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SCIBLU

Lund University

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Publications

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2015

Lauss M, Haq R, Cirenajwis H, et al. Genome-Wide DNA Methylation Analysis in Melanoma Reveals the Importance of CpG Methylation in MITF Regulation. J. Invest. Dermatol. 2015. doi:10.1038/jid.2015.61.

Langen B, Rudqvist N, Parris TZ, et al. Transcriptional response in normal mouse tissues after i.v. 211At administration - response related to absorbed dose, dose rate, and time. EJNMMI Res. 2015;5(1):1. doi:10.1186/s13550-014-0078-7.

Saal LH, Vallon-Christersson J, Häkkinen J, et al. The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine. Genome Med. 2015;7(1):20. doi:10.1186/s13073-015-0131-9.

Taneera J, Fadista J, Ahlqvist E, et al. Identification of novel genes for glucose metabolism based upon expression pattern in human islets and effect on insulin secretion and glycemia. Hum. Mol. Genet. 2015;24(7):1945-55. doi:10.1093/hmg/ddu610.

 

2014

Hall E, Volkov P, Dayeh T, et al. Sex differences in the genome-wide DNA methylation pattern and impact on gene expression, microRNA levels and insulin secretion in human pancreatic islets. Genome Biol. 2014;15(12):522. doi:10.1186/s13059-014-0522-z.

Holmgren G, Synnergren J, Bogestål Y, et al. Identification of novel biomarkers for doxorubicin-induced toxicity in human cardiomyocytes derived from pluripotent stem cells. Toxicology 2015;328:102-11. doi:10.1016/j.tox.2014.12.018.

Taneera J, Storm P, Groop L. Downregulation of type II diabetes mellitus and maturity onset diabetes of young pathways in human pancreatic islets from hyperglycemic donors. J. Diabetes Res. 2014;2014:237535. doi:10.1155/2014/237535.

Hansson B, Naurin S, Hasselquist D. Does inbreeding affect gene expression in birds? Biol. Lett. 2014;10(9):20140648-20140648. doi:10.1098/rsbl.2014.0648.

Hall E, Volkov P, Dayeh T, et al. Effects of palmitate on genome-wide mRNA expression and DNA methylation patterns in human pancreatic islets. BMC Med. 2014;12(1):103. doi:10.1186/1741-7015-12-103.

Safavi S, Hansson M, Karlsson K, Biloglav A, Johansson B, Paulsson K: Novel gene targets detected by genomic profiling in a consecutive series of 126 adult acute lymphoblastic leukemia cases. Haematologica 2014.

Karlsson A, Jonsson M, Lauss M, Brunnström H, Jönsson P, Borg A, Jönsson G, Ringner M, Planck M, Staaf J: Genome-wide DNA methylation analysis of lung carcinoma reveals one neuorendocrine and four adenocarcinoma epitypes associated with patient outcome. Clin Cancer Res 2014.

Styring E, Seinen J, Dominguez-Valentin M, Domanski HA, Jönsson M, von Steyern F V, Hoekstra HJ, Suurmeijer AJH, Nilbert M. Key roles for MYC, KIT and RET signaling in secondary angiosarcomas. Br J Cancer 2014, 111: 407–12

Jönsson J-M, Bartuma K, Dominguez-Valentin M, Harbst K, Ketabi Z, Malander S, et al. Distinct gene expression profiles in ovarian cancer linked to Lynch syndrome. Fam. Cancer (2014). doi:10.1007/s10689-014-9728-1

Jönsson J-M, Johansson I, Dominguez-Valentin M, Kimbung S, Jönsson M, Bonde JH, et al. Molecular subtyping of serous ovarian tumors reveals multiple connections to intrinsic breast cancer subtypes. PLoS One 2014, 9, e107643.

Styring E, Seinen J, Dominguez-Valentin M, et al. Key roles for MYC, KIT and RET signaling in secondary angiosarcomas. Br. J. Cancer 2014;111(2):407-12. doi:10.1038/bjc.2014.359.

Schüler E, Rudqvist N, Parris TZ, Langen B, Helou K, Forssell-Aronsson E. Transcriptional response of kidney tissue after 177Lu-octreotate administration in mice. Nucl. Med. Biol. 2014;41(3):238-247. doi:10.1016/j.nucmedbio.2013.12.001.

Roupé KM, Veerla S, Olson J, Stone EL, Sørensen OE, Hedrick SM, Nizet V: Transcription Factor Binding Site Analysis Identifies FOXO Transcription Factors as Regulators of the Cutaneous Wound Healing Process. PLoS One 2014, 9:e89274.

Samraj AK, Müller AH, Grell A-S, Edvinsson L: Role of unphosphorylated transcription factor STAT3 in late cerebral ischemia after subarachnoid hemorrhage. J Cereb Blood Flow Metab 2014.

Schüler E, Rudqvist N, Parris TZ, et al. Time- and dose rate-related effects of internal (177)Lu exposure on gene expression in mouse kidney tissue. Nucl. Med. Biol. 2014;41(10):825-32. doi:10.1016/j.nucmedbio.2014.07.010.

Rudqvist N, Schüler E, Parris TZ, Langen B, Helou K, Forssell-Aronsson E. Dose-specific transcriptional responses in thyroid tissue in mice after (131)I administration. Nucl. Med. Biol. 2015;42(3):263-8. doi:10.1016/j.nucmedbio.2014.11.006.

Dai X, Li L, Liu X, Hu W, Yang Y, Bai Z. Cooperation of DLC1 and CDK6 affects breast cancer clinical outcome. G3 (Bethesda). 2014;5(1):81-91. doi:10.1534/g3.114.014894.

 

2013

Kucharzewska P, Christianson HC, Welch JE, Svensson KJ, Fredlund E, Ringnér M, Mörgelin M, Bourseau-Guilmain E, Bengzon J, Belting M. Exosomes reflect the hypoxic status of glioma cells and mediate hypoxia-dependent activation of vascular cells during tumor development. Proc Natl Acad Sci U S A 2013, 110: 7312–7.

Langen B, Rudqvist N, Parris TZ, Schüler E, Helou K, Forssell-Aronsson E. Comparative analysis of transcriptional gene regulation indicates similar physiologic response in mouse tissues at low absorbed doses from intravenously administered 211At. J. Nucl. Med. 2013;54(6):990-8. doi:10.2967/jnumed.112.114462.

Safavi S, Forestier E, Golovleva I, Barbany G, Nord KH, Moorman A V, Harrison CJ, Johansson B, Paulsson K: Loss of chromosomes is the primary event in near-haploid and low-hypodiploid acute lymphoblastic leukemia. Leukemia 2013, 27:248–50.

Ekman M, Bhattachariya A, Dahan D, Uvelius B, Albinsson S, Swärd K: Mir-29 repression in bladder outlet obstruction contributes to matrix remodeling and altered stiffness. PLoS One 2013, 8:e82308.

Nord KH, Nilsson J, Arbajian E, Vult von Steyern F, Brosjö O, Cleton-Jansen A-M, Szuhai K, Hogendoorn PCW: Recurrent chromosome 22 deletions in osteoblastoma affect inhibitors of the wnt/beta-catenin signaling pathway. PLoS One 2013, 8:e80725.

Mohajeri A, Tayebwa J, Collin A, Nilsson J, Magnusson L, von Steyern FV, Brosjö O, Domanski HA, Larsson O, Sciot R, Debiec-Rychter M, Hornick JL, Mandahl N, Nord KH, Mertens F: 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, 52:873–86.

Rasmussen AA, Kandasamy D, Beck H, Crosby SD, Björnberg O, Schnackerz KD, Piskur J: Global expression analysis in the yeast Lachancea (Saccharomyces) kluyveri revealed new URC genes involved in pyrimidine catabolism. Eukaryot Cell 2013

Hashemi J, Fotouhi O, Sulaiman L, Kjellman M, Höög A, Zedenius J, Larsson C: Copy number alterations in small intestinal neuroendocrine tumors determined by array comparative genomic hybridization. BMC Cancer 2013, 13:505.

Langen B, Rudqvist N, Parris TZ, Schüler E, Helou K, Forssell-Aronsson E: Comparative analysis of transcriptional gene regulation indicates similar physiologic response in mouse tissues at low absorbed doses from intravenously administered 211At. J Nucl Med 2013, 54:990–8.

Danielsson A, Claesson K, Parris TZ, Helou K, Nemes S, Elmroth K, Elgqvist J, Jensen H, Hultborn R: Differential gene expression in human fibroblasts after alpha-particle emitter (211)At compared with (60)Co irradiation. Int J Radiat Biol 2013, 89:250–8.

Hall E, Dayeh T, Kirkpatrick CL, Wollheim CB, Dekker Nitert M, Ling C: DNA methylation of the glucagon-like peptide 1 receptor (GLP1R) in human pancreatic islets. BMC Med Genet 2013, 14:76.

Swärd K, Sadegh MK, Mori M, Erjefält JS, Rippe C: Elevated pulmonary arterial pressure and altered expression of Ddah1 and Arg1 in mice lacking cavin-1/PTRF. Physiol Rep 2013, 1

Therkildsen C, Jönsson G, Dominguez-Valentin M, Nissen A, Rambech E, Halvarsson B, Bernstein I, Borg Å, Nilbert M: Gain of chromosomal region 20q and loss of 18 discriminates between Lynch syndrome and familial colorectal cancer. Eur J Cancer 2013, 49:1226–1235.

Rönn T, Volkov P, Davegårdh C, Dayeh T, Hall E, Olsson AH, Nilsson E, Tornberg A, Dekker Nitert M, Eriksson K-F, Jones HA, Groop L, Ling C: A six months exercise intervention influences the genome-wide DNA methylation pattern in human adipose tissue. PLoS Genet 2013, 9:e1003572.

Johansson I, Ringnér M, Hedenfalk I: The Landscape of Candidate Driver Genes Differs between Male and Female Breast Cancer. PLoS One 2013, 8:e78299.

Johansson H, Albrekt A-S, Borrebaeck CAK, Lindstedt M: The GARD assay for assessment of chemical skin sensitizers. Toxicol In Vitro 2013, 27:1163–9.

Lundberg K, Albrekt A-S, Nelissen I, Santegoets S, de Gruijl TD, Gibbs S, Lindstedt M: 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, 8:e52875.

Planck M, Isaksson S, Veerla S, Staaf J: Identification of transcriptional subgroups in EGFR-mutated and EGFR/KRAS wild-type lung adenocarcinoma reveals gene signatures associated with patient outcome. Clin Cancer Res 2013, 19:5116–26.

Davidsson J, Veerla S, Johansson B: Constitutional trisomy 8 mosaicism as a model for epigenetic studies of aneuploidy. Epigenetics Chromatin 2013, 6:18.

Nord KH, Macchia G, Tayebwa J, Nilsson J, Vult von Steyern F, Brosjö O, Mandahl N, Mertens F: Integrative genome and transcriptome analyses reveal two distinct types of ring chromosome in soft tissue sarcomas. Hum Mol Genet 2013.

Dominguez-Valentin M, Therkildsen C, Veerla S, Jönsson M, Bernstein I, Borg A, Nilbert M: Distinct gene expression signatures in lynch syndrome and familial colorectal cancer type x. PLoS One 2013, 8:e71755.

Frings O, Augsten M, Tobin NP, Carlson J, Paulsson J, Pena C, Olsson E, Veerla S, Bergh J, Ostman A, Sonnhammer E: Prognostic Significance in Breast Cancer of a Gene Signature Capturing Stromal PDGF Signaling. The American journal of pathology 2013, 10.1016/j.ajpath.2013.02.018

Storry JR, Jöud M, Christophersen MK, Thuresson B, Akerström B, Sojka BN, Nilsson B, Olsson ML: Homozygosity for a null allele of SMIM1 defines the Vel-negative blood group phenotype. Nature genetics 2013, 10.1038/ng.2600

Engström KS, Hossain MB, Lauss M, Ahmed S, Raqib R, Vahter M, Broberg K: Efficient Arsenic Metabolism - The AS3MT Haplotype Is Associated with DNA Methylation and Expression of Multiple Genes Around AS3MT. PloS one 2013, 8:e5373210.1371.

Peña C, Céspedes MV, Bradic Lindh M, Kiflemariam S, Mezheyeuski A, Edqvist P-H, Hägglöf C, Birgisson H, Bojmar L, Jirstrom K, Sandström P, Olsson E, Veerla S, Gallardo A, Sjöblom T, Chang AC-M, Reddel RR, Mangues R, Augsten M, Ostman A: STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer. Cancer research 2012, 10.1158/0008-5472.CAN-12-1875.

Sivertsson L, Synnergren J, Jensen J, Björquist P, Ingelman-Sundberg M: Hepatic differentiation and maturation of human embryonic stem cells cultured in a perfused three-dimensional bioreactor. Stem Cells Dev 2013, 22:581–94.

 

2012

Olsson AH, Yang BT, Hall E, Taneera J, Salehi A, Nitert MD, Ling C: Decreased expression of genes involved in oxidative phosphorylation in human pancreatic islets from patients with type 2 diabetes. European journal of endocrinology / European Federation of Endocrine Societies 2011, 165:589–9510.1530/EJE-11-0282.

Hossain MB, Vahter M, Concha G, Broberg K: Environmental arsenic exposure and DNA methylation of the tumor suppressor gene p16 and the DNA repair gene MLH1: effect of arsenic metabolism and genotype. Metallomics 2012, 4:1167–75.

Taneera J, Jin Z, Jin Y, Muhammed SJ, Zhang E, Lang S, Salehi A, Korsgren O, Renström E, Groop L, Birnir B: γ-Aminobutyric acid (GABA) signalling in human pancreatic islets is altered in type 2 diabetes. Diabetologia 2012, 55:1985–9410.1007/s00125-012-2548-7.

Andersson SA, Olsson AH, Esguerra JLS, Heimann E, Ladenvall C, Edlund A, Salehi A,

Taneera J, Degerman E, Groop L, Ling C, Eliasson L: Reduced insulin secretion correlates with decreased expression of exocytotic genes in pancreatic islets from patients with type 2 diabetes. Molecular and cellular endocrinology 2012, 364:36–4510.1016/j.mce.2012.08.009.

Rudqvist N, Parris TZ, Schüler E, Helou K, Forssell-Aronsson E: Transcriptional response of BALB/c mouse thyroids following in vivo astatine-211 exposure reveals distinct gene expression profiles. EJNMMI Res 2012, 2:32.

Mahdi T, Hänzelmann S, Salehi A, Muhammed SJ, Reinbothe TM, Tang Y, Axelsson AS, Zhou Y, Jing X, Almgren P, Krus U, Taneera J, Blom AM, Lyssenko V, Esguerra JLS, Hansson O, Eliasson L, Derry J, Zhang E, Wollheim CB, Groop L, Renström E, Rosengren AH: Secreted Frizzled-Related Protein 4 Reduces Insulin Secretion and Is Overexpressed in Type 2 Diabetes. Cell Metabolism 2012, 16:625–63310.1016/j.cmet.2012.10.009.

Taneera J, Lang S, Sharma A, Fadista J, Zhou Y, Ahlqvist E, Jonsson A, Lyssenko V, Vikman P, Hansson O, Parikh H, Korsgren O, Soni A, Krus U, Zhang E, Jing X-J, Esguerra JLS, Wollheim CB, Salehi A, Rosengren A, Renström E, Groop L: A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets. Cell Metabolism 2012, 16:122–3410.1016/j.cmet.2012.06.006.

Li H, Engström K, Vahter M, Broberg K: Arsenic exposure through drinking water is associated with longer telomeres in peripheral blood. Chem Res Toxicol 2012, 25:2333–9.

Mohajeri A, Kindblom L-G, Sumathi VP, Brosjö O, Magnusson L, Nilsson J, Nord KH, Mertens F: SNP array and FISH findings in two pleomorphic hyalinizing angiectatic tumors. Cancer Genet 2012:673–676.

Ahlqvist K, Saamarthy K, Syed Khaja AS, Bjartell A, Massoumi R: Expression of Id proteins is regulated by the Bcl-3 proto-oncogene in prostate cancer. Oncogene 2012, 10.1038/onc.2012.175

Nord KH, Paulsson K, Veerla S, Wejde J, Brosjö O, Mandahl N, Mertens F: Retained heterodisomy is associated with high gene expression in hyperhaploid inflammatory leiomyosarcoma. Neoplasia (New York, N.Y.) 2012, 14:807–12.

Rudqvist N, Parris TZ, Schüler E, Helou K, Forssell-Aronsson E. Transcriptional response of BALB/c mouse thyroids following in vivo astatine-211 exposure reveals distinct gene expression profiles. EJNMMI Res. 2012;2(1):32. doi:10.1186/2191-219X-2-32.

Mertens F, Brosjö O, von Steyern FV, Nord KH, Mandahl N: The MDM2 SNP309 G allele is not preferentially amplified in bone and soft tissue tumors. Cancer Genet 2012:470–473.

Trombetta D, Macchia G, Mandahl N, Nord KH, Mertens F: Molecular genetic characterization of the 11q13 breakpoint in a desmoplastic fibroma of bone. Cancer Genet 2012:410–413.

Molenaar JJ, Koster J, Zwijnenburg DA, Sluis PV, Valentijn LJ, Ploeg IVD, Hamdi M, Nes JV, Westerman BA, Arkel JV, Ebus ME, Haneveld F, Lakeman A, Schild L, Molenaar P, Stroeken P, Noesel MMV, Øra I, Santo EE, Caron HN, Westerhout EM: Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature 2012, :2-810.1038/nature10910.

Sulaiman L, Haglund F, Hashemi J, Obara T, Nordenström J, Larsson C, Juhlin CC: Genome-wide and locus specific alterations in CDC73/HRPT2-mutated parathyroid tumors. PloS one 2012, 7:e4632510.1371.

Holm K, Grabau D, Lövgren K, Aradottir S, Gruvberger-Saal S, Howlin J, Saal LH, Ethier SP, Bendahl P-O, Stål O, Malmström P, Fernö M, Rydén L, Hegardt C, Borg Å, Ringnér M: Global H3K27 trimethylation and EZH2 abundance in breast tumor subtypes. Mol Oncol 2012, 6:494–506.

Harbst K, Staaf J, Lauss M, Karlsson A, Måsbäck A, Johansson I, Bendahl P-O, Vallon-Christersson J, Törngren T, Ekedahl H, Geisler J, Höglund M, Höglund M, Ringnér M, Ringnér M, Lundgren L, Jirström K, Olsson H, Ingvar C, Borg Å, Tsao H, Jönsson G: Molecular profiling reveals low- and high-grade forms of primary melanoma. Clin Cancer Res 2012, 18:4026–36.

Johansson I, Nilsson C, Berglund P, Lauss M, Ringnér M, Olsson H, Luts L, Sim E, Thorstensson S, Fjällskog M-L, Hedenfalk I: Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker. Breast Cancer Res 2012, 14:R31.

Asp J, Synnergren J, Jonsson M, Dellgren G, Jeppsson A: Comparison of human cardiac gene expression profiles in paired samples of right atrium and left ventricle collected in vivo. Physiol Genomics 2012, 44:89–98.

Synnergren J, Améen C, Jansson A, Sartipy P: Global transcriptional profiling reveals similarities and differences between human stem cell-derived cardiomyocyte clusters and heart tissue. Physiol Genomics 2012, 44:245–58.

 

2011

Lindqvist M, Nookaew I, Brinkenberg I, Samuelson E, Thörn K, Nielsen J, Harandi AM: Unraveling molecular signatures of immunostimulatory adjuvants in the female genital tract through systems biology. PloS one 2011, 6:e2044810.1371/journal.pone.0020448.


Riva M, Nitert MD, Voss U, Sathanoori R, Lindqvist A, Ling C, Wierup N: Nesfatin-1 stimulates glucagon and insulin secretion and beta cell NUCB2 is reduced in human type 2 diabetic subjects. Cell and tissue research 2011, 346:393-40510.1007/s00441-011-1268-5.

Schüler E, Parris TZ, Rudqvist N, Helou K, Forssell-Aronsson E. Effects of internal low-dose irradiation from 131I on gene expression in normal tissues in Balb/c mice. EJNMMI Res. 2011;1(1):29. doi:10.1186/2191-219X-1-29.

Olsson AH, Yang BT, Hall E, Taneera J, Salehi A, Nitert MD, Ling C: Decreased expression of genes involved in oxidative phosphorylation in human pancreatic islets from patients with type 2 diabetes. Eur J Endocrinol 2011, 165:589–95.

Lindgren D, Boström A-K, Nilsson K, Hansson J, Sjölund J, Möller C, Jirström K, Nilsson E, Landberg G, Axelson H, Johansson ME. Isolation and characterization of progenitor-like cells from human renal proximal tubules. The American Journal of Pathology 2011, 178(2):828-37.

Möller E, Hornick JL, Magnusson L, Veerla S, Domanski HA, Mertens F. FUS-CREB3L2/L1-positive sarcomas show a specific gene expression profile with upregulation of CD24 and FOXL1. Clinical Cancer Research 2011, 17:2646-56.

Olsson E, Honeth G, Bendahl P-O, Saal LH, Gruvberger-Saal S, Ringner M, Vallon-Christersson J, Jonsson G, Holm K, Lovgren K, Ferno M, Grabau D, Borg A, Hegardt C. CD44 isoforms are heterogeneously expressed in breast cancer and correlate with tumor subtypes and cancer stem cell markers. BMC cancer 2011, 11:418.

Johansson H, Lindstedt M, Albrekt A-S, Borrebaeck CAK: A genomic biomarker signature can predict skin sensitizers using a cell-based in vitro alternative to animal tests. BMC Genomics 2011, 12:399.

Synnergren J, Améen C, Lindahl A, Olsson B, Sartipy P: Expression of microRNAs and their target mRNAs in human stem cell-derived cardiomyocyte clusters and in heart tissue. Physiol Genomics 2011, 43:581–94.

Aburawi HE, Biloglav A, Johansson B, Paulsson K. Cytogenetic and molecular genetic characterization of the “high hyperdiploid” B-cell precursor acute lymphoblastic leukaemia cell line MHH-CALL-2 reveals a near-haploid origin. Br. J. Haematol. 2011;154(2):275-7. doi:10.1111/j.1365-2141.2011.08601.x.

 

2010

Jönsson G, Staaf J, Vallon-Christersson J, Ringnér M, Holm K, Hegardt C, Gunnarsson H, Fagerholm R, Strand C, Agnarsson BA, Kilpivaara O, Luts L, Heikkilä P, Aittomäki K, Blomqvist C, Loman N, Malmström P, Olsson H, Johannsson OT, Arason A, Nevanlinna H, Barkardottir RB, Borg A: Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics. Breast Cancer Res 2010, 12:R42.

Esbjörnsson J, Månsson F, Martínes-Arias W, Vincic E, Biaque AJ, da Silva ZJ, Fenyö EM, Norrgren H, Medstrand P. Frequent CXCR4 tropism of HIV-1 subtype A and CRF02_AG during late-stage disease - indication of an evolving epidemic in West Africa. Retrovirology 2010, 7:23.

Paulsson K, Haferlach C, Fonatsch C, Hagemeijer A, Andersen MK, Slovak ML, Johansson B: The idic(X)(q13) in myeloid malignancies: breakpoint clustering in segmental duplications and association with TET2 mutations. Hum Mol Genet 2010, 19:1507–14.

Olsson A, Björk A, Vallon-Christersson J, Isaacs JT, Leanderson T: Tasquinimod (ABR-215050), a quinoline-3-carboxamide anti-angiogenic agent, modulates the expression of thrombospondin-1 in human prostate tumors. Mol Cancer 2010, 9:107.

Holm K, Hegardt C, Staaf J, Vallon-Christersson J, Jönsson G, Olsson H, Borg A, Ringnér M. Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Research 2010, 12:R36.

Lindgren D, Frigyesi A, Gudjonsson S, Sjödahl G, Hallden C, Chebil G, Veerla S, Ryden T, Månsson W, Liedberg F, Höglund M: Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome. Cancer Res 2010, 70:3463–72.

Synnergren J, Heins N, Brolén G, Eriksson G, Lindahl A, Hyllner J, Olsson B, Sartipy P, Björquist P: Transcriptional profiling of human embryonic stem cells differentiating to definitive and primitive endoderm and further toward the hepatic lineage. Stem Cells Dev 2010, 19:961–78.

de Peppo GM, Svensson S, Lennerås M, Synnergren J, Stenberg J, Strehl R, Hyllner J, Thomsen P, Karlsson C: Human embryonic mesodermal progenitors highly resemble human mesenchymal stem cells and display high potential for tissue engineering applications. Tissue Eng Part A 2010, 16:2161–82.

Andréasson U, Edén P, Peterson C, Högerkorp C-M, Jerkeman M, Andersen N, Berglund M, Sundström C, Rosenquist R, Borrebaeck CAK, Ek S: Identification of uniquely expressed transcription factors in highly purified B-cell lymphoma samples. Am J Hematol 2010, 85:418–25.

Gustavsson E, Sernbo S, Andersson E, Brennan DJ, Dictor M, Jerkeman M, Borrebaeck CA, Ek S: SOX11 expression correlates to promoter methylation and regulates tumor growth in hematopoietic malignancies. Mol Cancer 2010, 9:187.

OSTERBERG L, LEVAN K, PARTHEEN K, DELLE U, OLSSON B, SUNDFELDT K, HORVATH G: Specific Copy Number Alterations Associated with Docetaxel/Carboplatin Response in Ovarian Carcinomas. Anticancer Res 2010, 30:4451–4458.

 

2009

Augsten M, Hägglöf C, Olsson E, Stolz C, Tsagozis P, Levchenko T, Frederick MJ, Borg A, Micke P, Egevad L, Ostman A. CXCL14 is an autocrine growth factor for fibroblasts and acts as a multi-modal stimulator of prostate tumor growth. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:3414-9.

Davidsson J, Lilljebjörn H, Andersson A, Veerla S, Heldrup J, Behrendtz M, Fioretos T, Johansson B. The DNA methylome of pediatric acute lymphoblastic leukemia. Human Molecular Genetics 2009, 18:4054-65.

Friberg PA, Larsson DGJ, Billig H. Transcriptional effects of progesterone receptor antagonist in rat granulosa cells. Molecular and Cellular Endocrinology 2010, 315(1-2):121-30.

Hallor KH, Sciot R, Staaf J, Heidenblad M, Rydholm A, Bauer HC, Aström K, Domanski HA, Meis JM, Kindblom L-G, Panagopoulos I, Mandahl N, Mertens F. Two genetic pathways, t(1;10) and amplification of 3p11-12, in myxoinflammatory fibroblastic sarcoma, haemosiderotic fibrolipomatous tumour, and morphologically similar lesions. The Journal of Pathology 2009, 217:716-27.

Hallor KH, Staaf J, Bovée JVMG, Hogendoorn PCW, Cleton-Jansen A-M, Knuutila S, Savola S, Niini T, Brosjö O, Bauer HCF, Vult von Steyern F, Jonsson K, Skorpil M, Mandahl N, Mertens F. Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors. Clinical Cancer Research  2009, 15:2685-94.

Osterberg L, Levan K, Partheen K, Staaf J, Sundfeldt K, Horvath G. High-resolution genomic profiling of carboplatin resistance in early-stage epithelial ovarian carcinoma. Cytogenetic and Genome Research 2009, 125:8-18.

Osterberg L, Levan K, Partheen K, Delle U, Olsson B, Sundfeldt K, Horvath G. Potential predictive markers of chemotherapy resistance in stage III ovarian serous carcinomas. BMC Cancer 2009, 9:368.

Persson H, Kvist A, Vallon-Christersson J, Medstrand P, Borg A, Rovira C. The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Nature Cell Biology 2009, 11:1268-71.

Tormin A, Brune JC, Olsson E, Valcich J, Neuman U, Olofsson T, Jacobsen S-E, Scheding S. Characterization of bone marrow-derived mesenchymal stromal cells (MSC) based on gene expression profiling of functionally defined MSC subsets. Cytotherapy 2009, 11:114-28.

Vallon-Christersson J, Nordborg N, Svensson M, Häkkinen J. BASE--2nd generation software for microarray data management and analysis. BMC Bioinformatics 2009, 10:330.

Veerla S, Lindgren D, Kvist A, Frigyesi A, Staaf J, Persson H, Liedberg F, Chebil G, Gudjonsson S, Borg A, Månsson W, Rovira C, Höglund M: MiRNA expression in urothelial carcinomas: important roles of miR-10a, miR-222, miR-125b, miR-7 and miR-452 for tumor stage and metastasis, and frequent homozygous losses of miR-31. Int J Cancer 2009, 124:2236–42.

Andréasson U, Dictor M, Jerkeman M, Berglund M, Sundström C, Linderoth J, Rosenquist R, Borrebaeck CAK, Ek S: Identification of molecular targets associated with transformed diffuse large B cell lymphoma using highly purified tumor cells. Am J Hematol 2009, 84:803–8.

 

2008

Brommesson S, Jönsson G, Strand C, Grabau D, Malmström P, Ringnér M, Fernö M, Hedenfalk I. Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs. BMC Clinical Pathology 2008, 8:6

Carneiro A, Isinger A, Karlsson A, Johansson J, Jönsson G, Bendahl P-O, Falkenback D, Halvarsson B, Nilbert M. Prognostic impact of array-based genomic profiles in esophageal squamous cell cancer. BMC Cancer 2008, 8:98.

Gunnarsson R, Staaf J, Jansson M, Ottesen AM, Göransson H, Liljedahl U, Ralfkiaer U, Mansouri M, Buhl AM, Smedby KE, Hjalgrim H, Syvänen A-C, Borg A, Isaksson A, Jurlander J, Juliusson G, Rosenquist R. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms. Genes, Chromosomes & Cancer 2008, 47:697-711.

Hallor KH, Teixeira MR, Fletcher CDM, Bizarro S, Staaf J, Domanski HA, von Steyern FV, Panagopoulos I, Mandahl N, Mertens F. Heterogeneous genetic profiles in soft tissue myoepitheliomas. Modern Pathology  2008, 21:1311.

Holst CM, Staaf J, Jönsson G, Hegardt C, Oredsson SM. Molecular mechanisms underlying N1, N11-diethylnorspermine-induced apoptosis in a human breast cancer cell line. Anti-Cancer Drugs 2008, 19:871-83.

Honeth G, Bendahl P-O, Ringnér M, Saal LH, Gruvberger-Saal SK, Lövgren K, Grabau D, Fernö M, Borg A, Hegardt C. The CD44+/CD24- phenotype is enriched in basal-like breast tumors. Breast Cancer Research : BCR 2008, 10(3).

Johansson VM, Miniotis MF, Hegardt C, Jönsson G, Staaf J, Berntsson PSH, Oredsson SM, Alm K. Effect of polyamine deficiency on proteins involved in Okazaki fragment maturation. Cell biology international 2008, 32:1467-77.

Kuchinskaya E, Heyman M, Nordgren A, Schoumans J, Staaf J, Borg A, Söderhäll S, Grandér D, Nordenskjöld M, Blennow E. Array-CGH reveals hidden gene dose changes in children with acute lymphoblastic leukaemia and a normal or failed karyotype by G-banding. British Journal of Haematology 2008, 140:572-7.

Lee J-J, Au AYM, Foukakis T, Barbaro M, Kiss N, Clifton-Bligh R, Staaf J, Borg A, Delbridge L, Robinson BG, Wallin G, Höög A, Larsson C. Array-CGH identifies cyclin D1 and UBCH10 amplicons in anaplastic thyroid carcinoma. Endocrine-Related Cancer 2008, 15:801-15.

Myhre L, Alm K, Hegardt C, Staaf J, Jönsson G, Larsson S, Oredsson SM. Different cell cycle kinetic effects of N1,N11-diethylnorspermine-induced polyamine depletion in four human breast cancer cell lines. Anti-Cancer Drugs 2008, 19:359-68.

Replogle K, Arnold AP, Ball GF, Band M, Bensch S, Brenowitz EA, Dong S, Drnevich J, Ferris M, George JM, Gong G, Hasselquist D, Hernandez AG, Kim R, Lewin HA, Liu L, Lovell PV, Mello CV, Naurin S, Rodriguez-Zas S, Thimmapuram J, Wade J, Clayton DF. The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution. BMC Genomics 2008, 9:131.

Saal LH, Gruvberger-Saal SK, Persson C, Lövgren K, Jumppanen M, Staaf J, Jönsson G, Pires MM, Maurer M, Holm K, Koujak S, Subramaniyam S, Vallon-Christersson J, Olsson H, Su T, Memeo L, Ludwig T, Ethier SP, Krogh M, Szabolcs M, Murty VVVS, Isola J, Hibshoosh H, Parsons R, Borg A. Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair. Nature Genetics 2008, 40:102-7.

Staaf J, Lindgren D, Vallon-Christersson J, Isaksson A, Göransson H, Juliusson G, Rosenquist R, Höglund M, Borg A, Ringnér M. Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biology 2008, 9(9):R136.

Staaf J, Törngren T, Rambech E, Johansson U, Persson C, Sellberg G, Tellhed L, Nilbert M, Borg A. Detection and precise mapping of germline rearrangements in BRCA1, BRCA2, MSH2, and MLH1 using zoom-in array comparative genomic hybridization (aCGH). Human Mutation 2008, 29:555-64.

Staaf J, Jönsson G, Ringnér M, Vallon-Christersson J. Normalization of array-CGH data: influence of copy number imbalances. BMC Genomics 2007, 8:382.

Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Höglund M, Borg A, Ringnér M. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics 2008, 9:40910.

Zhang Z-F, Ruivenkamp C, Staaf J, Zhu H, Barbaro M, Petillo D, Khoo SK, Borg A, Fan Y-S, Schoumans J. Detection of submicroscopic constitutional chromosome aberrations in clinical diagnostics: a validation of the practical performance of different array platforms. European Journal of Human Genetics 2008, 16:786-92.

Naurin S, Bensch S, Hansson B, Johansson T, Clayton DF, Albrekt A-S, VON Schantz T, Hasselquist D: TECHNICAL ADVANCES: A microarray for large-scale genomic and transcriptional analyses of the zebra finch (Taeniopygia guttata) and other passerines. Mol Ecol Resour 2008, 8:275–81.

Ortega-Paino E, Fransson J, Ek S, Borrebaeck CAK: Functionally associated targets in mantle cell lymphoma as defined by DNA microarrays and RNA interference. Blood 2008, 111:1617–24.

Andréasson U, Ek S, Merz H, Rosenquist R, Andersen N, Jerkeman M, Dictor M, Borrebaeck CAK: B cell lymphomas express CX3CR1 a non-B cell lineage adhesion molecule. Cancer Lett 2008, 259:138–45.

Ek S, Dictor M, Jerkeman M, Jirström K, Borrebaeck CAK: Nuclear expression of the non B-cell lineage Sox11 transcription factor identifies mantle cell lymphoma. Blood 2008, 111:800–5.

 

2007

Balciuniene J, Feng N, Iyadurai K, Hirsch B, Charnas L, Bill BR, Easterday MC, Staaf J, Oseth L, Czapansky-Beilman D, Avramopoulos D, Thomas GH, Borg A, Valle D, Schimmenti LA, Selleck SB. Recurrent 10q22-q23 deletions: a genomic disorder on 10q associated with cognitive and behavioral abnormalities. American Journal of Human Genetics 2007, 80:938-47.

Barbaro M, Oscarson M, Schoumans J, Staaf J, Ivarsson SA, Wedell A. Isolated 46,XY gonadal dysgenesis in two sisters caused by a Xp21.2 interstitial duplication containing the DAX1 gene. The Journal of Clinical Endocrinology and Metabolism 2007, 92:3305-13.

Huang J, Gusnanto A, O’Sullivan K, Staaf J, Borg A, Pawitan Y. Robust smooth segmentation approach for array CGH data analysis. Bioinformatics 2007, 23:2463-9.

Karlsson C, Andersson M-L, Collin M, Schmidtchen A, Björck L, Frick I-M. SufA--a novel subtilisin-like serine proteinase of Finegoldia magna. Microbiology 2007, 153:4208-18.

Vallon-Christersson J, Staaf J, Kvist A, Medstrand P, Borg A, Rovira C. Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray. BMC Genomics 2007, 8:295.

 

2006

Ek S, Björck E, Högerkorp C-M, Nordenskjöld M, Porwit-MacDonald A, Borrebaeck CAK: Mantle cell lymphomas acquire increased expression of CCL4, CCL5 and 4-1BB-L implicated in cell survival. Int J Cancer 2006, 118:2092–7.

Ek S, Andréasson U, Hober S, Kampf C, Pontén F, Uhlén M, Merz H, Borrebaeck CAK: From gene expression analysis to tissue microarrays: a rational approach to identify therapeutic and diagnostic targets in lymphoid malignancies. Mol Cell Proteomics 2006, 5:1072–81.

 

2005

Andersson N, Skrtic SM, Håkanson R, Ohlsson C: A gene expression fingerprint of mouse stomach ECL cells. Biochem Biophys Res Commun 2005, 332:404–10.

Arkblad EL, Tuck S, Pestov NB, Dmitriev RI, Kostina MB, Stenvall J, Tranberg M, Rydström J: A Caenorhabditis elegans mutant lacking functional nicotinamide nucleotide transhydrogenase displays increased sensitivity to oxidative stress. Free Radic Biol Med 2005, 38:1518–25.

Bachar O, Rose AC, Adner M, Wang X, Prendergast CE, Kempf A, Shankley NP, Cardell L-O: TNF alpha reduces tachykinin, PGE2-dependent, relaxation of the cultured mouse trachea by increasing the activity of COX-2. Br J Pharmacol 2005, 144:220–30.

Benson M, Jansson L, Adner M, Luts A, Uddman R, Cardell LO: Gene profiling reveals decreased expression of uteroglobin and other anti-inflammatory genes in nasal fluid cells from patients with intermittent allergic rhinitis. Clin Exp Allergy 2005, 35:473–8.

Gärdén P, Alm R, Häkkinen J: PROTEIOS: an open source proteomics initiative. Bioinformatics 2005, 21:2085–7.

Björck E, Ek S, Landgren O, Jerkeman M, Ehinger M, Björkholm M, Borrebaeck CAK, Porwit-MacDonald A, Nordenskjöld M: High expression of cyclin B1 predicts a favorable outcome in patients with follicular lymphoma. Blood 2005, 105:2908–15.

Ek S, Ortega E, Borrebaeck CAK: Transcriptional profiling and assessment of cell lines as in vitro models for mantle cell lymphoma. Leuk Res 2005, 29:205–13.

Flach C-F, Lange S, Jennische E, Lönnroth I, Holmgren J: Cholera toxin induces a transient depletion of CD8+ intraepithelial lymphocytes in the rat small intestine as detected by microarray and immunohistochemistry. Infect Immun 2005, 73:5595–602.

Göransson M, Elias E, Ståhlberg A, Olofsson A, Andersson C, Aman P: Myxoid liposarcoma FUS-DDIT3 fusion oncogene induces C/EBP beta-mediated interleukin 6 expression. Int J Cancer 2005, 115:556–60.

Hansson O, Donsmark M, Ling C, Nevsten P, Danfelter M, Andersen JL, Galbo H, Holm C: Transcriptome and proteome analysis of soleus muscle of hormone-sensitive lipase-null mice. J Lipid Res 2005, 46:2614–23.

Lantz M, Vondrichova T, Parikh H, Frenander C, Ridderstråle M, Asman P, Aberg M, Groop L, Hallengren B: Overexpression of immediate early genes in active Graves’ ophthalmopathy. J Clin Endocrinol Metab 2005, 90:4784–91.

Lindstedt M, Schiött A, Johnsen CR, Roggen E, Johansson-Lindbom B, Borrebaeck CAK: Individuals with occupational allergy to detergent enzymes display a differential transcriptional regulation and cellular immune response. Clin Exp Allergy 2005, 35:199–206.

Lindstedt M, Lundberg K, Borrebaeck CAK: Gene family clustering identifies functionally associated subsets of human in vivo blood and tonsillar dendritic cells. J Immunol 2005, 175:4839–46.

Lindstedt M, Schiött A, Bengtsson A, Larsson K, Korsgren M, Greiff L, Borrebaeck CAK: Genomic and functional delineation of dendritic cells and memory T cells derived from grass pollen-allergic patients and healthy individuals. Int Immunol 2005, 17:401–9.

Magnusson C, Svensson A, Christerson U, Tågerud S: Denervation-induced alterations in gene expression in mouse skeletal muscle. Eur J Neurosci 2005, 21:577–80.

Matsusaki M, Larsson K, Akagi T, Lindstedt M, Akashi M, Borrebaeck CAK: Nanosphere induced gene expression in human dendritic cells. Nano Lett 2005, 5:2168–73.

Nilsson A, Moller K, Dahlin L, Lundborg G, Kanje M: Early changes in gene expression in the dorsal root ganglia after transection of the sciatic nerve; effects of amphiregulin and PAI-1 on regeneration. Brain Res Mol Brain Res 2005, 136:65–74.

Ek S, Björck E, Högerkorp C-M, Nordenskjöld M, Porwit-MacDonald A, Borrebaeck CAK: Mantle cell lymphomas acquire increased expression of CCL4, CCL5 and 4-1BB-L implicated in cell survival. Int J Cancer 2006, 118:2092–7.

 

2004

Benson M, Carlsson L, Adner M, Jernås M, Rudemo M, Sjögren A, Svensson PA, Uddman R, Cardell LO: Gene profiling reveals increased expression of uteroglobin and other anti-inflammatory genes in glucocorticoid-treated nasal polyps. J Allergy Clin Immunol 2004, 113:1137–43.

Ek S, Björck E, Porwit-MacDonald A, Nordenskjöld M, Borrebaeck CAK: Increased expression of Ki-67 in mantle cell lymphoma is associated with de-regulation of several cell cycle regulatory components, as identified by global gene expression analysis. Haematologica 2004, 89:686–95.

Flach C-F, Lange S, Jennische E, Lönnroth I: Cholera toxin induces expression of ion channels and carriers in rat small intestinal mucosa. FEBS Lett 2004, 561:122–6.

Fransson J, Ek S, Ellmark P, Söderlind E, Borrebaeck CAK, Furebring C: Profiling of internalizing tumor-associated antigens on breast and pancreatic cancer cells by reversed genomics. Cancer Lett 2004, 208:235–42.

Hedtjärn M, Mallard C, Eklind S, Gustafson-Brywe K, Hagberg H: Global gene expression in the immature brain after hypoxia-ischemia. J Cereb Blood Flow Metab 2004, 24:1317–32.

Hedtjärn M, Mallard C, Hagberg H: Inflammatory gene profiling in the developing mouse brain after hypoxia-ischemia. J Cereb Blood Flow Metab 2004, 24:1333–51.

Lagergren A, Manetopoulos C, Axelson H, Sigvardsson M: Neuroblastoma and pre-B lymphoma cells share expression of key transcription factors but display tissue restricted target gene expression. BMC Cancer 2004, 4:80.

Månsson R, Tsapogas P, Akerlund M, Lagergren A, Gisler R, Sigvardsson M: Pearson correlation analysis of microarray data allows for the identification of genetic targets for early B-cell factor. J Biol Chem 2004, 279:17905–13.

Schiött A, Lindstedt M, Johansson-Lindbom B, Roggen E, Borrebaeck CAK: CD27- CD4+ memory T cells define a differentiated memory population at both the functional and transcriptional levels. Immunology 2004, 113:363–70.

Sonderegger M, Jeppsson M, Hahn-Hägerdal B, Sauer U: Molecular basis for anaerobic growth of Saccharomyces cerevisiae on xylose, investigated by global gene expression and metabolic flux analysis. Appl Environ Microbiol 2004, 70:2307–17.

Tivesten A, Barlind A, Caidahl K, Klintland N, Cittadini A, Ohlsson C, Isgaard J: Growth hormone-induced blood pressure decrease is associated with increased mRNA levels of the vascular smooth muscle KATP channel. J Endocrinol 2004, 183:195–202.

 

2003

Bilke S, Breslin T, Sigvardsson M: Probabilistic estimation of microarray data reliability and underlying gene expression. BMC Bioinformatics 2003, 4:40.

Högerkorp C-M, Bilke S, Breslin T, Ingvarsson S, Borrebaeck CAK: CD44-stimulated human B cells express transcripts specifically involved in immunomodulation and inflammation as analyzed by DNA microarrays. Blood 2003, 101:2307–13.

Lindstedt M, Johansson-Lindbom B, Borrebaeck CAK: Expression of CD137 (4-1BB) on human follicular dendritic cells. Scand J Immunol 2003, 57:305–10.

Tsapogas P, Breslin T, Bilke S, Lagergren A, Månsson R, Liberg D, Peterson C, Sigvardsson M: RNA analysis of B cell lines arrested at defined stages of differentiation allows for an approximation of gene expression patterns during B cell development. J Leukoc Biol 2003, 74:102–10.

Wahlbom CF, Cordero Otero RR, van Zyl WH, Hahn-Hägerdal B, Jönsson LJ: Molecular analysis of a Saccharomyces cerevisiae mutant with improved ability to utilize xylose shows enhanced expression of proteins involved in transport, initial xylose metabolism, and the pentose phosphate pathway. Appl Environ Microbiol 2003, 69:740–6.

 

2002

Benson M, Svensson PA, Carlsson B, Jernås M, Reinholdt J, Cardell LO, Carlsson L: DNA microarrays to study gene expression in allergic airways. Clin Exp Allergy 2002, 32:301–8.

Benson M, Carlsson B, Carlsson LMS, Wennergren G, Cardell LO: Increased expression of Vascular Endothelial Growth Factor-A in seasonal allergic rhinitis. Cytokine 2002, 20:268–73.

Ek S, Högerkorp C-M, Dictor M, Ehinger M, Borrebaeck CAK: Mantle cell lymphomas express a distinct genetic signature affecting lymphocyte trafficking and growth regulation as compared with subpopulations of normal human B cells. Cancer Res 2002, 62:4398–405.

Lindstedt M, Johansson-Lindbom B, Borrebaeck CAK: Global reprogramming of dendritic cells in response to a concerted action of inflammatory mediators. Int Immunol 2002, 14:1203–13.

Sigvardsson M, Clark DR, Fitzsimmons D, Doyle M, Akerblad P, Breslin T, Bilke S, Li R, Yeamans C, Zhang G, Hagman J: Early B-cell factor, E2A, and Pax-5 cooperate to activate the early B cell-specific mb-1 promoter. Mol Cell Biol 2002, 22:8539–51.