Publications

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 , Joaquin 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, Joaquin 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)

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

R. 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)

J. Kamhieh-Milz, R. Moftah, G. Bal, Matthias Futschik, V. Sterzer, O. Khorramshahi, M. Burow, G. Thiel, A. Stuke-Sontheimer, R. Chaoui, S. Kamhieh-Milz, and A. 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 (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, Joana Gonçalves 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 A. Hernández-Prieto, Rui S.R. 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 (Abstract, Pdf, Website of Database)

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, Supplementary Material)

Gürkan Bal, Julian Kamhieh-Milz, Tayseer Zaid, Matthias Futschik, Thomas Häupl, Abdulgabar Salama and Anja Moldenhauer (2012) Molecular profiling of the haematopoietic support of interleukin-stimulated human umbilical vein endothelial cells (HUVEC), Cell Transplantation 21(1):251-67(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, Patricc 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 (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 11:305 (pdf,html, Supplementary Materials)

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 11:R54 (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)


Presentations

José Pedro Pinto, Ravi Kalathur, Daniel V. Oliveira, Tânia Barata, Rui Machado, Susana Machado, Ivette Pacheco-Leyva, Joana M. Xavier, Bragança José, 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)

Rui Machado (2016) Identification of key factors of heart regeneration using a systems biology approach, ProRegeM, Annual Meeting 2016, Lisbon, Portugal

J Pinto, Machado, R Kalathur, DV Oliveira, T Barata, R Machado, S Machado, I Pacheco-Leyva, I Duarte, M Futschik (2016) StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. Bioinformatics Open Days, Braga, Portugal

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..9th International Meeting of the 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.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.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. 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 (abstract)

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 (abstract)

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 M.E Futschik (2014) StemCellNet: an interactive platform for network-oriented investigations in stem cell biology, Heart without Boarders, International Conference, Porto, Portugal (abstract)

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

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

Matthias E. Futschik (2014) Systems Biology: Can it help in the study of neurodegeneration? 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 Lecture, 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 , 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, Faro, Portugal

José 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, 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, ESF-EMBO Symposium, 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, ESF-EMBO Symposium, Pultusk, Poland

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

Miguel A. Hernández-Prieto and Matthias E. Futschik (2012) CyanoExpress: A Comprehensive Database for Evaluating the Transcriptional Response in Synechocystis, ISPP 2012, Porto, Portugal (pdf)

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, ISPP 2012, Porto, 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, STEM 2011, Lisbon, Portugal

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

Miguel A. Hernández-Prieto, Luisa Barreira, Claudia Steglich, João Varela, Wolfgang Hess & Matthias E. Futschik (2011) Concerted responses to iron availability in cyanobacteria, 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 Kalathurand 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)

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

Ravi K Kalathur, Gautam Chaurasia, Erich Wanker and Matthias.E. Futschik (2010) Molecular interaction networks in Huntington´s Disease, SINAL 2010, Faro, Portugal

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

M.E. 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