List of Genevia Technologies' Scientific references

2019

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

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 .

2017

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.

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.

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.

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.

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.

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.

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.

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.

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.