REFERENCES
Qlucore Omics Explorer has been used in:
C B Lajer, E Garnæs, L Friis-Hansen, B Norrild, M H Therkildsen, M Glud, M Rossing, H Lajer, D Svane, L Skotte, L Specht, C Buchwald and F C NielsenThe role of miRNAs in human papilloma virus (HPV)-associated cancers: bridging between HPV-related head and neck cancer and cervical cancer British Journal of Cancer 106, 2012
Felix Haglund, Ming Lu, Vladana Vukojevic, Inga-Lena Nilsson, Adam Andreasson, Mensur Džabic, Robert Bränström, Anders Höög, C. Christofer Juhlin, Catharina LarssonProlactin Receptor in Primary Hyperparathyroidism – Expression, Functionality and Clinical Correlations PLosONE, 2012
Harald Osmundsen, Anne-Marthe Jevnaker and Maria A. Landin Deoxyoligonucleotide Microarrays for Gene Expression Profiling in Murine Tooth Germs Odontogenesis, 2012
DR de la Bletiere, O Blanchet, P Cornillet-Lefebvre… Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples BMC Medical Genomics, 2012
G Macchia, D Trombetta, E Möller, F Mertens...FOSL1 as a candidate target gene for 11q12 rearrangements in desmoplastic fibroblastoma Laboratory Investigation, 2012
Pascale May-Panloup, Véronique Ferré-L'Hôtellier, Catherine Morinière, Charles Marcaillou, Sophie Lemerle, Marie-Claire Malinge, Anne Coutolleau,Nicolas Lucas3,Pascal Reynier, Philippe Descamps, Philippe Guardiola ;Molecular characterization of corona radiata cells from patients with diminished ovarian reserve using microarray and microfluidic-based gene expression profiling Human Reproduction, 2012
Ákos Végvária, Melinda Rezeli,Carina Sihlbom, Jari Häkkinen, Elisabet Carlsohn, Johan Malm, Hans Lilja, Thomas Laurell,György Marko-Varga ;Molecular microheterogeneity of prostate specific antigen in seminal fluid by mass spectrometry Clinical Biochemistry, 2011
Jimsgene Sanjmyatav, Thomas Steiner, Heiko Wunderlich, Julia Diegmann, Mieczyslaw Gajda, Kerstin Junker;A Specific Gene Expression Signature Characterizes Metastatic Potential in Clear Cell Renal Cell Carcinoma The Journal of Urology
D Sehic, J Karlsson, B Sandstedt…SIX1 protein expression selectively identifies blastemal elements in Wilms tumor Pediatric Blood & Cancer, 2011
Damien Reynaud1, Eric Pietras, Keegan Barry-Holson, Alain Mir, Mikhail Binnewies, Marion Jeanne, Olga Sala-Torra, Jerald P. Radich, Emmanuelle Passegué IL-6 Controls Leukemic Multipotent Progenitor Cell Fate and Contributes to Chronic Myelogenous Leukemia Development Cancer cell vol 20 Issue 5
Debra Rossouw, Dan Jacobson and Florian F. Bauer Transcriptional Regulation and the Diversification of Metabolism in Wine Yeast Strains Genetics
Killian JK, Bilke S, Davis S, Walker RL, Jaeger E, Killian MS, Waterfall JJ, Bibikova M, Fan JB, Smith WI Jr, Meltzer PS A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology Am J Pathol 2011
D Rossouw, N Jolly, D Jacobson...The effect of scale on gene expression: commercial versus laboratory wine fermentations. Applied Microbiology and Biotechnology
Naiara G Bediaga, Amelia Acha-Sagredo, Isabel Guerra, Amparo Viguri, Carmen Albaina, Irune Ruiz Diaz, Ricardo Rezola, ...DNA methylation epigenotypes in breast cancer molecular subtypes Breast Cancer Research 2010
Thibaut Lery, Mario Primicerio, Maria J. Esteban, Magnus Fontes, Yvon Maday, Volker Mehrmann, Goncalo Quadros, Wil Schilders, Andreas Schuppert and Heather Tewkesbury Health & BiologyEuropean Success Stories in Industrial Mathematics
L Kleynhans, N Du Plessis, GF Black, AG Loxton...Medroxyprogesterone Acetate Alters Mycobacterium Bovis BCG-Induced Cytokine Production in Peripheral Blood Mononuclear Cells of Contraceptive Users. PLoSone
Jessica Carlsson, Sabina Davidsson, Gisela Helenius, Mats Karlsson, Zelmina Lubovac, Ove Andrén, Björn Olsson and Karin Klinga-Levan A miRNA expression signature that separates between normal and malignant prostate tissues Cancer Cell International 2011
Frida Abel, Daniel Dalevi, Maria Nethander, Rebecka Jörnsten, Katleen De Preter, Joëlle Vermeulen, Raymond Stallings, Per Kogner, John Maris and Staffan Nilsson A 6-gene signature identifies four molecular subgroups of neuroblastoma Cancer Cell International 2011
H Johansson, M Lindstedt, AS Albrekt... A genomic biomarker signature can predict skin sensitizers using a cell-based in vitro alternative to animal tests. BMC Genomics, 2011
L Fagerberg, S Stromberg, A Elobeid, M Gry... Large-scale Protein Profiling in Human Cell Lines Using Antibody-based Proteomics. Journal of Proteome Research 2011
R Jimbo, J Fernandez-Rodriguez, YT Sul... Principal Component Analysis: A Novel Analysis to Evaluate the Characteristics of Osseointegration of Different Implant Surfaces. Implant Dentistry, 2011
M Fontes, C Soneson. The projection score-an evaluation criterion for variable subset selection in PCA visualization. BMC Bioinformatics 2011
E Möller, JL Hornick, L Magnusson, S Veerla... FUS-CREB3L2/L1–Positive Sarcomas Show a Specific Gene Expression Profile with Upregulation of CD24 and FOXL1 - Clinical Cancer Research, 2011
G Styger, D Jacobson... Identifying genes that impact on aroma profiles produced by Saccharomyces cerevisiae and the production of higher alcohols.Applied Microbiology and Biotechnology
CB Johansson, C Gretzer, R Jimbo, I Mattisson... Enhanced implant integration with hierarchically structured implants: a pilot study in rabbits. Clinical Oral Implants Research 2011
Ole Ammerpohl, Johann Pratschke, Clemens Schafmayer, Andrea Haake, Wladimir Faber, Oliver von Kampen, Mario Brosch, Bence Sipos, Witigo von Schönfels, Katharina Balschun, Christoph Röcken, Alexander Arlt, Bodo Schniewind, Jonas Grauholm, Holger Kalthoff, Peter Neuhaus,,Felix Stickel,,Stefan Schreiber,,Thomas Becker,,Reiner Siebert, Jochen Hampe. Distinct DNA methylation patterns in cirrhotic liver and hepatocellular carcinoma. International Journal of Cancer 2011
Anders Carlsson, Dirk M. Wuttge, Johan Ingvarsson, Anders A. Bengtsson, Gunnar Sturfelt, Carl A. K. Borrebaeck and Christer Wingren. Serum protein profiling of systemic lupus erythematosus and systemic sclerosis using recombinant antibody microarrays.Molecular & Cellular Proteomics
Måns Jergil, Maud Forsberg, Hugh Salter, Kenneth Stockling, Anne-Lee Gustafson, Lennart Dencker and Michael Stigson. Short-Time Gene Expression Response to Valproic Acid and Valproic Acid Analogs in Mouse Embryonic Stem Cells. Toxicological Sciences 2011
S. Bensa, O. Ammerpohl, J.I. Martin-Suberoa, M. Apparib, J. Richtera, O. Hiortc, R. Wernerc, F.G. Riepeb, R. Sieberta, P.-M. Holterhusb. Androgen Receptor Mutations Are Associated with Altered Epigenomic Programming as Evidenced by HOXA5 Methylation.Sexual Development, online publication feb 2011
Joana Heinzelmann, Brenda Henning, Jimsgene Sanjmyatav, Nicole Posorski, Thomas Steiner, Heiko Wunderlich, Mieczyslaw R. Gajda and Kerstin Junker. Specific miRNA signatures are associated with metastasis and poor prognosis in clear cell renal cell carcinoma.World Journal of Urology DOI: 10.1007/s00345-010-0633-4
Linda Dexlin-Mellby, Anna Sandström, Magnus Centlow, Sara Nygren, Stefan R. Hansson, Carl A. K. Borrebaeck, Christer Wingren. Proteomic expression analysis and comparison of protein and mRNA expression profiles in human malignant gliomas. PROTEOMICS – Clinical Applications Volume 4, Issue 10-11, pages 794–807, November 2010
Järås M, Johnels P, Hansen N, Agerstam H, Tsapogas P, Rissler M, Lassen C,Olofsson T, Bjerrum OW, Richter J, Fioretos T. Isolation and killing of candidate chronic myeloid leukemia stem cells by antibody targeting of IL-1 receptor accessory protein. Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16280-5
Karl Björk, Anita C. Hansson and Wolfgang H. Sommer. Genetic Variation and Brain Gene Expression in Rodent Models of Alcoholism: Implications for medication development. International Review of Neurobiology, Volume 91, pages 129-171
Linda Holmquist Mengelbier, Jenny Karlsson, David Lindgren, Ingrid Öra, Margareth Isaksson, Ildiko Frigyesi, Attila Frigyesi, Johannes Bras||, Bengt Sandstedt, and David Gisselsson. Deletions of 16q in Wilms Tumors Localize to Blastemal-Anaplastic Cells and Are Associatedwith Reduced Expression of the IRXB Renal Tubulogenesis Gene Cluster. The American Journal of Pathology 2010;177:2609-2621
Ulrika Andréasson, Patrik Edén, Carsten Peterson, Carl-Magnus Högerkorp, Mats Jerkeman, Niels Andersen, Mattias Berglund, Christer Sundström, Richard Rosenquist, Carl A.K. Borrebaeck, Sara Ek. Identification of uniquely expressed transcription factors in highly purified B-cell lymphoma samples. American Journal of Hematology. Volume 85, Issue 6, pages 418–425, June 2010
Linda Dexlin-Mellby, Anna Sandström, Magnus Centlow, Sara Nygren, Stefan R. Hansson, Carl A. K. Borrebaeck, Christer Wingren, Tissue proteome profiling of preeclamptic placenta using recombinant antibody microarrays, PROTEOMICS – Clinical Applications
Magnus Fontes. Statistical and knowledge supported visualization of multivariate data. Submitted to Proceedings from the conference in honour of Gunnar Sparr, Lund , Sweden 8-9 May 2008. Available online here.
Anders Carlsson, Oscar Persson, Johan Ingvarsson, Bengt Widegren, Leif Salford, Carl A. K. Borrebaeck, Christer Wingren, Plasma proteome profiling reveals biomarker patterns associated with prognosis and therapy selection in glioblastoma multiforme patients, PROTEOMICS – Clinical Applications, Volume 4, Issue 6-7, pages 591–602, July 2010
Gisselsson D, Lindgren D, Mengelbier LH, Ora I, Yeger H. Genetic bottlenecks and the hazardous game of population reduction in cell line based research. Experimental cell research, In Press, Available online 17 July 2010
Julia Richter, Ole Ammerpohl, Jose I Martin-Subero, Manuel Montesinos-Rongen, Marina Bibikova, Eliza Wickham-Garcia, Otmar D Wiestler, Martina Deckert and Reiner Siebert. Array-based DNA methylation profiling of primary lymphomas of the central nervous system. BMC Cancer 2009, 9:455.
Rehannah Borup , Maria Rossing , Ricardo Henao, Yohei Yamamoto, Annelise Krogdahl, Christian Godballe, Ole Winther, Katalin Kiss, Lise Christensen, Estrid Høgdall, Finn Bennedbæk, Finn Cilius Nielsen, Molecular signatures of thyroid follicular neoplasia, Endocrine-Related Cancer 2010; 17: 691-708
Astrid Enkelmann, Joana Heinzelmann, Ferdinand von Eggeling, Martina Walter, Alexander Berndt, Heiko Wunderlich and Kerstin Junker, Specific protein and miRNA patterns characterise tumour-associated fibroblasts in bladder cancer, Journal of Cancer Research and Clinical Oncology DOI: 10.1007/s00432-010-0932-6
Malin Lindstedt, Inge Nelissen, Sue Gibbs, Carl Borrebaeck. 2010. Mimicking the immunoregulatory properties of primary dendritic cells in vitro - A rational approach to design a test system. Toxicology Reviews. In press.
Mark J Alston , John Seers , Jay CD Hinton and Sacha Lucchini. BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets. BMC Bioinformatics 2010, 11:73
Charlotte Soneson, Henrik Lilljebjörn, Thoas Fioretos, Magnus Fontes.
Multivariate analysis of the relationship between SNP copy number and gene expression in leukemia - Presented at Statistical advances in Genome-scale Data Analysis - Workshop ETH, Ascona 2009
Erik Alexandersson, Jonas Å.H. Danielson, Johan Råde, Vamsi K. Moparthi, Magnus Fontes, Per Kjellbom and Urban Johanson. Transcriptional regulation of aquaporins in accessions of Arabidopsis in response to drought stress, The Plant Journal 2009.
Davidsson Josef; Lilljebjorn Henrik; Andersson Anna; Veerla Srinivas; Heldrup Jesper; Behrendtz Mikael; Fioretos Thoas; Johansson Bertil. The DNA methylome of pediatric acute lymphoblastic leukemia. Human Molecular Genetics 2009
Möller, Emily. EWSR1 and FUS fusion genes in Tumorigenesis. Dissertation at department of Clinical Genetics, Lund Uinversity 2010.
Early versions of Gene Expression Explorer have been used in the following references:
Andersson A, Olofsson T, Lindgren D, Nilsson B, Ritz C, Edén P, Lassen C, Råde J, Fontes M, Mörse H, Heldrup J, Behrendtz M, Mitelman F, Höglund M, Johansson B, Fioretos T. 2005. Molecular signatures in childhood acute leukemia and their correlations to expression patterns in normal hematopoietic subpopulations. Proc Natl Acad Sci USA 102:19069-19074.
Andersson A, Ritz C, Lindgren D, Edén P, Lassen C, Heldrup J, Olofsson T, Råde J, Fontes M, Porwit-McDonald A, Behrendtz M, Höglund M, Johansson B, Fioretos T. 2007. Microarray-based classification of a consecutive series of 121 childhood acute leukemias: prediction of leukemic and genetic subtype as well as of minimal residual disease status. Leukemia 21:1198-1203.
Workshops and books
T Léry, M Primicerio, ... European Success Stories in Industrial Mathematics. Springer
Sylvestre Burgos, Manh Hong Duong, Laura Friis Frølich, Daniel Høyer Iversen, Bogna Pawlowska, Matthias Voigt, Mikalai Zhudro. How to enhance the exploratory power of Qlucore Omics Explorer?. The 23rd ECMI Modelling Week, European Student Workshop on Mathematical Modelling in Industry and Commerce Wroclaw University of Technology, Poland, August 23-30, 2009. Report.