Professor Matthias Futschik
Profiles

Professor Matthias Futschik

Honorary Professor

School of Biomedical Sciences (Faculty of Health)

Biography

Biography

  • Professor in Bioinformatics at Plymouth University Peninsula Schools of Medicine and Dentistry (2016 - 2019)

Qualifications

I studied physics at the Eberhard Karls University (Tübingen, Germany), the Brown University (Rhode Island, USA) and the Humboldt University (Berlin, Germany), and carried out research work in the field of photobiophysics for my Master degree. In 1999, I went to Dunedin, New Zealand, where I pursued a PhD in Information Science at the University of Otago. My focus was the development of new computational methods for microarray data analysis and their application in cancer research. After working for some time in a spin-off company (Pacific Edge Biotech. Ltd) as senior bioinformatician, I returned to Berlin to take up a position as Assistant Professor at the Charité, Humboldt-University, where I became interested in the structure, function and regulation of molecular networks. In 2008, I moved to Faro,Portugal, to establish my own independent lab in the field of systems biology (SysBioLab, http://www.sysbiolab.eu) at the University of Algarve, where we combine experimental and computational methods to elucidate complex processes in living organisms ranging from gene regulation in cyanobacteria to differentiation of stem cells. I expended these lines of investigations in my position as Professor in Bioinformatics at the Plymouth University and collaborated with other local researchers in the fields of cancer and clinical neurosciences at the Institute of Translational and Stratified Medicine. Currently, I am working for the UK Health Security Agency (UKHSA) on the analysis of national wide Covid testing data.




Professional membership

  • · Member of the International Society of Computational Biology (ISCB)


Roles on external bodies

  • Biostatistican, UK Health Security Agency, London
  • Visiting professor at the University of Algarve
  • Honorary senior researcher at the Centre of Marine Science, University of Algarve, Faro, Portugal (webpage
  • Acting head of the SysBioLab at the University of Algarve, Portugal

Key publications

Eyre DW, Futschik M, Tunkel S, Wei J, Cole-Hamilton J, Saquib R, Germanacos N, Dodgson AR, Klapper PE & Sudhanva M (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 23, (8) 922-932 , DOI
Francis CM, Futschik ME, Huang J, Bai W, Sargurupremraj M, Teumer A, Breteler MMB, Petretto E, Ho ASR & Amouyel P (2022) 'Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities' Nature Communications 13, (1) , DOI
Dunn J, Lenis VP, Hilton DA, Warta R, Herold-Mende C, Hanemann CO & Futschik ME (2020) 'Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma' Cancers 12, (11) 3270-3270 , DOI Open access
Pinto JP, Machado RSR, Magno R, Oliveira DV, Machado S, Andrade RP, Bragança J, Duarte I & Futschik ME (2017) 'StemMapper: a curated gene expression database for stem cell lineage analysis' Nucleic Acids Research 46, (D1) D788-D793 , DOI Open access
Hernández-Prieto MA, Semeniuk TA, Giner-Lamia J & Futschik ME (2016) 'The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803' Scientific Reports 6, (1) , DOI Open access
Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RSR, Machado S, Pacheco-Leyva I, Duarte I & Futschik ME (2015) 'StemChecker: a web-based tool to discover and explore stemness signatures in gene sets' Nucleic Acids Research 43, (W1) W72-W77 , DOI Open access
View all publications
Teaching

Teaching

Teaching interests

My teaching interests comprise different areas of bioinformatics and systems biology and include genomics, transcriptomics, and network biology. I also give introductory courses in applied bioinformatics and statistics using R/Bioconductor.

I contributed to following modules at University of Plymouth:

  • BHCS1001 Biomedical Investigation and Experimentation
  • BHCS3001 Personal Research Project
  • BHCS3008 Current Developments in Biomedicial Sciences
  • BIOM5006 Research Project

Staff serving as external examiners

Research

Research

Research interests

My area of research comprises bioinformatics and systems biology with the aim to connect molecular mechanisms with their phenotypic manifestations in living organisms. I am interested in a wide range of biological processes ranging from gene regulation in bacteria to the determination of cell fate in organ development. To facilitate gaining knowledge from biological data, I have also led the development of databases and software tools, that are publicly available. Recent topics of my research include:

MOLECULAR NETWORKS IN HUMAN HEALTH AND DISEASE

Most functions within cells are carried out not by single molecules, but result from the collaborative interaction of numerous molecules such as proteins, nucleic acids or metabolites, which form miraculously complex networks. Understanding the functions of a molecular single component, thus, requires the knowledge of its various interactions to components in the organism and its environment. To set the groundwork for holistic studies of physiological and pathological processes in human, we have integrated various molecular interaction maps and established several publicly accessible resources for network-oriented investigations. In cooperation with other research groups, we utilize these resources, for instance, to detect changes of network structures during disease development and to identify novel molecular targets for therapies.

SYSTEMS BIOLOGY OF STEM CELLS 

Stem cells hold a great potential for medicine. They could provide a source for tissue and organ regeneration. For safe clinical application, however, we need fully understand how stem cells maintain the identity and which factors controls their differentiation towards other cell types. To achieve this, we have collected and integrated numerous molecular interaction data for stem cells in StemCellNet - a web-server for network-oriented investigations in stem cell biology. Additionally,we curated a large number of genetic signatures for stemness - the defining characteristic of stem cells - and included them in our StemChecker web-tool. Using these resources, we seek to reveal the complex mechanisms underlying stem cell maintenance differentiation using a systems biology approach to address the question how a pluripotent cell determines its specific fate based on its internal state and external cues.


Other research

GENE REGULATION IN CYANOBACTERIA

As cyanobacteria have the distinct capability to utilize solar energy as power supply for their metabolic processes, they emerged as ideal cellular production systems, combining plant-like photosynthesis with fast growth, small genome size and ease in genetic modification. To efficiently utilize and modify cyanobacteria in green biotechnology, a detailed knowledge of their gene regulatory networks is necessary. At present, however, such knowledge exists only in rudimentary form. To derive and validate detailed models of gene regulatory networks in cyanobacteria, we are combining experimental and computational approaches including transcriptome profiling and in silico reverse engineering. As basis for modelling the regulation of processes on systems-level, we have developed the CyanoEXpress database comprising the largest integrated gene expression dataset for the model cyanobacterium Synechocystis to date.

Grants & contracts

  •  ERAB (Collaborator): The role of the circulating microbiome in determining outcome in patients with alcohol related liver disease. (PI: Ashwin Dhanda, UoP) 2019
  • ARUK South West Network (Collaborator): Detection of low-allele frequency mosaic mutations.(PI: Elaine Green, UoP) 2018-2019

Publications

Publications

Key publications

Eyre DW, Futschik M, Tunkel S, Wei J, Cole-Hamilton J, Saquib R, Germanacos N, Dodgson AR, Klapper PE & Sudhanva M (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 23, (8) 922-932 , DOI
Francis CM, Futschik ME, Huang J, Bai W, Sargurupremraj M, Teumer A, Breteler MMB, Petretto E, Ho ASR & Amouyel P (2022) 'Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities' Nature Communications 13, (1) , DOI
Dunn J, Lenis VP, Hilton DA, Warta R, Herold-Mende C, Hanemann CO & Futschik ME (2020) 'Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma' Cancers 12, (11) 3270-3270 , DOI Open access
Pinto JP, Machado RSR, Magno R, Oliveira DV, Machado S, Andrade RP, Bragança J, Duarte I & Futschik ME (2017) 'StemMapper: a curated gene expression database for stem cell lineage analysis' Nucleic Acids Research 46, (D1) D788-D793 , DOI Open access
Hernández-Prieto MA, Semeniuk TA, Giner-Lamia J & Futschik ME (2016) 'The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803' Scientific Reports 6, (1) , DOI Open access
Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RSR, Machado S, Pacheco-Leyva I, Duarte I & Futschik ME (2015) 'StemChecker: a web-based tool to discover and explore stemness signatures in gene sets' Nucleic Acids Research 43, (W1) W72-W77 , DOI Open access

Key publications are highlighted

Journals
Articles
Diaz LR, Gil-Ranedo J, Jaworek KJ, Nsek N, Marques JP, Costa E, Hilton DA, Bieluczyk H, Warrington O & Hanemann CO (2024) 'Ribogenesis boosts controlled by HEATR1-MYC interplay promote transition into brain tumour growth' EMBO Reports , DOI Open access
Nonnenmacher T, Dandamudi N, Futschik ME, Tunkel SA, Kulasegaran-Shylini R, Germanacos N, Cole-Hamilton J, Blandford E, Goddard A & Hillier J (2023) 'PCR testing of traced contacts for SARS-CoV-2 in England, January to July 2021' Eurosurveillance 28, (44) , DOI
Reeve L, Tessier E, Trindall A, Abdul Aziz NIB, Andrews N, Futschik M, Rayner J, Didier’Serre A, Hams R & Groves N (2023) 'High attack rate in a large care home outbreak of SARS-CoV-2 BA.2.86, East of England, August 2023' Eurosurveillance 28, (39) , DOI
Fagg J, Beale R, Futschik ME, Turek E, Chapman D, Halstead S, Jones M, Cole-Hamilton J, Gunson R & Sudhanva M (2023) 'Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing' Journal of Clinical Virology 167, 105574-105574 , DOI
Kay O, Futschik ME, Turek E, Chapman D, Carr S, Sudhanva M, Klapper PE, Cox T, Hill M & Cole-Hamilton J (2023) 'Performance of self-collected saliva samples for SARS-CoV-2 mass testing in community settings' Journal of Clinical Virology Plus 3, (3) 100161-100161 , DOI
Eyre DW, Futschik M, Tunkel S, Wei J, Cole-Hamilton J, Saquib R, Germanacos N, Dodgson AR, Klapper PE & Sudhanva M (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 23, (8) 922-932 , DOI
Djeghloul D, Dimond A, Cheriyamkunnel S, Kramer H, Patel B, Brown K, Montoya A, Whilding C, Wang Y-F & Futschik ME (2023) 'Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis' Nature Structural & Molecular Biology 30, (4) 489-501 , DOI
Barata T, Duarte I & Futschik ME (2023) 'Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes' Genes 14, (3) 745-745 , DOI
Bonet F, Añez SB, Inácio JM, Futschik ME & Belo JA (2022) 'CCBE1 Is Essential for Epicardial Function during Myocardium Development' International Journal of Molecular Sciences 23, (20) 12642-12642 , DOI
Francis CM, Futschik ME, Huang J, Bai W, Sargurupremraj M, Teumer A, Breteler MMB, Petretto E, Ho ASR & Amouyel P (2022) 'Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities' Nature Communications 13, (1) , DOI
Wallach T, Mossmann ZJ, Szczepek M, Wetzel M, Machado R, Raden M, Miladi M, Kleinau G, Krüger C & Dembny P (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 16, (1) , DOI
Kuiper M, Bonello J, Fernández-Breis JT, Bucher P, Futschik ME, Gaudet P, Kulakovskiy IV, Licata L, Logie C & Lovering RC (2021) 'The gene regulation knowledge commons: the action area of GREEKC' Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1865, (1) 194768-194768 , DOI
Riediger M, Hernández-Prieto MA, Song K, Hess WR & Futschik ME (2021) 'Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria <i>Synechocystis</i> sp. PCC 6803 and PCC 6714' DNA Research 28, (6) , DOI
Machado R, Sachinidis A & Futschik ME (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) 2477-2477 , DOI
Inácio JM, von Gilsa Lopes J, Silva AM, Cristo F, Marques S, Futschik ME & Belo JA (2021) 'DAND5 Inactivation Enhances Cardiac Differentiation in Mouse Embryonic Stem Cells' Frontiers in Cell and Developmental Biology 9, , DOI
Dunn J, Lenis VP, Hilton DA, Warta R, Herold-Mende C, Hanemann CO & Futschik ME (2020) 'Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma' Cancers 12, (11) 3270-3270 , DOI Open access
Krynická V, Georg J, Jackson PJ, Dickman MJ, Hunter CN, Futschik ME, Hess WR & Komenda J (2019) 'Depletion of the FtsH1/3 Proteolytic Complex Suppresses the Nutrient Stress Response in the Cyanobacterium <i>Synechocystis</i> sp strain PCC 6803' The Plant Cell 31, (12) 2912-2928 , DOI
Santos JMA, Mendes-Silva L, Afonso V, Martins G, Machado RSR, Lopes JA, Cancela L, Futschik ME, Sachinidis A & Gavaia P (2019) 'Exogenous WNT5A and WNT11 proteins rescue CITED2 dysfunction in mouse embryonic stem cells and zebrafish morphants' Cell Death &amp; Disease 10, (8) , DOI
Dunn J, Ferluga S, Sharma V, Futschik M, Hilton DA, Adams CL, Lasonder E & Hanemann CO (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 Author Site , DOI Open access
Ghezzo MN, Fernandes MT, Pacheco-Leyva I, Rodrigues PM, Machado RS, Araujo MAS, Kalathur RK, Futschik ME, Alves N & dos Santos NR (2018) 'FoxN1-dependent thymic epithelial cells promote T-cell leukemia development' Carcinogenesis 39, (12) 1463-1476 , DOI Open access
Sabour D, Machado RSR, Pinto JP, Rohani S, Sahito RGA, Hescheler J, Futschik ME & 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 , DOI Open access
Giner-Lamia J, Hernández-Prieto M & E. Futschik M (2018) 'ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803' Bio-protocol 8, (12) , DOI Open access
Ho P-W, Klein M, Futschik M & Nevoigt E (2018) 'Glycerol positive promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae' FEMS Yeast Research Author Site , DOI Open access
Ghezzo MN, Fernandes MT, Machado RS, Pacheco-Leyva I, Araújo MAS, Kalathur RK, Futschik ME, Alves NL & dos Santos NR (2018) 'FoxN1-dependent thymic epithelial cells promote T-cell leukemia development' , DOI
Giner-Lamia J, Robles-Rengel R, Hernández-Prieto MA, Muro-Pastor MI, Florencio FJ & Futschik ME (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 , DOI Open access
Pinto JP, Machado RSR, Magno R, Oliveira DV, Machado S, Andrade RP, Bragança J, Duarte I & Futschik ME (2017) 'StemMapper: a curated gene expression database for stem cell lineage analysis' Nucleic Acids Research 46, (D1) D788-D793 , DOI Open access
Kalathur RKR, Pedro Pinto J, Sahoo B, Chaurasia G & Futschik ME (2017) 'HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington’s Disease' Scientific Reports 7, (1) , DOI Open access
Georg J, Kostova G, Vuorijoki L, Schön V, Kadowaki T, Huokko T, Baumgartner D, Müller M, Klähn S & Allahverdiyeva Y (2017) 'Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1' Current Biology , DOI Open access
Macedo JA, Schrama D, Duarte I, Tavares E, Renaut J, Futschik ME, Rodrigues PM & Melo EP (2017) 'Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells' BMC Genomics 18, (1) , DOI Open access
Giner-Lamia J, Pereira SB, Bovea-Marco M, Futschik ME, Tamagnini P & Oliveira P (2016) 'Extracellular Proteins: Novel Key Components of Metal Resistance in Cyanobacteria?' Frontiers in Microbiology 7, , DOI Open access
Hernández-Prieto MA, Semeniuk TA, Giner-Lamia J & Futschik ME (2016) 'The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803' Scientific Reports 6, (1) , DOI Open access
Bal G, Futschik ME, Hartl D, Ringel F, Kamhieh-Milz J, Sterzer V, Hoheisel JD, Alhamdani MSS & Salama A (2015) 'Identification of novel biomarkers in chronic immune thrombocytopenia (<scp>ITP</scp>) by microarray‐based serum protein profiling' British Journal of Haematology 172, (4) 602-615 , DOI
Doron S, Fedida A, Hernández-Prieto MA, Sabehi G, Karunker I, Stazic D, Feingersch R, Steglich C, Futschik M & Lindell D (2015) 'Transcriptome dynamics of a broad host-range cyanophage and its hosts' The ISME Journal 10, (6) 1437-1455 , DOI
Pells S, Koutsouraki E, Morfopoulou S, Valencia-Cadavid S, Tomlinson SR, Kalathur R, Futschik ME & De Sousa PA (2015) 'Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State' PLOS ONE 10, (7) e0131102-e0131102 , DOI Open access
Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RSR, Machado S, Pacheco-Leyva I, Duarte I & Futschik ME (2015) 'StemChecker: a web-based tool to discover and explore stemness signatures in gene sets' Nucleic Acids Research 43, (W1) W72-W77 , DOI Open access
Kalathur RKR, Giner-Lamia J, Machado S, Barata T, Ayasolla KRS & Futschik ME (2015) 'The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach' F1000Research 4, 103-103 , DOI Open access
Stroedicke M, Bounab Y, Strempel N, Klockmeier K, Yigit S, Friedrich RP, Chaurasia G, Li S, Hesse F & Riechers S-P (2015) 'Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity' Genome Research 25, (5) 701-713 , DOI
Hill R, Kalathur RKR, Colaço L, Brandão R, Ugurel S, Futschik M & Link W (2015) 'TRIB2 as a biomarker for diagnosis and progression of melanoma' Carcinogenesis 36, (4) 469-477 , DOI
Hill R, Kalathur RKR, Callejas S, Colaço L, Brandão R, Serelde B, Cebriá A, Blanco-Aparicio C, Pastor J & Futschik M (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) , DOI Open access
Hernández-Prieto MA, Semeniuk TA & Futschik ME (2014) 'Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria' Frontiers in Genetics 5, , DOI Open access
Pinto JP, Machado RSR, Xavier JM & Futschik ME (2014) 'Targeting molecular networks for drug research' Frontiers in Genetics 5, , DOI Open access
Pinto JP, Reddy Kalathur RK, Machado RSR, Xavier JM, Bragança J & Futschik ME (2014) 'StemCellNet: an interactive platform for network-oriented investigations in stem cell biology' Nucleic Acids Research 42, (W1) W154-W160 , DOI Open access
Kamhieh-Milz J, Moftah RFH, Bal G, Futschik M, Sterzer V, Khorramshahi O, Burow M, Thiel G, Stuke-Sontheimer A & Chaoui R (2014) 'Differentially Expressed MicroRNAs in Maternal Plasma for the Noninvasive Prenatal Diagnosis of Down Syndrome (Trisomy 21)' BioMed Research International 2014, 1-9 , DOI Open access
Kalathur RKR, Pinto JP, Hernández-Prieto MA, Machado RSR, Almeida D, Chaurasia G & Futschik ME (2013) 'UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks' Nucleic Acids Research 42, (D1) D408-D414 , DOI Open access
Wallach T, Schellenberg K, Maier B, Kalathur RKR, Porras P, Wanker EE, Futschik ME & Kramer A (2013) 'Dynamic Circadian Protein–Protein Interaction Networks Predict Temporal Organization of Cellular Functions' PLoS Genetics 9, (3) e1003398-e1003398 , DOI Open access
Hernández-Prieto MA, Schön V, Georg J, Barreira L, Varela J, Hess WR & Futschik ME (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 , DOI Open access
Hernández-Prieto MA, Schön V, Georg J, Barreira L, Varela J, Hess WR & Futschik ME (2012) 'Iron deprivation in Synechocystis: inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profiling' G3 (Bethesda, Md.) 2, (12) 1475-1495
Hernandez-Prieto MA (2012) 'CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803' Bioinformation 8, (13) 634-638 , DOI Open access
Kalathur RKR, Hernández-Prieto MA & Futschik ME (2012) 'Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database' BMC Neurology 12, (1) , DOI Open access
Chaurasia G & Futschik M (2011) 'The Integration and Annotation of the Human Interactome in the UniHI Database' 175-188 , DOI
Duong CT, 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 , DOI
Bal G, Kamhieh-Milz J, Futschik M, Häupl T, Salama A & Moldenhauer A (2011) 'Transcriptional Profiling of the Hematopoietic Support of Interleukin-Stimulated Human Umbilical Vein Endothelial Cells (HUVECs)' Cell Transplantation 21, (1) 251-267 , DOI
Moldenhauer A, Futschik M, Lu H, Helmig M, Götze P, Bal G, Zenke M, Han W & Salama A (2011) 'Interleukin 32 promotes hematopoietic progenitor expansion and attenuates bone marrow cytotoxicity' European Journal of Immunology 41, (6) 1774-1786 , DOI
Marras E, Travaglione A, Chaurasia G, Futschik M & Capobianco E (2010) 'Inferring modules from human protein interactome classes' BMC Systems Biology 4, (1) , DOI Open access
Russ J & Futschik ME (2010) 'Comparison and consolidation of microarray data sets of human tissue expression' BMC Genomics 11, (1) 305-305 , DOI Open access
Steglich C, Lindell D, Futschik M, Rector T, Steen R & Chisholm SW (2010) 'Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus' Genome Biology 11, (5) R54-R54 , DOI Open access
Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, Wright MA, Rector T, Steen R & McNulty N (2009) 'Choreography of the Transcriptome, Photophysiology, and Cell Cycle of a Minimal Photoautotroph, Prochlorococcus' PLoS ONE 4, (4) e5135-e5135 , DOI Open access
Gsponer J, Futschik ME, Teichmann SA & Babu MM (2008) 'Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation' Science 322, (5906) 1365-1368 , DOI
Chaurasia G, Malhotra S, Russ J, Schnoegl S, Hänig C, Wanker EE & Futschik ME (2008) 'UniHI 4: new tools for query, analysis and visualization of the human protein–protein interactome' Nucleic Acids Research 37, (suppl_1) D657-D660 , DOI Open access
Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW & Hess WR (2008) 'Correction: The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus' PLoS Genetics 4, (11) , DOI
Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW & Hess WR (2008) 'The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus' PLoS Genetics 4, (8) e1000173-e1000173 , DOI Open access
Futschik ME & 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 , DOI
FUTSCHIK ME, TSCHAUT A, CHAURASIA G & HERZEL H (2007) 'GRAPH-THEORETICAL COMPARISON REVEALS STRUCTURAL DIVERGENCE OF HUMAN PROTEIN INTERACTION NETWORKS' Genome Informatics 2007 , DOI
Futschik ME, Chaurasia G, Tschaut A, Russ J, Babu MM & Herzel H (2007) 'Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network' Journal of Integrative Bioinformatics 4, (3) 198-207 , DOI
Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R & Hess WR (2007) 'Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution' Nature 449, (7158) 83-86 , DOI
Futschik ME, Chaurasia G & Herzel H (2007) 'Comparison of human protein–protein interaction maps' Bioinformatics 23, (5) 605-611 , DOI
Chaurasia G, Iqbal Y, Hänig C, Herzel H, Wanker EE & Futschik ME (2006) 'UniHI: an entry gate to the human protein interactome' Nucleic Acids Research 35, (suppl_1) D590-D594 , DOI Open access
Steglich C, Futschik M, Rector T, Steen R & Chisholm SW (2006) 'Genome-Wide Analysis of Light Sensing in<i>Prochlorococcus</i>' Journal of Bacteriology 188, (22) 7796-7806 , DOI
Kumar L, Futschik M & Herzel H (2006) 'DNA motifs and sequence periodicities' In Silico Biol 6, (1-2) 71-78 Author Site
Chaurasia G, Herzel H, Wanker EE & Futschik ME (2006) 'Systematic functional assessment of human protein-protein interaction maps' Genome Inform 17, (1) 36-45 Author Site
FUTSCHIK ME & CARLISLE B (2005) 'NOISE-ROBUST SOFT CLUSTERING OF GENE EXPRESSION TIME-COURSE DATA' Journal of Bioinformatics and Computational Biology 03, (04) 965-988 , DOI
Futschik ME & Crompton T (2004) 'OLIN: optimized normalization, visualization and quality testing of two-channel microarray data' Bioinformatics 21, (8) 1724-1726 , DOI
Futschik M & Crompton T (2004) 'Model selection and efficiency testing for normalization of cDNA microarray' Genome Biology 5, (8) R60-R60 , DOI Open access
Futschik ME, 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 , DOI
Futschik ME, Sullivan M, Reeve A & Kasabov N (2003) 'Prediction of clinical behaviour and treatment for cancers' Appl Bioinformatics 2, (3 Suppl) S53-S58 Author Site
Humar B, Graziano F, Cascinu S, Catalano V, Ruzzo AM, Magnani M, Toro T, Burchill T, Futschik ME & Merriman T (2002) 'Association of CDH1 haplotypes with susceptibility to sporadic diffuse gastric cancer' Oncogene 21, (53) 8192-8195 , DOI
Futschik M, Jeffs A, Pattison S, Kasabov N, Sullivan M, Merrie A & Reeve A (2002) 'Gene Expression Profiling of Metastatic and Nonmetastatic Colorectal Cancer Cell Lines' Genome Letters 1, (1) 26-34 , DOI
Chapters
Futschik ME, Morkel M, Schäfer R & Sers C (2020) 'Chapter 7 The human transcriptome: implications for understanding, diagnosing, and treating human disease' Essential Concepts in Molecular Pathology Elsevier 113-138 , DOI
Futschik ME, Morkel M, Schäfer R & Sers C (2020) 'The human transcriptome: implications for understanding, diagnosing, and treating human disease' Essential Concepts in Molecular Pathology Elsevier 113-138 , DOI
Futschik ME, Morkel M, Schäfer R & Sers C (2018) 'Chapter 7 The Human Transcriptome Implications for Understanding, Diagnosing, and Treating Human Disease' Molecular Pathology Elsevier 135-164 , DOI
Futschik ME, Morkel M, Schäfer R & Sers C (2018) 'The Human Transcriptome' Molecular Pathology Elsevier 135-164 , DOI
Futschik ME, Morkel M, Schäfer R & Sers C (2017) 'The Human Transcriptome: Implications for the Understanding, Diagnosing and Treating of Human Diseas' in Coleman W Molecular Pathology The Molecular Basis of Human Disease Academic Press 136-164 Publisher Site
Hernandez-Prieto MA, Kalathur RKR & Futschik ME (2014) 'Molecular Networks – Representation and Analysis' Springer Handbook of Bio-/Neuroinformatics Springer Berlin Heidelberg 399-418 , DOI
Allen MJ, Tiwari B, Futschik ME & Lindell D (2010) 'Construction of microarrays and their application to virus analysis' Manual of Aquatic Viral Ecology American Society of Limnology and Oceanography 34-56 , DOI
Chaurasia G & Futschik ME (2009) 'Interactomics and Cancer' An Omics Perspective on Cancer Research Springer Netherlands 167-182 , DOI
Futschik ME, Kemmner W, Schäfer R & Sers C (2009) 'Chapter 7 The Human Transcriptome: Implications for the Understanding of Human Disease' Molecular Pathology Elsevier 123-149 , DOI
Futschik ME, Kemmner W, Schäfer R & Sers C (2009) 'The Human Transcriptome: Implications for the Understanding of Human Disease' Molecular Pathology Elsevier 123-149 , DOI
Conference Papers
Futschik M (2012) 'B02 Huntington's disease and its therapeutic target genes: a global functional profile based on the HD research crossroads database' BMJ A6.1-A6 , DOI
Ayasolla KR, Kalathur RK & Futschik ME (2010) 'A16 Endoplasmic reticulum stress: an initiator of neuroinflammation in Huntington's disease?' BMJ A5.3-A5 , DOI
Kalathur RK & Futschik ME (2010) 'A31 Network based analyses of Huntington's disease' BMJ A10.2-A10 , DOI
Ayasolla KR, Kalathur RK & Futschik ME (2010) 'A32 A systems biology approach towards deciphering the unfolded protein response in Huntington's disease' BMJ A10.3-A10 , DOI
Wallach T, Futschik M, Millan PP, Wendt S, Wanker EE & Kramer A (2009) 'A mammalian circadian interactome' 8-8
Futschik ME, Chaurasia G & Wanker E (2008) 'Disentangling molecular interaction networks for chorea Huntington' A1-A1
Futschik ME & Herzel H (2007) 'Are we overestimating the number of cell-cycling genes? The impact of background models for time series data' 2-14
Chaurasia G, Herzel H & Futschik ME (2007) 'Comparison and integration of large-scale human protein-protein interaction maps' 300-300
Futschik ME, Chaurasia G, Wanker E & Herzel H (2006) 'Comparison of human protein-protein interaction maps' 21-32
Moldenhauer A, Selders L, Genter G, Hieronymus T, Ruau D, Lun A, Futschik M, Kiesewetter H, Zenke M & Salama A (2005) 'Cocultures of umbilical cord blood hematopoietic progenitor cells and umbilical cord endothelium' 131B-132B
Kasabov N, Middlemiss M & Futschik M (2001) 'Knowledge based neural networks for on-line and off-line modeling and rule extraction' 240-244
Futschik ME & Kasabov NK 'Fuzzy clustering of gene expression data' 2002 IEEE World Congress on Computational Intelligence. 2002 IEEE International Conference on Fuzzy Systems. FUZZ-IEEE'02 IEEE , DOI
Presentations and posters
Dunn J, Hanemann O, Ferluga S, Lasonder E, Sharma V, Hilton D, Adams C & Futschik M Dunn J, Hanemann O, Ferluga S, Lasonder E, Sharma V, Hilton D, Adams C & Futschik M 'PO-522 Global proteome and phosphoprotein profiling of meningiomas reveals novel potential therapeutic targets and biomarkers' , DOI
Hanemann CO, Dunn J, Ferluga S, Sharma V, Futschik M, Hilton D, Adams C & Lasonder E Hanemann CO, Dunn J, Ferluga S, Sharma V, Futschik M, Hilton D, Adams C & Lasonder E 'PROTEOMIC ANALYSIS OF MENINGIOMA DISCOVERS NEW PATHWAYS AND THEIR ACTIVATION INCLUDING NEK9 AND AKT' Author Site , DOI
Laraba L, Ferluga S, Ercolano E, Adams C, Shivane A, Edwards P, Futschik M, Lenis V, de Guibert JG & Moller S Laraba L, Ferluga S, Ercolano E, Adams C, Shivane A, Edwards P, Futschik M, Lenis V, de Guibert JG & Moller S 'The cancer stem cell marker ALDH1A1 is upregulated and drives proliferation in merlin null meningioma and schwannoma' Author Site , DOI
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Additional information

Links

Some R/Bioconductor packages that I have developed:
  • OLIN webpage: Bioconductor package for optimised normalisation of microarray data and detection of hybridisation artefacts
  • Mfuzz webpage: Bioconductor package for clustering and visualisation of time series gene expression data
  • Cycle webpage: Bioconductor package for detection of periodically expressed genes in time series expression data