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M. Annala, W. Struss, E. Warner, K. Beja, G. Vandekerkhove, A. Wong, D. Khalaf, I. Seppälä, A. So, G. Lo, R. Aggarwal, E. Small, M. Nykter, M. Gleave, K. Chi, A. Wyatt. Treatment Outcomes and Tumor Loss of Heterozygosity in Germline DNA Repair-deficient Prostate Cancer. Eur Urol, 72(1):34-42, 2017.

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K. Veskimäe, S. Staff, A. Grönholm, M. Pesu, M. Laaksonen, M. Nykter, J. Isola, J. Mäenpää. Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry. Tumour Biol, 37(9):11991-11999, 2016.

A. Wyatt, A. Azad, S. Volik, M. Annala, K. Beja, B. McConeghy, A. Haegert, E. Warner, F. Mo, S. Brahmbhatt, R. Shukin, S. Le Bihan, M. Gleave, M. Nykter, C. Collins, K. Chi. Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer. JAMA Oncol, 2(12):1598-1606, 2016.

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R. Nurminen, T. Rantapero, S. Wong, D. Fischer, R. Lehtonen, T. Tammela, M. Nykter, T. Visakorpi, T. Wahlfors, J. Schleutker. Expressional profiling of prostate cancer risk SNPs at 11q13.5 identifies DGAT2 as a new target gene. Genes Chromosomes Cancer, 55(8):661-73, 2016.

P. Ruusuvuori, M. Valkonen, M. Nykter, T. Visakorpi, L. Latonen. Feature-based analysis of mouse prostatic intraepithelial neoplasia in histological tissue sections. J Pathol Inform, 7:5, 2016.

L. Sjöblom, O. Saramäki, M. Annala, K. Leinonen, J. Nättinen, T. Tolonen, T. Wahlfors, M. Nykter, G. Bova, J. Schleutker, T. Tammela, H. Lilja, T. Visakorpi. Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer. PLoS One, 11(3)e0150241, 2016.

E. Alarmo, R. Havunen, S. Häyrynen, S. Penkki, J. Ketolainen, M. Nykter, A. Kallioniemi. Bone morphogenetic protein 4 regulates microRNA expression in breast cancer cell lines in diverse fashion. Genes Chromosomes Cancer, 55(3):227-36, 2016.

C. Chua, Y. Liu, K. Granberg, L. Hu, H. Haapasalo, M. Annala, D. Cogdell, M. Verploegen, L. Moore, G. Fuller, M. Nykter, W. Cavenee, W. Zhang. IGFBP2 potentiates nuclear EGFR-STAT3 signaling. Oncogene, 35(6):738-47, 2016.

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The Cancer Genome Atlas Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell, 163(4):1011-25, 2015.

A. Ylipää, K. Kivinummi, A. Kohvakka, M. Annala, L. Latonen, M. Scaravilli, K. Kartasalo, S. Leppänen, S. Karakurt, J. Seppälä, O. Yli-Harja, T. Tammela, W. Zhang, T. Visakorpi, M. Nykter. Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer. Cancer Res, 75(19):4026-31, 2015.

J. Rane, A. Ylipää, R. Adamson, V. Mann, M. Simms, A. Collins, T. Visakorpi, M. Nykter, N. Maitland. Construction of therapeutically relevant human prostate epithelial fate map by utilising miRNA and mRNA microarray expression data. Br J Cancer, 113(4):611-5, 2015.

K. Nordfors, J. Haapasalo, K. Mäkelä, K. Granberg, M. Nykter, M. Korja, T. Paavonen, H. Haapasalo, Y. Soini. Twist predicts poor outcome of patients with astrocytic glioma. J Clin Pathol, 2015.

K. Kaukoniemi, H. Rauhala, M. Scaravilli, L. Latonen, M. Annala, R. Vessella, M. Nykter, T. Tammela, T. Visakorpi. Epigenetically altered miR-193b targets cyclin D1 in prostate cancer. Cancer Med, 4(9):1417-25, 2015.

C. Chua, Y. Liu, K. Granberg, L. Hu, H. Haapasalo, M. Annala, D. Cogdell, M. Verploegen, L. Moore, G. Fuller, M. Nykter, W. Cavenee, W. Zhang. IGFBP2 potentiates nuclear EGFR-STAT3 signaling. Oncogene, 2015.

S. Marttila, L. Kananen, S. Häyrynen, J. Jylhävä, T. Nevalainen, A. Hervonen, M. Jylhä, M. Nykter, M. Hurme. Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression. BMC Genomics, 16:179, 2015.

G. Gundem, P. Van Loo, B. Kremeyer, L. Alexandrov, J. Tubio, E. Papaemmanuil, D. Brewer, H. Kallio, G. Högnäs, M. Annala, K. Kivinummi, V. Goody, C. Latimer, S. O'Meara, K. Dawson, W. Isaacs, M. Emmert-Buck, M. Nykter, C. Foster, Z. Kote-Jarai, D. Easton, H. Whitaker, D. Neal, C. Cooper, R. Eeles, T. Visakorpi, P. Campbell, U. McDermott, D. Wedge, G. Bova. The evolutionary history of lethal metastatic prostate cancer. Nature, 520(7547):353-7, 2015.

M. Annala, K. Kivinummi, J. Tuominen, S. Karakurt, K. Granberg, L. Latonen, A. Ylipää, L. Sjöblom, P. Ruusuvuori, O. Saramäki, K. Kaukoniemi, O. Yli-Harja, R. Vessella, T. Tammela, W. Zhang, T. Visakorpi, M. Nykter. Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer. Oncotarget, 6(8):6235-50, 2015.

K. Turner, Y. Sun, P. Ji, K. Granberg, B. Bernard, L. Hu, D. Cogdell, X. Zhou, O. Yli-Harja, M. Nykter, I. Shmulevich, W. Yung, G. Fuller, W. Zhang. Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression. Proc Natl Acad Sci U S A, 112(11):3421-6, 2015.

M. Scaravilli, K. Porkka, A. Brofeldt, M. Annala, T. Tammela, G. Jenster, M. Nykter, T. Visakorpi. MiR-1247-5p is overexpressed in castration resistant prostate cancer and targets MYCBP2. Prostate, 75(8):798-805, 2015.

K. Veskimäe, S. Staff, F. Tabaro, M. Nykter, J. Isola, J. Mäenpää. Microarray analysis of differentially expressed genes in ovarian and fallopian tube epithelium from risk-reducing salpingo-oophorectomies. Genes Chromosomes Cancer, 54(5):276-87, 2015.

J. Rane, M. Scaravilli, A. Ylipää, D. Pellacani, V. Mann, M. Simms, M. Nykter, A. Collins, T. Visakorpi, N. Maitland. MicroRNA expression profile of primary prostate cancer stem cells as a source of biomarkers and therapeutic targets. Eur Urol, 67(1):7-10, 2015.

X. Li, Y. Liu, K. Granberg, Q. Wang, L. Moore, P. Ji, J. Gumin, E. Sulman, G. Calin, H. Haapasalo, M. Nykter, I. Shmulevich, G. Fuller, F. Lang, W. Zhang. Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma. Oncogene, 34(13):1619-28, 2015.

Duffy DJ, Krstic A, Halasz M, Schwarzl T, Fey D, Iljin K, Mehta JP, Killick K, Whilde J, Turriziani B, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W. (2015). Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma. Oncotarget, 6(41), 43182–201.


J. Yang, M. Annala, P. Ji, G. Wang, H. Zheng, D. Codgell, X. Du, Z. Fang, B. Sun, M. Nykter, K. Chen, W. Zhang. Recurrent LRP1-SNRNP25 and KCNMB4-CCND3 fusion genes promote tumor cell motility in human osteosarcoma. J Hematol Oncol, 7(1):76, 2014.

M. Annala, K. Kivinummi, K. Leinonen, J. Tuominen,W. Zhang, T. Visakorpi, and M. Nykter. DOT1L-HES6 fusion drives androgen independent growth in prostate cancer. EMBO Molecular Medicine, 6(9):1121-3, 2014.

X. Li, Y. Liu, K. J. Granberg, Q. Wang, L. M. Moore, P. Ji, J. Gumin, G. Calin, H. Haapasalo, M. Nykter, I. Shmulevich, G. N. Fuller, F. F. Lang, and W. Zhang. Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma. Oncogene, 34(13):1619-28, 2014.

Q. Huang, T. Whitington, P. Gao, J. F. Lindberg, Y. Yang, J. Sun, M.- R. Väisänen, R. Szulkin, M. Annala, J. Yan, L. A. Egevad, K. Zhang, R. Lin, A. Jolma, M. Nykter, A. Manninen, F. Wiklund, M. H. Vaarala, T. Visakorpi, J. Xu, J. Taipale, and G.-H. Wei. A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding. Nature Genetics, 46(2):126-135, 2014.

P. Ruusuvuori, J. Lin, A. C. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, and A. M. Dudley. Quantitative analysis of colony morphology in yeast. Biotechniques, 56(1):18-27, 2014.

T. Liuksiala, K. Teittinen, K. Granberg, M. Heinäniemi, M. Annala, M. Mäki, M. Nykter, and O. Lohi. Overexpression of SNORD114-3 marks acute promyelocytic leukemia, Leukemia, 28:233-236, 2014.


J. Lin, R. Kreisberg, A. Kallio, A. M. Dudley, M. Nykter, I. Shmulevich, P. May, and R. Autio. POMO - plotting omics analysis results for multiple organisms, BMC Genomics, 14:918, 2013.

H. Turpeinen, A. Oksanen, V. Kivinen, S. Kukkurainen, A. Uusimäki, M. Rämet, M. Parikka, V. P. Hytönen, M. Nykter, and M. Pesu. Proprotein convertase subtilisin/kexin type 7 (PCSK7) is essential for the zebrafish development and bioavailability of transforming growth factor beta 1a (TGF1a), The Journal of Biological Chemistry, 288(51):36610-36623, 2013.

K. Leinonen, O. Saramäki, B. Furusato, T. Kimura, H. Takahashi, S. Egawa, H. Suzuki, K. Keiger, S. H. Hahm, W. Isaacs, T. T. Tolonen, U.-H. Stenman, T. L. J. Tammela, M. Nykter, G. S. Bova, and T. Visakorpi. Loss of PTEN is associated with aggressive behavior in ERG positive prostate cancer, Cancer Epidemiology Biomarkers & Prevention, 22(12):2333-2344, 2013.

T. Manninen, H. Huttunen, P. Ruusuvuori, and M. Nykter. Leukemia prediction using sparse logistic regression, PLoS ONE, 8(8):e72932, 2013.

L. Kong, K.-L. Aho, K. Granberg, R. Lund, L. Järvenpää, J. Seppälä, P. Gokhale, K. Leinonen, L. Hahne, J. Mäkelä, K. Laurila, H. Pukkila, E. Närvä, O. Yli-Harja, P. W. Andrews, M. Nykter, R. Lahesmaa, C. Roos, and R. Autio. Estools data@hand, a gene expression data analysis resource for stem cell research community, Nature Methods, 10(9):814815, 2013.

A. Ylipää, O. Yli-Harja, W. Zhang, and M. Nykter. Characterization of aberrant pathways across human cancers, BMC Systems Biology, 7(Suppl 1):S1, 2013.

R. J. Lund, M. R. Emami, I. Barbaric, V. Kivinen, M. Jones, D. Baker, P. Gokhale, M. Nykter, R. Lahesmaa, P. W. Andrews. Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases, Stem Cell Research, 11:1022-1036, 2013.

S. Marttila, J. Jylhävä, T. Nevalainen, M. Nykter, M. Jylhä, A. Hervonen, L. Tserel, P. Peterson, M. Hurme. Transcriptional Analysis Reveals Gender-Specific Changes in the Aging of the Human Immune System, PLoS ONE, 8(6):e66229, 2013.

M. Heinäniemi, M. Nykter, R. Kramer, A. Wienecke-Baldacchino, L. Sinkkonen, J. X. Zhou, R. Kreisberg, S. A. Kauffman, S. Huang, and I. Shmulevich. Gene-pair expression signatures reveal lineage control, Nature Methods, 10:577-583, 2013.

A. Sadot, S. Sarbu, J. Kesseli, H. Amir-Kroll, W. Zhang, M. Nykter, and I. Shmulevich. Information-theoretic analysis of the dynamics of an executable biological model, PLoS ONE, 8(3):e59303, 2013.

T. Mäki-Marttunen, J. Kesseli, and M. Nykter. Balance between noise and information flow maximizes set complexity of network dynamics, PLoS ONE, 8(3):e56523, 2013.

N. Aghaeepour, G. Finak, The FlowCAP Consortium, The DREAM Consortium, H. Hoos, T. R. Mosmann, R. Brinkman, R. Gottardo, and R. H. Scheuermann. Critical assessment of automated flow cytometry data analysis techniques, Nature Methods, 10(3):228-238, 2013.

D. Yang, Y. Sun, L. Hu, H. Zheng, P. Ji, C. V. Pecot, Y. Zhao, S. Reynolds, H. Cheng, R. Rupaimoole, D. Cogdell, M. Nykter, R. Broaddus, C. Rodriguez-Aguayo, G. Lopez-Berestein, J. Liu, I. Shmulevich, A. K. Sood, K. Chen, and W. Zhang. Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer, Cancer Cell, 23(2):186-199, 2013.

M. T. Weirauch, A. Cote, R. Norel, M. Annala, Y. Zhao, T. J. Riley, J. S. Rodriguez, T. Cokelaer, A. Vedenko, S. Talukder, DREAM5 consortium, H. J. Bussemaker, Q. D. Morris, M. L. Bulyk, G. Stolovitzky, and T. R. Hughes. Evaluation of methods for modeling transcription factor sequence specificity, Nature Biotechnology, 31(2):126-134, 2013.

B. C. Parker, M. Annala, D. Cogdell, K. Granberg, Y. Sun, P. Ji, J. Gumin, H. Zheng, L. Hu, X. Li, O. Yli-Harja, H. Haapasalo, T. Visakorpi, X. Liu, C.-G. Liu, R. Sawaya, G. N. Fuller, K. Chen, F. L. Lang, M. Nykter, and W. Zhang. FGFR3-TACC3 fusion escapes miR-99a regulation and promotes tumorigenesis in glioblastoma, Journal of Clinical Investigations, 123(2):855-865, 2013.

L. M. Moore, V. Kivinen, Y. Liu, M. Annala, D. Cogdell, X. Liu, C.-G. Liu, R. Sawaya, O. Yli-Harja, I. Shmulevich, G. N. Fuller, W. Zhang, M. Nykter, Transcriptome and Small RNA Deep Sequencing Reveals Deregulation of miRNA Biogenesis in Human Glioma ,Journal of Pathology , 229(3):449-459, 2013.

Hongisto V, Jernström S, Fey V, Mpindi JP, Kleivi Sahlberg K, Kallioniemi O, Perälä M. (2013) High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells. PLoS One. 8(10):e77232.

He T, Haapa-Paananen S, Kaminskyy VO, Kohonen P, Fey V, Zhivotovsky B, Kallioniemi O, Perälä M. (2013) Inhibition of the mitochondrial pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase by doxorubicin and brequinar sensitizes cancer cells to TRAIL-induced apoptosis. Oncogene. [Epub ahead of print]

K. M. Holmes, M. Annala, C. Y. X. Chua, S. M. Dunlap, Y. Liu, N. Hugen, L. M. Moore, D. Cogdell, L. Hu, M. Nykter, K. Hess, G. N. Fuller, W. Zhang, Insulin-like growth factor-binding protein 2-driven glioma progression is prevented by blocking a clinically significant integrin, integrin-linked kinase, and NF-kB network, Proceedings of the National Academy of Sciences USA, 109(9):3475-3480, 2012.

Vainio P, Mpindi JP, Kohonen P, Fey V, Mirtti T, Alanen KA, Perälä M, Kallioniemi O, Iljin K (2012) High-Throughput Transcriptomic and RNAi Analysis Identifies AIM1, ERGIC1, TMED3 and TPX2 as Potential Drug Targets in Prostate Cancer. PLoS One. 7(6):e39801. Epub 2012 Jun 28

Vainio P, Gupta S, Ketola K, Mirtti T, Mpindi JP, Kohonen P, Fey V, Perala M, Smit F, Verhaegh G, Schalken J, Alanen KA, Kallioniemi O, Iljin K (2011) Arachidonic Acid Pathway Members PLA2G7, HPGD, EPHX2, and CYP4F8 Identified as Putative Novel Therapeutic Targets in Prostate Cancer. Am J Pathol 178: 525-536

Pollari S, Leivonen SK, Perälä M, Fey V, Käkönen SM, Kallioniemi O (2012) Identification of microRNAs inhibiting TGF-β-induced IL-11 production in bone metastatic breast cancer cells. PLoS One.7(5):e37361. Epub 2012 May 21

J. Yang, A. Ylipää, Y. Sun, H. Zheng, K. Chen, M. Nykter, J. Trent, N. Ratner, D. C. Lev, W. Zhang, Genomic and Molecular Characterization of Malignant Peripheral Nerve Sheath Tumor Identifies the IGF1R Pathway as a Primary Target for Treatment, Clinical Cancer Research, 17(24):7563-7573, 2011.

T. Mäki-Marttunen, J. Acimovic, M. Nykter, J. Kesseli, K. Ruohonen, O. Yli-Harja, M.-L. Linne, Information diversity in structure and dynamics of simulated neuronal networks, Frontiers in Computational Neuroscience, 5(26), 2011.

M. Annala, K. Laurila, H. Lähdesmäki, M. Nykter, A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays, PLoS ONE, 6(5):e20059, 2011.

H. Cheng, L. Zhang, D. E. Cogdell, H. Zheng, A. J. Schetter, M. Nykter, C. C. Harris, K. Chen, S. R. Hamilton, W. Zhang, Circulating Plasma MiR-141 Is a Novel Biomarker for Metastatic Colon Cancer and Predicts Poor Prognosis, PLoS ONE, 6(3):e17745, 2011.

A. Ylipää, K. Hunt, J. Yang, A. Lazar, K. Torres, D. Lev, M. Nykter, R. Pollock, J. Trent, and W. Zhang, Integrative Genomic Characterization and a Genomic Staging System for Gastrointestinal Stromal Tumors, Cancer, 117(2):380-389, 2011.

A. Ylipää, O. Yli-Harja, W. Zhang, and M. Nykter, A Systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas, Chinese Journal of Cancer, 30(1):27-38, 2011.

D. Yang, A. Ylipää, J. Yang, K. Hunt, R. Pollock, J. Trent, O. Yli-Harja, I. Shmulevich, M. Nykter, and W. Zhang, An integrated study of aberrant gene copy number and gene expression in GIST and LMS, Technology in Cancer Research & Treatment, 9(2):171-178, 2010.

D. J. Galas, M. Nykter, G. W. Carter, N. D. Price, and I. Shmulevich, Biological information as set-based complexity, IEEE Transactions on Information Theory, 56(2):667-677, 2010.

Ketola K, Vainio P, Fey V, Kallioniemi O, Iljin K (2010) Monensin is a potent inducer of oxidative stress and inhibitor of androgen signaling leading to apoptosis in prostate cancer cells. Mol Cancer Ther 9: 3175-3185

Pöllänen E, Fey V, Tormakangas T, Ronkainen PH, Taaffe DR, Takala T, Koskinen S, Cheng S, Puolakka J, Kujala UM, Suominen H, Sipila S, Kovanen V (2010) Power training and postmenopausal hormone therapy affect transcriptional control of specific co-regulated gene clusters in skeletal muscle. Age (Dordr) 32: 347-363

V. Litvak, S. A. Ramsey, A. G. Rust, D. E. Zak, K. A. Kennedy, A. E. Lampano, M. Nykter, I. Shmulevich, and A. Aderem, Transcription factor C/EBPd plays a key role in a regulatory circuit that discriminates transient and persistent TLR4-induced inflammatory signals,Nature Immunology, 10(4):437-443, 2009.

M. Nykter, H. Lähdesmäki, A. Rust, V. Thorsson, and I. Shmulevich, A data integration framework for prediction of transcription factor targets: a BCL6 case study, Annals of the New York Academy of Sciences, 1158:205-214, 2009.

Huvila J, Brandt A, Rojas CR, Pasanen S, Talve L, Hirsimaki P, Fey V, Kytomaki L, Saukko P, Carpen O, Soini JT, Grenman S, Auranen A (2009) Gene expression profiling of endometrial adenocarcinomas reveals increased apolipoprotein E expression in poorly differentiated tumors. Int J Gynecol Cancer 19: 1226-1231

Iljin K, Ketola K, Vainio P, Halonen P, Kohonen P, Fey V, Grafstrom RC, Perala M, Kallioniemi O (2009) High-throughput cell-based screening of 4910 known drugs and drug-like small molecules identifies disulfiram as an inhibitor of prostate cancer cell growth. Clin Cancer Res 15: 6070-6078

Harma H, Rozwandowicz-Jansen A, Martikkala E, Frang H, Hemmila I, Sahlberg N, Fey V, Perala M, Hanninen P (2009) A new simple cell-based homogeneous time-resolved fluorescence QRET technique for receptor-ligand interaction screening. J Biomol Screen 14: 936-943

Steiner S, Dietzel L, Schroter Y, Fey V, Wagner R, Pfannschmidt T (2009) The role of phosphorylation in redox regulation of photosynthesis genes psaA and psbA during photosynthetic acclimation of mustard. Mol Plant 2: 416-429

M. Nykter, N. D. Price, M. Aldana, S. Ramsey, S. A. Kauffman, L. Hood, O. Yli-Harja, and I. Shmulevich, Gene Expression Dynamics in the Macrophage Exhibit Criticality, Proceedings of the National Academy of Sciences USA, 105(6):1897-1900, 2008.

M. Nykter, N. D. Price, A. Larjo, T. Aho, S. A. Kauffman, O. Yli-Harja, and I. Shmulevich, Critical networks exhibit maximal information diversity in structure-dynamics relationships, Physical Review Letters, 100(058702), 2008.

A. Niemistö*, M. Nykter*, T. Aho, H. Jalovaara, K. Marjanen, M. Ahdesmäki, P. Ruusuvuori, M. Tiainen, M.-L. Linne, and O. Yli-Harja, Computational methods for estimation of cell cycle distributions of synchronized yeast cells, EURASIP Journal on Bioinformatics and Systems Biology, 2007(46150), 2007. (*equally contributing authors)

M. Nykter, T. Aho, M. Ahdesmäki, P. Ruusuvuori, A. Lehmussola, and O. Yli-Harja, Simulation of Microarray Data with Realistic Characteristics, BMC Bioinformatics,7(349), 2006.

A. Harjunpää, M. Taskinen, M. Nykter, M.-L. Karjalainen-Lindsberg, H. Nyman, O. Monni, S. Hemmer, O. Yli-Harja, S. Hautaniemi, S. Meri, and S. Leppä, Differential gene expression in non-malignant tumor microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP, British Journal of Haematology, 135(1), 2006.

M. Nykter, K. K. Hunt, R. E. Pollock, A. K. El-Naggar, E. Taylor, I. Shmulevich, O. Yli-Harja, and W. Zhang, Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies, Technology in Cancer Research & Treatment, 5(2):177-182, 2006.

Fey V, Wagner R, Brautigam K, Pfannschmidt T (2005) Photosynthetic redox control of nuclear gene expression. J Exp Bot 56: 1491-1498

Fey V, Wagner R, Bräutigam K, Wirtz M, Hell R, Dietzmann A, Leister D, Oelmüller R, Pfannschmidt T (2005) Retrograde plastid redox signals in the expression of nuclear genes for chloroplast proteins of Arabidopsis thaliana. J Biol Chem 280: 5318-5328