Publications

2012

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.

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.

2011

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.

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.

2010

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.

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. 

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.

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. 

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. 

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