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Computational Biology

We are part of Academy of Finland Center of Excellence in Tumor Genetics

Publications 2006-2019

2019

  1. Jayaram, A, Wingate, A, Wetterskog, D, Conteduca, V, Khalaf, D, Sharabiani, MTA et al.. Plasma Androgen Receptor Copy Number Status at Emergence of Metastatic Castration-Resistant Prostate Cancer: A Pooled Multicohort Analysis. JCO Precis Oncol. 2019;3 :. doi: 10.1200/PO.19.00123. PubMed PMID:32923850 PubMed Central PMC7446348.
  2. Lindfors, K, Lin, J, Lee, HS, Hyöty, H, Nykter, M, Kurppa, K et al.. Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study. Gut. 2020;69 (8):1416-1422. doi: 10.1136/gutjnl-2019-319809. PubMed PMID:31744911 PubMed Central PMC7234892.
  3. Ritch, E, Fu, SYF, Herberts, C, Wang, G, Warner, EW, Schönlau, E et al.. Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer. Clin Cancer Res. 2020;26 (5):1114-1125. doi: 10.1158/1078-0432.CCR-19-1623. PubMed PMID:31744831 .
  4. Khalaf, DJ, Annala, M, Taavitsainen, S, Finch, DL, Oja, C, Vergidis, J et al.. Optimal sequencing of enzalutamide and abiraterone acetate plus prednisone in metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase 2, crossover trial. Lancet Oncol. 2019;20 (12):1730-1739. doi: 10.1016/S1470-2045(19)30688-6. PubMed PMID:31727538 .
  5. Granberg, KJ, Raita, A, Lehtinen, B, Tiihonen, AM, Kesseli, J, Annala, M et al.. Moderate-to-strong expression of FGFR3 and TP53 alterations in a subpopulation of choroid plexus tumors. Histol Histopathol. 2020;35 (7):673-680. doi: 10.14670/HH-18-180. PubMed PMID:31660579 .
  6. Harjula, SE, Saralahti, AK, Ojanen, MJT, Rantapero, T, Uusi-Mäkelä, MIE, Nykter, M et al.. Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio). Dev Comp Immunol. 2020;103 :103523. doi: 10.1016/j.dci.2019.103523. PubMed PMID:31626817 .
  7. Genitsch, V, Kollár, A, Vandekerkhove, G, Blarer, J, Furrer, M, Annala, M et al.. Morphologic and genomic characterization of urothelial to sarcomatoid transition in muscle-invasive bladder cancer. Urol Oncol. 2019;37 (11):826-836. doi: 10.1016/j.urolonc.2019.09.025. PubMed PMID:31585777 .
  8. Moradi, E, Marttinen, M, Häkkinen, T, Hiltunen, M, Nykter, M. Supervised pathway analysis of blood gene expression profiles in Alzheimer’s disease. Neurobiol Aging. 2019;84 :98-108. doi: 10.1016/j.neurobiolaging.2019.07.004. PubMed PMID:31522136 .
  9. 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;38 (50):7473-7490. doi: 10.1038/s41388-019-0956-6. PubMed PMID:31444413 .
  10. Valkonen, M, Isola, J, Ylinen, O, Muhonen, V, Saxlin, A, Tolonen, T 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. 2020;39 (2):534-542. doi: 10.1109/TMI.2019.2933656. PubMed PMID:31398111 .
  11. Genitsch, V, Kollár, A, Vandekerkhove, G, Blarer, J, Furrer, M, Annala, M et al.. Morphologic and genomic characterization of urothelial to sarcomatoid transition in muscle-invasive bladder cancer. Urol Oncol. 2019;37 (9):573.e19-573.e29. doi: 10.1016/j.urolonc.2019.06.021. PubMed PMID:31358384 .
  12. 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.
  13. Taavitsainen, S, Annala, M, Ledet, E, Beja, K, Miller, PJ, Moses, M et al.. Evaluation of Commercial Circulating Tumor DNA Test in Metastatic Prostate Cancer. JCO Precis Oncol. 2019;3 :. doi: 10.1200/PO.19.00014. PubMed PMID:32914020 PubMed Central PMC7446428.
  14. 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 .
  15. Hotte, SJ, Chi, KN, Joshua, AM, Tu, D, Macfarlane, RJ, Gregg, RW et al.. A Phase II Study of PX-866 in Patients With Recurrent or Metastatic Castration-resistant Prostate Cancer: Canadian Cancer Trials Group Study IND205. Clin Genitourin Cancer. 2019;17 (3):201-208.e1. doi: 10.1016/j.clgc.2019.03.005. PubMed PMID:31056399 .
  16. 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 .
  17. 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.
  18. 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.
  19. Sundahl, N, Vandekerkhove, G, Decaestecker, K, Meireson, A, De Visschere, P, Fonteyne, V et al.. Randomized Phase 1 Trial of Pembrolizumab with Sequential Versus Concomitant Stereotactic Body Radiotherapy in Metastatic Urothelial Carcinoma. Eur Urol. 2019;75 (5):707-711. doi: 10.1016/j.eururo.2019.01.009. PubMed PMID:30665814 .
  20. 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 .
  21. Gubina, N, Naudi, A, Stefanatos, R, Jove, M, Scialo, F, Fernandez-Ayala, DJ et al.. Essential Physiological Differences Characterize Short- and Long-Lived Strains of Drosophila melanogaster. J Gerontol A Biol Sci Med Sci. 2019;74 (12):1835-1843. doi: 10.1093/gerona/gly143. PubMed PMID:29945183 .

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Publications 2018

  1. 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.
  2. 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:30234142 PubMed Central PMC6142899.
  3. 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 .
  4. 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.
  5. 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.
  6. 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 .
  7. 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 .
  8. 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.
  9. 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 .
  10. 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 .
  11. 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.
  12. 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 .
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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 .
  19. 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 .
  20. 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 .
  21. 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 .

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Publications 2017

  1. Karvonen, H, Chiron, D, Niininen, W, Ek, S, Jerkeman, M, Moradi, E et al.. Crosstalk between ROR1 and BCR pathways defines novel treatment strategies in mantle cell lymphoma. Blood Adv. 2017;1 (24):2257-2268. doi: 10.1182/bloodadvances.2017010215. PubMed PMID:29296874 PubMed Central PMC5737127.
  2. Kivinummi, K, Urbanucci, A, Leinonen, K, Tammela, TLJ, Annala, M, Isaacs, WB et al.. The expression of AURKA is androgen regulated in castration-resistant prostate cancer. Sci Rep. 2017;7 (1):17978. doi: 10.1038/s41598-017-18210-3. PubMed PMID:29269934 PubMed Central PMC5740165.
  3. Wyatt, AW, Annala, M, Aggarwal, R, Beja, K, Feng, F, Youngren, J et al.. Concordance of Circulating Tumor DNA and Matched Metastatic Tissue Biopsy in Prostate Cancer. J. Natl. Cancer Inst. 2017;109 (12):. doi: 10.1093/jnci/djx118. PubMed PMID:29206995 .
  4. Hyysalo, A, Ristola, M, Mäkinen, ME, Häyrynen, S, Nykter, M, Narkilahti, S et al.. Laminin α5 substrates promote survival, network formation and functional development of human pluripotent stem cell-derived neurons in vitro. Stem Cell Res. 2017;24 :118-127. doi: 10.1016/j.scr.2017.09.002. PubMed PMID:28926760 .
  5. 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 .
  6. Beltran, H, Wyatt, AW, Chedgy, EC, Donoghue, A, Annala, M, Warner, EW et al.. Impact of Therapy on Genomics and Transcriptomics in High-Risk Prostate Cancer Treated with Neoadjuvant Docetaxel and Androgen Deprivation Therapy. Clin. Cancer Res. 2017;23 (22):6802-6811. doi: 10.1158/1078-0432.CCR-17-1034. PubMed PMID:28842510 PubMed Central PMC5690882.
  7. Kytola, V, Topaloglu, U, Miller, LD, Bitting, RL, Goodman, MM, D Agostino, RB Jr et al.. Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center. Theranostics. 2017;7 (11):2914-2923. doi: 10.7150/thno.20355. PubMed PMID:28824725 PubMed Central PMC5562225.
  8. Vandekerkhove, G, Todenhöfer, T, Annala, M, Struss, WJ, Wong, A, Beja, K et al.. Circulating Tumor DNA Reveals Clinically Actionable Somatic Genome of Metastatic Bladder Cancer. Clin. Cancer Res. 2017;23 (21):6487-6497. doi: 10.1158/1078-0432.CCR-17-1140. PubMed PMID:28760909 .
  9. Zhang, K, Myllymäki, SM, Gao, P, Devarajan, R, Kytölä, V, Nykter, M et al.. Oncogenic K-Ras upregulates ITGA6 expression via FOSL1 to induce anoikis resistance and synergizes with αV-Class integrins to promote EMT. Oncogene. 2017;36 (41):5681-5694. doi: 10.1038/onc.2017.177. PubMed PMID:28604746 PubMed Central PMC5658677.
  10. Urbanucci, A, Barfeld, SJ, Kytölä, V, Itkonen, HM, Coleman, IM, Vodák, D et al.. Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer. Cell Rep. 2017;19 (10):2045-2059. doi: 10.1016/j.celrep.2017.05.049. PubMed PMID:28591577 PubMed Central PMC5675034.
  11. Lin, J, Kramna, L, Autio, R, Hyöty, H, Nykter, M, Cinek, O et al.. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples. BMC Genomics. 2017;18 (1):378. doi: 10.1186/s12864-017-3721-7. PubMed PMID:28506246 PubMed Central PMC5430618.
  12. Tarkkonen, K, Hieta, R, Kytölä, V, Nykter, M, Kiviranta, R. Comparative analysis of osteoblast gene expression profiles and Runx2 genomic occupancy of mouse and human osteoblasts in vitro. Gene. 2017;626 :119-131. doi: 10.1016/j.gene.2017.05.028. PubMed PMID:28502869 .
  13. Lund, RJ, Rahkonen, N, Malonzo, M, Kauko, L, Emani, MR, Kivinen, V et al.. RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. Stem Cell Reports. 2017;8 (5):1442-1454. doi: 10.1016/j.stemcr.2017.04.016. PubMed PMID:28494942 PubMed Central PMC5425787.
  14. Yang, M, Topaloglu, U, Petty, WJ, Pagni, M, Foley, KL, Grant, SC et al.. Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages. J Hematol Oncol. 2017;10 (1):100. doi: 10.1186/s13045-017-0468-1. PubMed PMID:28472989 PubMed Central PMC5418716.
  15. Lehtinen, B, Raita, A, Kesseli, J, Annala, M, Nordfors, K, Yli-Harja, O et al.. Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas. BMC Cancer. 2017;17 (1):310. doi: 10.1186/s12885-017-3274-9. PubMed PMID:28468611 PubMed Central PMC5415775.
  16. Quigley, D, Alumkal, JJ, Wyatt, AW, Kothari, V, Foye, A, Lloyd, P et al.. Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors. Cancer Discov. 2017;7 (9):999-1005. doi: 10.1158/2159-8290.CD-17-0146. PubMed PMID:28450426 PubMed Central PMC5581695.
  17. Valkonen, M, Kartasalo, K, Liimatainen, K, Nykter, M, Latonen, L, Ruusuvuori, P et al.. Metastasis detection from whole slide images using local features and random forests. Cytometry A. 2017;91 (6):555-565. doi: 10.1002/cyto.a.23089. PubMed PMID:28426134 .
  18. Afyounian, E, Annala, M, Nykter, M. Segmentum: a tool for copy number analysis of cancer genomes. BMC Bioinformatics. 2017;18 (1):215. doi: 10.1186/s12859-017-1626-8. PubMed PMID:28407731 PubMed Central PMC5390478.
  19. Granberg, KJ, Annala, M, Lehtinen, B, Kesseli, J, Haapasalo, J, Ruusuvuori, P et al.. Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas. Neuro-oncology. 2017;19 (9):1206-1216. doi: 10.1093/neuonc/nox028. PubMed PMID:28379477 PubMed Central PMC5570261.
  20. Valkonen, M, Ruusuvuori, P, Kartasalo, K, Nykter, M, Visakorpi, T, Latonen, L et al.. Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models. Sci Rep. 2017;7 :44831. doi: 10.1038/srep44831. PubMed PMID:28317907 PubMed Central PMC5357939.
  21. Annala, M, Struss, WJ, Warner, EW, Beja, K, Vandekerkhove, G, Wong, A et al.. Treatment Outcomes and Tumor Loss of Heterozygosity in Germline DNA Repair-deficient Prostate Cancer. Eur. Urol. 2017;72 (1):34-42. doi: 10.1016/j.eururo.2017.02.023. PubMed PMID:28259476 .
  22. Ampuja, M, Rantapero, T, Rodriguez-Martinez, A, Palmroth, M, Alarmo, EL, Nykter, M et al.. Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer. BMC Genomics. 2017;18 (1):68. doi: 10.1186/s12864-016-3428-1. PubMed PMID:28077088 PubMed Central PMC5225521.
  23. Grönroos, T, Teppo, S, Mehtonen, J, Laukkanen, S, Liuksiala, T, Nykter, M et al.. Overexpression of PTP4A3 in ETV6-RUNX1 acute lymphoblastic leukemia. Leuk. Res. 2017;54 :1-6. doi: 10.1016/j.leukres.2016.12.005. PubMed PMID:28063378 .
  24. Annala, M, Nappi, L, Azad, AA, Mo, F, Fazli, L, Chi, KN et al.. Molecular Dissection of Complete Response to Receptor Tyrosine Kinase Inhibition in Type II Papillary Renal Cell Carcinoma. Clin Genitourin Cancer. 2017;15 (1):e145-e150. doi: 10.1016/j.clgc.2016.05.019. PubMed PMID:27324055 .

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Publications 2016

  1. Grönroos, T, Teppo, S, Mehtonen, J, Laukkanen, S, Liuksiala, T, Nykter, M et al.. Overexpression of PTP4A3 in ETV6-RUNX1 acute lymphoblastic leukemia. Leuk. Res. 2017;54 :1-6. doi: 10.1016/j.leukres.2016.12.005. PubMed PMID:28063378 .
  2. Ulman, V, Svoboda, D, Nykter, M, Kozubek, M, Ruusuvuori, P. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry A. 2016;89 (12):1057-1072. doi: 10.1002/cyto.a.23031. PubMed PMID:27922735 .
  3. Teppo, S, Laukkanen, S, Liuksiala, T, Nordlund, J, Oittinen, M, Teittinen, K et al.. Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia. Genome Res. 2016;26 (11):1468-1477. doi: 10.1101/gr.193649.115. PubMed PMID:27620872 PubMed Central PMC5088590.
  4. Määttä, K, Rantapero, T, Lindström, A, Nykter, M, Kankuri-Tammilehto, M, Laasanen, SL et al.. Whole-exome sequencing of Finnish hereditary breast cancer families. Eur. J. Hum. Genet. 2016;25 (1):85-93. doi: 10.1038/ejhg.2016.141. PubMed PMID:27782108 PubMed Central PMC5159774.
  5. Veskimäe, K, Staff, S, Grönholm, A, Pesu, M, Laaksonen, M, Nykter, M et al.. Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry. Tumour Biol. 2016;37 (9):11991-11999. doi: 10.1007/s13277-016-5062-6. PubMed PMID:27155850 .
  6. Cordova, ZM, Grönholm, A, Kytölä, V, Taverniti, V, Hämäläinen, S, Aittomäki, S et al.. Myeloid cell expressed proprotein convertase FURIN attenuates inflammation. Oncotarget. 2016;7 (34):54392-54404. doi: 10.18632/oncotarget.11106. PubMed PMID:27527873 PubMed Central PMC5342350.
  7. Annala, M, Nappi, L, Azad, AA, Mo, F, Fazli, L, Chi, KN et al.. Molecular Dissection of Complete Response to Receptor Tyrosine Kinase Inhibition in Type II Papillary Renal Cell Carcinoma. Clin Genitourin Cancer. 2017;15 (1):e145-e150. doi: 10.1016/j.clgc.2016.05.019. PubMed PMID:27324055 .
  8. Wyatt, AW, Azad, AA, Volik, SV, Annala, M, Beja, K, McConeghy, B et al.. Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer. JAMA Oncol. 2016;2 (12):1598-1606. doi: 10.1001/jamaoncol.2016.0494. PubMed PMID:27148695 PubMed Central PMC5097690.
  9. Bova, GS, Kallio, HM, Annala, M, Kivinummi, K, Högnäs, G, Häyrynen, S et al.. Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer. Cold Spring Harb Mol Case Stud. 2016;2 (3):a000752. doi: 10.1101/mcs.a000752. PubMed PMID:27148588 PubMed Central PMC4853517.
  10. Nurminen, R, Rantapero, T, Wong, SC, Fischer, D, Lehtonen, R, Tammela, TL et al.. Expressional profiling of prostate cancer risk SNPs at 11q13.5 identifies DGAT2 as a new target gene. Genes Chromosomes Cancer. 2016;55 (8):661-73. doi: 10.1002/gcc.22368. PubMed PMID:27113481 .
  11. Ruusuvuori, P, Valkonen, M, Nykter, M, Visakorpi, T, Latonen, L. Feature-based analysis of mouse prostatic intraepithelial neoplasia in histological tissue sections. J Pathol Inform. 2016;7 :5. doi: 10.4103/2153-3539.175378. PubMed PMID:26955503 PubMed Central PMC4763506.
  12. Sjöblom, L, Saramäki, O, Annala, M, Leinonen, K, Nättinen, J, Tolonen, T et al.. Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer. PLoS ONE. 2016;11 (3):e0150241. doi: 10.1371/journal.pone.0150241. PubMed PMID:26939004 PubMed Central PMC4777373.
  13. Chedgy, EC, Annala, M, Beja, K, Warner, EW, Gleave, ME, Chi, KN et al.. Moving Toward Personalized Care: Liquid Biopsy Predicts Response to Cisplatin in an Unusual Case of BRCA2-Null Neuroendocrine Prostate Cancer. Clin Genitourin Cancer. 2016;14 (2):e233-6. doi: 10.1016/j.clgc.2015.12.023. PubMed PMID:26797585 .
  14. Alarmo, EL, Havunen, R, Häyrynen, S, Penkki, S, Ketolainen, J, Nykter, M et al.. Bone morphogenetic protein 4 regulates microRNA expression in breast cancer cell lines in diverse fashion. Genes Chromosomes Cancer. 2016;55 (3):227-36. doi: 10.1002/gcc.22324. PubMed PMID:26684238 .
  15. Chua, CY, Liu, Y, Granberg, KJ, Hu, L, Haapasalo, H, Annala, MJ et al.. IGFBP2 potentiates nuclear EGFR-STAT3 signaling. Oncogene. 2016;35 (6):738-47. doi: 10.1038/onc.2015.131. PubMed PMID:25893308 PubMed Central PMC4615268.

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Publications 2015

  1. Chedgy, EC, Annala, M, Beja, K, Warner, EW, Gleave, ME, Chi, KN et al.. Moving Toward Personalized Care: Liquid Biopsy Predicts Response to Cisplatin in an Unusual Case of BRCA2-Null Neuroendocrine Prostate Cancer. Clin Genitourin Cancer. 2016;14 (2):e233-6. doi: 10.1016/j.clgc.2015.12.023. PubMed PMID:26797585 .
  2. Alarmo, EL, Havunen, R, Häyrynen, S, Penkki, S, Ketolainen, J, Nykter, M et al.. Bone morphogenetic protein 4 regulates microRNA expression in breast cancer cell lines in diverse fashion. Genes Chromosomes Cancer. 2016;55 (3):227-36. doi: 10.1002/gcc.22324. PubMed PMID:26684238 .
  3. Cancer Genome Atlas Research Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015;163 (4):1011-25. doi: 10.1016/j.cell.2015.10.025. PubMed PMID:26544944 PubMed Central PMC4695400.
  4. Ylipää, A, Kivinummi, K, Kohvakka, A, Annala, M, Latonen, L, Scaravilli, M et al.. Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer. Cancer Res. 2015;75 (19):4026-31. doi: 10.1158/0008-5472.CAN-15-0217. PubMed PMID:26282172 .
  5. Rane, JK, Ylipää, A, Adamson, R, Mann, VM, Simms, MS, Collins, AT et al.. Construction of therapeutically relevant human prostate epithelial fate map by utilising miRNA and mRNA microarray expression data. Br. J. Cancer. 2015;113 (4):611-5. doi: 10.1038/bjc.2015.262. PubMed PMID:26203762 PubMed Central PMC4647689.
  6. Nordfors, K, Haapasalo, J, Mäkelä, K, Granberg, KJ, Nykter, M, Korja, M et al.. Twist predicts poor outcome of patients with astrocytic glioma. J. Clin. Pathol. 2015;68 (11):905-12. doi: 10.1136/jclinpath-2015-202868. PubMed PMID:26163539 .
  7. Kaukoniemi, KM, Rauhala, HE, Scaravilli, M, Latonen, L, Annala, M, Vessella, RL et al.. Epigenetically altered miR-193b targets cyclin D1 in prostate cancer. Cancer Med. 2015;4 (9):1417-25. doi: 10.1002/cam4.486. PubMed PMID:26129688 PubMed Central PMC4567026.
  8. Chua, CY, Liu, Y, Granberg, KJ, Hu, L, Haapasalo, H, Annala, MJ et al.. IGFBP2 potentiates nuclear EGFR-STAT3 signaling. Oncogene. 2016;35 (6):738-47. doi: 10.1038/onc.2015.131. PubMed PMID:25893308 PubMed Central PMC4615268.
  9. Marttila, S, Kananen, L, Häyrynen, S, Jylhävä, J, Nevalainen, T, Hervonen, A et al.. Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression. BMC Genomics. 2015;16 :179. doi: 10.1186/s12864-015-1381-z. PubMed PMID:25888029 PubMed Central PMC4404609.
  10. Gundem, G, Van Loo, P, Kremeyer, B, Alexandrov, LB, Tubio, JMC, Papaemmanuil, E et al.. The evolutionary history of lethal metastatic prostate cancer. Nature. 2015;520 (7547):353-357. doi: 10.1038/nature14347. PubMed PMID:25830880 PubMed Central PMC4413032.
  11. Annala, M, Kivinummi, K, Tuominen, J, Karakurt, S, Granberg, K, Latonen, L et al.. Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer. Oncotarget. 2015;6 (8):6235-50. doi: 10.18632/oncotarget.3359. PubMed PMID:25749039 PubMed Central PMC4467434.
  12. Turner, KM, Sun, Y, Ji, P, Granberg, KJ, Bernard, B, Hu, L et al.. Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (11):3421-6. doi: 10.1073/pnas.1414573112. PubMed PMID:25737557 PubMed Central PMC4371922.
  13. Scaravilli, M, Porkka, KP, Brofeldt, A, Annala, M, Tammela, TL, Jenster, GW et al.. MiR-1247-5p is overexpressed in castration resistant prostate cancer and targets MYCBP2. Prostate. 2015;75 (8):798-805. doi: 10.1002/pros.22961. PubMed PMID:25731699 .
  14. Veskimäe, K, Staff, S, Tabaro, F, Nykter, M, Isola, J, Mäenpää, J et al.. Microarray analysis of differentially expressed genes in ovarian and fallopian tube epithelium from risk-reducing salpingo-oophorectomies. Genes Chromosomes Cancer. 2015;54 (5):276-87. doi: 10.1002/gcc.22241. PubMed PMID:25706666 .
  15. Rane, JK, Scaravilli, M, Ylipää, A, Pellacani, D, Mann, VM, Simms, MS et al.. MicroRNA expression profile of primary prostate cancer stem cells as a source of biomarkers and therapeutic targets. Eur. Urol. 2015;67 (1):7-10. doi: 10.1016/j.eururo.2014.09.005. PubMed PMID:25234358 .
  16. Li, X, Liu, Y, Granberg, KJ, Wang, Q, Moore, LM, Ji, P et al.. Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma. Oncogene. 2015;34 (13):1619-1628. doi: 10.1038/onc.2014.98. PubMed PMID:24747968 PubMed Central PMC4205227.

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Publications 2014

  1. Yang, J, Annala, M, Ji, P, Wang, G, Zheng, H, Codgell, D et al.. Recurrent LRP1-SNRNP25 and KCNMB4-CCND3 fusion genes promote tumor cell motility in human osteosarcoma. J Hematol Oncol. 2014;7 :76. doi: 10.1186/s13045-014-0076-2. PubMed PMID:25300797 PubMed Central PMC4197299.
  2. Rane, JK, Scaravilli, M, Ylipää, A, Pellacani, D, Mann, VM, Simms, MS et al.. MicroRNA expression profile of primary prostate cancer stem cells as a source of biomarkers and therapeutic targets. Eur. Urol. 2015;67 (1):7-10. doi: 10.1016/j.eururo.2014.09.005. PubMed PMID:25234358 .
  3. Annala, M, Kivinummi, K, Leinonen, K, Tuominen, J, Zhang, W, Visakorpi, T et al.. DOT1L-HES6 fusion drives androgen independent growth in prostate cancer. EMBO Mol Med. 2014;6 (9):1121-3. doi: 10.15252/emmm.201404210. PubMed PMID:25006183 PubMed Central PMC4197859.
  4. Li, X, Liu, Y, Granberg, KJ, Wang, Q, Moore, LM, Ji, P et al.. Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma. Oncogene. 2015;34 (13):1619-1628. doi: 10.1038/onc.2014.98. PubMed PMID:24747968 PubMed Central PMC4205227.
  5. Parker, BC, Engels, M, Annala, M, Zhang, W. Emergence of FGFR family gene fusions as therapeutic targets in a wide spectrum of solid tumours. J. Pathol. 2014;232 (1):4-15. . PubMed PMID:24588013 .
  6. Ruusuvuori, P, Lin, J, Scott, AC, Tan, Z, Sorsa, S, Kallio, A et al.. Quantitative analysis of colony morphology in yeast. BioTechniques. 2014;56 (1):18-27. doi: 10.2144/000114123. PubMed PMID:24447135 PubMed Central PMC3996921.
  7. Huang, Q, Whitington, T, Gao, P, Lindberg, JF, Yang, Y, Sun, J et al.. A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding. Nat. Genet. 2014;46 (2):126-35. doi: 10.1038/ng.2862. PubMed PMID:24390282 .
  8. Annala, M, Mykrä, H, Tolkkinen, M, Kauppila, T, Muotka, T. Are biological communities in naturally unproductive streams resistant to additional anthropogenic stressors?. Ecol Appl. ;24 (8):1887-97. . PubMed PMID:29185660 .
  9. Liuksiala, T, Teittinen, KJ, Granberg, K, Heinäniemi, M, Annala, M, Mäki, M et al.. Overexpression of SNORD114-3 marks acute promyelocytic leukemia. Leukemia. 2014;28 (1):233-6. doi: 10.1038/leu.2013.250. PubMed PMID:23979522 .

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Publications 2013

  1. Lin, J, Kreisberg, R, Kallio, A, Dudley, AM, Nykter, M, Shmulevich, I et al.. POMO–Plotting Omics analysis results for Multiple Organisms. BMC Genomics. 2013;14 :918. doi: 10.1186/1471-2164-14-918. PubMed PMID:24365393 PubMed Central PMC3880012.
  2. Ylipää, A, Yli-Harja, O, Zhang, W, Nykter, M. Characterization of aberrant pathways across human cancers. BMC Syst Biol. 2013;7 Suppl 1 :S1. doi: 10.1186/1752-0509-7-S1-S1. PubMed PMID:24267866 PubMed Central PMC3750561.
  3. Turpeinen, H, Oksanen, A, Kivinen, V, Kukkurainen, S, Uusimäki, A, Rämet, M et al.. Proprotein convertase subtilisin/kexin type 7 (PCSK7) is essential for the zebrafish development and bioavailability of transforming growth factor β1a (TGFβ1a). J. Biol. Chem. 2013;288 (51):36610-23. doi: 10.1074/jbc.M113.453183. PubMed PMID:24178295 PubMed Central PMC3868773.
  4. Brennan, CW, Verhaak, RG, McKenna, A, Campos, B, Noushmehr, H, Salama, SR et al.. The somatic genomic landscape of glioblastoma. Cell. 2013;155 (2):462-77. doi: 10.1016/j.cell.2013.09.034. PubMed PMID:24120142 PubMed Central PMC3910500.
  5. Leinonen, KA, Saramäki, OR, Furusato, B, Kimura, T, Takahashi, H, Egawa, S et al.. Loss of PTEN is associated with aggressive behavior in ERG-positive prostate cancer. Cancer Epidemiol. Biomarkers Prev. 2013;22 (12):2333-44. doi: 10.1158/1055-9965.EPI-13-0333-T. PubMed PMID:24083995 PubMed Central PMC4086660.
  6. Manninen, T, Huttunen, H, Ruusuvuori, P, Nykter, M. Leukemia prediction using sparse logistic regression. PLoS ONE. 2013;8 (8):e72932. doi: 10.1371/journal.pone.0072932. PubMed PMID:24023658 PubMed Central PMC3758279.
  7. Kong, L, Aho, KL, Granberg, K, Lund, R, Järvenpää, L, Seppälä, J et al.. ESTOOLS Data@Hand: human stem cell gene expression resource. Nat. Methods. 2013;10 (9):814-5. doi: 10.1038/nmeth.2576. PubMed PMID:23985726 .
  8. Liuksiala, T, Teittinen, KJ, Granberg, K, Heinäniemi, M, Annala, M, Mäki, M et al.. Overexpression of SNORD114-3 marks acute promyelocytic leukemia. Leukemia. 2014;28 (1):233-6. doi: 10.1038/leu.2013.250. PubMed PMID:23979522 .
  9. Lund, RJ, Emani, MR, Barbaric, I, Kivinen, V, Jones, M, Baker, D et al.. Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases. Stem Cell Res. 2013;11 (3):1022-36. doi: 10.1016/j.scr.2013.07.002. PubMed PMID:23941963 .
  10. Marttila, S, Jylhävä, J, Nevalainen, T, Nykter, M, Jylhä, M, Hervonen, A et al.. Transcriptional analysis reveals gender-specific changes in the aging of the human immune system. PLoS ONE. 2013;8 (6):e66229. doi: 10.1371/journal.pone.0066229. PubMed PMID:23776639 PubMed Central PMC3679079.
  11. Zhang, W, Nykter, M, Chen, K. Next generation sequencing applications in cancer research. Cancer Lett. 2013;340 (2):149-50. doi: 10.1016/j.canlet.2013.05.026. PubMed PMID:23764479 .
  12. Cancer Genome Atlas Research Network, Kandoth, C, Schultz, N, Cherniack, AD, Akbani, R, Liu, Y et al.. Integrated genomic characterization of endometrial carcinoma. Nature. 2013;497 (7447):67-73. doi: 10.1038/nature12113. PubMed PMID:23636398 PubMed Central PMC3704730.
  13. Heinäniemi, M, Nykter, M, Kramer, R, Wienecke-Baldacchino, A, Sinkkonen, L, Zhou, JX et al.. Gene-pair expression signatures reveal lineage control. Nat. Methods. 2013;10 (6):577-83. doi: 10.1038/nmeth.2445. PubMed PMID:23603899 PubMed Central PMC4131748.
  14. Sadot, A, Sarbu, S, Kesseli, J, Amir-Kroll, H, Zhang, W, Nykter, M et al.. Information-theoretic analysis of the dynamics of an executable biological model. PLoS ONE. 2013;8 (3):e59303. doi: 10.1371/journal.pone.0059303. PubMed PMID:23527156 PubMed Central PMC3602105.
  15. Mäki-Marttunen, T, Kesseli, J, Nykter, M. Balance between noise and information flow maximizes set complexity of network dynamics. PLoS ONE. 2013;8 (3):e56523. doi: 10.1371/journal.pone.0056523. PubMed PMID:23516395 PubMed Central PMC3596377.
  16. Yang, D, Sun, Y, Hu, L, Zheng, H, Ji, P, Pecot, CV et al.. Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer. Cancer Cell. 2013;23 (2):186-99. doi: 10.1016/j.ccr.2012.12.020. PubMed PMID:23410973 PubMed Central PMC3603369.
  17. Aghaeepour, N, Finak, G, FlowCAP Consortium, DREAM Consortium, Hoos, H, Mosmann, TR et al.. Critical assessment of automated flow cytometry data analysis techniques. Nat. Methods. 2013;10 (3):228-38. doi: 10.1038/nmeth.2365. PubMed PMID:23396282 PubMed Central PMC3906045.
  18. Annala, MJ, Parker, BC, Zhang, W, Nykter, M. Fusion genes and their discovery using high throughput sequencing. Cancer Lett. 2013;340 (2):192-200. doi: 10.1016/j.canlet.2013.01.011. PubMed PMID:23376639 PubMed Central PMC3675181.
  19. Weirauch, MT, Cote, A, Norel, R, Annala, M, Zhao, Y, Riley, TR et al.. Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol. 2013;31 (2):126-34. doi: 10.1038/nbt.2486. PubMed PMID:23354101 PubMed Central PMC3687085.
  20. Parker, BC, Annala, MJ, Cogdell, DE, Granberg, KJ, Sun, Y, Ji, P et al.. The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. J. Clin. Invest. 2013;123 (2):855-65. doi: 10.1172/JCI67144. PubMed PMID:23298836 PubMed Central PMC3561838.
  21. Patel, LR, Nykter, M, Chen, K, Zhang, W. Cancer genome sequencing: understanding malignancy as a disease of the genome, its conformation, and its evolution. Cancer Lett. 2013;340 (2):152-60. doi: 10.1016/j.canlet.2012.10.018. PubMed PMID:23111104 PubMed Central PMC3632661.
  22. Moore, LM, Kivinen, V, Liu, Y, Annala, M, Cogdell, D, Liu, X et al.. Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma. J. Pathol. 2013;229 (3):449-59. doi: 10.1002/path.4109. PubMed PMID:23007860 PubMed Central PMC3857031.

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Publications 2012

  1. Patel, LR, Nykter, M, Chen, K, Zhang, W. Cancer genome sequencing: understanding malignancy as a disease of the genome, its conformation, and its evolution. Cancer Lett. 2013;340 (2):152-60. doi: 10.1016/j.canlet.2012.10.018. PubMed PMID:23111104 PubMed Central PMC3632661.
  2. Holmes, KM, Annala, M, Chua, CY, Dunlap, SM, Liu, Y, Hugen, N et al.. Insulin-like growth factor-binding protein 2-driven glioma progression is prevented by blocking a clinically significant integrin, integrin-linked kinase, and NF-κB network. Proc. Natl. Acad. Sci. U.S.A. 2012;109 (9):3475-80. doi: 10.1073/pnas.1120375109. PubMed PMID:22345562 PubMed Central PMC3295320.

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Publications 2011

  1. Yang, J, Ylipää, A, Sun, Y, Zheng, H, Chen, K, Nykter, M et al.. Genomic and molecular characterization of malignant peripheral nerve sheath tumor identifies the IGF1R pathway as a primary target for treatment. Clin. Cancer Res. 2011;17 (24):7563-73. doi: 10.1158/1078-0432.CCR-11-1707. PubMed PMID:22042973 PubMed Central PMC3243813.
  2. Mäki-Marttunen, T, Aćimović, J, Nykter, M, Kesseli, J, Ruohonen, K, Yli-Harja, O et al.. Information diversity in structure and dynamics of simulated neuronal networks. Front Comput Neurosci. 2011;5 :26. doi: 10.3389/fncom.2011.00026. PubMed PMID:21852970 PubMed Central PMC3151619.
  3. Annala, M, Laurila, K, Lähdesmäki, H, Nykter, M. A linear model for transcription factor binding affinity prediction in protein binding microarrays. PLoS ONE. 2011;6 (5):e20059. doi: 10.1371/journal.pone.0020059. PubMed PMID:21637853 PubMed Central PMC3102690.
  4. Cheng, H, Zhang, L, Cogdell, DE, Zheng, H, Schetter, AJ, Nykter, M et al.. Circulating plasma MiR-141 is a novel biomarker for metastatic colon cancer and predicts poor prognosis. PLoS ONE. 2011;6 (3):e17745. doi: 10.1371/journal.pone.0017745. PubMed PMID:21445232 PubMed Central PMC3060165.
  5. Yli-Harja, O, Ylipää, A, Nykter, M, Zhang, W. Cancer systems biology: signal processing for cancer research. Chin J Cancer. 2011;30 (4):221-5. . PubMed PMID:21439242 PubMed Central PMC4013347.
  6. Ylipää, A, Yli-Harja, O, Zhang, W, Nykter, M. A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas. Chin J Cancer. 2011;30 (1):27-40. . PubMed PMID:21192842 PubMed Central PMC4012261.
  7. Ylipää, A, Hunt, KK, Yang, J, Lazar, AJ, Torres, KE, Lev, DC et al.. Integrative genomic characterization and a genomic staging system for gastrointestinal stromal tumors. Cancer. 2011;117 (2):380-9. doi: 10.1002/cncr.25594. PubMed PMID:20818650 PubMed Central PMC3008331.

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Publications 2010

  1. Ylipää, A, Hunt, KK, Yang, J, Lazar, AJ, Torres, KE, Lev, DC et al.. Integrative genomic characterization and a genomic staging system for gastrointestinal stromal tumors. Cancer. 2011;117 (2):380-9. doi: 10.1002/cncr.25594. PubMed PMID:20818650 PubMed Central PMC3008331.
  2. Yang, D, Ylipaa, A, Yang, J, Hunt, K, Pollock, R, Trent, J et al.. An integrated study of aberrant gene copy number and gene expression in GIST and LMS. Technol. Cancer Res. Treat. 2010;9 (2):171-8. doi: 10.1177/153303461000900206. PubMed PMID:20218739 .
  3. Galas, DJ, Nykter, M, Carter, GW, Price, ND, Shmulevich, I. Biological Information as Set-Based Complexity. IEEE Trans Inf Theory. 2010;56 (2):667-677. doi: 10.1109/TIT.2009.2037046. PubMed PMID:27857450 PubMed Central PMC5110148.

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Publications 2009

  1. Nykter, M, Lähdesmäki, H, Rust, A, Thorsson, V, Shmulevich, I. A data integration framework for prediction of transcription factor targets. Ann. N. Y. Acad. Sci. 2009;1158 :205-14. doi: 10.1111/j.1749-6632.2008.03758.x. PubMed PMID:19348642 PubMed Central PMC2771581.
  2. Litvak, V, Ramsey, SA, Rust, AG, Zak, DE, Kennedy, KA, Lampano, AE et al.. Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat. Immunol. 2009;10 (4):437-43. doi: 10.1038/ni.1721. PubMed PMID:19270711 PubMed Central PMC2780024.

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Publications 2008

  1. Nykter, M, Price, ND, Larjo, A, Aho, T, Kauffman, SA, Yli-Harja, O et al.. Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys. Rev. Lett. 2008;100 (5):058702. doi: 10.1103/PhysRevLett.100.058702. PubMed PMID:18352443 .
  2. Nykter, M, Price, ND, Aldana, M, Ramsey, SA, Kauffman, SA, Hood, LE et al.. Gene expression dynamics in the macrophage exhibit criticality. Proc. Natl. Acad. Sci. U.S.A. 2008;105 (6):1897-900. doi: 10.1073/pnas.0711525105. PubMed PMID:18250330 PubMed Central PMC2538855.

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Publications 2007

  1. Niemistö, A, Nykter, M, Aho, T, Jalovaara, H, Marjanen, K, Ahdesmäki, M et al.. Computational methods for estimation of cell cycle phase distributions of yeast cells. EURASIP J Bioinform Syst Biol. 2007; :46150. doi: 10.1155/2007/46150. PubMed PMID:18354733 PubMed Central PMC3171340.
  2. Ruusuvuori, P, Nykter, M, Mäkiraatikka, E, Lehmussola, A, Korpelainen, T, Erkkilä, T et al.. Microarray simulator as educational tool. Conf Proc IEEE Eng Med Biol Soc. 2007;2007 :5920-3. doi: 10.1109/IEMBS.2007.4353695. PubMed PMID:18003361 .

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Publications 2006

  1. Harjunpää, A, Taskinen, M, Nykter, M, Karjalainen-Lindsberg, ML, Nyman, H, Monni, O et al.. Differential gene expression in non-malignant tumour microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP. Br. J. Haematol. 2006;135 (1):33-42. doi: 10.1111/j.1365-2141.2006.06255.x. PubMed PMID:16925574 .
  2. Nykter, M, Aho, T, Ahdesmäki, M, Ruusuvuori, P, Lehmussola, A, Yli-Harja, O et al.. Simulation of microarray data with realistic characteristics. BMC Bioinformatics. 2006;7 :349. doi: 10.1186/1471-2105-7-349. PubMed PMID:16848902 PubMed Central PMC1574357.
  3. Nykter, M, Hunt, KK, Pollock, RE, El-Naggar, AK, Taylor, E, Shmulevich, I et al.. Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies. Technol. Cancer Res. Treat. 2006;5 (2):177-82. doi: 10.1177/153303460600500209. PubMed PMID:16551137 .

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