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REFERENCES

Qlucore Omics Explorer references for different types of data:

See downloadable document with examples. For a full list see below. 

 

2017

Berkley E. Gryder, Marielle E. Yohe, Hsien-Chao Chou, Xiaohu Zhang, Joana Marques, Marco Wachtel, Beat Schaefer, Nirmalya Sen, Young Song, Alberto Gualtieri, Silvia Pomella, Rossella Rota, Abigail Cleveland, Xinyu Wen, Sivasish Sindiri, Jun S. Wei, Frederic G. Barr, Sudipto as, Thorkell Andresson, Rajarshi Guha, Madhu Lal-Nag, Marc Ferrer, Jack F. Shern, Keji Zhao, Craig J. Thomas, Javed Khan. PAX3-FOXO1 establishes myogenic super enhancers and confers BET bromodomain vulnerability. Cancer Discovery, 2017

 

Hao Hu, Michael E. Wisniewski, Ahmed Abdelfattah, Xiaodong Zheng. Biocontrol activity of a cold-adapted yeast from Tibet against gray mold in cherry tomato and its action mechanism. Extremophiles, 2017

 

Carolyn D. Kramer, Alexandra M. Simas, Xianbao He, Robin R. Ingalls, Ellen O. Weinberg, Caroline Attardo Genco. Distinct roles for dietary lipids and Porphyromonas gingivalis infection on atherosclerosis progression and the gut microbiotaAnaerobe, 2017

 

Selena Ferrian, Claudia Manca, Sugnet Lubbe, Francesca Conradie, Nazir Ismail, Gilla Kaplan, Clive M. Gray , Dorothy Fallows. A combination of baseline plasma immune markers can predict therapeutic response in multidrug resistant tuberculosis. PLOS One, 2017

 

Bohdan B. Khomtchouk , James R. Hennessy, Claes Wahlestedt. shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics. PLOS One, 2017

 

Sebastian Marwitz, Sofia Depner, Dmytro Dvornikov, Ruth Merkle, Magdalena Szczygiel, Karin Müller-Decker, Philippe Lucarelli, Marvin Wäsch, Heimo Mairbäurl, Klaus F. Rabe, Christian Kugler, Ekkehard Vollmer, Martin Reck, Swetlana Scheufele, Maren Kröger, Ole Ammerpohl, Reiner Siebert,
Torsten Goldmann, Ursula Klingmüller. Downregulation of the TGF-ß pseudoreceptor BAMBI in non-small cell lung cancer enhances TGF-ß signaling and invasionCancer Research, 2017 

 

C Unger, N Kramer, D Unterleuthner, M Scherzer, A Burian, A Rudisch, M Stadler, M Schlederer, D Lenhardt, A Riedl, S Walter, A Wernitznig, L Kenner, M Hengstschläger, J Schüler, W Sommergruber and H Dolznig. Stromal-derived IGF2 promotes colon cancer progression via paracrine and autocrine mechanisms. Oncogene, 2017

 

Rachel Waller, Emily F. Goodall, Marta Milo, Jonathan Cooper-Knock, Marc Da Costa, Esther Hobson, Mbombe Kazoka, Helen Wollff, Paul R. Heath, Pamela J. Shaw*, Janine Kirby. Serum miRNAs miR-206, 143-3p and 374b-5p as potential biomarkers for amyotrophic lateral sclerosis (ALS). Neurobiology of Aging, 2017 

 

KF Mose, M Burton, M Thomassen, F Andersen, T. A. Kruse, Q. Tan, L. Skov, M. A. Røpke, T. Litman,
O. Clemmensen, B. W. Kristensen, P. S. Friedmann, K. E. Andersen. The gene expression and immunohistochemical time-course of diphenylcyclopropenone induced contact allergy in healthy humans following repeated epicutaneous challenges. Experimental Dermatology, 2017

 

Vinko Palada. Molecular mechanisms of muscle pain associated with myotonic dystrophy type II. Dissertation, Freie University of Berlin, 2017

 

JD Rasinger, AK Lundebye, SJ Penglase, S Ellingsen. Methylmercury Induced Neurotoxicity and the Influence of Selenium in the Brains of Adult Zebrafish (Danio rerio). International Journal of Molecular Sciences, 2017. 

 

W Zhang, MM Morshed, K Noyan, A Russom. Quantitative humoral profiling of the HIV-1 proteome in elite controllers and patients with very long-term efficient antiretroviral therapy. Scientific Reports, 2017 

 

Melanie Spitzwieser, Elisabeth Entfellner, Bettina Werner, Walter Pulverer, Georg Pfeiler, Stefan Hacker and Margit Cichna-Mark. Hypermethylation of CDKN2A exon 2 in tumor, tumor-adjacent and tumor-distant tissues from breast cancer patients. BMC Cancer, 2017

 

Kathrin S. Zeller, Andy Forreryd,  Tim Lindberg, Robin Gradin, Aakash Chawade, Malin Lindstedt. The GARD platform for potency assessment of skin sensitizing chemicalsALTEX Online, 2017

 

Thoas Fioretos, Marcus Järås. Anti-IL1RAP Antibodies and Their Use for Treating HumanFPO, 2017

 

Maria Rossing, Christina Westmose Yde,  Astrid Sehested, Olga Østrup, David Scheie, Volodia Dangouloff-Ros, Birgit Geoerger, Gilles Vassal, Karsten Nysom. Genomic diagnostics leading to the identification of a TFG-ROS1 fusion in a child with possible atypical meningioma. Cancer Genetics, 2017

 

Isaac Engel, Grégory Seumois, Lukas Chavez, Daniela Samaniego-Castruita, Brandie White, Ashu Chawla, Dennis Mock, Pandurangan Vijayanand & Mitchell Kronenberg. Innate-like functions of natural killer T cell subsets result from highly divergent gene programs. Nature Immunology, 2017 

 

Martin Nue Møller, Svend Kirkeby, Jonas Vikeså, Finn Cilius Nielsen, Per Cayé-Thomasen. The human endolymphatic sac expresses natriuretic peptides. Laryngoscope, 2017

 

Megha Rajasekhar, Anton M. Olsson, Kathryn J.A. Steel, Mirella Georgouli, Ushan Ranasinghe, Christine Brender Read. Klaus S. Frederiksen, Leonie S. Taams. MicroRNA-155 contributes to enhanced resistance to apoptosis in monocytes from patients with rheumatoid arthritis. Journal of Autoimmunity, 2017

 

Afnan Ali Al Sultan. The effects of TAR DNA binding protein mutations on RNA processing associated with
Amyotrophic Lateral Sclerosis. Sheffield Institute for Translational Neuroscience University of Sheffield, 2016

 

James E. Scriven, Lisa M. Graham, Charlotte Schutz, Thomas J. Scriba, Katalin A. Wilkinson, Robert J. Wilkinson, David R. Boulware, Britta C. Urban, David G. Lalloo,  Graeme Meintjes. A glucuronoxylomannan-associated immune signature, characterized by monocyte deactivation and raised IL-10, is a predictor of death in cryptococcal meningitis. Journal of Infectious Diseases Advance Access, 2016 

 

Catherine C Bell, Volker M Lauschke, Sabine U Vorrink, Henrik Palmgren, Roger Duffin, Tommy B Andersson and Magnus Ingelman-Sundberg. Transcriptional, functional and mechanistic comparisons of stem cell-derived hepatocytes, HepaRG cells and 3D human hepatocyte spheroids as predictive in vitro systems for drug-induced liver injury. Drug Metabolism and Disposition, 2017

 

Paul J. Planet, Dane Parker,Taylor S. Cohen, Hannah Smith, Justinne D. Leon, Chanelle Ryan, Tobin J. Hammer,Noah Fierer, Emily I. Chen,Alice S. Prince. Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection. mBio, 2017

 

A Schridde, C C Bain,  J U Mayer, J Montgomery, E Pollet, , B Denecke, S W F Milling, S J Jenkins, M Dalod, S Henri, B Malissen, O Pabst and A Mcl Mowat. Tissue-specific differentiation of colonic macrophages requires TGFß receptor-mediated signaling. Mucosal Immunology, 2017

 

Sung Yun Jung, Jong Min Choi, Maxime W.C. Rousseaux, Anna Malovannaya, Jean J Kim, Joachim Kutzera, Yi Wang, Yin Huang, Weimin Zhu, Suman Maity, Huda Yahya Zoghbi and Jun Qin. An anatomically resolved mouse brain proteome reveals Parkinson disease-relevant pathways. Molecular and Cellular Proteomics, 2017

 

Sumadi Lukman Anwar, Ulrich Lehmann. DNA methylation and expression of Homeobox gene family as diagnostic and prognostic markers in human hepatocellular carcinoma. JOURNAL OF THE MEDICAL SCIENCES, 2017

 

Sumadi Lukman Anwar, Till Krech, Britta Hasemeier, Elisa Schipper, Nora Schweitzer, Arndt Vogel, Hans Kreipe, Reena Buurman, Britta Skawran, Ulrich Lehmann. hsa-mir-183 is frequently methylated and related to poor survival in human hepatocellular carcinoma. World Journal of Gastroenterology, 2017

 

Aminatou Kone, Antoine Dara, Amadou Niangaly, Indranil Sinha, David Brodin, Bakary Fofana, Souleymane Dama, Demba Dembele, Bakary Sidibe, Nouhoum Diallo, Mahamadou Thera, Issaka Sagara, Karin Wright, Anders Björkman, Jose Gil, Ogobara Doumbo, Abdoulaye Djimde. EFFECT OF ARTESUNATE MONOTHERAPY ON PLASMODIUM FALCIPARUM IN VIVO GENOMIC EXPRESSION. BMJ Global Health, 2017

 

Qinghua Cao, Fang Liu, Kaiyuan Ji, Ni Liu, Yuan He, Wenhui Zhang and Liantang Wang. MicroRNA-381 inhibits the metastasis of gastric cancer by targeting TMEM16A expression. Journal of Experimental & Clinical Cancer Research, 2017

 

Dania Zhivaki, Sébastien Lemoine, Annick Lim, Ahsen Morva, Pierre-Olivier Vidalain, Liliane Schandene, Nicoletta Casartelli, Marie-Anne Rameix-Welti, Pierre-Louis Hervé, Edith Dériaud, Benoit Beitz, Maryline Ripaux-Lefevre, Jordi Miatello, Brigitte Lemercier, Valerie Lorin, Delphyne Descamps, Jenna Fix, Jean-François Eléouët, Sabine Riffault, Olivier Schwartz, Fabrice Porcheray, Françoise Mascart, Hugo Mouquet, Xiaoming Zhang, Pierre Tissières, Richard Lo-Man. Respiratory Syncytial Virus Infects Regulatory B Cells in Human Neonates via Chemokine Receptor CX3CR1 and Promotes Lung Disease Severity. Immunity, 2017

 

K. Hoff, A. Kahlert, E. Audain, H. Milting, R. Siebert, H.-H. Kramer, O. Ammerpohl, M.-P. Hitz. Differential DNA-Methylation Pattern in Cardiac Tissue Samples from Patients with Congenital Heart Disease. The Thoracic and Cardiovascular Surgeon, 2017 

 

Souren Mkrtchian,  Kian Leong Lee, Jessica Kåhlin, Anette Ebberyd, Lorenz Poellinger, Malin Jonsson Fagerlund,  Lars I. Eriksson, Hypoxia regulates microRNA expression in the human carotid bodyExperimental Cell Research, 2017.

 

Robert F. Stanley, Richard T. Piszczatowski, Boris Bartholdy, Kelly Mitchell, Wendy M. McKimpson, Swathi Narayanagari, Dagmar Walter, Tihomira I. Todorova, Cassandra Hirsch, Hideki Makishima, Britta Will, Christine McMahon, Kira Gritsman, Jaroslaw P. Maciejewski, Richard N. Kitsis, Ulrich Steidl. A myeloid tumor suppressor role for NOL3JEM, The Journal of Experimental Medicine, 2017

 

R Mesnage, M Arno, GE Séralini, MN Antoniou. Transcriptome and metabolome analysis of liver and kidneys of rats chronically fed NK603 Roundup-tolerant genetically modified maize. Environmental Sciences Europe, 2017

 

Anna K. Wakeland, Francesca Soncin, Matteo Moretto-Zita, Ching-Wen Chang, Mariko Horii, Don Pizzo, Katharine K. Nelson, Louise C. Laurent, Mana M. Parast'Correspondence information about the author Mana M. Parast. Hypoxia Directs Human Extravillous Trophoblast Differentiation in a Hypoxia-Inducible Factor–Dependent Manner. The American Journal of Pathology, 2017

Marcin Golec, Matthias Wielscher, Marta Kinga Lemieszek, Klemens Vierlinger, Czeslawa Skórska, Sophia Huetter, Jolanta Sitkowska, Barbara Mackiewicz, Anna Góra-Florek, Rolf Ziesche, Hagai Yanai, Vadim E. Fraifeld, Janusz Milanowski,Jacek Dutkiewicz. Middle age enhances expression of innate immunity genes in a female mouse model of pulmonary fibrosis. Biogerontology, 2017

 

Høj Thomsen L. Fog-Tonnesen M, Nielsen Fink L. Norlin J, de Vinuesa A.G, Krarup Hansen T, de Heer E, ten Dijke P, Rosendahl A. Smad2 Phosphorylation in Diabetic Kidney Tubule Epithelial Cells Is Associated with Modulation of Several Transforming Growth Factor-ß Family Members. Nephron, 2017

 

K. Dale, J.D. Rasinger, K.L. Thorstensen, S. Penglase, S. Ellingsen. Vitamin E reduces endosulfan-induced toxic effects on morphology and behavior in early development of zebrafish (Danio rerio). Food and Chemical Toxicology, 2017

 

Cancan Peng Wenli Ma Wei Xia Wenling Zheng. Integrated analysis of differentially expressed genes and pathways in triple-negative breast cancer. Molecular Medicine Reports, 2017

 

Deborah A. Weighill, Daniel Jacobson. Network Metamodeling: Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network Topology. Advances in Biochemical Engineering/Biotechnology, 2017 

 

2016 

Igor Stzepourginski, Giulia Nigro, Jean-Marie Jacob, Sophie Dulauroy, Philippe J. Sansonetti, Gérard Eberl and Lucie Peduto. CD34+ mesenchymal cells are a major component of the intestinal stem cells niche at homeostasis and after injury. PNAS, 2016

 

Julia Hengst, Christine Susanne Falk,  Verena Schlaphoff, Katja Deterding, Michael Peter Manns, Markus Cornberg, Heiner Wedemeyer. Direct-Acting Antiviral–Induced Hepatitis C Virus Clearance Does Not Completely Restore the Altered Cytokine and Chemokine Milieu in Patients With Chronic Hepatitis CThe Journal of Infectious Diseases, 2016.

 

Henning Kempf, , Ruth Olmer, , Alexandra Haase, , Annika Franke, , Emiliano Bolesani, , Kristin Schwanke, , Diana Robles-Diaz, Michelle Coffee, Gudrun Göhring, Gerald Dräger, Oliver Pötz, Thomas Joos, Erik Martinez-Hackert, Axel Haverich, Falk F. R. Buettner, Ulrich Martin, Robert Zweigerdt. Bulk cell density and Wnt/TGFbeta signalling regulate mesendodermal patterning of human pluripotent stem cells. Nature Communications, 2016

 

Mariacarla Andreozzi,  Cristina Quintavalle, David Benz, Luca Quagliata, Matthias Matter, Diego Calabrese, Nadia Tosti, Christian Ruiz, Francesca Trapani, Luigi Tornillo, Alfredo Fusco, §, Markus H Heim, Charlotte KY Ng, Pierlorenzo Pallante, Luigi M Terracciano, Salvatore Piscuoglio. HMGA1 Expression in Human Hepatocellular Carcinoma Correlates with Poor Prognosis and Promotes Tumor Growth and Migration in in vitro Models. Neoplasia, 2016 

 

Anja Ziegler, Helen Everett, Eman Hamza, Mattia Garbani, Vinzenz Gerber, Eliane Marti and Falko Steinbach. Equine dendritic cells generated with horse serum have enhanced functionality in comparison to dendritic cells generated with fetal bovine serum. BMC Veterinary Research, 2016

 

Mr Luke Jennings, Dr. Helen Elizabeth Colley, Dr. Jane Ong, Dr. Foti Panagakos, Dr. James Masters, Dr. Harsh Trivedi, Dr. Craig Murdoch, and Dr. Simon Whawell. Development and characterisation of in vitro human oral mucosal equivalents derived from immortalised oral keratinocytes. Tissue Engineering Part C: Methods, 2016

 

Franck Limonier, Katleen Van Steendam, Geneviève Waeterloos, Koen Brusselmans, Myriam Sneyers, Dieter Deforce. An application of mass spectrometry for quality control of biologicals: highly sensitive profiling of plasma residuals in human plasma-derived immunoglobulin. Journal of Proteomics, 2016

 

Michael J. A. Williams, L. Vicky Phillips, Ivor F. Galvin, Richard W. Bunton, Gregory T. Jones. Integrated microRNA and messenger RNA analysis in aortic stenosis. Scientific Reports, 2016

 

Sadhvi Nithiananthan, Aileen Crawford, Johnathan Cooper Knock, Daniel W. Lambert,
Simon A. Whawell. Physiological Fluid Flow Moderates Fibroblast Responses to TGF-ß1. Journal of Cellular Biochemistry, 2016

 

Danielle Ahn,  Hernán Peñaloza, Zheng Wang, Matthew Wickersham, Dane Parker, Purvi Patel, Antonius Koller, Emily I. Chen, Susan M. Bueno, Anne-Catrin Uhlemann, and Alice Prince. Acquired resistance to innate immune clearance promotes Klebsiella pneumoniae ST258 pulmonary infection. JCI insight, 2016

 

Stephen J. Walker, Daniel P. Beavers, John Fortunato & Arthur Krigsman. A Putative Blood-Based Biomarker for Autism Spectrum Disorder-Associated Ileocolitis. Scientific Reports, 2016

 

Pål A. Olsvik, , Marc H.G. Berntssen, Liv Søfteland. In vitro toxicity of pirimiphos-methyl in Atlantic salmon hepatocytes. Toxicology in Vitro, 2016

 

Tiziano Donnarumma, George R. Young,  Julia Merkenschlager, Urszula Eksmond, Nadine Bongard, Stephen L. Nutt, Claude Boyer, Ulf Dittmer, Vu Thuy Khanh Le-Trilling, Mirko Trilling, Wibke Bayer, George Kassiotis. Opposing Development of Cytotoxic and Follicular Helper CD4 T Cells Controlled by the TCF-1-Bcl6 Nexus. Cell Reports, 2016

 

J. Keith Killian, Lambert C.J. Dorssers, Britton Trabert, Ad J.M. Gillis, Michael B. Cook, Yonghong Wang, Joshua J. Waterfall, Holly Stevenson, William I. Smith Jr., Natalia Noyes, Parvathy Retnakumar, J. Hans Stoop, J. Wolter Oosterhuis, Paul S. Meltzer, Katherine A. McGlynn and Leendert H.J. Looijenga. Imprints and DPPA3 are bypassed during pluripotencyand differentiation-coupled methylation reprogramming in testicular germ cell tumors. Genome Research, 2016

 

Michael H. Limberg, Julia Schulte, Tita Aryani, Regina Mahr, Meike Baumgart, Michael Bott,
Wolfgang Wiechert, Marco Oldiges. Metabolic profile of 1,5-diaminopentane producing Corynebacterium glutamicum under scale-down conditions: Blueprint for robustness to bioreactor inhomogeneities. Biotechnology and Bioengineering, 2016 

 

Samaneh Masoumi, Aditya Harisankar,  Aileen Gracias, Fabian Bachinger, Temesgen Fufa, Gayathri Chandrasekar, Frank Gaunitz, Julian Walfridsson, and Satish S Kitambi. Understanding cytoskeleton regulators in glioblastoma multiforme for therapy design. Drug Design, Development and Therapy, 2016

 

P Delfani, G Sturfelt, B Gullstrand, A Carlsson, M Kassandra, C A K Borrebaeck, A A Bengtsson, and C Wingren. Deciphering systemic lupus erythematosus-associated serum biomarkers reflecting apoptosis and disease activity. Lupus, 2016

 

J. Hengst, Falk, V. Schlaphoff, K. Deterding, M.P. Manns, M. Cornbergand H. Wedemeyer. DAA-induced HCV clearance does not completely restore the altered cytokine and chemokine milieu in patients with chronic hepatitis C. The Journal of Infectious Diseases, 2016

 

Marie Szymanowski,  Maria Salomon Estebanez, Raja Padidela, Bing Han, Karolina Mosinska, 
Adam Stevens, Lena Damaj, Florence Pihan-Le Bars, Emilie Lascouts, Rachel Reynaud, 
Catherine Ferreira, Claire Bansept, Pascale de Lonlay,  Cécile Saint-Martin, Mark J. Dunne, 
Indraneel Banerjee, Jean-Baptiste Arnoux. mTOR inhibitors for the treatment of severe congenital hyperinsulinism: perspectives on limited therapeutic success. The Journal of Endoctrinology & Metabolism, 2016

 

Melanie R. Hassler, Walter Pulverer, Ranjani Lakshminarasimhan, Andreas Weinhaeusel, Suzanne D. Turner, Gerda Egger. Insights into the Pathogenesis of Anaplastic LargeCell Lymphoma through Genome-wide DNA Methylation Profiling. Cell Reports, 2016

 

Annette Bernhard, Marc H.G. Berntssen, , Anne-Katrine Lundebye, , Anita Røyneberg Alvheim, Lene Secher Myrmel, , Even Fjære, , Bente E. Torstensen, Karsten Kristiansen, , Lise Madsen, Trond Brattelid, Josef D. Rasinger. Marine fatty acids aggravate hepatotoxicity of a-HBCD in juvenile female BALB/c mice. Food and Chemical Toxicology, 2016

 

Hristo Georgiev, Inga Ravens, Charaf Benarafa, Reinhold Förster & Günter Bernhardt. Distinct gene expression patterns correlate with developmental and functional traits of iNKT subsets.
Nature Communications, 2016

 

Michael K. Skinner. Ovary Systems Biology. Lecture at Washington State university, 2016

 

Sebastian Marwitz, Sofia Depner, Dmytro Dvornikov, Ruth Merkle, Magdalena Szczygiel, Karin Müller-Decker, Philippe Lucarelli, Marvin Wäsch, Heimo Mairbäurl, Klaus F. Rabe, Christian Kugler, Ekkehard Vollmer, Martin Reck, Swetlana Scheufele, Maren Kröger, Ole Ammerpohl, Reiner Siebert, Torsten Goldmann, Ursula Klingmüller. Downregulation of the TGF-ß pseudoreceptor BAMBI in non-small cell lung cancer enhances TGF-ß signaling and invasion. Cancer Research AACR, 2016 


Ann-Cathrine Larsen; Lauge H. Mikkelsen; Rehannah Borup; Katalin Kiss; Peter B. Toft; Christian von Buchwald; Sarah E. Coupland; Jan U. Prause; Steffen Heegaard. MicroRNA Expression Profile in Conjunctival Melanoma. IOVS, 2016

 

Zeng MN, Ma WL, Zheng W. Bioinformatics analysis of microRNA comprehensive regulatory network in B- cell acute lymphoblastic leukemia. NCBI PubMed, 2016

 

Volker M. Lauschke, Sabine U. Vorrink, Sabrina M. Moro, Fatemah Reyazee, Åsa Nordling, Delilah F. Hendriks, Catherine C. Bell, Rowena Sison-Young, B. Kevin Park, 
Christopher E. Goldring, Ewa Ellis, Inger Johansson, Souren Mkrtchian, Tommy B. Andersson, Magnus Ingelman-Sundberg. Massive rearrangements of cellular miRNA signatures are key drivers of hepatocyte dedifferentiation. Hepatology, 2016

 

Elena Matsa, Paul W. Burridge, Kun-Hsing Yu,  John H. Ahrens1, Vittavat Termglinchan, Haodi Wu, Chun Liu, Praveen Shukla, Nazish Sayed, Jared M. Churko, Ningyi Shao, Nicole A. Woo, Alexander S. Chao, Joseph D. Gold1, Ioannis Karakikes,  Michael P. Snyder, Joseph C. Wu. Transcriptome Profiling of Patient-Specific Human iPSC-Cardiomyocytes Predicts Individual Drug Safety and Efficacy Responses In Vitro. Cell Stem Cell, 2016

 

Alejandra Urrutia,  Darragh Duffy, Vincent Rouilly, Céline Posseme, Raouf Djebali, Gabriel Illanes, Valentina Libri, Benoit Albaud, David Gentien, Barbara Piasecka, Milena Hasan, Magnus Fontes,  Lluis Quintana-Murci, Matthew L. Albert. Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses. Cell Reports, 2016

 

Bruno Stuhlmüller, Karsten Mans, Neeraj Tandon, Marc O. Bonin, Biljana Smiljanovic, Till A. Sörensen, Pascal Schendel, Peter Martus, Joachim Listing, Jacqueline Detert, Marina Backhaus, Thomas Neumann, Robert J. Winchester, Gerd-R. Burmester, Thomas Häupl. Genomic stratification by expression of HLA-DRB4 alleles identifies differential innate and adaptive immune transcriptional patterns - A strategy to detect predictors of methotrexate response in early rheumatoid arthritis. Clincal Immunology, 2016 

 

W Dunn, A Burgun, MO Krebs, B Rance. Exploring and visualizing multidimensional data in translational research platforms. Briefings in Bioinformatics, 2016

 

Fang Liu, Yuan He, Qinghua Cao, Ni Liu, and Wenhui Zhang. TBL1XR1 Is Highly Expressed in Gastric Cancer and Predicts Poor Prognosis. Disease Markers, 2016

 

Dongfeng Chen, Junxiong Zheng, Natalija Gerasimcik, Kristina Lagerstedt, Helene Sjögren, Jonas Abrahamsson, Linda Fogelstrand, Inga-Lill Mårtensson. The Expression Pattern of the Pre-B Cell Receptor Components Correlates with Cellular Stage and Clinical Outcome in Acute Lymphoblastic Leukemia. PLOSOne, 2016

 

Olga Bogatyrova. Mutations in regulators of the epigenome and their effects on the DNA methylome.  Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany, 2016

 

A Forreryd, KS Zeller, T Lindberg, H Johansson, M Lindstedt. From genome-wide arrays to tailor-made biomarker readout – Progress towards routine analysis of skin sensitizing chemicals with GARD. Toxicology in Vitro, 2016

 

Ariz Akhter, Muhammad Kashif Mughal, Ghaleb Elyamany, Gary Sinclair, Raja Zahratul Azma, Noraidah Masir, Salwati Shuib, Fariborz Rashid-Kolvear, Meer-Taher Shabani-Rad, Douglas Allan Stewart and Adnan Mansoor. Diagnostic Pathology, 2016

 

Bjørn Henrik Hansen, Kai K. Lie, Trond R. Størseth, Trond Nordtug, Dag Altin & Pål A. Olsvik. Exposure of first-feeding cod larvae to dispersed crude oil results in similar transcriptional and metabolic responses as food deprivation. Journal of Toxicology and Environmental Health, 2016

 

J Carlos Villaescusa, Bingsi Li, Enrique M Toledo, Pia Rivetti di Val Cervo, Shanzheng Yang, Simon RW Stott, Karol Kaiser, Saiful Islam, Daniel Gyllborg, Rocio Laguna-Goya, Michael Landreh, Peter Lönnerberg, Anna Falk, Tomas Bergman, Roger A Barker, Sten Linnarsson, Licia Selleri, View ORCID ProfileErnest Arenas. A PBX1 transcriptional network controls dopaminergic neuron development and is impaired in Parkinson's disease. The Embo Journal, 2016

 

Rowena L. Sison-Young, Volker M. Lauschke, Esther Johann, Eliane Alexandre, Sébastien Antherieu, Hélène Aerts, Helga H. J. Gerets, Gilles Labbe, Delphine Hoët, Martina Dorau, Christopher A. Schofield, Cerys A. Lovatt, Julie C. Holder, Simone H. Stahl, Lysiane Richert, Neil R. Kitteringham, Robert P. Jones, Mohamed Elmasry, Richard J. Weaver, Philip G. Hewitt, Magnus Ingelman-Sundberg, Chris E. Goldring, B. Kevin Park. A multicenter assessment of single-cell models aligned to standard measures of cell health for prediction of acute hepatotoxicity. Archives of Toxicology, 2016

 

Abrahan Hernández-Hernández, Ingrid Lilienthal, Nanaho Fukuda, Niels Galjart, and Christer Höög. CTCF contributes in a critical way to spermatogenesis and male fertility. Scientific Reports, 2016

 

Sine V. Winther, Tomi Tuomainen, Rehannah Borup, Pasi Tavi, Gudrun Antoons, and Morten B. Thomsen. Potassium Channel Interacting Protein 2 (KChIP2) is not a transcriptional regulator of cardiac electrical remodeling. Scientific Reports, 2016

 

Sofia Waldemarson, Emila Kurbasic, Morten Krogh, Paolo Cifani, Tord Berggård, Åke Borg and Peter James. Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples. Breast Cancer Research. 2016

 

Mohammed Ashrafi MB, ChB, Anil Sebastian PhD, Barbara Shih PhD, Nicholas Greaves PhD,
Teresa Alonso-Rasgado PhD, Mohamed Baguneid MD, Ardeshir Bayat MB, BS, PhD. Whole genome microarray data of chronic wound debridement prior to application of dermal skin substitutes. Wound Repair and Regeneration, 2016

 

Christopher James Collins, Yawo A. Mondjinou, Bradley P. Loren, Sandra Torregrosa-Allen, Christopher J Simmons, Bennett D. Elzey, Nadia Ayat, Zheng-Rong Lu, and David H Thompson. Influence of Molecular Structure on the In Vivo Performance of Flexible Rod Polyrotaxanes. Biomacromolecules, 2016

 

Payam Delfani, Linda Dexlin Mellby, Malin Nordström, Andreas Holmér, Mattias Ohlsson, Carl A. K. Borrebaeck, Christer Wingren. Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics. PLOS One, 2016

 

Francesco Nicoli, Email author, Mkunde Chachage†, Petra Clowes, Asli Bauer, Dickens Kowour, Barbara Ensoli, Aurelio Cafaro, Leonard Maboko, Michael Hoelscher, Riccardo Gavioli, Elmar Saathoff and Christof Geldmacher. Association between different anti-Tat antibody isotypes and HIV disease progression: data from an African cohort. BMC Infectious Diseases, 2016

 

Kevin A. Link, Shan Lin, Mahesh Shresth, Melissa Bowman, Mark Wunderlich, Clara D. Bloomfield, Gang Huang,c, and James C. Mulloy. Supraphysiologic levels of the AML1-ETO isoform AE9a are essential for transformation. PNAS, 2016

 

H. Sun, P. Liu, L. K. Nolan and S. J. Lamont. Thymus transcriptome reveals novel pathways in response to avian pathogenic Escherichia coli infection. Poultry Science Oxford Journals, 2016 

 

WC Plaisted, A Zavala, E Hingco, H Tran, R Coleman, Thomas E. Lane, Jeanne F. Loring, Craig M. Walsh. Remyelination Is Correlated with Regulatory T Cell Induction Following Human Embryoid Body-Derived Neural Precursor Cell Transplantation in a Viral Model of Multiple Sclerosis, PLOS One, 2016 

 

M Pudenz. Impact of soy isoflavones on DNA methylation in rat mammary glands-Dose-response aspects, critical time windows, and influence on carcinogenesis. Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, 2016

 

Zineb Mounir, Joshua M Korn, Thomas Westerling, Fallon Lin, Christina A Kirby, Markus Schirle, 

Gregg McAllister, Greg Hoffman, Nadire Ramadan, Anke Hartung, Yan Feng,  David Randal Kipp, 
Christopher Quinn, Michelle Fodor, Jason Baird, Marie Schoumacher, Ronald Meyer, James Deeds, Gilles Buchwalter, Travis Stams, Nicholas Keen, William R Sellers, Myles Brown, Raymond A Pagliarini. ERG signaling in prostate cancer is driven through PRMT5-dependent methylation
of the Androgen Receptor. eLife, 2016

 

Ann-Cathrine Larsen.  Conjunctival malignant melanoma in Denmark: epidemiology, treatment and prognosis with special emphasis on tumorigenesis and genetic profile. Acta Ophthalmologica, 2016

 

Julia Kolarova, Susanne Bens, Ole Ammerpohl, Alina C. Hilger, Rong Zhang, Heiko Reutter,
Reiner Siebert. PLAGL1 epimutation and bladder exstrophy: Coincidence or concurrent etiology?  Birth Defects Research Part A: Clinical and Molecular Teratology, 2016

 

Vicente Martinez-Redondo, Paulo R. Jannig, Jorge C Correia1, Duarte M.S. Ferreira, Igor Cervenka, Jessica M. Lindvall, Indranil Sinha, Manizheh Izadi, Amanda T. Pettersson-Klein1, Leandro Z. Agudelo, Alfredo Gimenez-Cassina1, Patricia C. Brum, Karin Dahlman-Wright1 and Jorge L. Ruas3. Peroxisome proliferator-activated receptor gamma coactivator-1alpha isoforms selectively regulate multiple splicing events on target genes. The Journal of Biological Chemistry, 2016

 

Oluwajoba O. Akinjo,a Timothy W. Gant and Emma L. Marczylo.  Perturbation of epigenetic processes by doxorubicin in the mouse testis. Toxicology Research, 2016.

 

Henrik Lilljebjörn, Rasmus Henningsson, Axel Hyrenius-Wittsten, Linda Olsson, Christina Orsmark-Pietras, Sofia von Palffy, Maria Askmyr, Marianne Rissler, Martin Schrappe, Gunnar Cario, Anders Castor, Cornelis J. H. Pronk, Mikael Behrendtz, Felix Mitelman, Bertil Johansson, Kajsa Paulsson, Anna K. Andersson, Magnus Fontes & Thoas Fioretos. Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia. Nature Communications 7, 2016

 

Aline Dupont , Felix Sommer, Kaiyi Zhang, Urska Repnik, Marijana Basic, André Bleich, Mark Kühnel, Fredrik Bäckhed, Yael Litvak, Marcus Fulde, Ilan Rosenshine, Mathias W. Hornef. Age-Dependent Susceptibility to Enteropathogenic Escherichia coli (EPEC) Infection in Mice. PLOS Pathogens, 2016

 

Catherine C. Bell, Delilah F. G. Hendriks,  Sabrina M. L. Moro, Ewa Ellis,  Joanne Walsh, Anna Renblom, ,Lisa Fredriksson Puigvert,  Anita C. A. Dankers, Frank Jacobs, Jan Snoeys, Rowena L, Sison-Young, Rosalind E. Jenkins, Åsa Nordling, Souren Mkrtchian, B. Kevin Park, Neil R. Kitteringham, Christopher E. P. Goldring, Volker M. Lauschke, Magnus Ingelman-Sundberg. Characterization of primary human hepatocyte spheroids as a model system for drug-induced liver injury, liver function and disease. Scientific Reports, Nature, 2016

 

T Weiss, S Taschner-Mandl, H Dodig , F Rifatbegovic, C Frech, IM Ambros, PF Ambros. Schwann cells secrete factors that impair neuroblastoma growth. Klinische Pädiatrie, (Clinical Research and Practice in Pediatrics), 2016

 

Gitte L. Christensen, Maria L. B. Jacobsen, Anna Wendt, Ines G. Mollet, Josefine Friberg, Klaus S. Frederiksen, Michael Meyer, Christine Bruun, Lena Eliasson. Bone morphogenetic protein 4 inhibits insulin secretion from rodent beta cells through regulation of calbindin1 expression and reduced voltage-dependent calcium currents. Diabetologia, 2016

 

Gregory T. Jones, PhD; L. Victoria Phillips; Michael J.A. Williams, MBChB; Andre M. van Rij, MBChB; Tasnuva D. Kabir, MBChB, PhD. Two C-C Family Chemokines, Eotaxin and RANTES, Are Novel
Independent Plasma Biomarkers for Abdominal Aortic Aneurysm. The Journal of the American Heart Association, 2016

 

Tiphaine Parrot, Mathilde Allard, Romain Oger, Houssem Benlalam, Diane Raingeard de la Blétière, Anne Coutolleau, Laurence Preisser, Juliette Desfrançois, Amir Khammari, Brigitte Dréno, Nathalie Labarrière, Yves Delneste, Philippe Guardiola and Nadine Gervois. IL-9 promotes the survival and function of human melanoma-infiltrating CD4+CD8+ double-positive T cells. European Journal of Immunology, 2016

 

Ignacio Sancho-Martinez, Emmanuel Nivet, Yun Xia, Tomoaki Hishida, Aitor Aguirre, Alejandro Ocampo, Li Ma, Robert Morey, Marie N. Krause, Andreas Zembrzycki, Olaf Ansorge, Eric Vazquez-Ferrer, Ilir Dubova, Pradeep Reddy, David Lam, Yuriko Hishida, Min-Zu Wu, Concepcion Rodriguez Esteban, Dennis O’Leary, Geoffrey M. Wahl. Establishment of human iPSC-based models for the study and targeting of glioma initiating cells. Nature Communications, 2016

 

Somsundar Veppil Muralidharan. TARGETING MYC-DRIVEN TUMOURS BETing on ATR. Department of Surgery Institute of Clinical Sciences Sahlgrenska Academy at University of Gothenburg - Theses, 2016

 

Hristo Georgiev,  Inga Ravens, Charaf Benarafa, Reinhold Förster, Günter Bernhardt. Distinct gene expression patterns correlate with developmental and functional traits of iNKT subsets. Nature Communications 2016

 

Willem J. du Plessis, Léanie Kleynhans, Nelita du Plessis, Kim Stanley, Stephanus T. Malherbe, Elizna Maasdorp, Katharina Ronacher, Novel N. Chegou, Gerhard Walzl, Andre G. Loxton. The Functional Response of B Cells to Antigenic Stimulation: A Preliminary Report of Latent Tuberculosis. PLOS One, 2016

 

N. E. U. Hermansen, R. Borup, M. K. Andersen, A. J. Vangsted2, N. T. Clausen, D. L. Kristensen, F. C. Nielsen and P. Gimsing. Gene expression risk signatures maintain prognostic power in multiple myeloma despite microarray probe set translation. International Journal of Laboratory Hematology, 2016 

 

Ai Ing Lim, Silvia Menegatti,  Jacinta Bustamante, Lionel Le Bourhis, Matthieu Allez,  Lars Rogge, Jean-Laurent Casanova, Hans Yssel, and James P. Di Santo. IL-12 drives functional plasticity of human group 2 innate lymphoid cells. The Journal of Experimental Medicine, 2016

 

Rabih Moshouraba,  Vinko Paladac, Stefanie Grunwaldc, Ulrike Griebenc, Gary R. Lewina, Simone Spulerc. A Molecular Signature of Myalgia in Myotonic Dystrophy 2EBioMedicine, 2016

 

Wafa Kammoun-Rebai, Ikbel Naouar, Valentina Libri, Matthew Albert, Hechmi Louzir, Amel Meddeb-Garnaoui and Darragh Duffy. Protein biomarkers discriminate Leishmania major-infected and non-infected individuals in areas endemic for cutaneous leishmaniasis. BMC Infectious Diseases, 2016

 

Marc H.G. Berntssena, Robin Ørnsruda, Josef Rasingera, Liv Søftelanda, Erik-Jan Locka, Kjersti Kolåsa, Mari Morenb, Ketil Hyllande, Joana Silvac, Johan Johansend, Kai Liea. Dietary vitamin A supplementation ameliorates the effects of poly-aromatic hydrocarbons in Atlantic salmon (Salmo salar). Aquatic Toxicology, 2016

 

Pablo Carbonell-Bejerano , Virginia Rodríguez, Silvia Hernáiz, Carolina Royo, Silvia Dal Santo, Mario Pezzotti, José Miguel Martínez-Zapater. Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method. Theoretical and Experimental Plant Physiology, 2016

 

Wen Cheng, Chuanbao Zhang, Xiufang Ren, Yang Jiang, Sheng Han, Yang Liu, Jinquan Cai, Mingyang Li, Kuanyu Wang, Yanwei Liu, Huimin Hu, Qingbin Li, Pei Yang, Zhaoshi Bao, Anhua Wu. Bioinformatic analyses reveal a distinct Notch activation induced by STAT3 phosphorylation in the mesenchymal subtype of glioblastoma. Journal of Neurosurgery, 2016

 

József Prechl , Krisztián Papp, Zoltán Hérincs, Hajna Péterfy, Veronika Lóránd, Zoltán Szittner, Andone Estonba, Paolo Rovero, Ilaria Paolini, Jokin del Amo, Maria Uribarri, Maria Claudia Alcaro, Otsanda Ruiz-Larrañaga, Paola Migliorini, László Czirják. Serological and Genetic Evidence for Altered Complement System Functionality in Systemic Lupus Erythematosus: Findings of the GAPAID Consortium. PLOS One, 2016

 

Anna Afasizheva, Alexus Devine, Heather Tillman, King Leung Fung, Wilfred D. Vieira, Benjamin H. Blehm, Yorihisa Kotobuki, Ben Busby, Emily I. Chen and Kandice Tanner. Mitogen-activated protein kinase signaling causes malignant melanoma cells to differentially alter extracellular matrix biosynthesis to promote cell survival. BMC Cancer, 2016

 

Bilgin Candar-Cakir, Ercan Arican, Baohong Zhang. Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes. Plant Biotechnology Journal, 2016

 

Kirsty Meldrum, Timothy W. Gant, Sameirah Macchiaruloa and Martin O. Leonard. Bronchial epithelial innate and adaptive immunity signals are induced by polycyclic aromatic hydrocarbons. Toxicology Research, 2016

 

R Vangoitsenhoven, H Wolden-Kirk, K Lemaire...Effect of a transcriptional inactive or absent vitamin D receptor on beta-cell function and glucose homeostasis in miceEffect of a transcriptional inactive or absent vitamin D receptor on beta-cell function and glucose homeostasis in mice. The Journal of Steroid Biochemistry and Molecular Biology, 2016

 

Carl Arne Krister Borrebaeck, Christer Lars Bertil Wingren. METHODS AND ARRAYS FOR USE IN THE SAME.

 

Shankar Thangamani,  Haroon Mohammad, , Mostafa F. N. Abushahba,Tiago J. P. Sobreira, Victoria E. Hedrick,  Lake N. Pau & Mohamed N. Seleem. Antibacterial activity and mechanism of action of auranofin against multi-drug resistant bacterial pathogens. Scientific Reports, 2016

 

Lisa M Nilsson, Lydia C. Green, Somsundar Veppil Muralidharan, Dagsu Demir, Martin Welin, Joydeep Bhadury, Derek Logan, Björn Walse, and Jonas A. Nilsson. Cancer differentiation agent hexamethylene bisacetamide was likely the first BET bromodomain inhibitor in clinical trials, Cancer Research 2016

 

Pål A. Olsvika, Liv Søftelanda, Ernst M. Hevrøya, Josef D. Rasingera, Rune Waagbøa. Fish pre-acclimation temperature only modestly affects cadmium toxicity in Atlantic salmon hepatocytes. Journal of Thermal Biology, 2016

 

Oliver Popp, Dirk Müller, Katharina Didzus, Wolfgang Paul, Florian Lipsmeier,  Florian Kirchner, Jens Niklas, Klaus Mauch, Nicola Beaucamp. A hybrid approach identifies metabolic signatures of high-producers for Chinese hamster ovary clone selection and process optimization. Biotechnology and Bioengineering, 2016

 

Catherine Leclerc, Jacques Haeich, Francisco Aulestia, Marie-Claude
Kilhoffer, Andrew L. Miller, Isabelle N´eant, Sarah E. Webb, Etienne Schaeffer,
Marie-Pierre Junier, Herv´e Chneiweiss, Marc Moreau. Calcium signaling orchestrates glioblastoma development: Facts and conjunctures. BBA - Molecular Cell Research, 2016

 

J Davidsson, B Johansson. Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p. Epigenetics, 2016

 

Matthew Timothy Tierney, Anastasia Gromova, Francesca Boscolo Sesillo,  David Sala, Caroline Spenlé,  Gertraud Orend,  Alessandra Sacco. Autonomous Extracellular Matrix Remodeling Controls a Progressive Adaptation in Muscle Stem Cell Regenerative Capacity during Development. Cell Reports, 2016 

 

Sasha A. Singh, Allison B. Andraski, Brett Pieper, Wilson Goh , Carlos O. Mendivil, 
Frank M. Sacks, Masanori Aikawa. Multiple apolipoprotein kinetics measured in human
HDL by high-resolution/accurate mass parallel reaction monitoring. Journal of Lipid Research, 2016

 

V Kuci, L Nordström, P Conrotto, S Ek. SOX11 and HIG-2 are cross-regulated and affect growth in mantle cell lymphoma.  Leukemia & Lymphoma, 2016

 

Matthias S. Matter, Jens U. Marquardt, Jesper B. Andersen, Cristina Quintavalle, 
Nikolay Korokhov, Jim K. Stauffer, Kosuke Kaji, Thomas Decaens, Luca Quagliata, Fathi Elloumi, Tanya Hoang, Alfredo Molinolo, Elizabeth A. Conner, Achim Weber, Mathias Heikenwalder, Valentina M. Factor, Snorri S. Thorgeirsson. Oncogenic driver genes and the inflammatory microenvironment dictate liver tumor phenotype. Hepatology, 2016

 

Britta C. Martel, Thomas Litman, Andreas Hald, Hanne Norsgaard, Paola Lovato, Beatrice Dyring-Andersen, Lone Skov, Kristian Thestrup-Pedersen, Søren Skov, Kresten Skak and Lars K. Poulsen. Distinct molecular signatures of mild extrinsic and intrinsic atopic dermatitis, Experimental Dermatology, 2016

 

CC Oakes, M Seifert, Y Assenov, L Gu, M Przekopowitz. DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nature Genetics, 2016

 

MA Taylor, M Wappett, O Delpuech, H Brown. Enhanced MAPK signaling drives ETS1-mediated induction of miR-29b leading to downregulation of TET1 and changes in epigenetic modifications in a subset of lung SCC. Oncogene, 2016

 

Ahrens M, Ammerpohl O, von Schönfels W, Kolarova J, Bens S, Itzel T, Teufel A, Herrmann A, Brosch M, Hinrichsen H, Erhart W, Egberts J, Sipos B, Schreiber S, Häsler R, Stickel F, Becker T, Krawczak M, Röcken C, Siebert R, Schafmayer C, Hampe J. DNA methylation analysis in nonalcoholic fatty liver disease suggests distinct disease-specific and remodeling signatures after bariatric surgery. Cell Metabolism, 2016

 

Julia Merkenschlager, Mickaël J. Ploquin, Urszula Eksmond, Rakieb Andargachew, Georgina Thorborn, Andrew Filby, Marion Pepper, Brian Evavold & George Kassiotis. Stepwise B-cell-dependent expansion of T helper clonotypes diversifies the T-cell response. Nature Communication, 2016

 

Hongyan Suna, Ran Bib, Peng Liub, Lisa K. Nolanc, Susan J. Lamonta. Combined analysis of primary lymphoid tissues' transcriptomic response to extra-intestinal Escherichia coli (ExPEC) infection. Developmental & Comparative Immunology, 2016

 

F Schmid, Q Wang, M R Huska, M A Andrade-Navarro, M Lemm, I Fichtner, M Dahlmann, D Kobelt, W Walther, J Smith, P M Schlag and U Stein. SPON2, a newly identified target gene of MACC1, drives colorectal cancer metastasis in mice and is prognostic for colorectal cancer patient survival. Oncogene, 2016

 

 

2015

Kirsten C. G. Van Dycke, Jeroen L. A. Pennings, Conny T. M. van Oostrom, Linda W. M. van Kerkhof, Harry van Steeg, Gijsbertus T. J. van der Horst, Wendy Rodenburg. Biomarkers for Circadian Rhythm Disruption Independent of Time of Day. PLOS One, 2015

 

Rebekka Petra Diepold, Plasticity genes in gene x environment interactions: expression and inheritance in a mouse model of anxiety. Dissertation Faculty of Biology Ludwig Maximilians University in Munich, 2015

 

Sarah J. Chapplea, Thomas P. Keeleya, Daniela Mastronicolaa, Matthew Arnob, Gema Vizcay-Barrenac, Roland Fleckc, Richard C.M Siowa, Giovanni E. Manna. Bach1 differentially regulates distinct Nrf2-dependent genes in human venous and coronary artery endothelial cells adapted to physiological oxygen levels. Free Radical Biology and Medicine,  2015

 

Daniel Berglind,, Patrick Müller, Mikaela Willmer, Indranil Sinha, Per Tynelius, Erik Näslund, Karin Dahlman-Wright, Finn Rasmussen. Differential methylation in inflammation and type 2 diabetes genes in siblings born before and after maternal bariatric surgery. Obesity, 2015

 

Sandra Mattua, Francesca Fornaria, Luca Quagliataa, Andrea Perra, Maria Maddalena Angioni, Annalisa Petrelli, Silvia Menegon, Andrea Morandi, Paola Chiarugi, Giovanna Maria Ledda-Columbano, Laura Gramantieri, Luigi Terracciano, Silvia Giordanocorrespondenceemail, Amedeo Columbano. The metabolic gene HAO2 is down regulated in mouse, rat and human hepatocellular carcinoma and correlates with metastasis and poor survival. Journal of Hepatology, 2015

 

Julie Prudhomme, Agnès Dubois, Pablo Navarro, Danielle Arnaud, Philip Avner, and Céline Morey. A rapid passage through a two-active-X-chromosome state accompanies the switch of imprinted X-inactivation patterns in mouse trophoblast stem cells. Epigenetics Chromatin, 2015

 

Ute Warnecke-Eberz , Ralf Metzger, Arnulf H. Hölscher, Uta Drebber, Elfriede Bollschweiler. Diagnostic marker signature for esophageal cancer from transcriptome analysis. Tumor Biology, 2015

 

Firoz Shah, César Nicolás, Johan Bentzer, Magnus Ellström, Mark Smits, Francois Rineau,
Björn Canbäck, Dimitrios Floudas, Robert Carleer, Gerald Lackner, Jana Braesel, Dirk Hoffmeister,
Bernard Henrissat, Dag Ahrén, Tomas Johansson, David S. Hibbett, Francis Martin, Per Persson,
Anders Tunlid. Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors. New Pytologist, 2015

 

Mustimbo E. P. Roberts, Brandon W. Higgs, Philip Brohawn, Fernanda Pilataxi, Xiang Guo, Michael Kuziora, Russell P. Bowler, Wendy I. White. CD4+ T-Cell Profiles and Peripheral Blood Ex-Vivo Responses to T-Cell Directed Stimulation Delineate COPD Phenotypes. Chronic Obstructive Pulmonary Diseases Foundation, 2015

 

James L Reading, Bart Vaes, Caroline Hull, Shereen Sabbah, Thomas Hayday, Nancy S Wang, Anthony DiPiero, Nicholas A Lehman, Jen M Taggart, Fiona Carty, Karen English, Jef Pinxteren, Robert Deans, Anthony E Ting and Timothy IM Tree. Suppression of IL-7-dependent Effector T-cell Expansion by Multipotent Adult Progenitor Cells and PGE2The American Society of Gene & Cell Therapy, 2015

 

J Karlsson, A Valind, D Gisselsson. BCOR internal tandem duplication and YWHAE–NUTM2B/E fusion are mutually exclusive events in clear cell sarcoma of the kidney. Genes, Chromosomes and Cancer, 2015

 

C De Leonibus, P Chatelain, C Knight, P Clayton and A Stevens. Effect of summer daylight exposure and genetic background on growth in growth hormone-deficient children. The Pharmacogenomics Journal, 2015

 

Umut Cagina, Olivia F. Duncana,  Ariana P. Gatta, Marc S. Dionneb, Sean T. Sweeneyc, Joseph M. Batemana. Mitochondrial retrograde signaling regulates neuronal function. PNAS, 2015

 

M Pellino. Gene expression analysis and transcriptome evolution in apomicts: a case study in Boechera and Ranunculus. Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany,  2015

 

Sumadi Lukman Anwar, Till Krech, Britta Hasemeier, Elisa Schipper, Nora Schweitzer, Arndt Vogel, Hans Kreipe, Ulrich Lehmann. Loss of DNA methylation at imprinted loci is a frequent event in hepatocellular carcinoma and identifies patients with shortened survival. Clinical Epigenetics, 2015

 

Carolina Roya, , Pablo Carbonell-Bejerano, Rafael Torres-Pérez, Anna Nebish, Óscar Martínez, Manuel Rey, Rouben Aroutiounian, Javier Ibáñez and José M.Martínez-Zapater.  Developmental, transcriptome, and genetic alterations associated with parthenocarpy in the grapevine seedless somatic variant Corinto bianco. Journal of Experimental Botany, Oxford Journals, 2015

 

Helene Kretzmer, Stephan H Bernhart, Wei Wang, Andrea Haake, Marc A Weniger, Anke K Bergmann, Matthew J Betts, Enrique Carrillo-de-Santa-Pau, Gero Doose, Jana Gutwein, Julia Richter, Volker Hovestadt, Bingding Huang, Daniel Rico, Frank Jühling, Julia Kolarova, Qianhao Lu, Christian Otto, Rabea Wagener, Judith Arnolds, Birgit Burkhardt, Alexander Claviez, Hans G Drexler, Sonja Eberth, Roland Eils. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nature Genetics, 2015

 

Anna S. Gerdtsson, Núria Malats, Anna Säll, , Francisco X. Real,, Miquel Porta,  Petter Skoog, 
Helena Persson,  Christer Wingren, Carl A.K. Borrebaeck. A multicenter trial defining a serum protein signature associated with pancreatic ductal adenocarcinoma. International Journal of Proteomics, 2015

 

Emila Kurbasic, Martin Sjöström, Morten Krogh, Elin Folkesson, Dorthe Grabau, Karin Hansson, Lisa Rydén, Sofia Waldemarson, Peter James Emma Niméus. Changes in glycoprotein expression between primary breast tumour and synchronous lymph node metastases or asynchronous distant metastases. Clinical Proteomics, 2015

 

Maria Wik Markhus , Josef Daniel Rasinger, Marian Kjellevold Malde, Livar Frøyland, Siv Skotheim, Hanne Cecilie Braarud, Kjell Morten Stormark, Ingvild Eide Graff. Docosahexaenoic Acid Status in Pregnancy Determines the Maternal Docosahexaenoic Acid Status 3-, 6-and 12 Months Postpartum. Results from a Longitudinal Observational Study. PLOS One, 2015

 

Armand Valsesia, Pierre Chatelain, Adam Stevens, Valentina Peterkova, Alicia Belgorosky, Mohamad Maghnie, Franco Antoniazzi, Ekaterina Koledova, Jerome Wojcik, Pierre Farmer, Benoit Destenaves and Peter E Clayton. Growth hormone (GH) deficiency status combined with GH receptor polymorphism affects response to GH in children. European Journal of Endocrinology, 2015

 

GJ Walter, V Fleskens, KS Frederiksen, M Rajasekhar. Phenotypic, functional and gene expression profiling of peripheral CD45RA+ and CD45RO+ CD4+ CD25+ CD127low regulatory T cells in rheumatoid arthritis. Arthritis & Rheumatology, 2015

 

Julia K. Seibert, Luca Quagliata, Cristina Quintavalle, Thomas G. Hammond, Luigi Terracciano and Alex Odermatt. A role for the dehydrogenase DHRS7 (SDR34C1) in prostate cancer. Cancer Medicine, 2015

 

Yu-Chieh Wang,  Jason W. Stein, Candace L. Lynch, Ha T. Tran, Chia-Yao Lee,  Ronald Coleman,   Adam Hatch,  Victor G. Antontsev,  Hun S. Chy,  Carmel M. O’Brien,   Shashi K. Murthy, Andrew L. Laslett,  Suzanne E. Peterson and Jeanne F. Loring. Glycosyltransferase ST6GAL1 contributes to the regulation of pluripotency in human pluripotent stem cells. Scientific Reports, 2015 

 

A Stucki-Koch, G Hauck, H Kreipe, K Hussein. MicroRNA expression profiles in BCR-ABL-negative primary myelofibrosis with chromosome 7q defects. Journal of Hematopathology, 2015

 

S Coffey, MJA Williams, LV Phillips, GT Jones. Circulating microRNA Profiling Needs Further Refinement Before Clinical Use in Patients With Aortic Stenosis,  Journal of the American Heart Association, 2015

 

R Mesnage, M Arno, M Costanzo, M Malatesta. Transcriptome profile analysis reflects rat liver and kidney damage following chronic ultra-low dose Roundup exposure. Environmental Health, 2015

 

N Ravi. Genetic analysis of Anaplastic Thyroid Cancer. Degree Projects in Molecular Biology. Lund University, 2015

 

JL Deuve, A Bonnet-Garnier, N Beaujean, P Avner. Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome. Epigenetics, 2015

 

NE van der Sligte, FJG Scherpen, A ter Elst, V Guryev. Effect of IKZF1 deletions on signal transduction pathways in Philadelphia chromosome negative pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Experimental Hematology & Oncology, 2015

 

RD Abeles, CG Antoniades, DL Shawcross, W Khamri. PWE-114 Modulation of non-canonical nfkb pathways may underlie the anti-inflammatory, resolution-like activation of circulating cd14hi monocytes in hyper-acute liver failure. Gut, 2015

 

A Sharma, MA Jamil, N Nuesgen, F Schreiner, L Priebe. DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrationsClinical Epigenetics, 2015

 

MN Møller, S Kirkeby, J Vikeså, FC Nielsen. Expression of histamine receptors in the human endolymphatic sac: the molecular rationale for betahistine use in Menieres disease. European Archives of European Archives of Oto-Rhino-Laryngology, 2015

 

Natalia Torow, Kai Yu, Kasra Hassani, Jenny Freitag, Olga Schulz, Marijana Basic, Anne Brennecke, Tim Sparwasser, Norbert Wagner, André Bleich, Matthias Lochner, Siegfried Weiss, Reinhold Förster, Oliver Pabst & Mathias W. Hornef. Active suppression of intestinal CD4+TCRaß+ T-lymphocyte maturation during the postnatal period. Nature Communications, 2015

 

N Torow, O Dittrich-Breiholz, MW Hornef. Transcriptional profiling of intestinal CD4+ T cells in the neonatal and adult mice. Genomics Data, 2015

 

AK Coussens, RJ Wilkinson, AR Martineau. Phenylbutyrate Is Bacteriostatic against Mycobacterium tuberculosis and Regulates the Macrophage Response to Infection, Synergistically with 25-Hydroxy-Vitamin D3. PLOS Pathogens, 2015

 

Schiøler Schultz. Extracellular matrix proteins as drivers of inflammation in rheumatoid arthritis. Industrial PhD Thesis, University of Copenhagen, 2015

 

Juliane Lippmann, Frederik Gwinner, Camille Rey, Uyanga Tamira, Helen K. W. Lawd, Benno Schwikowski,  Jost Enninga. Bacterial internalization, localization and effectors shape the Epithelial Immune Response during Shigella Infection. Infection and Immunity, 2015

 

V Schlaphoff, K Deterding, S Hardtke, J Hengst, C Falk, B Bremer, MP Manns, M Cornberg and H Wedemeyer. Serum biomarker profile can predict the outcome of acute HCV infection. Journal of Viral Hepatitis, 2015

 

M Wöbse, V Schlaphoff, A Wranke, M Cornberg,CS Falk, C Yur daydin, MP Manns,H Wedemeyer, S Hardtke and HIDIT-2 study-group. Plasma cytokine and chemokine patterns during PEG_IFNa-2a therapy of chronic hepatitis delta.  Journal of Viral Hepatitis, 2015

 

K Grinnemo, O Simonson, M Corbascio, C Sylvén. DERIVATION AND SELF-RENEWAL OF ISI1+ CELLS AND USES THEREOFUS. FPO IP Research and Communities, Patent 20,150,164,958, 2015

 

AK Coussens, CE Naude, R Goliath, G Chaplin, Robert J. Wilkinson, Nina G. Jablonski. High-dose vitamin D3 reduces deficiency caused by low UVB exposure and limits HIV-1 replication in urban Southern Africans.  PNAS, 2015 

 

JE Simpson, PG Ince, T Minett, FE Matthews, PR Heath. Neuronal DNA damage response-associated dysregulation of signalling pathways and cholesterol metabolism at the earliest stages of Alzheimer-type pathology. Neuropathology and Applied Neurobiology, 2015

 

MS Trivedi, EI Chen, D Awad, A Koller, P Patel. Identifying predictors of taxane-induced peripheral neuropathy using shotgun proteomics technologyJournal of Clinical Oncology, 2015 

 

S Muhie, R Hammamieh, C Cummings, D Yang, M Jett. Stress-caused anergy of leukocytes towards Staphylococcal enterotoxin B and exposure transcriptome signatures. Genes and Immunity, 2015

 

Y Xiao, S Zijl, L Wang, DC de Groot, MJ van Tol. Identification of the Common Origins of Osteoclasts, Macrophages, and Dendritic Cells in Human Hematopoiesis.  Stem Cell Reports, 2015

 

J Kolarova, I Tangen, S Bens, G Gillessen-Kaesbach. Array-based DNA-methylation analysis in individuals with developmental delay/intellectual disability and normal molecular karyotype.  European Journal of Medical Genetics, 2015

 

SE Khorsandi, A Quaglia, S Salehi, W Jassem.  The microRNA Expression Profile in Donation after Cardiac Death (DCD) Livers and Its Ability to Identify Primary Non Function. PLOS One, 2015

 

S Owusu Sekyere, PV Suneetha, S Hardtke, CS Falk. Type I Interferon Elevates Co-regulatory Receptor Expression on CMV- and EBV-specific CD8 T cells in Chronic Hepatitis CFrontiers in Immunology,  2015

 

A Badr, P Angers, Y Desjardins. Comprehensive analysis of in vitro to ex vitro transition of tissue cultured potato plantlets grown with or without sucrose using metabolic profiling techniquePlant Cell, Tissue and Organ Culture (PCTOC), 2015

 

M Lindstedt, C Borrebaeck, H Johansson, A Albrekt. Method for Identifying Agents Capable of Inducing Respiratory Sensitization and Array and Analytical Kits for Use in the Method US Patent 20,150,111,771, 2015

 

Y Wang, P Lavender, J Watson, M Arno, T Lehner. Stress activated DC induce dual homeostatic and inflammasome pathways, which may elicit CD4+ memory T cells and IFN stimulated gene, Journal of Biological Chemistry, 2015

 

SE Bates, R Eisch, A Ling, D Rosing, M Turner. Romidepsin in peripheral and cutaneous T-cell lymphoma: mechanistic implications from clinical and correlative data, British Journal of Haematology, 2015

 

S Bustany, J Cahu, P Guardiola, B Sola. Cyclin D1 sensitizes myeloma cells to endoplasmic reticulum stress-mediated apoptosis by activating the unfolded protein response pathway, BMC Cancer, 2015

 

Z Li, Z Qiao, W Zheng, W Ma. Network Cluster Analysis of Protein–Protein Interaction Network–Identified Biomarker for Type 2 Diabetes, Diabetes Technology & Therapeutics, 2015

 

PM Tørring, MJ Larsen, AD Kjeldsen, LB Ousager. Global Gene Expression Profiling of Telangiectasial Tissue from Patients with Hereditary Haemorrhagic Telangiectasia. Microvascular Research, 2015

 

KP Sørensen, M Thomassen, Q Tan, M Bak, S Cold. ] Long non-coding RNA expression profiles predict metastasis in lymph node-negative breast cancer independently of traditional prognostic markers. Breast Cancer Research, 2015

 

Ufuk Kirik, Karin Hansson, Morten Krogh, Mats Jönsson, Mef Nilbert, Peter James, Ana Carneiro.  Discovery-Based Protein Expression Profiling Identifies Distinct Subgroups and Pathways in Leiomyosarcomas. Molecular Cancer Research, 2015

 

GL Christensen, MLB Jacobsen, A Wendt, IG Mollet. Bone morphogenetic protein 4 inhibits insulin secretion from rodent beta cells through regulation of calbindin1 expression and reduced voltage-dependent calcium current. Diabetologia, 2015

 

R Gonzalez, I Garitaonandia, R Semechkin. Derivation of Neural Stem Cells and Dopaminergic Neurons from Human Pluripotent Stem Cells. US Patent 20,150,087,541, 2015

 

K Hollevoet, E Mason-Osann, F Müller, I Pastan. ] Methylation-associated partial down-regulation of mesothelin causes resistance to anti-mesothelin immunotoxins in a pancreatic cancer cell line. PLoS One, 2015

 

A Forreryd, H Johansson, AS Albrekt, CAK Borrebaeck. Prediction of Chemical Respiratory Sensitizers Using GARD, a Novel. PLOS One, 2015

 

MN Møller, S Kirkeby, J Vikeså, FC Nielsen. Gene expression demonstrates an immunological capacity of the human endolymphatic sac. The Laryngoscope, 2015

 

AK Östberg, U Dahlgren, YT Sul, CB Johansson. Inflammatory cytokine release is affected by surface morphology and chemistry of titanium implants.  Journal of Materials Science, 2015

 

J Kolarova, O Ammerpohl, J Gutwein, M Welzel, I Baus. In vivo Investigations of the Effect of Short-and Long-Term Recombinant Growth Hormone Treatment on DNA-Methylation in Humans. PLOS One, 2015

 

J Vikeså, AKH Møller, B Kaczkowski, R Borup. Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin. BMC Cancer, 2015 

 

KCM Denninger, T Litman, T Marstrand, K Moller. Kinetics of gene expression and bone remodelling in the clinical phase of collagen induced arthritis. Arthritis Research & Therapy, 2015

 

R Stella, G Biancotto, G Arrigoni, F Barrucci, R Angeletti. Proteomics for the detection of indirect markers of steroids treatment in bovine muscle. Proteomics, 2015.

 

H S Schultz, L M Nitze, L H Zeuthen, P Keller, A Gruhler, J Pass, J Chen, L Guo, A J Fleetwood, J A Hamilton, M W Berchtold, S Panina. Collagen Induces Maturation of Human Monocyte-Derived Dendritic Cells by Signaling through Osteoclast-Associated Receptor. Journal of Immunology, 2015


A K Andersson, J Ma, J Wang, X Chen, A Larson Gedman, J Dang, J Nakitandwe, L Holmfeldt, M Parker et al. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nature Genetics, 2015

 

N Nüsgen, W Goering, A Dauksa, A Biswas, M Ahmer, I Dimitriou, A Sharma et al. Inter-locus as well as intra-locus heterogeneity in LINE-1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs. Clinical Epigenetics, 2015

 

S Muhie, A Gautam, J Meyerhoff, N Chakraborty, R Hammamieh, M Jett. Brain transcriptome profiles in mouse model simulating features of post-traumatic stress disorder. Molecular Brain, 2015

 

D Marancik, G Gao, B Paneru, H Ma, A G Hernandez, M Salem, J Yao, Y Palti, G D Wiens. Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Frontiers, 2015


M Negrini, G Cutrona, C Bassi, et al. microRNAome expression in chronic lymphocytic leukemia: comparison with normal B cell subsets and correlations with 
prognostic and clinical parameters. Clinical Cancer Research, 2015

 

H Kempf, R Olmer, C Kropp, M Rückert, M Jara-Avaca, D Robles-Diaz et al. Controlling Expansion and Cardiomyogenic Differentiation of Human Pluripotent Stem Cells in Scalable Suspension Culture. Stem Cell Reports, 2015

 

L Berglin. Biliary epithelial cells, the immune system and PSC pathogenesis. Karolinska Institutet, 2015


Z X Chen, K Wallis, S M Fell, et al. RNA helicase A is a downstream mediator of KIF1Bß tumor suppressor function in neuroblastoma. Cancer Discovery, 2015

 

D Heckmann, C Urban, K Weber, K Kannenberg, G Binder. Decreased expression of cell proliferation-related genes in clonallyderived skin fibroblasts from children with Silver-Russell syndrome is independent of the degree of 11p15 ICR1 hypomethylation. Clinical Epigenetics 2015

 

U Warnecke-Eberz, S-H Chon, A H Hölscher, U Drebber, E Bollschweiler. Exosomal onco-miRs from serum of patients with adenocarcinoma of the esophagus: comparison of miRNA profiles of exosomes and matching tumor. Tumor Biology 2015

 

L Chen, R Coleman, R Leang, H Tran, A Kopf, C M Walsh, I Sears-Kraxberger, O Steward, W B Macklin, J F Loring, T E Lane. Human Neural Precursor Cells Promote Neurologic Recovery in a Viral
Model of Multiple Sclerosis Stem Cell Reports, 2015

 

2014

Anastasia Petrova, Anna Celli, Laureen Jacquet,  Dimitra Dafou, Debra Crumrine,  Melanie Hupe, Matthew Arno, Carl Hobbs, Aleksandra Cvoro,  Panagiotis Karagiannis,  Liani Devito, Richard Sun, Lillian C. Adame, Robert Vaughan,  John A. McGrath,  Theodora M. Mauro and Dusko Ilic. 3D In Vitro Model of a Functional Epidermal Permeability Barrier from Human Embryonic Stem Cells and Induced Pluripotent Stem Cells. Stem Cell Reports, NCBI, 2014

 

P Wäster, I Rosdahl, K Öllinger. Cell fate regulated by nuclear factor-?B- and activator protein-1-dependent signalling in human melanocytes exposed to ultraviolet A and ultraviolet BPMC, 2014

 

J K Killian, M Miettinen, R L Walker, Y Wang, et al. Recurrent epimutation of SDHC in gastrointestinal stromal tumors  Science Translational Medicine, 2014

 

H Ma, R Morey, R C O'Neil et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature, 2014

 

S Wee, M Niklasson, V D Marinescu, A Segerman, L Schmidt, A Hermansson, P Dirks, K Forsberg-Nilsson, B Westermark, L Uhrbom, S Linnarsson, S Nelander, M Andäng. Selective Calcium Sensitivity in Immature Glioma Cancer Stem Cells. PLOS One, 2014

 

B B Khomtchouk, D J Van Booven, C Wahlestedt. HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline Source Code for Biology and Medicine, 2014

 

S J Li, M Dhaenens, A Garmyn, E Verbrugghe, P Van Rooij, S De Saeger, M Eeckhout, R Ducatelle, S Croubels, F Haesebrouck, D Deforce, F Pasmans, A Martel. Exposure of Aspergillus fumigatus to T-2 toxin results in a stress response associated with exacerbation of aspergillosis in poultry. World Mycotoxin Journal, 2014

 

M N Møller, S Kirkeby, J Vikeså, F C Nielsen, P Cayé-Thomasen. Gene Expression in the Human Endolymphatic Sac: The Solute Carrier Molecules in Endolymphatic Fluid Homeostasis. Otology & Neurotology, 2014

 

M Askmyr, H Ågerstam, H Lilljebjörn, N Hansen, C Karlsson, S von Palffy, N Landberg, C Högberg, C Lassen, M Rissler, J Richter, M Ehinger, M Järås, T Fioretos. Modeling chronic myeloid leukemia in immunodeficient mice reveals expansion of aberrant mast cells and accumulation of pre-B cells. Blood Cancer Journal, 2014

 

J Karlsson, H Lilljebjörn, L Holmquist Mengelbier, A Valind, M Rissler, I Øra, T Fioretos, D Gisselsson. Activation of human telomerase reverse transcriptase through gene fusion in clear cell sarcoma of the kidney. Cancer Letter, 2014

 

A Gronert Álvarez, P Fytili, P V Suneetha, R M Kraft Anke, C Brauner, J Schlue , T Krech, F Lehner, C Meyer-Heithuis, E Jäckel, J Klempnauer, M M Manns, M Cornberg, H Wedemeyer. Comprehensive phenotyping of regulatory T cells after liver transplantation. Liver Transplantation, 2014

 

N Skrbo, G-O Hjortland, A Kristian, R Holm, S Nord, L Prasmickaite, O Engebraaten, G M Mælandsmo, T Sørlie, K Andersen. Differential In Vivo Tumorigenicity of Distinct Subpopulations from a Luminal-Like Breast Cancer Xenograft. PLOS One, 2014

 

D Usoskin, A Furlan, S Islam, H Abdo, P Lönnerberg, D Lou, J Hjerling-Leffler, J Haeggström, O Kharchenko, P V Kharchenko, S Linnarsson, P Ernfors. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nature Neuroscience, 2014

 

D Berglind. Maternal obesity surgery: Effects in women, spouses and offspring. Karolinka Institutet, 2014

 

A Spadonia, M Guidarellia, J Phillipsb, M Maria, M Wisniewski. Transcriptional profiling of apple fruit in response to heat treatment: Involvement of a defense response during Penicillium expansum infection Postharvest Biology and Technology, 2014 

 

G Chirumbolo, F Ulbar, G Tolomelli, R Lewis, F Bonifazi, G Bandini, M Arpinati. A novel multiparameter risk score of chronic GVHD based on the measurement of IP10 (CXCL10) and plasmacytoid DC (pDC) in the peripheral blood at 3 months aftertransplant. Haematol, 2014 

 

K-M Andersson, D Kumar, J Bentzer, E Friman, D Ahrén, A Tunlid. Interspecific and host-related gene expression patterns in nematode-trapping fungi. BMC Genomics, 2014 

 

H Kempf, R Olmer, C Kropp, M Rückert, M Jara-Avaca, D Robles-Diaz, A Franke, DA Elliott, D Wojciechowski, M Fischer, AR Lara, G Kensah, I Gruh, A Haverich, U Martin, R Zweigerdt.  Controlling Expansion and Cardiomyogenic Differentiation of Human Pluripotent Stem Cells in Scalable Suspension Culture.  Stem Cell Reports, 2014 

 

J Roessler, O Ammerpohl, J Gutwein, D Steinemann, B Schlegelberger, V Weyer, M Sariyar, R Geffers, N Arnold, R Schmutzler, CR Bartram, T Heinrich, M Abbas, W Antonopoulos, E Schipper, B Hasemeier, H Kreipe & U Lehmann.  The CpG island methylator phenotype in breast cancer is associated with the lobular subtype.  Epigenomics, 2014 

 

S G Musharraf, AJ Siddiqui & S Mazhar.  Direct infusion ESI–MS analysis for metabolite profiling of human plasma using various fractionation techniques.  Bioanalysis, 2014 

 

S J Walker, M Colaco, DS Koslov, T Keys, RJ Evans, G H Badlani, K-E Andersson.  Transcriptome analysis of bladder biopsy from interstitial cystitis/bladder pain syndrome patients.  Genomics Data, 2014 

 

R Hoque, A Farooq, F Gorelick, W Z Mehal.  Beta-hydroxybutyrate and niacin protect the murine liver from acute inflammatory injury via activation of the Gpr109 receptor.  Hepatology, 2014 

 

D D Burra, O Berkowitz, P E Hedley, J Morris, S Resjö, F Levander, E Liljeroth, E Andreasson, E Alexandersson.  Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosumleading to resistance against Phytophthora infestans.  BioMed Central Plant Biology, 2014 

 

J Ouyang, W Ma, BW Zheng.  Stem Cells Gene Expression Profile After Hypochlorous acid Treatment.  Leaders in Pharmaceutical Business Intelligence, 2014 

 

A Dauksa, A Gulbinas, Z Endzinas, J Oldenburg, O El-Maarri.  DNA Methylation at Selected CpG Sites in Peripheral Blood Leukocytes Is Predictive Of Gastric Cancer.  Anticancer Research, 2014 

 

M Nordström, C Wingren, C Rose, A Bjartell, C Becker, H Lilja, K Borrebaeck.  Identification of plasma protein profiles associated with risk groups of prostate cancer patients. PROTEOMICS - Clinical Applications, 2014 

 

D Ansari, R Andersson, M P Bauden, B Andersson.... Protein deep sequencing applied to biobank samples from patients with pancreatic cancer. Journal of Cancer Research and Clinical Oncology, 2014 

 

S Marwitz, J Kolarova, M Reck, N Reinmuth, C Kugler. The tissue is the issue: improved methylome analysis from paraffin-embedded tissues by application of the HOPE technique. Laboratory Investigation, 2014 

 

P Sui, H Watanabe, M H Ossipov, G Bakalkin. Proteomics of Neuropathic Pain: Proteins and Signaling Pathways Affected in a Rat Model.  Journal of Proteome research…, 2014

 

M Negrini, G Cutrona, C Bassi, S Fabris, B Zagatti. MicroRNAome expression in chronic lymphocytic leukemia: comparison with normal B cell subsets and correlations with prognostic and clinical parameters. Clinical Cancer Research, 2014

 

B Ayoglu, A Chaouch, H Lochmüller, L Politano. Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies.  EMBO Molecular Medicine, 2014

 

M J Larsen, M Thomassen, Q Tan, K P Sørensen.  Microarray-basedRNA profiling of breast cancer: Batch effect removal improves cross-platform consistency. BioMed Research International, 2014 

 

L M Wolfe, R D Thiagarajan, F Boscolo, V Taché. Banking Placental Tissue: An Optimized Collection Procedure for Genome-Wide Analysis of Nucleic Acids. Placenta, 2014

 

X Zhang, B Mozeleski, S Lemoine, E Dériaud, A Lim. CD4 T Cells with Effector Memory Phenotype and Function Develop in the Sterile Environment of the Fetus. Science Translational Medicine…, 2014

 

V L Luchenko, T Litman, A R Chakraborty, A Heffner. Histone deacetylase inhibitor-mediated cell death is distinct from its global effect on chromatin. Molecular Oncology, 2014

 

K Hamre, S Penglase, J D Rasinger, K H Skjærven. Ontogeny of redox regulation in Atlantic cod (< i> Gadus morhua</i>) larvae, Free Radical Biology and Medicine,  2014

 

M Colaco, D S Koslov, T Keys, R J Evans, G H Badlani...Correlation of Gene Expression with Bladder Capacity in Interstitial Cystitis/Bladder Pain Syndrome. The Journal of Urology, 2014

 

A Forreryd, H Johansson, A S Albrekt, M Lindstedt.  Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization. BMC Genomics, 2014

 

S Noack, V Seiffart, E Willbold, S Laggies, A Winkel. Periostin secreted by mesenchymal stem cells supports tendon formation in an ectopic mouse model. Stem Cells and Development, 2014

 

J Kozlowska, L S Vermeer, G B Rogers, N Rehnnuma. Combined Systems Approaches Reveal Highly Plastic Responses to Antimicrobial Peptide Challenge in Escherichia coli. PLOS Pathogens, 2014

 

T Bengtsson, D Weighill, E Proux-Wéra, F Levander.  Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach. BMC Genomics. 2014 

 

L Jønson, J Christiansen, TVO Hansen, J Vikeså. IMP3 RNP Safe Houses Prevent miRNA-Directed< i> HMGA2</i> mRNA Decay in Cancer and Development. Cell Reports, 2014

 

CT Wallington-Beddoe, JA Powell, D Tong, SM Pitson. Sphingosine Kinase 2 Promotes Acute Lymphoblastic Leukemia by Enhancing MYC Expression. Cancer Research, 2014

 

JD Rasinger, TS Carroll, AK Lundebye, C Hogstrand. Cross-omics gene and protein expression profiling in juvenile female mice highlights disruption of calcium and zinc signalling in the brain following dietary exposure to CB-153, BDE-47, HBCD or TCDD. Toxicology, 2014

 

H Johansson, F Rydnert, J Kühnl, AG Schepky. GARD in-House Validation–A Proof of Concept. Toxicological Sciences, 2014

 

F Pauly, KE Smedby, M Jerkeman, H Hjalgrim.  Identification of B-cell lymphoma subsets by plasma protein profiling using recombinant antibody microarrays. Leukemia Research, 2014

 

D Duffy, V Rouilly, V Libri, M Hasan, B Beitz, M David, A Urrutia, A Bisiaux, ST LaBrie, A Dubois, IG Boneca, C Delval, S Thomas, L Rogge, M Schmolz, L Quintana-Murci, and ML Albert for The Milieu Interieur Consortium. Functional Analysis via Standardized Whole-Blood Stimulation Systems Defines the Boundaries of a Healthy Immune Response to Complex Stimuli. Immunity, 2014

 

Darragh Duffy, Rasha Mamdouh, Melissa Laird, Charlotte Soneson ,Lenaig Le Fouler, Maï El-Daly,7,Armanda Casrouge, Jérémie Decalf, Amal Abbas, Noha Sharaf Eldin, Magnus Fontes, Mohamed Abdel-Hamid, Mostafa K. Mohamed, Mona Rafik, Arnaud Fontanet andMatthew L. Albert. The ABCs of viral hepatitis that define biomarker signatures of acute viral hepatitis. Hepatology, 2014

 

M Fontes, C Soneson. METHOD FOR ROBUST COMPARISON OF DATA. US Patent 20,140,074,864, 2014

 

A Stevens, C Bonshek,  A WhatmoreI Butcher...Insights into the pathophysiology of catch-up compared with non-catch-up growth in children born small for gestational age: an integrated analysis of metabolic and transcriptomic data.The Pharmacogenomics Journal, 2014

 

PM Tørring, MJ Larsen, AD Kjeldsen, LB Ousager. Long Non-Coding RNA Expression Profiles in Hereditary Haemorrhagic Telangiectasia. PLOS ONE, 2014

 

S Resjö, A Ali, HJG Meijer, MF Seidl, B Snel, M Sandin. Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members. Journal of Proteome, 2014…

 

KM Roupé, S Veerla, J Olson, EL Stone, OE Sørensen. Transcription Factor Binding Site Analysis Identifies FOXO Transcription Factors as Regulators of the Cutaneous Wound Healing Process. PLOS ONE, 2014

 

AS Albrekt, H Johansson, A Börje, C Borrebaeck. Skin sensitizers differentially regulate signaling pathways in MUTZ-3 cells in relation to their individual potency. BMC Pharmacology and …, 2014

 

C Friemel, O Ammerpohl, J Gutwein, AG Schmutzler. Array-based DNA methylation profiling in male infertility reveals allele-specific DNA methylation in< i> PIWIL1</i> and< i> PIWIL2</i. Fertility and Sterility, 2014

 

ML Wissing, SG Kristensen, CY Andersen. Identification of new ovulation-related genes in humans by comparing the transcriptome of granulosa cells before and after ovulation triggering in the same controlled. Human Reproduction, 2014

 

AP Vitins, AS Kienhuis, EN Speksnijder. Mechanisms of amiodarone and valproic acid induced liver steatosis in mouse in vivo act as a template for other hepatotoxicity models. Archives of Toxicology, 2014

 

N Bayatti, J Cooper-Knock, JJ Bury, M Wyles, PR Heath. Comparison of Blood RNA Extraction Methods Used for Gene Expression Profiling in Amyotrophic Lateral Sclerosis. PLOS ONE, 2014

 

ZX Chen, K Wallis, SM Fell, VR Sobrado, MC Hemmer. RNA helicase A is a downstream mediator of KIF1Bß tumor suppressor function in neuroblastoma. Cancer Discovery, 2014

 

MJ Larsen, M Thomassen, Q Tan, AV Lænkholm. RNA profiling reveals familial aggregation of molecular subtypes in non-BRCA1/2 breast cancer families. BMC Medical Genomics, 2014

J Karlsson, L Holmquist Mengelbier, CD Ciornei. Clear cell sarcoma of the kidney demonstrates an embryonic signature indicative of a primitive nephrogenic origin. Genes, Chromosomes and Cancer, 2014 

 

CAK Borrebaeck, G Sturfelt, C Wingren. Recombinant Antibody Microarray for Profiling the Serum Proteome of SLE. Systemic Lupus Erythematosus, 2014

 

HG Evans, U Roostalu, GJ Walter, NJ Gullick. TNF-a blockade induces IL-10 expression in human CD4+ T cells. Nature Communications, 2014

MJ Larsen, M Thomassen, Q Tan, AV Lænkholm. RNA profiling reveals familial aggregation of molecular subtypes in non-BRCA1/2 breast cancer families. BMC Medical Genomics, 2014

 

N Bayatti, J Cooper-Knock, JJ Bury, M Wyles, PR Heath. Comparison of Blood RNA Extraction Methods Used for Gene Expression Profiling in Amyotrophic Lateral Sclerosis. PLOS ONE, 2014

 

N ZX Chen, K Wallis, SM Fell, VR Sobrado, MC Hemmer.  RNA helicase A is a downstream mediator of KIF1Bß tumor suppressor function in neuroblastoma. Cancer Discovery, 2014


J Michalek, E Izbicka, RT Streeper, C Louden. METHODS OF IDENTIFICATION AND DIAGNOSIS
OF LUNG DISEASES USING CLASSIFICATION SYSTEMS AND KITS THEREOF. US Patent 20,140,024,553, 2014

 

T Fioretos, M Jaras. Anti-IL1RAP Antibodies and Their Use for Treating Human. US Patent 20,140,017,167, 2014

 

M Abbas, J Salem, A Stucki-Koch, M Rickmann, Expression of angiogenic factors is increased in metastasised renal cellcarcinomas. Springer Link, 2014  

 

Tania Witte , Christoph Plass1, and Clarissa Gerhauser. Pan-cancer patterns of DNA methylation, Genome Medicine 2014

 

2013

M Thibonnier. MIRNA MODULATORS OF THERMOGENESIS. US Patent 20,130,331,433, 2013. 

 

A Wilbertz, S Fey, J Obländer, V Nowak, J Vogler. Array-Based Integrative Analysis Of Epigenomic and Transcriptomic Alterations In CD71+ Bone Marrow Erythroprogenitor Cells From Patients With Myelodysplastic …Blood, 2013

 

L Al-Khalili, TC Barbosa, J Östling, J Massart. Profiling of human myotubes reveals an intrinsic proteomic signature associated with type 2 diabetes. Translational Proteomics, 2013

 

X Lin, J Li, G Yin, Q Zhao, D Elias, AE Lykkesfeldt. Integrative analyses of gene expression and DNA methylation profiles in breast cancer cell line models of tamoxifen-resistance indicate a potential. Breast Cancer Research, 2013

 

G Macchia, KH Nord, G D'Alessandro, J Nilsson. Rearrangements of chromosome bands 15q12-q21 are secondary to HMGA2 deregulation in conventional lipoma. Oncology Reports

 

L Quagliata, M Andreozzi, M Kovac, L Tornillo. SH2D4A is frequently downregulated in hepatocellular carcinoma and cirrhotic nodules. European Journal of Cancer, 2013

 

KP Sørensen, M Thomassen, Q Tan, M Bak, S Cold. Long non-coding RNA HOTAIR is an independent prognostic marker of metastasis in estrogen receptor-positive primary breast cance. Breast Cancer Research …, 2013

 

J Heinzelmann, A Unrein, U Wickmann, S Baumgart. MicroRNAs with Prognostic Potential for Metastasis in Clear Cell Renal Cell Carcinoma: A Comparison of Primary Tumors and Distant Metastases. Annals of Surgical Oncology, 2013

 

M Fontes. COMPUTER-IMPLEMENTED METHOD FOR ANALYZING MULTIVARIATE DATA. US Patent 20,130,304,783, 2013

 

KH Nord, J Nilsson, E Arbajian, FV von Steyern. Recurrent Chromosome 22 Deletions in Osteoblastoma Affect Inhibitors of the Wnt/Beta-Catenin Signaling Pathway. PLOS ONE, 2013

 

T Meerupati, KM Andersson, E Friman, D Kumar. Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi. PLOS Genetics, 2013

 

L Vilanova, M Wisniewski, J Norelli, I Viñas, R Torres. Transcriptomic Profiling of Apple in Response to Inoculation with a Pathogen (Penicillium expansum) and a Non-pathogen (Penicillium digitatum). Plant Molecular Biology Reporter

 

CAK Borrebaeck, LBC Wingren. BIOMARKER SIGNATURES AND USES THEREOF. US Patent 20,130,288,912, 2013

 

S Lunemann, DFG Malone, J Hengst, K Port. Compromised function of natural killer cells in acute and chronic viral hepatitis. Journal of Infectious …, 2013

 

SG Musharraf, S Mazhar, AJ Siddiqui, MI Choudhary. Metabolite Profiling of Human Plasma by Different Extraction Methods through Gas Chromatography-Mass Spectrometry-An
Objective Comparison. Analytica Chimica Acta, 2013

 

D Duffy, R Saleh, M Laird, C Soneson, LL Fouler. The ABCs of viral hepatitis that define biomarker signatures of acute viral hepatitis. Hepatology, 2013

 

M Lindstedt, CAK Borrebaeck, H Johansson, A Albrekt. Analytical Methods and Arrays for Use in the Same. US Patent 20,130,274,134, 2013

 

Clayton P, Chatelain P, Tatò L, Yoo HW, Ambler GR, Belgorosky A, Quinteiro S, Deal C, Stevens A, Raelson J, Croteau P,Destenaves B, Olivier C. A pharmacogenomic approach to the treatment of children with GH deficiency or Turner syndrome. Eur J Endocrinol, 2013.

 

R Ratzer, HB Søndergaard, JR Christensen, L Börnsen. Gene expression analysis of relapsing–remitting, primary progressive and secondary progressive multiple sclerosis. Multiple Sclerosis Journal, 2013.

 

R Albrechtsen, M Kveiborg, D Stautz, J Vikeså, JB Noer. ADAM12 redistributes and activates MMP-14, resulting in gelatin degradation, reduced apoptosis, and increased tumor growth. Journal of Cell Science, 2013.


O Ammerpohl, S Bens, M Appari, R Werner, B Korn. Androgen Receptor Function Links Human Sexual Dimorphism to DNA Methylation. PLOS ONE, 2013. 

 

Y Li, M Moretto-Zita, F Soncin, A Wakeland, L Wolfe. BMP4-directed trophoblast differentiation of human embryonic stem cells is mediated through a ?Np63+ cytotrophoblast stem cell state. Development, 2013. 

 

A Mohajeri, J Tayebwa, A Collin, J Nilsson. Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor. Genes, Chromosomes & Cancer, 2013

 

S Goyama, J Schibler, L Cunningham, Y Zhang, Y Rao. Transcription factor RUNX1 promotes survival of acute myeloid leukemia cells. The Journal of Clinical Investigaton, 2013

 

J Davidsson, S Veerla, B Johansson. Constitutional trisomy 8 mosaicism as a model for epigenetic studies of aneuploidy. Epigenetics & Chromatin, 2013

 

P Mur, M Mollejo, Y Ruano, ÁR de Lope, C Fiaño. Codeletion of 1p and 19q determines distinct gene methylation and expression profiles in IDH-mutated oligodendroglial tumors. Acta Neuropathologica, 2013.

 

L Freitag, C von Kaisenberg, H Kreipe, K Hussein. Expression analysis of leukocytes attracting cytokines in chronic histiocytic intervillositis of the placenta.  Int J Clin Exp Pathol, 2013.

 

F Rineau, F Shah, MM Smits, P Persson, T Johansson. Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus. The ISME Journal, 2013.

 

K JÄÄGER. Differentiation and heterogeneity of mesenchymal stem cells. Thesis/Science Dep of Gene Technology, Tallin University of Technology.

 

A Stevens, D Hanson, A Whatmore, B Destenaves. Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks. BMC Genomics, 2013.

 

J Davidsson, S Veerla, B Johansson. Constitutional trisomy 8 mosaicism as a model for epigenetic studies of aneuploidy. Epigenetics & Chromatin, 2013.

 

AK Coussens, RJ Wilkinson, V Nikolayevskyy. Ethnic Variation in Inflammatory Profile in Tuberculosis. PLoS Pathogens, 2013.

 

V O'brien, C Hillier. CELL CHARACTERISATION. US Patent 20,130,196,875, 2013

 

F Shah, F Rineau, B Canbäck, T Johansson, A Tunlid. The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus. New Phytologist, 2013

 

S Abdelhady, SS Kitambi, V Lundin, R Aufschnaiter. Erg Channel Is Critical in Controlling Cell Volume during Cell Cycle in Embryonic Stem Cells. PLOS ONE, 2013.

 

M Ahrens, O Ammerpohl, W von Schönfels, J Kolarova. DNA Methylation Analysis in Nonalcoholic Fatty Liver Disease Suggests Distinct Disease-Specific and Remodeling Signatures after Bariatric Surgery. Cell Metabolism, 2013.

 

F Rineau, F Shah, MM Smits, P Persson, T Johansson. Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus. The ISME Journal, 2013. 

 

K Jääger. Differentiation and heterogeneity of mesenchymal stem cells. Thesis on natural and exact sciences, Tallin University of Technology, Faculty of Science Dep of Gene Technology, 2013.

 

P Mur, M Mollejo, Y Ruano, ÁR de Lope, C Fiaño. Codeletion of 1p and 19q determines distinct gene methylation and expression profiles in IDH-mutated oligodendroglial tumors. Acta Neuropathologica, 2013.

 

L Freitag, C von Kaisenberg, H Kreipe, K Hussein. Expression analysis of leukocytes attracting cytokines in chronic histiocytic intervillositis of the placenta. Int J Clin Exp Pathol, 2013.

 

F Rineau, F Shah, MM Smits, P Persson, T Johansson. Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus. The ISME Journal, 2013

 

SAB Hermsen, TE Pronk, EJ van den Brandhof. Transcriptomic analysis in the developing zebrafish embryo after compound exposure: individual gene expression and pathway regulation. Toxicology and Applied Pharmacology, 2013

 

A Mohajeri, J Tayebwa, A Collin, J Nilsson. Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene …Genes, Chromosomes & Cancer, 2013

 

KM Andersson, T Meerupati, F Levander, E Friman. Characterization of the proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum. Applied and Environmental Microbiology, 2013

 

Martin.J Larsen, Torben A.Kruse, Anne-Vibeke Laenkholm, Martin Bak, Anne E.Lykkesfeldt, Kristina P.Sörensen, Thomas v.O Hansen, Bent Ejlertsen, Anne-Marie Gerdes, Mads Thomassen. Classifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling. PLOS One, 2013

 

A Harish, A Tunlid, CG Kurland. Rooted phylogeny of the three superkingdoms. Biochimie, 2013

S.Salehi, H.C Brereton, M.J Arno, , D.Darling, A.Quaglia, J.O Grady, N.Heaton, V.R Aluvihare. Human Liver Regeneration Is Characterized by the Coordinated Expression of Distinct MicroRNA Governing Cell Cycle Fate. American Journal of Transplantation.  May 2013

 

D Chen, A Persson, Y Sun, LG Salford, DG Nord. Better Prognosis of Patients with Glioma
Expressing FGF2-Dependent PDGFRA Irrespective of Morphological Diagnosis. PLOS ONE, 2013

 

A  Stevens, P Clayton, L Tatò, HW Yoo. Pharmacogenomics of insulin-like growth
factor-I generation during GH treatment in children with GH deficiency or Turner
syndrome. The pharmacogenomics , 2013 

 

JK Killian, SY Kim, M Miettinen, C Smith, M Merino. Succinate dehydrogenase mutation
underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discovery, 2013

 

R Gonzalez, I Garitaonandia, T Abramihina. Deriving dopaminergic neurons for
clinical use. A practical approach. Scientific Reports, 2013 

 

S Ohrt-Nissen, KBV Døssing, M Rossing, C Lajer. Characterization of miRNA expression in
human degenerative lumbar discs. Connective Tissue …, 2013

 

D Jacobson, AR Monforte, AC Silva Ferreira. Untangling the chemistry of Port wine aging with the use of GC-FID, multivariate statistics and network reconstruction.  Journal of Agricultural and Food Chemistry 2013

D Joshi, S Salehi, H Brereton, M Arno, A Quaglia. Distinct MicroRNA profiles are associated with severity of HCV recurrence and acute cellular rejection after liver transplant. Liver Transplantation, 2013

 

ED Foucher, S Blanchard, L Preisser, E Garo, N Ifrah. IL-34 Induces the Differentiation of Human Monocytes into Immunosuppressive Macrophages. Antagonistic Effects of GM-CSF and IFN?. PLOS ONE, 2013

 

SL Anwar, C Albat, T Krech, B Hasemeier, E Schipper. Concordant hypermethylation of intergenic microRNA genes in human hepatocellular carcinoma as new diagnostic and prognostic marker. International Journal of Cancer, 2013

 

K Lundberg, AS Albrekt, I Nelissen, S Santegoets. Transcriptional Profiling of Human Dendritic Cell Populations and Models-Unique Profiles of In Vitro Dendritic Cells and Implications on Functionality and Applicability. PLOS ONE, 2013

 

2012 

Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Höög A, Juhlin CC, Hartman J, Larsson. Evidence of a functional estrogen receptor in parathyroid adenomas. J Clin Endocrinol Metab, 2012

 

Mlisana K, Naicker N, Werner L, Roberts L, van Loggerenberg F, Baxter C,
Passmore JA, Grobler AC, Sturm AW, Williamson C, Ronacher K, Walzl G, Abdool
Karim SS. Symptomatic vaginal discharge is a poor predictor of sexually transmitted infections and genital tract inflammation in high-risk women in South AfricaJ Infect Dis, 2012

 

RT Streeper, E Izbicka, SH Baek. METHODS OF IDENTIFICATION, ASSESSMENT,
PREVENTION AND THERAPY OF LUNG DISEASES AND KITS THEREOF. US Patent 20,120,302,455, 2012

 

S Alagaratnam, NJ Harrison, AC Bakken, AM Hoff. Transforming pluripotency: an exon-level
study of malignancy-specific transcripts in human embryonal carcinoma and
embryonic stem cells. Stem Cells and Development

 

OJ Matthew, PF Laura, PR Francesca, MB Peter. Functional characterisation of long
chain prenyl diphosphate synthases from tomato. Biochemical Journal, 2013


Muhie, R Hammamieh, C Cummings, D Yang, M Jett. Transcriptome characterization of immune
suppression from battlefield-like stress. Genes and Immunity, 2012

 

F Yadetie, OA Karlsen, A Lanzén, K Berg, P Olsvik. Global transcriptome analysis of
Atlantic cod (Gadus morhua) liver after in vivo methylmercury exposure suggests effects on energy metabolism. Aquatic Toxicology, 2012

 

H Johansson, AS Albrekt, Carl Borrebaeck, M Lindstedt. The GARD assay for assessment of
chemical skin sensitizers. Toxicology in Vitro, 2012

 

YF Wong, PD Wilson, RJ Unwin, JT Norman, M Arno. Retinoic Acid Receptor-Dependent,
Cell-Autonomous, Endogenous Retinoic Acid Signaling and Its Target Genes in
Mouse Collecting Duct Cells. PLOS ONE, 2012

 

J Carlsson, G Helenius, M Karlsson, O Andrén. Differences in microRNA expression during tumor development in thetransition and peripheral zones of the prostate. oru.diva-portal.org

 

M FONTES, C SONESON. Method for robust comparison of data. WO Patent 2,012,123,374, 2012

 

KH Nord, K Paulsson, S Veerla, J Wejde, O Brosjö. Retained Heterodisomy Is Associated with
High Gene Expression in Hyperhaploid Inflammatory Leiomyosarcoma. Neoplasia 2012

 

T Fioretos, M Järås. Novel Agents and Uses Thereof. US Patent 20,120,225,059, 2012

 

AK Coussens, RJ Wilkinson, Y Hanifa, V Nikolayevskyy. Vitamin D accelerates resolution of inflammatory responses during tuberculosis treatment. Proceedings of the National Academy of Sciences of the United States of America,  PNAS, 2012.

 

A Sandström, R Andersson, R Segersvärd, ZM Löhr. Serum proteome profiling of pancreatitis
using recombinant antibody microarrays reveals disease-associated biomarker.  Proteomics-Clinical,  2012

 

P Sekyrova, J Östblom. Blebbing as a physical force in cancer EMT-Parallels with mitosis. Seminars in Cancer Biology, 2012

 

K Jääger, S Islam, P Zajac, S Linnarsson. RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis-and Adipose-Derived Stromal Stem Cells. PLoS ONE, 2012

 

C Eckmann-Scholz, S Bens, J Kolarova. DNA-Methylation Profiling of Fetal Tissues Reveals Marked Epigenetic Differences between Chorionic and Amniotic Samples. PLoS ONE, 2012

 

PR Young, JG Lashbrooke, E Alexandersson.  The genes and enzymes of the carotenoid biosynthetic pathway in Vitis vinifera L. BMC Genomics, 2012

 

B Sadeghi, H Al-Chaqmaqchi, S Al-Hashmi. Early-phase GVHD gene expression profile in target versus non-target tissues: kidney, a possible target?  Bone Marrow,  2012

 

J Taneera, S Lang, A Sharma, J Fadista, Y Zhou. A Systems Genetics Approach Identifies Genes and Pathways for Type 2 Diabetes in Human Islets. Cell Metabolism, 2012

 

J Gaedcke, M Grade, J Camps, R Sokilde. The rectal cancer microRNAome-microRNA expression in rectal cancer and matched normal mucosa. Clinical Cancer Research, 2012

 

KA Serikawa, S Jacobsen, D Lundsgaard, BA Fox. Detection of gene expression signatures related to underlying disease and treatment in rheumatoid arthritis patients. Modern Rheumatology, 2012

 

MB Lyng, AV Lænkholm, R Søkilde, KH Gravgaard. Global MicroRNA Expression Profiling of High-Risk ER+ Breast Cancers from Patients Receiving Adjuvant Tamoxifen Mono-Therapy: A DBCG Study. PLoS ONE, 2012

 

C Riou, BP Peixoto, L Roberts, K Ronacher. Effect of Standard Tuberculosis Treatment on Plasma Cytokine Levels in Patients with Active Pulmonary Tuberculosis; PLoS ONE, 2012

 

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

 

2011-2010

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.