Scientific references

2019

Tiihonen J, Koskuvi M, Storvik M, Hyötyläinen I, Gao Y, Puttonen KA, Giniatullina R, Poguzhelskaya E, Ojansuu I, Vaurio O, Cannon TD, Lönnqvist J, Therman S, Suvisaari J, Kaprio J, Cheng L, Hill AF, Lähteenvuo M, Tohka J, Giniatullin R, Lehtonen Š, Koistinaho J. Sex-specific transcriptional and proteomic signatures in schizophrenia. Nat Commun. 2019 Sep 2;10(1):3933. doi: 10.1038/s41467-019-11797-3. PMID: 31477693

Tiihonen J, Koskuvi M, Lähteenvuo M, Virtanen PLJ, Ojansuu I, Vaurio O, Gao Y, Hyötyläinen I, Puttonen KA, Repo-Tiihonen E, Paunio T, Rautiainen MR, Tyni S, Koistinaho J, Lehtonen Š. Neurobiological roots of psychopathy. Mol Psychiatry. 2019 Aug 27. doi: 10.1038/s41380-019-0488-z. PMID:31455857

Pölönen, P, Jawahar Deen, A, Leinonen, HM, Jyrkkänen, HK, Kuosmanen, S, Mononen, M et al.. Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma. Oncogene. 2019; :. doi: 10.1038/s41388-019-0956-6. PubMed PMID:31444413 .

Valkonen, M, Isola, J, Isola, J, Ylinen, O, Muhonen, V, Saxlin, A et al.. Cytokeratin-supervised deep learning for automatic recognition of epithelial cells in breast cancers stained for ER, PR, and Ki-67. IEEE Trans Med Imaging. 2019; :. doi: 10.1109/TMI.2019.2933656. PubMed PMID:31398111 .

Mehtonen, J, Pölönen, P, Häyrynen, S, Dufva, O, Lin, J, Liuksiala, T et al.. Data-driven characterization of molecular phenotypes across heterogeneous sample collections. Nucleic Acids Res. 2019;47 (13):e76. doi: 10.1093/nar/gkz281. PubMed PMID:31329928 PubMed Central PMC6648337.

Yang, J, Ylipää, A, Sun, Y, Zheng, H, Chen, K, Nykter, M et al.. Editor's Note: Genomic and Molecular Characterization of Malignant Peripheral Nerve Sheath Tumor Identifies the IGF1R Pathway as a Primary Target for Treatment. Clin. Cancer Res. 2019;25 (10):3195. doi: 10.1158/1078-0432.CCR-19-1144. PubMed PMID:31092619 .

Pölönen, P, Mehtonen, J, Lin, J, Liuksiala, T, Häyrynen, S, Teppo, S et al.. Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies. Cancer Res. 2019;79 (10):2466-2479. doi: 10.1158/0008-5472.CAN-18-2970. PubMed PMID:30940663 .

Lehtipuro, S, Nykter, M, Granberg, KJ. Modes of immunosuppression in glioblastoma microenvironment. Oncotarget. 2019;10 (9):920-921. doi: 10.18632/oncotarget.26643. PubMed PMID:30847018 PubMed Central PMC6398170.

Viiri, LE, Rantapero, T, Kiamehr, M, Alexanova, A, Oittinen, M, Viiri, K et al.. Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation. Sci Rep. 2019;9 (1):3562. doi: 10.1038/s41598-019-39215-0. PubMed PMID:30837492 PubMed Central PMC6401154.

Vandekerkhove, G, Struss, WJ, Annala, M, Kallio, HML, Khalaf, D, Warner, EW et al.. Circulating Tumor DNA Abundance and Potential Utility in De Novo Metastatic Prostate Cancer. Eur. Urol. 2019;75 (4):667-675. doi: 10.1016/j.eururo.2018.12.042. PubMed PMID:30638634 .

2018

Tikkanen T, Leroy B, Fournier JL, Risques RA, Malcikova J, Soussi T. Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing. Hum Mutat. 2018 Jul;39(7):925-933. doi: 10.1002/humu.23543. Epub 2018 May 17. PMID:29696732

Annala, M, Taavitsainen, S, Vandekerkhove, G, Bacon, JVW, Beja, K, Chi, KN et al.. Frequent mutation of the FOXA1 untranslated region in prostate cancer. Commun Biol. 2018;1 :122. doi: 10.1038/s42003-018-0128-1. PubMed PMID:30272002 PubMed Central PMC6123809.

Latonen, L, Nykter, M, Visakorpi, T. Proteomics of prostate cancer - revealing how cancer cells master their messy genomes. Oncoscience. 2018;5 (7-8):216-217. doi: 10.18632/oncoscience.453. PubMed PMID:30234142PubMed Central PMC6142899.

Lin, J, Kimura, BY, Oikarinen, S, Nykter, M. Bioinformatics Assembling and Assessment of Novel Coxsackievirus B1 Genome. Methods Mol. Biol. 2018;1838 :261-272. doi: 10.1007/978-1-4939-8682-8_18. PubMed PMID:30129002 .

Jylhä, A, Nättinen, J, Aapola, U, Mikhailova, A, Nykter, M, Zhou, L et al.. Comparison of iTRAQ and SWATH in a clinical study with multiple time points. Clin Proteomics. 2018;15 :24. doi: 10.1186/s12014-018-9201-5. PubMed PMID:30069167 PubMed Central PMC6065059.

Veskimäe, K, Scaravilli, M, Niininen, W, Karvonen, H, Jaatinen, S, Nykter, M et al.. Expression Analysis of Platinum Sensitive and Resistant Epithelial Ovarian Cancer Patient Samples Reveals New Candidates for Targeted Therapies. Transl Oncol. 2018;11 (5):1160-1170. doi: 10.1016/j.tranon.2018.07.010. PubMed PMID:30056367 PubMed Central PMC6079561.

Chedgy, EC, Vandekerkhove, G, Herberts, C, Annala, M, Donoghue, AJ, Sigouros, M et al.. Biallelic tumour suppressor loss and DNA repair defects in de novo small-cell prostate carcinoma. J. Pathol. 2018;246 (2):244-253. doi: 10.1002/path.5137. PubMed PMID:30015382 .

Kallio, HML, Hieta, R, Latonen, L, Brofeldt, A, Annala, M, Kivinummi, K et al.. Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases. Br. J. Cancer. 2018;119 (3):347-356. doi: 10.1038/s41416-018-0172-0. PubMed PMID:29988112 .

Harjula, SE, Ojanen, MJT, Taavitsainen, S, Nykter, M, Rämet, M. Interleukin 10 mutant zebrafish have an enhanced interferon gamma response and improved survival against a Mycobacterium marinum infection. Sci Rep. 2018;8 (1):10360. doi: 10.1038/s41598-018-28511-w. PubMed PMID:29985419 PubMed Central PMC6037744.

Gubina, N, Naudi, A, Stefanatos, R, Jove, M, Scialo, F, Fernandez-Ayala, DJ et al.. Essential physiological differences characterise short- and long-lived strains of Drosophila melanogaster. J. Gerontol. A Biol. Sci. Med. Sci. 2018; :. doi: 10.1093/gerona/gly143. PubMed PMID:29945183 .

Luoto, S, Hermelo, I, Vuorinen, EM, Hannus, P, Kesseli, J, Nykter, M et al.. Computational Characterization of Suppressive Immune Microenvironments in Glioblastoma. Cancer Res. 2018;78 (19):5574-5585. doi: 10.1158/0008-5472.CAN-17-3714. PubMed PMID:29921698 .

Nordfors, K, Haapasalo, J, Afyounian, E, Tuominen, J, Annala, M, Häyrynen, S et al.. Erratum: Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma. Cold Spring Harb Mol Case Stud. 2018;4 (3):. doi: 10.1101/mcs.a003129. PubMed PMID:29858379 PubMed Central PMC5983177.

Park, ES, Yan, JP, Ang, RA, Lee, JH, Deng, X, Duffy, SP et al.. Isolation and genome sequencing of individual circulating tumor cells using hydrogel encapsulation and laser capture microdissection. Lab Chip. 2018;18 (12):1736-1749. doi: 10.1039/c8lc00184g. PubMed PMID:29762619 .

Kartasalo, K, Latonen, L, Vihinen, J, Visakorpi, T, Nykter, M, Ruusuvuori, P et al.. Comparative analysis of tissue reconstruction algorithms for 3D histology. Bioinformatics. 2018;34 (17):3013-3021. doi: 10.1093/bioinformatics/bty210. PubMed PMID:29684099 PubMed Central PMC6129300.

Uusi-Mäkelä, MIE, Barker, HR, Bäuerlein, CA, Häkkinen, T, Nykter, M, Rämet, M et al.. Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio). PLoS ONE. 2018;13 (4):e0196238. doi: 10.1371/journal.pone.0196238. PubMed PMID:29684067 PubMed Central PMC5912780.

Gao, Q, Liang, WW, Foltz, SM, Mutharasu, G, Jayasinghe, RG, Cao, S et al.. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018;23 (1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050. PubMed PMID:29617662 PubMed Central PMC5916809.

Nordfors, K, Haapasalo, J, Afyounian, E, Tuominen, J, Annala, M, Häyrynen, S et al.. Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma. Cold Spring Harb Mol Case Stud. 2018;4 (2):. doi: 10.1101/mcs.a002246. PubMed PMID:29602769 PubMed Central PMC5880256.

Latonen, L, Afyounian, E, Jylhä, A, Nättinen, J, Aapola, U, Annala, M et al.. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat Commun. 2018;9 (1):1176. doi: 10.1038/s41467-018-03573-6. PubMed PMID:29563510 PubMed Central PMC5862881.

Haapasalo, J, Nordfors, K, Granberg, KJ, Kivioja, T, Nykter, M, Haapasalo, H et al.. NRF2, DJ1 and SNRX1 and their prognostic impact in astrocytic gliomas. Histol. Histopathol. 2018;33 (8):791-801. doi: 10.14670/HH-11-973. PubMed PMID:29441509 .

Annala, M, Vandekerkhove, G, Khalaf, D, Taavitsainen, S, Beja, K, Warner, EW et al.. Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer. Cancer Discov. 2018;8 (4):444-457. doi: 10.1158/2159-8290.CD-17-0937. PubMed PMID:29367197 .

Högnäs, G, Kivinummi, K, Kallio, HML, Hieta, R, Ruusuvuori, P, Koskenalho, A et al.. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am. J. Surg. Pathol. 2018;42 (1):103-115. doi: 10.1097/PAS.0000000000000961. PubMed PMID:28984675 .

Nättinen, J, Jylhä, A, Aapola, U, Enríquez-de-Salamanca, A, Pinto-Fraga, J, López-Miguel, A et al.. Topical fluorometholone treatment and desiccating stress change inflammatory protein expression in tears. Ocul Surf. 2018;16 (1):84-92. doi: 10.1016/j.jtos.2017.09.003. PubMed PMID:28918083 .

Basenko EY, Pulman JA, Shanmugasundram A, Harb OS, Crouch K, Starns D,Warrenfeltz S, Aurrecoechea C, Stoeckert CJ Jr, Kissinger JC, Roos DS, Hertz-Fowler C. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. J Fungi (Basel). 2018 Mar 20;4(1). pii: E39. doi: 10.3390/jof4010039. PubMed PMID: 30152809; PubMed Central PMCID: PMC5872342.

Huot B, Castroverde CDM, Velásquez AC, Hubbard E, Pulman JA, Yao J, Childs KL, Tsuda K, Montgomery BL, He SY. Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis. Nat Commun. 2017 Nov 27;8(1):1808. doi: 10.1038/s41467-017-01674-2. PubMed PMID: 29180698; PubMed Central PMCID: PMC5704021.

Kaikkonen, E., Rantapero, T., Zhang, Q., Taimen, P., Laitinen, V., Kallajoki, M.,Jambulingam, D., Ettala, O., Knaapila, J., Boström, P. J., Wahlström, G.,Sipeky, C., Pursiheimo, J. P., Tammela, T., Kellokumpu-Lehtinen, P. L.,Fey, V., Maehle, L., Wiklund, F., Wei, G. H., Schleutker, J.(2018). ANO7 is associated with aggressive prostate cancer. International Journal of Cancer, 143(10), 2479–2487. https://doi.org/10.1002/ijc.31746

Tsafou, K., Katschnig, A. M., Radic-Sarikas, B., Mutz, C. N., Iljin, K., Schwentner, R., Kauer, M. O., Mühlbacher K., Aryee, D. N. T., Westergaard, D., Haapa-Paananen, S., Fey, V., Superti-Furga, G., Toretsky, J., Brunak, S., Kovar, H. (2018). Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers. Oncotarget, 9(57), 31018–31031. https://doi.org/10.18632/oncotarget.25760

2017

Sugano Y, Cianciolo Cosentino C, Loffing-Cueni D, Neuhauss SCF, Loffing J. Pflugers Arch. Comparative transcriptomic analysis identifies evolutionarily conserved gene products in the vertebrate renal distal convoluted tubule. 2017 Aug;469(7-8):859-867. doi: 10.1007/s00424-017-2009-8. Epub 2017 Jun 27. PMID:28656378

A. Urbanucci, S. Barfeld, V. Kytölä, H. Itkonen, I. Coleman, D. Vodák, L. Sjöblom, X. Sheng, T. Tolonen, S. Minner, C. Burdelski, K. Kivinummi, A. Kohvakka, S. Kregel, M. Takhar, M. Alshalalfa, E. Davicioni, N. Erho, P. Lloyd, R. Karnes, A. Ross, E. Schaeffer, D. Vander Griend, S. Knapp, E. Corey, F. Feng, P. Nelson, F. Saatcioglu, K. Knudsen, T. Tammela, G. Sauter, T. Schlomm, M. Nykter, T. Visakorpi, I. Mills. Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer.
Cell Rep, 19(10):2045-2059, 2017.

M. Valkonen M, Kartasalo K, Liimatainen K, Nykter M, Latonen L, Ruusuvuori P. Metastasis detection from whole slide images using local features and random forests. Cytometry A, 91(6):555-565, 2017.

E. Afyounian, M. Annala, M. Nykter. Segmentum: a tool for copy number analysis of cancer genomes. BMC Bioinformatics, 18(1):215, 2017.

M. Valkonen, P. Ruusuvuori, K. Kartasalo, M. Nykter, T. Visakorpi, L. Latonen. Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models. Sci Rep, 7:44831, 2017.

K. Granberg, M. Annala, B. Lehtinen, J. Kesseli, J. Haapasalo, P. Ruusuvuori, O. Yli-Harja, T. Visakorpi, H. Haapasalo, M. Nykter, W. Zhang. Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas. Neuro Oncol, 2017.

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.

T. Grönroos, S. Teppo, J. Mehtonen, S. Laukkanen, T. Liuksiala, M. Nykter, M. Heinäniemi, O. Lohi. Overexpression of PTP4A3 in ETV6-RUNX1 acute lymphoblastic leukemia. Leuk Res, 54:1-6, 2017.

J. Lin, L. Kramna, R. Autio, H. Hyöty, M. Nykter, O. Cinek. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples. BMC Genomics, 18(1):378, 2017.

R. Lund, N. Rahkonen, M. Malonzo, L. Kauko, M. Emani, V. Kivinen, E. Närvä, E. Kemppainen, A. Laiho, H. Skottman, O. Hovatta, O. Rasool, M. Nykter, H. Lähdesmäki, R. Lahesmaa. RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA(+) and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. Stem Cell Reports, 8(5):1442-1454, 2017.

B. Lehtinen, A. Raita, J. Kesseli, M. Annala, K. Nordfors, O. Yli-Harja, W. Zhang, T. Visakorpi, M. Nykter, H. Haapasalo, K. Granberg. Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas. BMC Cancer, 17(1):310, 2017.

K. Tarkkonen, R. Hieta, V. Kytölä, M. Nykter, R. Kiviranta. Comparative analysis of osteoblast gene expression profiles and Runx2 genomic occupancy of mouse and human osteoblasts in vitro. Gene, S0378-1119(17)30362-1, 2017.

M. Yang, U. Topaloglu, W. Petty, M. Pagni, K. Foley, S. Grant, M. Robinson, R. Bitting, A. Thomas, A. Alistar, R. Desnoyers, M. Goodman, C. Albright, M. Porosnicu, M. Vatca, S. Qasem, B. DeYoung, V. Kytola, M. Nykter, K. Chen, E. Levine, E. Staren, R. D'Agostino, R. Petro, W. Blackstock, B. Powell, E. Abraham, B. Pasche, W. Zhang. Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages. J Hematol Oncol, 10(1):100, 2017.

Bowman MJ, Pulman JA, Liu TL, Childs KL. A modified GC-specific MAKER geneannotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa. BMC Bioinformatics. 2017 Nov 25;18(1):522. doi:10.1186/s12859-017-1942-z. PubMed PMID: 29178822; PubMed Central PMCID:PMC5702205.

Poliner E, Pulman JA, Zienkiewicz K, Childs K, Benning C, Farré EM. A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and geneticengineering of the eicosapentaenoic acid pathway for enhanced long-chainpolyunsaturated fatty acid production. Plant Biotechnol J. 2018Jan;16(1):298-309. doi: 10.1111/pbi.12772. Epub 2017 Jul 13. PubMed PMID:28605577; PubMed Central PMCID: PMC5785352.

Wiersma AT, Pulman JA, Brown LK, Cowger C, Olson EL. Identification of Pm58from Aegilops tauschii. Theor Appl Genet. 2017 Jun;130(6):1123 1133. doi:10.1007/s00122-017-2874-8. Epub 2017 Mar 3. PubMed PMID: 28255671.

Kangas R., Törmäkangas T., Fey V., Pursiheimo J., Miinalainen I., Alen M., Kaprio J., Sipilä S., Säämänen A.M., Kovanen V., Laakkonen E.K. (2017). Aging and serum exomiR content in women-effects of estrogenic hormone replacement therapy. Sci Rep. 7:42702. doi: 10.1038/srep42702.

He, T., Surdez, D., Rantala, J. K., Haapa-Paananen, S., Ban, J., Kauer, M., Tomazou, E., Fey, V., Alonso, J., Kovar, H., Delattre, O., Iljin, K. (2017). High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability. Gene. http://doi.org/10.1016/j.gene.2016.10.021

2016

K. Määttä, T. Rantapero, A. Lindström, M. Nykter, M. Kankuri-Tammilehto, S. Laasanen, J. Schleutker. Whole-exome sequencing of Finnish hereditary breast cancer families. Eur J Hum Genet, 25(1):85-93, 2016.

V. Ulman, D. Svoboda, M. Nykter, M. Kozubek, P. Ruusuvuori. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry A, 89(12):1057-1072, 2016.

G. Bova, H. Kallio, M. Annala, K. Kivinummi, G. Högnäs, S. Häyrynen, T. Rantapero, V. Kivinen, W. Isaacs, T. Tolonen, M. Nykter, T. Visakorpi. Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer. Cold Spring Harb Mol Case Stud, 2(3):a000752, 2016.

S. Teppo, S. Laukkanen, T. Liuksiala, J. Nordlund, M. Oittinen, K. Teittinen, T. Grönroos, P. St-Onge, D. Sinnett, A. Syvänen, M. Nykter, K. Viiri, M. Heinäniemi, O. Lohi. Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia. Genome Res, 26(11):1468-1477, 2016.

Z. Cordova, A. Grönholm, V. Kytölä, V. Taverniti, S. Hämäläinen, S. Aittomäki, W. Niininen, I. Junttila, A. Ylipää, M. Nykter, M. Pesu.
Myeloid cell expressed proprotein convertase FURIN attenuates inflammation. Oncotarget, 7(34):54392-54404, 2016.

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.

G. Bova, H. Kallio, M. Annala, K. Kivinummi, G. Högnäs, S. Häyrynen, T. Rantapero, V. Kivinen, W. Isaacs, T. Tolonen, M. Nykter, T. Visakorpi. Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer. Cold Spring Harb Mol Case Stud, 2(3)a000752, 2016.

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.

Pulman JA, Childs KL, Sgambelluri RM, Walton JD. Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera. BMC Genomics. 2016 Dec 15;17(1):1038. PubMed PMID: 27978833; PubMed Central PMCID: PMC5159998.

Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, CrouchK, Doherty R, Falke D, Fischer S, Gajria B, Harb OS, Heiges M, Hertz-Fowler C, HuS, Iodice J, Kissinger JC, Lawrence C, Li W, Pinney DF, Pulman JA, Roos DS,Shanmugasundram A, Silva-Franco F, Steinbiss S, Stoeckert CJ Jr, Spruill D, Wang H, Warrenfeltz S, Zheng J. EuPathDB: the eukaryotic pathogen genomics databaseresource. Nucleic Acids Res. 2017 Jan 4;45(D1):D581-D591. doi:10.1093/nar/gkw1105. Epub 2016 Nov 29. PubMed PMID: 27903906; PubMed Central PMCID: PMC5210576.

Duffy, D. J., Krstic, A., Schwarzl, T., Halasz, M., Iljin, K., Fey, D., Haley, B., Whilde, J., Haapa-Paananen, S., Fey, V., Fischer, M., Westermann, F., Henrich, K., Bannert, S., Higgins, D. G., Kolch, W. (2016). Wnt signalling is a bi-directional vulnerability of cancer cells. Oncotarget, 5. http://doi.org/10.18632/oncotarget.11203

Laajala, T. D., Jumppanen, M., Huhtaniemi, R., Fey, V., Kaur, A., Knuuttila, M., Aho, E., Oksala, R., Westermarck, J., Mäkelä, S., Poutanen, M., Aittokallio, T. (2016). Optimized design and analysis of preclinical intervention studies in vivo. Scientific Reports 6:30723. http://doi.org/10.1038/srep30723

Cantisani MC, Parascandolo A, Perälä M, Allocca C, Fey V, Sahlberg N, Merolla F, Basolo F, Laukkanen MO, Kallioniemi OP, Santoro M, Castellone MD. (2016). A loss-of-function genetic screening identifies novel mediators of thyroid cancer cell viability. Oncotarget, 7(19), 28510–22. http://doi.org/10.18632/oncotarget.8577

Ketola K., Viitala M., Kohonen P., Fey V., Culig Z., Kallioniemi O., Iljin K. (2016). High-throughput cell-based compound screen identifies pinosylvin methyl ether and tanshinone IIA as inhibitors of castration-resistant prostate cancer. J Mol Biochem. 30;5(1):12-22.

2015

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. http://doi.org/10.18632/oncotarget.6568

2014

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.

2005-2013

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