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  • PL 63 (Haartmaninkatu 8)

    00014

    Finland

  • PL 63 (Haartmaninkatu 8), B524b

    HELSINGIN YLIOPISTO

    Finland

20032019
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Publications 2003 2019

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2019

ALDH1A1-related stemness in high-grade serous ovarian cancer is a negative prognostic indicator but potentially targetable by EGFR/mTOR-PI3K/aurora kinase inhibitors

Kaipio, K., Chen, P., Roering, P., Huhtinen, K., Mikkonen, P., Östling, P., Lehtinen, L., Mansuri, N., Korpela, T., Potdar, S., Hynninen, J., Auranen, A., Grénman, S., Wennerberg, K., Hautaniemi, S. & Carpén, O., 9 Oct 2019, In : Journal of Pathology. n/a, n/a

Research output: Contribution to journalArticleScientificpeer-review

Anagrelide for Gastrointestinal Stromal Tumor

Pulkka, O-P., Gebreyohannes, Y. K., Wozniak, A., Mpindi, J-P., Tynninen, O., Icay, K., Cervera, A., Keskitalo, S., Murumägi, A., Kulesskiy, E., Laaksonen, M., Wennerberg, K., Varjosalo, M., Laakkonen, P., Lehtonen, R., Hautaniemi, S., Kallioniemi, O., Schöffski, P., Sihto, H. & Joensuu, H., 1 Mar 2019, In : Clinical Cancer Research. 25, 5, p. 1676-1687 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Anduril 2: Upgraded large-scale data integration framework

Cervera, A., Rantanen, V., Ovaska, K., Laakso, M., Nuñez-Fontarnau, J., Alkodsi, A., Casado, J., Facciotto, C., Häkkinen, A., Louhimo, R., Karinen, S., Zhang, K., Lavikka, K., Lyly, L., Pal Singh, M. & Hautaniemi, S., 2019, In : Bioinformatics. 35, 19, p. 3815-3817 3 p.

Research output: Contribution to journalArticleScientificpeer-review

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Distinct subtypes of diffuse large B-cell lymphoma defined by hypermutated genes

Alkodsi, A., Cervera, A., Zhang, K., Louhimo, R., Meriranta, L., Pasanen, A., Leivonen, S-K., Holte, H., Leppä, S., Lehtonen, R. & Hautaniemi, S., Nov 2019, In : Leukemia. 33, 11, p. 2662-2672 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses

Isoviita, V-M., Salminen, L., Azar, J., Lehtonen, R., Roering, P., Carpen, O. M., Hietanen, S., Grénman, S., Hynninen, J., Färkkilä, A. & Hautaniemi, S., 27 Aug 2019, In : JCO Clinical Cancer Informatics. 3, p. 1-16 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Oikkonen, J., Zhang, K., Salminen, L., Schulman, I., Lavikka, K., Andersson, N., Ojanperä, E., Hietanen, S., Grénman, S., Lehtonen, R., Huhtinen, K., Carpén, O., Hynninen, J., Färkkilä, A. & Hautaniemi, S., 3 May 2019, In : JCO Precision Oncology. 3, p. 1-12 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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2018

A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients

Tumiati, M., Hietanen, S., Hynninen, J., Pietilä, E., Färkkilä, A., Kaipio, K., Roering, P., Huhtinen, K., Alkodsi, A., Li, Y., Lehtonen, R., Erkan, E. P., Tuominen, M. M., Lehti, K., Hautaniemi, S. K., Vähärautio, A., Grenman, S., Carpen, O. & Kauppi, L., 15 Sep 2018, In : Clinical Cancer Research. 24, 18, p. 4482-4493 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Clinical Value of 18F-fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in Response Evaluation after Primary Treatment of Advanced Epithelial Ovarian Cancer

Hynninen, J., Laasik, M., Vallius, T., Kemppainen, J., Grönroos, S., Virtanen, J., Casado, J., Hautaniemi, S., Grenman, S., Seppänen, M. & Auranen, A., Aug 2018, In : Clinical Oncology. 30, 8, p. 507-514 8 p.

Research output: Contribution to journalArticleScientificpeer-review

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Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer

Kondelin, J., Salokas, K., Saarinen, L., Ovaska, K., Rauanheimo, H., Plaketti, R-M., Hamberg, J., Liu, X., Yadav, L., Gylfe, A. E., Cajuso, T., Hänninen, U. A., Palin, K., Ristolainen, H., Katainen, R., Kaasinen, E., Tanskanen, T., Aavikko, M., Taipale, M., Taipale, J. & 17 others, Renkonen-Sinisalo, L., Lepistö, A., Koskensalo, S., Böhm, J., Mecklin, J-P., Ongen, H., Dermitzakis, E. T., Kilpivaara, O., Vahteristo, P., Turunen, M., Hautaniemi, S., Tuupanen, S., Karhu, A., Välimäki, N., Varjosalo, M., Pitkänen, E. & Aaltonen, L. A., 2018, In : EMBO molecular medicine. 10, 9, 20 p., e8552.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Dynamic visualization of multi-level molecular data: The Director package in R

Icay, K., Liu, C. & Hautaniemi, S., Jan 2018, In : Computer Methods and Programs in Biomedicine. 153, p. 129-136 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Evolutionary history of metastatic breast cancer reveals minimal seeding from axillary lymph nodes

Ullah, I., Karthik, G-M., Alkodsi, A., Kjallquist, U., Stalhammar, G., Lovrot, J., Martinez, N-F., Lagergren, J., Hautaniemi, S., Hartman, J. & Bergh, J., 2 Apr 2018, In : Journal of Clinical Investigation. 128, 4, p. 1355-1370 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Glycomic Profiling Highlights Increased Fucosylation in Pseudomyxoma Peritonei

Saarinen, L. A., Nummela, P., Leinonen, H., Heiskanen, A., Thiel, A., Haglund, C., Lepistö, A., Satomaa, T., Hautaniemi, S. & Ristimäki, A., 2 Aug 2018, In : Molecular & Cellular Proteomics. 17, 11, p. 2107-2118 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Identifying differentially methylated sites in samples with varying tumor purity

Häkkinen, A., Alkodsi, A., Facciotto, C., Zhang, K., Kaipio, K., Leppa, S., Carpen, O., Grenman, S., Hynninen, J., Hietanen, S., Lehtonen, R. & Hautaniemi, S., 15 Sep 2018, In : Bioinformatics. 34, 18, p. 3078-3085 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Let-7 microRNA controls invasion-promoting lysosomal changes via the oncogenic transcription factor myeloid zinc finger-1

Tvingsholm, S. A., Hansen, M. B., Clemmensen, K. K. B., Brix, D. M., Rafn, B., Frankel, L. B., Louhimo, R., Moreira, J., Hautaniemi, S., Gromova, I., Jäättelä, M. & Kallunki, T., Feb 2018, In : Oncogenesis. 7, 15 p., 14.

Research output: Contribution to journalArticleScientificpeer-review

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Lymphatic endothelium stimulates melanoma metastasis and invasion via MMP14-dependent Notch3 and beta 1-integrin activation

Pekkonen, P., Alve, S., Balistreri, G., Gramolelli, S., Tatti-Bugaeva, O., Paatero, I., Niiranen, O., Tuohinto, K., Perala, N., Taiwo, A., Zinovkina, N., Repo, P., Icay, K., Ivaska, J., Saharinen, P., Hautaniemi, S., Lehti, K. & Ojala, P. M., 1 May 2018, In : eLife. 7, 28 p., 32490.

Research output: Contribution to journalArticleScientificpeer-review

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Mathematical Modeling Predicts Response to Chemotherapy and Drug Combinations in Ovarian Cancer

Kozlowska, E., Färkkilä, A., Vallius, T., Carpen, O., Kemppainen, J., Grenman, S., Lehtonen, R., Hynninen, J., Hietanen, S. & Hautaniemi, S., 15 Jul 2018, In : Cancer Research. 78, 14, p. 4036-4044 9 p.

Research output: Contribution to journalArticleScientificpeer-review

PerPAS: Topology-Based Single Sample Pathway Analysis Method

Liu, C., Lehtonen, R. & Hautaniemi, S., 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 3, p. 1022-1027 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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PROX1 is a transcriptional regulator of MMP14

Gramolelli, S., Cheng, J., Martinez-Corral, I., Vähä-Koskela, M., Elbasani, E., Kaivanto, E., Rantanen, V., Tuohinto, K., Hautaniemi, S., Bower, M., Haglund, C., Alitalo, K., Mäkinen, T., Petrova, T. V., Lehti, K. & Ojala, P. M., 22 Jun 2018, In : Scientific Reports. 8, 13 p., 9531.

Research output: Contribution to journalArticleScientificpeer-review

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2017

Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma

Leivonen, S-K., Taskinen, M., Cervera, A., Karjalainen-Lindsberg, M-L., Delabie, J., Holte, H., Lehtonen, R., Hautaniemi, S. & Leppa, S., 25 Aug 2017, In : Blood cancer journal. 7, 10 p., 596.

Research output: Contribution to journalArticleScientificpeer-review

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Deltex-1 mutations predict poor survival in diffuse large B-cell lymphoma

Meriranta, L., Pasanen, A., Louhimo, R., Cervera, A., Alkodsi, A., Autio, M., Taskinen, M., Rantanen, V., Karjalainen-Lindsberg, M-L., Holte, H., Delabie, J., Lehtonen, R., Hautaniemi, S. & Leppä, S., May 2017, In : Haematologica. 102, 5, p. E195-E198 4 p.

Research output: Contribution to journalArticleScientific

Open Access
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DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival

Fleischer, T., Klajic, J., Aure, M. R., Louhimo, R., Pladsen, A. V., Ottestad, L., Touleimat, N., Laakso, M., Halvorsen, A. R., Alnaes, G. I. G., Riis, M. L. H., Helland, A., Hautaniemi, S., Lonning, P. E., Naume, B., Borresen-Dale, A-L., Tost, J. & Kristensen, V. N., 3 Jan 2017, In : Oncotarget. 8, 1, p. 1074-1082 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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MicroRNAs regulate key cell survival pathways and mediate chemosensitivity during progression of diffuse large B- cell lymphoma

Leivonen, S-K., Icay, K., Jäntti, K., Siren, I., Liu, C., Alkodsi, A., Cervera, A., Ludvigsen, M., Hamilton-Dutoit, S. J., d'Amore, F., Karjalainen-Lindsberg, M-L., Delabie, J., Holte, H., Lehtonen, R., Hautaniemi, S. & Leppä, S., 15 Dec 2017, In : Blood cancer journal. 7, 11 p., 654.

Research output: Contribution to journalArticleScientificpeer-review

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Multiple components of PKA and TGF-beta pathways are mutated in pseudomyxoma peritonei

Saarinen, L., Nummela, P., Thiel, A., Lehtonen, R., Järvinen, P., Järvinen, H., Aaltonen, L. A., Lepisto, A., Hautaniemi, S. & Ristimaki, A., 20 Apr 2017, In : PLoS One. 12, 4, 16 p., 0174898.

Research output: Contribution to journalArticleScientificpeer-review

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2016

Complete androgen insensitivity syndrome caused by a deep intronic pseudoexon-activating mutation in the androgen receptor gene

Känsäkoski, J., Jaaskelainen, J., Jaaskelainen, T., Tommiska, J., Saarinen, L., Lehtonen, R., Hautaniemi, S., Frilander, M. J., Palvimo, J. J., Toppari, J. & Raivio, T., 9 Sep 2016, In : Scientific Reports. 6, 7 p., 32819.

Research output: Contribution to journalArticleScientificpeer-review

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Data integration to prioritize drugs using genomics and curated data

Louhimo, R. I., Laakso, M., Belitskin, D., Klefstrom, J., Lehtonen, R. & Hautaniemi, S., 26 May 2016, In : BioData mining. 9, 13 p., 21.

Research output: Contribution to journalArticleScientificpeer-review

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Language-Agnostic Reproducible Data Analysis Using Literate Programming

Vassilev, B., Louhimo, R., Ikonen, E. & Hautaniemi, S., 6 Oct 2016, In : PLoS One. 11, 10, 14 p., 0164023.

Research output: Contribution to journalArticleScientificpeer-review

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Novel Mad2-targeting miR-493-3p controls mitotic fidelity and cancer cells' sensitivity to paclitaxel

Tambe, M., Pruikkonen, S., Maki-Jouppila, J., Chen, P., Elgaaen, B. V., Straume, A. H., Huhtinen, K., Carpen, O., Lonning, P. E., Davidson, B., Hautaniemi, S. & Kallio, M. J., 15 Mar 2016, In : Oncotarget. 7, 11, p. 12267-12285 19 p.

Research output: Contribution to journalArticleScientificpeer-review

Oncogenic Herpesvirus Utilizes Stress-Induced Cell Cycle Checkpoints for Efficient Lytic Replication

Balistreri, G., Viiliainen, J., Turunen, M., Diaz, R., Lyly, L., Pekkonen, P., Rantala, J., Ojala, K., Sarek, G., Teesalu, M., Denisova, O., Peltonen, K., Julkunen, I., Varjosalo, M., Kainov, D., Kallioniemi, O., Laiho, M., Taipale, J., Hautaniemi, S. & Ojala, P. M., Feb 2016, In : PLoS Pathogens. 12, 2, 26 p., 1005424.

Research output: Contribution to journalArticleScientificpeer-review

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Par6G suppresses cell proliferation and is targeted by loss-of-function mutations in multiple cancers

Marques, E., Englund, J. I., Tervonen, T. A., Virkunen, E., Laakso, M., Myllynen, M., Mäkelä, A., Ahvenainen, M., Lepikhova, T., Monni, O., Hautaniemi, S. & Klefstrom, J., 17 Mar 2016, In : Oncogene. 35, 11, p. 1386-1398 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

SePIA: RNA and small RNA sequence processing, integration, and analysis

Icay, K., Chen, P., Cervera Taboada, A., Rantanen, V., Lehtonen, R. & Hautaniemi, S., 20 May 2016, In : BioData mining. 9, 18 p., 20.

Research output: Contribution to journalArticleScientificpeer-review

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Transmembrane Prostatic Acid Phosphatase (TMPAP) Delays Cells in G1 Phase of the Cell Cycle

Araujo, C. L., Quintero, I. B., Ovaska, K., Herrala, A. M., Hautaniemi, S. & Vihko, P. T., 1 Feb 2016, In : Prostate. 76, 2, p. 151-162 12 p.

Research output: Contribution to journalArticleScientificpeer-review

2015

AIP inactivation leads to pituitary tumorigenesis through defective G alpha(i)-cAMP signaling

Tuominen, I., Heliovaara, E., Raitila, A., Rautiainen, M-R., Mehine, M., Katainen, R., Donner, I., Aittomaki, V., Lehtonen, H. J., Ahlsten, M., Kivipelto, L., Schalin-Jantti, C., Arola, J., Hautaniemi, S. & Karhu, A., 26 Feb 2015, In : Oncogene. 34, 9, p. 1174-1184 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data

Alkodsi, A., Louhimo, R. & Hautaniemi, S., Mar 2015, In : Briefings in Bioinformatics. 16, 2, p. 242-254 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model

Marjonen, H., Sierra, A., Nyman, A., Rogojin, V., Grohn, O., Linden, A-M., Hautaniemi, S. & Kaminen-Ahola, N., 13 May 2015, In : PLoS One. 10, 5, 20 p., 0124931.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Identification of Prognostic Groups in High-Grade Serous Ovarian Cancer Treated with Platinum-Taxane Chemotherapy

Chen, P., Huhtinen, K., Kaipio, K., Mikkonen, P., Aittomaki, V., Lindell, R., Hynninen, J., Auranen, A., Grenman, S., Lehtonen, R., Carpen, O. & Hautaniemi, S., 1 Aug 2015, In : Cancer Research. 75, 15, p. 2987-2998 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Identification of sample-specific regulations using integrative network level analysis

Liu, C., Louhimo, R., Laakso, M., Lehtonen, R. & Hautaniemi, S., 28 Apr 2015, In : BMC Cancer. 15, 11 p., 319.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer

Heinonen, H., Lepikhova, T., Sahu, B., Pehkonen, H. M., Pihlajamaa, P., Louhimo, R., Gao, P., Wei, G-H., Hautaniemi, S., Jänne, O. A. & Monni, O. M., 2015, In : International Journal of Cancer. 137, 10, p. 2374-2383 10 p.

Research output: Contribution to journalArticleScientificpeer-review

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MMP16 Mediates a Proteolytic Switch to Promote Cell-Cell Adhesion, Collagen Alignment, and Lymphatic Invasion in Melanoma

Tatti, O., Gucciardo, E., Pekkonen, P., Holopainen, T., Louhimo, R., Repo, P., Maliniemi, P., Lohi, J., Rantanen, V., Hautaniemi, S., Alitalo, K., Ranki, A., Ojala, P. M., Keski-Oja, J. & Lehti, K., 15 May 2015, In : Cancer Research. 75, 10, p. 2083-2094 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Origins and Impacts of New Mammalian Exons

Merkin, J. J., Chen, P., Alexis, M. S., Hautaniemi, S. K. & Burge, C. B., 31 Mar 2015, In : Cell Reports. 10, 12, p. 1992-2005 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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Workflow for automated quantification of cerebromicrovascular gelatinase activity

Mattila, O. S., Rantanen, V., Saksi, J., Strbian, D., Pikkarainen, T., Hautaniemi, S. & Lindsberg, P. J., Jan 2015, In : Microvascular Research. 97, p. 19-24 6 p.

Research output: Contribution to journalArticleScientificpeer-review

2014

Adipocyte morphology and implications for metabolic derangements in acquired obesity

Heinonen, S., Saarinen, L., Naukkarinen, J., Rodriguez, A., Fruhbeck, G., Hakkarainen, A., Lundbom, J., Lundbom, N., Vuolteenaho, K., Moilanen, E., Arner, P., Hautaniemi, S., Suomalainen, A., Kaprio, J., Rissanen, A. & Pietilainen, K. H., Nov 2014, In : International Journal of Obesity. 38, 11, p. 1423-1431 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Anima: modular workflow system for comprehensive image data analysis

Rantanen, V., Valori, M. & Hautaniemi, S., 30 Jul 2014, In : Frontiers in Bioengineering and Biotechnology. 2, p. 25 25.

Research output: Contribution to journalArticleScientificpeer-review

Biclustering Methods: Biological Relevance and Application in Gene Expression Analysis

Oghabian, A., Kilpinen, S., Hautaniemi, S. & Czeizler, E., 20 Mar 2014, In : PLoS One. 9, 3, 10 p., 90801.

Research output: Contribution to journalArticleScientificpeer-review

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Characterising metabolically healthy obesity in weight-discordant monozygotic twins

Naukkarinen, J., Heinonen, S., Hakkarainen, A., Lundbom, J., Vuolteenaho, K., Saarinen, L. A., Hautaniemi, S., Rodriguez, A., Fruehbeck, G., Pajunen, P., Hyotylainen, T., Oresic, M., Moilanen, E., Suomalainen Wartiovaara, A., Lundbom, N., Kaprio, J., Rissanen, A. & Pietiläinen, K. H., Jan 2014, In : Diabetologia. 57, 1, p. 167-176 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Dectin-1 Pathway Activates Robust Autophagy-Dependent Unconventional Protein Secretion in Human Macrophages

Ohman, T., Teirila, L., Lahesmaa-Korpinen, A-M., Cypryk, W., Veckman, V., Saijo, S., Wolff, H., Hautaniemi, S., Nyman, T. A. & Matikainen, S., 15 Jun 2014, In : Journal of Immunology. 192, 12, p. 5952-5962 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Deregulation of COMMD1 Is Associated with Poor Prognosis in Diffuse Large B-cell Lymphoma

Taskinen, M., Louhimo, R., Koivula, S., Chen, P., Rantanen, V., Holte, H., Delabie, J., Karjalainen-Lindsberg, M-L., Bjorkholm, M., Fluge, O., Pedersen, L. M., Fjorden, K., Jerkeman, M., Eriksson, M., Hautaniemi, S. & Leppä, S., 13 Mar 2014, In : PLoS One. 9, 3, 11 p., 91031.

Research output: Contribution to journalArticleScientificpeer-review

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Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes

Maliniemi, P., Hahtola, S., Ovaska, K., Jeskanen, L., Väkevä, L., Jäntti, K., Stadler, R., Michonneau, D., Fraitag, S., Hautaniemi, S. & Ranki, A., 2014, In : Orphanet journal of rare diseases. 9, 15 p., 160.

Research output: Contribution to journalArticleScientificpeer-review

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Prostatic acid phosphatase is the main acid phosphatase with 5 '-ectonucleotidase activity in the male mouse saliva and regulates salivation

Araujo, C. L., Quintero, I. B., Kipar, A., Herrala, A. M., Pulkka, A. E., Saarinen, L., Hautaniemi, S. & Vihko, P., Jun 2014, In : American Journal of Physiology: Cell Physiology. 306, 11, p. C1017-C1027 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Systeemibiologian keinoin kohti henkilökohtaista lääketiedettä

Hautaniemi, S., 2014, In : Suomen lääkärilehti. 69, 16-17, p. 1214-1215 2 p.

Research output: Contribution to journalArticleProfessional