel microarray data, Bioinformatics, 21(8):1724-6 (pdf)

M. Futschik and T. Crompton (2004) Model selection and efficiency testing for normalization of cDNA microarray, Genome Biology, 5(8):R60 (pdf)

M.E. Futschik, M. Sullivan, A. Reeve, N. Kasabov (2003) Prediction of clinical behaviour and treatment for cancers, Applied Bioinformatics, 3(2): S53-58 (pdf)

M.E. Futschik, A. Reeve and N. Kasabov (2003) Evolving connectionist systems for knowledge discovery from gene expression data of gene expression data of cancer tissue, Artificial Intelligence in Medicine, 28: 165-189, 2003 (pdf)

B. Humar, F. Graziano, S. Cascinu, V. Catalano, A.M. Ruzzo, M. Magnani, T. Turo, M.E. Futschik, T.Merriman and P. Guilford, (2002) Association of CDH1 haplotypes with susceptibility to sporadic diffuse gastric cancer, Oncogene, 21(53): 8192-8195 (pdf)

M. Futschik, A. Jeffs, S. Pattison, N. Kasabov, M. Sullivan, A. Merrie and A. Reeve (2002) Gene expression profiling of metastatic and non-metastatic colorectal cancer cell-lines,Genome Letters, vol.1, No.1, 26-34 (pdf)

C. Brown, G. Jacobs, M. Schreiber, J. Magnum, J. McNaughton, M. Cambray, M. Futschik, Major, O. Rackham, W. Tate, P. Stockwell, C. Thompson and N. Kasabov, (2000) Using bioinformatics to investigate post-transcriptional control of gene expression, NZ Bio Science, 7(4), 11-12


Presentations

Miguel A. Hernandez-Prieto, Trudi Semeniuk, Joaquín Giner-Lamia, and Matthias E. Futschik (2018) Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis - a comprehensive study based on CyanoEXpress, PHYCONET Annual Conference, London, UK

Matthias Futschik (2018) Deciphering the gene regulatory networks of cyanobacteria, Keynote talk at the 3rd Early Career Researcher Symposium on Cyanobacteria, Freiburg, Germany

Matthias Futschik (2017) Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803, Contributed talk, 10th European Workshop on the Molecular Biology of Cyanobacteria (Abstractbook, Page 35), Cluj-Napoca, Romania

José Pedro Pinto, Ravi Kalathur, Daniel V. Oliveira, Tânia Barata, Rui Machado, Susana Machado, Ivette Pacheco-Leyva, Joana M. Xavier, José Bragança , Isabel Duarte and Matthias Futschik (2016) SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology, Poster presentation, 9th International Meeting of the Stem Cell Network NRW (Abstractbook, Abstract 103, Page 124), Müster, Germany Lisbon, Portugal

Rui S. R. Machado, José P. Pinto, Davood Sabour, José Bragança, A. Sachinidis and Matthias E. Futschik (2017) HEARTI ToolBox: An online platform for the analysis in silico of cardiomyogenesis, Poster presentation, 9th International Meeting of the Stem Cell Network NRW (Abstractbook, Abstract 60, Page 81), Müster, Germany

Matthias Futschik (2017) The many faces of stem cells: Meta-analysis of stemness signatures, Contributed talk, 7th Bioinformatics and Stem Cells Satellite Meeting,Müster, Germany

José Pedro Pinto, Ravi Kalathur, Daniel V. Oliveira, Tânia Barata, Rui Machado, Susana Machado, Ivette Pacheco-Leyva, Joana M. Xavier, José Bragança , Isabel Duarte and Matthias Futschik (2016) SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology, INFORUM 2016, Lisbon, Portugal

M Futschik, J Giner-Lamia, M Hernandez-Prieto (2016) CyanoEXpress: An interactive web-tool for exploration and visualization of gene expression data from cyanobacteria, NorPlantBio 2016, Trondheim, Norway (abstract)

M Hernandez-Prieto, T Semeniuk, J Giner-Lamia, M Futschik (2016) Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis, NorPlantBio 2016, Trondheim, Norway (abstract)

Isabel Duarte, D.Oliveira, T. Justo, J. Bragança and M. Futschik (2015) Predicting Cardiac Novel Splice Variantes from RNAseq data, Bioinformatics for the Life Sciences, Universidade do Minho, Braga, Portugal

DV Oliveira, I Duarte, RS Machado, I Pacheco-Leyva, T Justo, JP Pinto, S Machado, JA Belo, J Bragança & ME Futschik (2015) From Stem Cells 2 Heart: Finding novel candidate isoforms and genes for cardiomyogenesis. Poster presentation. 9th International Meeting of Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

RS Machado, JP Pinto, DV Oliveira, I. Duarte, S Machado, J Bragança & M Futschik (2015) A meta-analysis study of stem cell differentiation in the context of cardiogenesis. Poster presentation. 9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

S Machado, R Kalathur, DV Oliveira, T Barata, R Machado, I Pacheco-Leyva, I Duarte, M Futschik, J Pinto (2015) StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. Oral presentation. 9th International Meeting of the Portuguese society for Stem cells and Cell therapies Oeiras. Portugal.

JP Pinto, R Kalathur, RS Machado, J Xavier, J Bragança & ME Futschik (2015) StemCellNet: an interactive platform for network -oriented investigations in stem cell biology. Poster presentation. 9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

Matthias Futschik, Joaquín Giner-Lamia and Miguel Hernández-Prieto(2015) Transcriptional regulation and coordination of photosynthetic genes in Synechocystis: a comprehensive study based on CyanoEXpress, ISPP 2015, Tübingen, Germany

Joaquin Giner-Lamia, Miquel Bovea-Marco, Miguel A. Hernández-Prieto and Matthias E. Futschik (2015) CyanoEXpress: An enhanced tool for on-line analysis and visualization of gene expression data from cyanobacteria, ISPP 2015, Tübingen, Germany

Isabel Duarte, D.Oliveira, T. Justo, J. Bragança, J Belo and M. Futschik (2015) From Stem Cells 2 Heart: Estudo do Impacto do Splice Alternativo durante o Desenvolvimento Cardiaco, Molecular Genetics Anual Seminar Series, Universidade do Algarve, Faro, Portugal

J. Pinto, R. Kalathur, R. Machado , J. Xavier, J. Bragança, and Matthias E. Futschik (2014) StemCellNet: an interactive platform for network-oriented investigations in stem cell biology, Poster Presentation, Heart without Boarders International Conference, Porto, Portugal (Abstract Book, Page 45)

I. Duarte, T. Justo, J. Pinto, D.Oliveira, J. Bragança, J. Belo and Matthias Futschik (2014) From Stem Cells 2 heart: Elucidating the role of alternative splicing in cardiomyogenesis, Poster Presentation, Heart without Boarders, International Conference, Porto, Portugal (Abstract Book Page 52)

D Oliveira, R. Machado, I. Pacheco-Leyva, I. Duarte, T. Justo , J. Pinto, J. Belo, J. Bragança and Matthias Futschik (2014) From Stem Cells 2 heart: Finding novel candidate genes for cardiomyogenesis, Poster Presentation, Heart without Boarders, International Conference, Porto, Portugal (Abstract Book Page 72)

Matthias E. Futschik (2014) Systems Biology: Can it help in the study of neurodegeneration? Invited Talk, 1st Neuroimmunology Workshop, ICM, Paris, France.

Matthias E. Futschik (2013) How Synechocystis adapts to changes in environment: A meta-analysis of its transcriptional responses, Invited Talk, CyanoFactory Meeting, Porto, Portugal

Rui S.R. Machado, José Pedro B. G. P. Pinto, José Bragança and Matthias E. Futschik (2013) What a heart makes or breaks: A meta-analysis of gene expression profiles, Poster presentation, 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, Faro, Portugal

Josá Pedro B. G. P. Pinto, Rui S.R. Machado, Ravi K.R. Kalathur, and Matthias E. Futschik (2013) StemCellNet: A web-based Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells, Poster presentation, 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, Faro, Portugal

Miguel A. Hernández-Prieto and Matthias E. Futschik (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, Poster presentation, ESF-EMBO Symposium Molecular Bioenergetics Of Cyanobacteria: Shaping The Environment Pultusk, Poland

Matthias E. Futschik (2013) How the internal world of Synechocystis adapts to the ever-changing world outside: A comprehensive meta-analysis of its transcriptional responses, Oral presentation, ESF-EMBO Symposium Molecular Bioenergetics Of Cyanobacteria: Shaping The Environment, Pultusk, Poland

Miguel A. Hernández-Prieto and Matthias E. Futschik (2012) CyanoExpress: A Comprehensive Database for Evaluating the Transcriptional Response in Synechocystis, Poster Presentation, P157, International Symposium on Phototrophic Prokaryotes 2012, Porto, Portugal (Poster pdf, Abstract png)

Miguel A. Hernández-Prieto, Verena Schön, Claudia Steglich, Wolfgang Hess and Matthias E. Futschik (2012) Simultaneous profiling of coding and non-coding RNAs from Synechocystis under iron-limiting conditions, Poster Presentation P158, International Symposium on Phototrophic Prokaryotes 2012, Porto, Portugal (Abstract png)

Matthias Futschik (2012) UniHI: Network biology goes to the bench, Contributed Talk, 3nd Meeting of the Institute for Biotechnology and Bioengineering, Lisboa, Portugal

Ravi Kalathur, Kameshwar Ayasolla and Matthias Futschik (2012) The Unfolded Protein Response and its potential role in Huntington's disease; Nature Precedings, dx.doi.org/10.1038/npre.2012.7145.1 (html)

Ravi K Kalathur and Matthias.E. Futschik (2011) The UniHI Database: A Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells, Poster Presentation, Cell Symposia: Stem Cell Programming & Reprogramming 2011, Lisbon, Portugal

Matthias E. Futschik and Miguel A. Hernández-Prietoa (2011) The Transcriptional Landscape of the Cyanobacterium Synechocystis, Poster Presentation, 8th European Workshop on Molecular Biology of Cyanobacteria, Naantali, Finland

Matthias.E. Futschik (2011) Network biology, a key to understand the complexity of molecular systems, University of Otago, NZ

Matthias.E. Futschik (2011) Concepts and applications of network biology, Auckland University of Technology, NZ

Matthias Futschik (2010) Chorea Huntington: A thousand changes due to a single mutation, Contributed Talk, 2nd Meeting of the Institute for Biotechnology and Bioengineering, Universidade do Minho, Braga, Portugal (pdf)

Ravi K Kalathur and Matthias.E. Futschik (2010) Network-based analyses of Huntington's disease; Nature Precedings; dx.doi.org/10.1038/npre.2012.7078.1 (html)

Kameshwar Ayasolla, Ravi Kalathur and Matthias Futschik (2010) A systems biology approach towards deciphering the unfolded protein response in Huntington's disease; Nature Precedings; dx.doi.org/10.1038/npre.2012.7078.1 (html)

Kameshwar Ayasolla, Ravi Kalathur and Matthias Futschik (2010) ER stress: an initiator of neuroinflammation in Huntington's disease? J Neurol Neurosurg Psychiatry 81:A5 doi:10.1136/jnnp.2010.222570.16 (abstract)

Matthias Futschik (2010) A Network Perspective on Signalling, 4th National Meeting on Signal Transduction, SINAL 2010, Invited Talk, Faro, Portugal

Miguel A. Hernández-Prietoa, Luisa Barreira, João Varela & Matthias E. Futschik (2010) Concerted responses to iron availability in cyanobacteria, SINAL 2010, Faro, Portugal

M. Futschik (2009) Disentangling molecular interaction networks for Huntington's Disease, Weizmann Institute, Rehovot, Israel

Matthias Futschik (2009) Disentangling molecular interaction networks for Chorea Huntington, Invited Talk, Institute for Systems Biology, Seattle, US.

ME Futschik (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 Sciences- Irvine, California, US

Matthias Futschik, Gautam Chaurasia and Erich Wanker, Disentangling molecular intaction networks for Chorea Huntington, European Huntington's Diesease Network Meeting, Lisbon, Portugal, 2008 (html)

M. Futschik, Large-scale human protein-protein interacton maps: A tool for finding the magical bullets against complex diseases, Invited Talk, Protein-Protein Interactions as Drug Targets Symposium, Berlin, Germany, 2008

M. Futschik, Network biology, a key to understand the complexity of molecular systems, Invited Talk, University of Algarve, Faro, Portugal, 2007

M. Futschik and Hanspeter Herzel, Are we overestimating the number of cell-cycling genes? The impact of background models, Contributed Talk, German Conference on Bioinformatics, Potsdam, Germany, 2007 (Lecture Notes in Informatics, 115, 2-14: html,pdf)

M.E. Futschik, Gautam Chaurasia, Anna Tschaut, Jenny Russ, M. Madan Babu and Hanspeter Herzel (2007) Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Networks, Contributed Talk, International workshop in Integrative Bioinformatics, Ghent, Belgim

M.E. Futschik, Anna Tschaut, Gautam Chaurasia, and Hanspeter Herzel (2007) Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks, Contributed Talk, International Workshop on Bioinformatics and Systems Biology, Tokyo, Japan

M.E. Futschik (2007) Concurrency between and coherency within human PPI maps HUPO PSI, Spring Meeting, Lyon, France

M.E. Futschik, G. Chaurasia, E. Wanker and H. Herzel, Comparison of Human Protein-Protein Interaction Maps (2006) German Conference on Bioinformatics 2006, Contributed Talk, Tübingen, Germany (Lecture Notes in Informatics, P 83, 21-32, pdf)

M.E. Futschik, G. Chaurasia, E. Wanker and H. Herzel (2006) Comparison and integration of human protein interaction maps, Comparison of Human Protein-Protein Interaction Maps, Contributed Talk, Interactome Networks, Wellcome Trust/Cold Spring Harbour Laboratory Conference, Hinxton, Cambridge

M.E. Futschik, C. Hänig, G. Chaurasia, E. Wanker and H. Herzel, UniHI: Unifying Large-Scale Maps of the Human Protein Interactome, Poster, ISMB 2006, Fortaleza, Brasil

M. Futschik, S. Legewie and H. Herzel (2005) Prometheus under the microscope: Modelling the complex dynamics of liver regeneration, Contributed Talk, European Conference on Mathematical and Theoretical Biology, Dresden, Germany

C. Steglich, M. Futschik, D. Lindell, W.R. Hess and S. W. Chisholm (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, Roscoff, France

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

M. Futschik and S. Legewie (2004), Prometheus under the microscope, Systems-Biological approaches to liver regeneration , Invited Talk, Freiburger Zentrum für Datenanalyse und Modellbildung, Freiburg, Germany

M.E. Futschik (2004) Microarray data analysis - Gold-mining in a minefield, Invited Talk, Mathematical Interdisciplinary Research Day: Genetic Networks, Warwick Mathematical Instituts, UK (pdf)

M.E. Futschik (2004) Microarrays & Expression Profiling, Bioinformatics summer school in Sile-Istanbul/Turkey (Link)

M.E. Futschik (2004),Microarray data analysis I-V, Summer school on cell biology and mathematical modelling in Hvar/Croatia (Link)

M.E. Futschik, M. Sullivan, A. Reeve and N. Kasabov (2003) Modular Decision System and Information Integration for Improved Disease Outcome prediction, ECCB 2003, Oral presentation, Proceedings of the ECCB, pp.13-15, Paris, France (ps,pdf).

M.E. Futschik, M. Sullivan, A. Reeve and N. Kasabov (2003) Modular decision system and information integration for cancer outcome prediction. Currents in Computational Molecular Biology 2003, R. Sprang, P. Bézat and M. Vingron (eds.), RECOMB 2003, Berlin, Germany.

M.E. Futschik, M. Sullivan, A. Reeve and N. Kasabov (2003) Prediction of clinical behaviours and treatment for cancers. New Zealand Bioinformatics Conference, Wellington, NZ

M.E. Futschik and N.K. Kasabov (2002). Fuzzy clustering of gene expression data, Proceedings of World Congress of Computational Intelligence WCCI 2002, Hawaii, IEEE Press (html, pdf)

M.E. Futschik and N.K. Kasabov (2001). Revealing the Fine-Structures: Wavelet-based fuzzy clustering of gene expression data, ISMB 2001 - Programme and Abstracts, Copenhagen, p.47 (html)

N. Kasabov and M. Futschik (2001) Evolving Fuzzy Neural Networks for Knowledge Discovery from Gene Expression Data - A Case Study, RECOMB'2001 Proceedings - Currents in Computational Molecular Biology 2001, T. Lengauer and D. Sankoff (eds), Montreal, Canada, pp. 175-177

N. Kasabov and M.J. Middlemiss and M.E. Futschik (2001). Knowledge Based Neural Networks for On-Line and Off-Line Modeling and Rule Extraction in Bioinformatics, CGBI'2001 Atlantic Symposium on Computational Biology, Genome Information Systems and Technology, Durham, North Carolina, USA

M.E. Futschik, C. Brown and N. Kasabov (2000). Clustering of gene expression data by evolving self-organising maps, The 10th annual Queenstown Molecular Biology Meeting, Queenstown, New Zealand

M.E. Futschik, M. Schreiber, C. Brown and N. Kasabov (1999) Comparative studies of neural network models for ribosome binding site recognition, Proceedings of the ICONIP/ANZIIS/ANNES'99 Workshop , Dunedin, New Zealand, pp. 141-146

M. Futschik, M.Schreiber, C.M. Brown, and N. Kasabov (1999). Comparative Studies of Neural Network Models for mRNA Analysis, Poster and Software Demonstrations , ISMB 1999, Heidelberg, p. 43 (ps)


Patents

Nikola Kirilov Kasabov,Matthias Erwin Futschik, Michael James Sullivan and Anthony Edmund Reeve. Medical decision support system utilising gene expression and clinical information and method for use. European Patent EP03788512.6-2108, issued 20/7/2016 (pdf)

Anthony Edmund Reeve, Mathias Erwin Futschik, Michael James Sullivan, Nikola Kirilov Kasabov and Parry John Guilford. Medical applications of adaptive learning systems using gene expression data. US Patent US7370021B2, granted 6/5/2008 (pdf)

Anthony Edmund Reeve, Matthias Erwin Futschik, Michael James Sullivan, Nikola Kirilov Kasabov, Parry John Guilford, Medical Applications Of Adaptive Learning Systems And Diagnostic Kits, New Zealand Patent Application, NZ547894A (published 28/3/2008)

Anthony Edmund Reeve, Matthias Erwin Futschik, Michael James Sullivan, Nikola Kirilov Kasabov, Parry John Guilford, Medical Applications Of Adaptive Learning Systems, New Zealand Patent Application, NZ 537160A (published 29/9/2006)