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. Ehteshami Bejnordi, B, Veta, M, Johannes van Diest, P, van Ginneken, B, Karssemeijer, N, Litjens, G et al.. Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer. JAMA. 2017;318 (22):2199-2210. doi: 10.1001/jama.2017.14585. PubMed PMID:29234806 PubMed Central PMC5820737.
  4. 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 .
  5. 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 .
  6. 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 .
  7. 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.
  8. Latonen, L, Scaravilli, M, Gillen, A, Hartikainen, S, Zhang, FP, Ruusuvuori, P et al.. In Vivo Expression of miR-32 Induces Proliferation in Prostate Epithelium. Am. J. Pathol. 2017;187 (11):2546-2557. doi: 10.1016/j.ajpath.2017.07.012. PubMed PMID:28827140 .
  9. 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.
  10. 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 .
  11. 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.
  12. 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.
  13. 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.
  14. 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 .
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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 .
  20. 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.
  21. 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.
  22. 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.
  23. 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 .
  24. 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.
  25. 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 .
  26. Huttunen, M, Turkki, P, Mäki, A, Paavolainen, L, Ruusuvuori, P, Marjomäki, V et al.. Echovirus 1 internalization negatively regulates epidermal growth factor receptor downregulation. Cell. Microbiol. 2017;19 (3):. doi: 10.1111/cmi.12671. PubMed PMID:27665309 .
  27. 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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Earlier publications

For complete publications list see here.

Disclaimer: Above publications lists are automatically generated from pubmed. Thus, they may not be exhaustive and may contain publications not related to Computational Biology group.