Contact information

Sampsa Hautaniemi, Prof.

Biomedicum Helsinki, B524b
P.O.Box 63 (Haartmaninkatu 8)
00014 UNIVERSITY OF HELSINKI
phone +358 2941 25419

firstname.lastname@helsinki.fi

Twitter @HautaniemiLab


Affiliations

 

Publications

2017

  • Liu C, Lehtonen R, Hautaniemi S.
    PerPAS: Topology-based single sample pathway analysis method.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics., 2017, e-pub ahead of print.
    [link to pdf]

  • Meriranta L, Pasanen A, Louhimo R, Cervera A, Alkodsi A, Autio M, Taskinen M, Rantanen V, Karjalainen-Lindsberg ML, Holte H, Delabie J, Lehtonen R, Hautaniemi S, Leppä S.
    Deltex-1 mutations predict poor survival in diffuse large B-cell lymphoma.
    Haematologica, 2017, 102(5):e195-e198.
    [link to pdf]

  • Fleischer T, Klajic J, Aure MR, Louhimo R, Pladsen AV, Ottestad L, Touleimat N, Laakso M, Halvorsen AR, Alnæs GI, Riis ML, Helland Å, Hautaniemi S, Lønning PE, Naume B, Børresen-Dale AL, Tost J, Kristensen VN.
    DNA methylation signature (SAM40) identifies subgroups of the luminal A breast cancer samples with distinct survival.
    Oncotarget, 2017, 8(1):1074-1082.
    [link to pdf]

2016

  • Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S.
    SePIA: RNA and small RNA sequence processing, integration, and analysis.
    BioData Mining, 2016, 9:20.
    [link to pdf]

  • Vassilev B, Louhimo R, Ikonen E, Hautaniemi S.
    Language-agnostic reproducible data analysis using literate programming.
    PLoS One, 2016, 11(10):e0164023.
    [link to pdf]

  • Känsäkoski J, Jääskeläinen J, Jääskeläinen T, Tommiska J, Saarinen L, Lehtonen R, Hautaniemi S, Frilander MJ, Palvimo JJ, Toppari J, Raivio T.
    Complete androgen insensitivity syndrome caused by a deep intronic pseudoexon-activating mutation in the androgen receptor gene.
    Scientific Reports, 2016, 6:32819.
    [link to pdf]

  • Louhimo R, Laakso M, Belitskin D, Klefström J, Lehtonen R, Hautaniemi S.
    Data integration to prioritize drugs using genomics and curated data
    BioData Mining, 2016, 26;9:21.
    [link to pdf]

  • Balistreri G, Viiliäinen 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 PM.
    Oncogenic herpesvirus utilizes stress-induced cell cycle checkpoints for efficient lytic replication
    PLoS Pathogens, 2016, 12(2):e1005424.
    [link to pdf]

  • Tambe M, Pruikkonen S, Mäki-Jouppila J, Chen P, Elgaaen BV, Straume AH, Huhtinen K, Cárpen O, Lønning PE, Davidson B, Hautaniemi S, Kallio MJ.
    Novel Mad2-targeting miR-493-3p controls mitotic fidelity and cancer cells' sensitivity to paclitaxel
    Oncotarget, 2016, 7(11):12267-12285.
    [link to pdf]

  • Araujo CL, Quintero IB, Ovaska K, Herrala AM, Hautaniemi S, Vihko PT.
    Transmembrane prostatic acid phosphatase (TMPAP) delays cells in G1 phase of the cell cycle
    The Prostate, 2016, 76(2):151-62.
    [link to pdf]

  • Almangush A, Karhunen M, Hautaniemi S, Salo T, Leivo I.
    Prognostic value of tumour budding in oesophageal cancer: a meta-analysis
    Histopathology, 2016, 68(2):173-82. Review.
    [link to pdf]

  • Marques E, Englund JI, Tervonen TA, Virkunen E, Laakso M, Myllynen M, Mäkelä A, Ahvenainen M, Lepikhova T, Monni O, Hautaniemi S, Klefström J.
    Par6G suppresses cell proliferation and is targeted by loss-of-function mutations in multiple cancers
    Oncogene, 2016, 35, 1386–1398.
    [link to pdf]

2015

  • Chen P, Huhtinen K, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grenman S, Lehtonen R, Carpén O, Hautaniemi S.
    Identification of prognostic groups in high-grade serous ovarian cancer treated with platinum-taxane chemotherapy
    Cancer Research, 75(15):2987-98, 2015.
    [link to pdf] [download supplement]

  • Heinonen H, Lepikhova T, Sahu B, Pehkonen H, Pihlajamaa P, Louhimo R, Gao P, Wei GH, Hautaniemi S, Jänne OA, Monni O.

    Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer
    International Journal of Cancer, 15;137(10):2374-83, 2015
    [link to pdf]

  • Marjonen H, Sierra A, Nyman A, Rogojin V, Gröhn O, Linden AM, Hautaniemi S, Kaminen-Ahola N.
    Early maternal alcohol consumption alters hippocampal DNA methylation, gene expression and volume in a mouse model
    PLoS One, 2015, 13;10(5):e0124931.
    [link to pdf]

  • Liu C, Louhimo R, Laakso M, Lehtonen R, Hautaniemi S.
    Identification of sample-specific regulations using integrative network level analysis
    BMC Cancer, 2015, 15:319.
    [link to pdf]

  • 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 PM, Keski-Oja J, Lehti K.
    MMP16 mediates a proteolytic switch to promote cell-cell adhesion, collagen alignment, and lymphatic invasion in melanoma
    Cancer Research, 2015, 15;75(10):2083-94.
    [link to pdf]

  • Merkin JJ, Chen P, Alexis MS, Hautaniemi SK, Burge CB.
    Origins and impacts of new mammalian exons
    Cell Reports, 2015, 10(12):1992-2005.
    [link to pdf]

  • Nummela P, Saarinen L, Thiel A, Järvinen P, Lehtonen R, Lepistö A, Järvinen H, Aaltonen LA, Hautaniemi S, Ristimäki A.
    Genomic profile of pseudomyxoma peritonei analyzed using next-generation sequencing and immunohistochemistry
    International Journal of Cancer, 2015, 136(5):E282-9.
    [link to pdf]

  • Mattila OS, Rantanen V, Saksi J, Strbian D, Pikkarainen T, Hautaniemi S, Lindsberg P.
    Workflow for automated quantification of cerebromicrovascular gelatinase activity
    Microvascular Research, 2015, 97:19-24.
    [link to pdf]

  • Tuominen I, Heliövaara E, Raitila A, Rautiainen MR, Mehine M, Katainen R, Donner I, Aittomäki V, Lehtonen HJ, Ahlsten M, Kivipelto L, Schalin-Jäntti C, Arola J, Hautaniemi S, Karhu A.
    AIP inactivation leads to pituitary tumorigenesis through defective G.i-cAMP signaling
    Oncogene, 2015, 34(9):1174-84.
    [link to pdf]

2014

  • Rantanen V, Valori M, Hautaniemi S.
    Anima: Modular workflow system for comprehensive image data analysis
    Frontiers in Bioengineering and Biotechnology, 2014, 2:25.
    [link to pdf]

  • Norrmén C, Figlia G, Lebrun-Julien F, Pereira JA, Trötzmüller M, Köfeler HC, Rantanen V, Wessig C, van Deijk AL, Smit AB, Verheijen MH, Rüegg MA, Hall MN, Suter U.
    mTORC1 controls PNS myelination along the mTORC1-RXRγ-SREBP-lipid biosynthesis axis in Schwann cells
    Cell Reports, 2014, pii: S2211-1247(14)00769-4. [Epub ahead of print]
    [link to pdf]

  • Öhman T, Teirilä L, Lahesmaa-Korpinen AM, Cypryk W, Veckman V, Saijo S, Wolff H, Hautaniemi S, Nyman TA, Matikainen S.
    Dectin-1 pathway activates robust autophagy-dependent unconventional protein secretion in human macrophages
    Journal of Immunology, 2014, 192(12):5952-62.
    [link to pdf]

  • Araujo CL, Quintero IB, Kipar A, Herrala AM, Pulkka AE, Saarinen L, Hautaniemi S, Vihko P.
    Prostatic acid phosphatase is the main acid phosphatase with 5'-ectonucleotidase activity in the male mouse saliva and regulates salivation
    American Journal of Physiology: Cell Physiology, 2014, 306(11):C1017-27.
    [link to pdf]

  • Oghabian A, Kilpinen S, Hautaniemi S, Czeizler E.
    Biclustering methods: biological relevance and application in gene expression analysis
    PLoS One, 2014, 9(3):e90801.
    [link to pdf]

  • Alkodsi A, Louhimo R, Hautaniemi S.
    Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data
    Briefings in Bioinformatics, 2014, 16(2):242-54.
    [link to pdf]

  • Heinonen S, Saarinen L, Naukkarinen J, Rodríguez A, Frühbeck G, Hakkarainen A, Lundbom J, Lundbom N, Vuolteenaho K, Moilanen E, Arner P, Hautaniemi S, Suomalainen A, Kaprio J, Rissanen A, Pietiläinen KH.
    Adipocyte morphology and implications for metabolic derangements in acquired obesity
    International Journal of Obesity, 2014, 38(11):1423-31.
    [link to pdf]

  • Taskinen M, Louhimo R, Koivula S, Chen P, Rantanen V, Holte H, Karjalainen-Lindsberg M-L, Björkholm M, Fluge O, Moller Pedersen L, Fjorden K, Jerkeman M, Erikkson M, Hautaniemi S, Leppä S.
    Deregulation of COMMD1 is associated with poor prognosis in diffuse large B-cell lymphoma
    PLoS ONE, 2014, 9(3): e91031.
    [link to pdf]

  • Pihlajamaa P, Sahu B, Lyly L, Aittomäki V, Hautaniemi S, Jänne OA.
    Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs

    The EMBO Journal, 2014, 33(4):312-26.
    [link to pdf]

  • Savilahti EM, Kuitunen M, Valori M, Rantanen V, Bardina L, Gimenez G, Mäkelä MJ, Hautaniemi S, Savilahti E, Sampson HA.
    Changes in IgE and IgG4 epitope binding profiles associated with the outcome of oral immunotherapy in cow's milk allergy
    Pediatric Allergy and Immunology, 2014, 25(3):227-35.
    [link to pdf]

  • Naukkarinen J, Heinonen S, Hakkarainen A, Lundbom J, Vuolteenaho K, Saarinen L, Hautaniemi S, Rodriguez A, Frühbeck G, Pajunen P, Hyötyläinen T, Orešič M, Moilanen E, Suomalainen A, Lundbom N, Kaprio J, Rissanen A, Pietiläinen KH.
    Characterising metabolically healthy obesity in weight-discordant monozygotic twins
    Diabetologia, 2014, 57(1):167–176.
    [link to pdf]

2013

  • Aure MR, Leivonen SK, Fleischer T, Zhu Q, Overgaard J, Alsner J, Tramm T,
    Louhimo R, Alnæs GI, Perälä M, Busato F, Touleimat N, Tost J, Børresen-Dale AL,Hautaniemi S, Troyanskaya OG, Lingjærde OC, Sahlberg KK, Kristensen VN.
    Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors
    Genome Biology, 2013, 14(11):R126.
    [link to pdf]

  • Keuschnigg J, Karinen S, Auvinen K, Irjala H, Mpindi J-P, Kallioniemi O, Hautaniemi S, Jalkanen S, Salmi M.
    Plasticity of blood- and lymphatic endothelial cells and marker identification
    PLoS One, 2013, 8(9): e74293.
    [link to pdf]

  • Gerling M, Nousiainen K, Hautaniemi S, Krueger S, Fritzsche B, Homann N, Bruch H-P, Auer G, Roblick UJ, Ried T, Habermann JK.
    Aneuploidy-associated gene expression signatures characterize malignant transformation in ulcerative colitis
    Inflammatory Bowel Diseases, 2013, 19(4):691-703.
    [link to pdf]

  • Airas N, Näreaho A, Lindén J, Valo E, Hautaniemi S, Jokelainen P, Sukura A.
    Early trichinella spiralis and trichinella nativa infections induce similar gene expression profiles in rat jejunal mucosa
    Experimental Parasitology, 2013, 135(2):363-9.
    [link to pdf]

  • Louhimo R, Laakso M, Heikkinen T, Laitinen S, Manninen P, Rogojin V, Miettinen M, Blomqvist C, Liu J, Nevanlinna H, Hautaniemi S.
    Identification of genetic markers with synergistic survival effect in cancer
    BMC Systems Biology, 2013, 7(Suppl 1):S2.
    [link to pdf]

  • Aho V, Ollila H, Rantanen V, Kronholm E, Surakka I, van Leeuwen WMA, Lehto M, Matikainen S, Ripatti S, Härmä M, Sallinen M, Salomaa V,Jauhiainen M, Alenius H, Paunio T, Porkka-Heiskanen T.
    Partial sleep restriction activates immune response-related gene expression pathways: Experimental and epidemiological studies in humans
    PLoS ONE, 8(10): e77184.
    [link to pdf]

  • Matilainen O, Arpalahti L, Rantanen V, Hautaniemi S, Holmberg CI.
    Insulin/IGF-1 signaling regulates proteasome activity through the eubiquitinating enzyme UBH-4
    Cell Reports, 2013, 27;3(6):1980-95.
    [link to pdf]

  • Gylfe AE, Kondelin J, Turunen M, Ristolainen H, Katainen R, Pitkänen E, Kaasinen E, Rantanen V, Tanskanen T, Varjosalo M, Lehtonen H, Palin K, Taipale M, Taipale J, Renkonen-Sinisalo L, Järvinen H, Böhm J, Mecklin JP, Ristimäki A, Kilpivaara O, Tuupanen S, Karhu A, Vahteristo P, Aaltonen LA.
    Identification of candidate oncogenes in human colorectal cancers with microsatellite instability
    Gastroenterology, 2013, 145(3):540-543.e22.
    [link to pdf]

  • Af Hällström TM, Zhao H, Tian J,Rantanen V, Reese SW, Nolley R, Laiho M, Peehl DM.
    A tissue graft model of DNA damage response in the normal and malignant human prostate
    The Journal of Urology, 2013, pii: S0022-5347(13)05363-9.
    [link to pdf]

  • Quintero IB, Herrala AM, Araujo CL, Pulkka AE, Hautaniemi S, Ovaska K, Pryazhnikov E, Kulesskiy E, Ruuth MK, Soini Y, Sormunen RT, Khirug L, Vihko P.
    Transmembrane prostatic acid phosphatase (TMPAP) interacts with snapin and deficient mice develop prostate adenocarcinoma

    PLoS ONE, 2013, 8(9): e73072.
    [link to pdf]

  • Ovaska K, Matarese F, Grote K, Charapitsa I, Cervera A, Liu C, Reid G, Seifert M, Stunnenberg HG, Hautaniemi S.
    Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer
    PLoS Computational Biology, 2013, 9(6): e1003100.
    [link to pdf]

  • Aarne N, Laine J, Hänninen T, Rantanen V, Seitsonen J, Ruokolainen J, Kontturi E.

    Controlled hydrophobic functionalization of natural fibers by self-assembly of amphiphilic diblock copolymer micelles
    ChemSusChem, 2013, 6(7): 1203–1208
    [link to pdf]

  • Ylivinkka I, Hu Y, Chen P, Rantanen V, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M.
    Netrin-1 induced activation of Notch signaling mediates glioblastoma cell invasion
    Journal of Cell Science, 2013 Jun 1;126(Pt 11):2459-69.
    [link to pdf]

  • Haapa-Paananen S,  Chen P,  Hellström K,  Kohonen P, Hautaniemi S, Kallioniemi O,  Perälä M.
    Functional profiling of precursor microRNAs identifies microRNAs essential for glioma proliferation
    PLoS One, 2013; 8(4): e60930.
    [link to pdf]

  • Mustjoki S, Auvinen K, Kreutzman A, Rousselot P, Hernesniemi S, Melo T, Lahesmaa-Korpinen A-M, Hautaniemi S, Bouchet S, Molimard M, Smykla R, Lee FY, Vakkila J, Jalkanen S, Salmi M, Porkka K.
    Rapid mobilization of cytotoxic lymphocytes induced by dasatinib therapy in leukemia patients
    Leukemia, 2013 Apr;27(4):914-24.
    [link to pdf]

  • Jamshidi M, Schmidt MK, Dörk T, Garcia-Closas M, Heikkinen T, Cornelissen S, van den Broek AJ, Schürmann P, Meyer A, Park-Simon TW, Figueroa J, Sherman M, Lissowska J, Keong GT, Irwanto A, Laakso M, Hautaniemi S, Aittomäki K, Blomqvist C, Liu J, Nevanlinna H.
    Germline variation in TP53 regulatory network genes associates with breast cancer survival and treatment outcome
    International Journal of Cancer, 2013 May 1; 132(9):2044-2055.
    [link to pdf]

  • Sahu B, Laakso M, Pihlajamaa P, Ovaska K, Sinielnikov I, Hautaniemi S, Jänne O.
    FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells
    Cancer Research, 2013 Mar 1;73(5):1570-80.
    [link to pdf] [Anduril report]

  • Carlsson E, Krohn K, Ovaska K, Lindberg P, Häyry V, Maliniemi P, Lintulahti A, Korja M, Kivisaari R, Hussein S, Sarna S, Niiranen K, Hautaniemi S, Haapasalo H, Ranki A.
    Neuron navigator 3 alterations in nervous system tumors associate with tumor malignancy grade and prognosis
    Genes, Chromosomes and Cancer, 2013 Feb;52(2):191-201.
    [link to pdf]

  • Ovaska K, Lyly L, Sahu B, Jänne O, Hautaniemi S.
    Genomic region operation kit for flexible processing of deep sequencing data
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013 Jan-Feb;10(1):200-6.
    [link to pdf]

2012

  • Merkin J, Russell C, Chen P, Burge CB.
    Evolutionary dynamics of gene and isoform regulation in mammalian tissues
    Science, 2012 Dec 21;338(6114):1593-9.
    [link to pdf]

  • Karhemo PR, Ravela S, Laakso M, Ritamo I, Tatti O, Mäkinen S, Goodison S, Stenman UH, Hölttä E, Hautaniemi S, Valmu L, Lehti K, Laakkonen P.
    An optimized isolation of biotinylated cell surface proteins reveals novel players in cancer metastasis
    Journal of Proteomics, 2012 Dec 21;77:87-100.
    [link to pdf]

  • Jalkanen SE, Lahesmaa-Korpinen A-M, Heckman CA, Rantanen V, Porkka K, Hautaniemi S, Mustjoki S.
    Phosphoprotein profiling predicts response to tyrosine kinase inhibitor therapy in chronic myeloid leukemia patients.
    Experimental Hematology, 2012 Sep;40(9):705-714.e3.
    [link to pdf]

  • Jäämaa S, Sankila A, Rantanen V, Peltonen K, Järvinen PM, Af Hällström TM, Ruutu M, Taari K, Andersson LC, Laiho M.
    Contrasting DNA damage checkpoint responses in epithelium of the human seminal vesicle and prostate
    The Prostate, 2012 Jul 1;72(10):1060-70.
    [link to pdf]

  • Hu Y, Ylivinkka I, Chen P, Li L, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M.
    Netrin-4 promotes glioblastoma cell proliferation through integrin beta-4 signaling
    Neoplasia, 2012 Mar; 14(3): 219-227.
    [link to pdf]

  • Karinen S, Saarinen S, Lehtonen R, Rastas P, Vahteristo P, Aaltonen L A, Hautaniemi S.
    Rule-based induction method for haplotype comparison and identification of candidate disease loci
    Genome Medicine, 2012 Mar 19;4(3):21.
    [link to pdf]

  • Louhimo R, Lepikhova T, Monni O, Hautaniemi S.
    Comparative analysis of algorithms for integration of copy number and expression data
    Nature Methods, 2012 Feb; 9(4):351-5.
    [link to pdf]

  • Rafn B, Friberg Nielsen C, Hagel Andersen S, Szyniarowski P, Corcelle-Termeau E, Valo E, Fehrenbacher N, Olsen C, Daugaard M, Egebjerg C, Bøttzauw T, Kohonen P, Nylandsted J, Hautaniemi S, Moreira J, Jäättelä M, Kallunki T.
    ErbB2-driven breast cancer cell invasion depends on a complex signaling network activating myeloid zinc finger-1-dependent cathepsin B expression
    Molecular Cell, 2012 Mar; 45(6):764-76.
    [link to pdf]

  • Tuupanen S, Yan J, Turunen M, Gylfe A, Kaasinen E, Li L, Eng C, Culver D, Kalady M, Pennison M, Paschke B, de la Chapelle A, Hampel H, Henderson B, Le Marchand L, Hautaniemi S, Askhtorab H, Smoot D, Sandler R, Keku T, Kupfer S, Ellis N, Haiman C, Taipale T, Aaltonen LA.
    Characterization of the colorectal cancer associated enhancer MYC-335 at 8q24: the role of rs67491583
    Cancer Genetics, 2012 Jan; 205(1-2):25-33.
    [link to pdf]

  • Niemelä M, Kauko O, Sihto H, Mpindi JP, Nicorici D, Pernilä P, Kallioniemi OP, Joensuu H, Hautaniemi S, Westermarck J.
    CIP2A signature reveals the MYC dependency of CIP2A-regulated phenotypes and its clinical association with breast cancer subtypes
    Oncogene, 2012 Sep 27;31(39):4266-78.
    [link to pdf]

  • Mathiasen D, Egebjerg C, Khanna A, Daugaard M, Rafn B, Bøttzauw T, Friberg C, Tuomela S, Valo E, Willumsen B, Hautaniemi S, Lahesmaa R, Westermarck J, Jäättelä M, Kallunki T.
    Identification of a c-Jun N-terminal kinase 2 dependent signal amplification cascade that regulates c-Myc levels in ras transformation
    Oncogene, 2012 Jan 19;31(3):390-40.
    [link to pdf]

  • Balestrieri C, Vanoni M, Hautaniemi S, Alberghina L, Chiaradonna F.
    Integrative transcriptional analysis between human and mouse cancer cells provides a common set of transformation associated genes
    Biotechnology Advances, 2012 Jan-Feb;30(1):16-29.
    [link to pdf]

  • Alhopuro P, Sammalkorpi H, Niittymäki I, Biström M, Raitila A, Saharinen J, Nousiainen K, Lehtonen HJ, Heliövaara E, Puhakka J, Tuupanen S, Sousa S, Seruca R, Ferreira AM, Hofstra RM, Mecklin JP, Järvinen H, Ristimäki A, Orntoft TF, Hautaniemi S, Arango D, Karhu A, Aaltonen LA.
    Candidate driver genes in microsatellite-unstable colorectal cancer
    International Journal of Cancer, 2012 Apr 1;130(7):1558-66.
    [link to pdf]

  • Blom H, Rönnlund D, Scott L, Spicarova Z, Rantanen V, Widengren J, Aperia A, Brismar H.
    Nearest neighbor analysis of dopamine D1 receptors and Na+-K+-ATPases in dendritic spines dissected by STED microscopy
    Microscopy Research and Technique, 2012 Feb;75(2):220-8.
    [link to pdf]

2011

  • Cheng F, Pekkonen P, Laurinavicius S, Sugiyama N, Henderson S, Gunther T, Rantanen V, Kaivanto E, Aavikko M, Sarek G, Hautaniemi S, Biberfeld P, Aaltonen LA, Grundhoff A, Boshoff C, Alitalo K, Lehti K, Ojala P.
    KSHV-initiated notch activation leads to membrane-type-1 matrix metalloproteinase-dependent lymphatic endothelial-to-mesenchymal transition
    Cell Host & Microbe, 2011 Dec 15; 10(6):577-590.
    [link to pdf]

  • Mattila OS, Strbian D, Saksi J, Pikkarainen TO, Rantanen V, Tatlisumak T, Lindsberg PJ.
    Cerebral mast cells mediate blood-brain barrier disruption in acute experimental ischemic stroke through perivascular gelatinase activation
    Stroke, 2011 Dec;42(12):3600-5.
    [link to pdf]

  • Leppä E, Linden A-M, Vekovischeva OY, Rantanen V, Toppila E, Höger H, Sieghart W, Wulff P, Wisden W, Korpi ER.
    Removal of GABAA receptor gamma2 subunits from parvalbumin neurons causes wide-ranging behavioral alterations
    PLoS One, 2011 Dec;42(12):3600-5.
    [link to pdf]

  • Lahesmaa-Korpinen AM, Jalkanen SE, Chen P, Valo E, Núñez-Fontarnau J, Rantanen V, Oghabian A, Vakkila J, Porkka K, Mustjoki S, Hautaniemi S.
    FlowAnd: Comprehensive computational framework for flow cytometry data analysis

    Journal of Proteomics and Bioinformatics
    , 2011 Nov 4: 245-249.
    [link to pdf]

  • Rodriguez-Martinez A, Alarmo EL, Saarinen L, Ketolainen J, Nousiainen K, Hautaniemi S, Kallioniemi A.
    Analysis of BMP4 and BMP7 signaling in breast cancer cells unveils time-dependent transcription patterns and highlights a common synexpression group of genes
    BMC Medical Genomics, 2011 Nov 25;4:80.
    [link to pdf]

  • Cowley MJ, Pinese M, Kassahn KS, Waddell N, Pearson JV, Grimmond SM, Biankin AV, Hautaniemi S, Wu J.
    PINA v2.0: mining interactome modules
    Nucleic Acids Research, 2011 Nov 8. 2012 Jan;40(Database issue):D862-5.
    [link to pdf]

  • Habermann JK, Bundgen NK, Gemoll T, Hautaniemi S, Lundgren C, Wangsa D, Doering J, Bruch HP, Nordstroem B, Roblick UJ, Jornvall H, Auer G, Ried T.
    Genomic instability influences the transcriptome and proteome in endometrial cancer subtypes
    Molecular Cancer, 2011 Oct 31;10(1):132.
    [link to pdf]

  • Maliniemi P, Carlsson E, Kaukola A, Ovaska K, Niiranen K, Saksela O, Jeskanen L, Hautaniemi S, Ranki A.
    NAV3 copy number changes and target genes in basal and squamous cell cancers
    Experimental Dermatology, 2011 Nov;20(11):926-31.
    [link to pdf]

  • Moore HM, Bai B, Boisvert F-M, Latonen L, Rantanen V, Simpson V, Pepperkok R, Lamond AI, Laiho M.
    Quantitative proteomics and dynamic imaging of the nucleolus reveals distinct responses to UV and ionizing radiation
    Molecular & Cellular Proteomics, 2011 Oct;10(10):M111.009241.
    [link to pdf]

  • Sahu B, Laakso M, Ovaska K, Mirtti T, Lundin J, Rannikko A, Sankila A, Turunen JP, Lundin M, Konsti J, Vesterinen T, Nordling S, Kallioniemi O, Hautaniemi S, Jänne O.
    Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signaling and prostate cancer
    The EMBO Journal, 2011 Sep 13;30(19):3962-76.
    [link to pdf] [Anduril report]

  • Pihlajamaa P, Zhang FP, Saarinen L, Mikkonen L, Hautaniemi S, Jänne O.
    The phytoestrogen genistein is a tissue-specific androgen receptor modulator
    Endocrinology, 2011 Nov;152(11):4395-405.
    [link to pdf]

  • Chen P, Lepikhova T, Hu YZ, Monni O, Hautaniemi S.
    Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants
    Nucleic Acids Research, 2011 Oct;39(18):e123.
    [link to pdf] [website]

  • Heinonen M, Hemmes A, Salmenkivi K, Abdelmohsen K, Vilén ST, Laakso M, Leidenius M, Salo T, Hautaniemi S, Gorospe M, Heikkilä P, Haglund C, Ristimäki A.
    Role of RNA binding protein HuR in ductal carcinoma in situ of the breast
    The Journal of Pathology, 2011 Mar 7; 224: 529–539.
    [link to pdf]

  • Karinen S, Heikkinen T, Nevanlinna H, Hautaniemi S.
    Data integration workflow for search of disease driving genes and genetic variants
    PLoS ONE, 2011 Apr; 6(4).
    [link to pdf] [website]

  • Louhimo R, Hautaniemi S.
    CNAmet: an R package for integrating copy number, methylation and expression data
    Bioinformatics, 2011 Mar 15;27(6):887-8.
    [link to pdf] [website]

  • Koivula S, Valo E, Raunio A, Hautaniemi S, Leppä S.
    Rituximab regulates signaling pathways and alters gene expression associated with cell death and survival in diffuse large B-cell lymphoma
    Oncology Reports, 2011 Apr;25(4):1183-90.
    [link to pdf]

  • Niittymäki I, Gylfe A, Laine L, Laakso M, HJ Lehtonen, Kondelin J, Tolvanen J, Nousiainen K, Pouwels J, Järvinen H, Nuorva K, Mecklin JP, Mäkinen M, Ristimäki A, Ørntoft TF, Hautaniemi S, Karhu A, Kallio MJ, Aaltonen LA.
    High frequency of TTK mutations in microsatellite-unstable colorectal cancer and evaluation of their effect on spindle-assembly checkpoint
    Carcinogenesis, 2011 Mar;32(3):305-11.
    [link to pdf]

2010

  • Ovaska K, Laakso M, Haapa-Paananen S, Louhimo R, Chen P, Aittomäki V, Valo E, Nunez-Fontarnau J, Rantanen V, Karinen S, Nousiainen K, Lahesmaa-Korpinen A-M, Miettinen M, Saarinen L, Kohonen P, Wu J, Westermarck J, Hautaniemi S.
    Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
    Genome Medicine, 2010, 2:65.
    [link to pdf] [website] [results website] [commentary]

  • Jäämaa S, Kiviharju-af Hällström T, Sankila A, Rantanen V, Koistinen H, Stenman U-H, Zhang Z, Yang Z, De Marzo A, Taari K, Ruutu M, Andersson L, Laiho M.
    DNA damage recognition via activated ATM and p53 pathway in nonproliferating human prostate tissue
    Cancer Research, 2010 Nov 1;70(21):8630-41.
    [link to pdf]

  • Lahesmaa-Korpinen A-M, Carlson SM, White FM, Hautaniemi S.
    Integrated data management and validation platform for phosphorylated tandem mass spectrometry data
    Proteomics, 2010 Oct;10(19):3515-24.
    [link to pdf]

  • Laakso M, Hautaniemi S.
    Integrative platform to translate gene sets to networks
    Bioinformatics, 2010 Jul 15;26(14):1802-3.
    [link to pdf] [website]

  • Alhopuro P, Björklund M, Sammalkorpi H, Turunen M, Tuupanen S, Biström M, Niittymäki I, Lehtonen HJ, Kivioja T, Launonen V, Saharinen J, Nousiainen
    K, Hautaniemi S, Nuorva K, Mecklin JP, Järvinen H, Orntoft T, Arango D,
    Lehtonen R, Karhu A, Taipale J, Aaltonen LA.
    Mutations in the circadian gene CLOCK in colorectal cancer
    Molecular Cancer Research, 2010 Jul;8(7):952-60.
    [link to pdf]

  • Dias JD, Liikanen I, Guse K, Foloppe J, Sloniecka M, Diaconu I, Rantanen V, Eriksson M, Hakkarainen T, Lusky M, Erbs P, Escutenaire S, Kanerva A, Pesonen S, Cerullo V, Hemminki A.
    Targeted chemotherapy for head and neck cancer with a chimeric oncolytic adenovirus coding for bifunctional suicide protein FCU1
    Clinical Cancer Research, 2010 May 1;16(9):2540-9.
    [link to pdf]

  • Taskinen M, Valo E, Karjalainen-Lindsberg ML, Hautaniemi S, Meri S, Leppä S.
    Signal transducers and activators of transcription 5a-dependent cross-talk between follicular lymphoma cells and tumor microenvironment characterizes a group of patients with improved outcome after R-CHOP
    Clinical Cancer Research, 2010 May 1;16(9):2615-23.
    [link to pdf]

  • Savilahti EM, Karinen S, Salo H, Klemetti P, Saarinen KM, Klemola T, Kuitunen M, Hautaniemi S, Savilahti E, Vaarala O.
    Combined T regulatory cell and Th2 expression profile identifies children with cow's milk allergy
    Clinical Immunology, 2010 Jul;136(1):16-20.
    [link to pdf]

  • Savilahti EM, Rantanen V, Lin J, Karinen S, Saarinen KM, Goldis M, Mäkelä M, Hautaniemi S, Savilahti E, Sampson H.
    Early recovery from cow's milk allergy is associated with decreasing IgE and increasing IgG4 binding to cow's milk epitopes
    Journal of Allergy and Clinical Immunology, 2010 Jun;125(6):1315-1321.
    [link to pdf]

  • Enzerink A, Rantanen V, Vaheri A.
    Fibroblast nemosis induces angiogenic responses of endothelial cells
    Experimental Cell Research, 2010 Mar 10;316(5):826-35.
    [link to pdf]

2009

  • Rajecki M, Hällström TA, Hakkarainen T, Nokisalmi P, Hautaniemi S, Nieminen AI, Tenhunen M, Rantanen V, Desmond RA, Chen DT, Guse K, Stenman UH, Gargini R, Kapanen M, Klefström J, Kanerva A, Pesonen S, Ahtiainen L, Hemminki A.
    Mre11 inhibition by oncolytic adenovirus associates with autophagy and underlies synergy with ionizing radiation
    International Journal of Cancer, 2009 Jun 2;125(10):2441-2449.
    [link to pdf]

  • Blomster HA, Hietakangas V, Wu J, Kouvonen P, Hautaniemi S, Sistonen L.
    Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites
    Molecular & Cellular Proteomics, 2009 Jun;8(6):1382-90.
    [link to pdf]

  • Backlund M, Paukku K, Daviet L, De Boer R, Kalkkinen N, Valo E, Hautaniemi S, Ehsan A, Kontula K, Lehtonen J.
    Posttranscriptional regulation of angiotensin II type 1 receptor expression by glyceraldehyde 3-phosphate dehydrogenase
    Nucleic Acids Research, 2009 Apr;37(7):2346-58.
    [link to pdf]

  • Wu J, Vallenius T, Ovaska K, Westermarck J, Mäkelä TP, Hautaniemi S.
    Integrated network analysis platform for protein-protein interactions
    Nature Methods, 2009 Jan;6(1):75-77.
    [link to pdf] [web site]

  • Habermann J, Doering J, Hautaniemi S, Roblick W, Bündgen N, Nicorici D, Kronenwett U, Rathnagiriswaran S, Mettu TK, Ma Y, Krüger S, Bruch HP, Auer G, Guo NL, Ried T.
    The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome
    International Journal of Cancer, 2009 Apr 1;124(7):1552-64.
    [link to pdf]

2008

  • Ovaska K, Laakso M, Hautaniemi S.
    Fast Gene Ontology based clustering for microarray experiments
    BioData Mining, 2008 Nov 21;1(1):11.
    [link to pdf] [download]

  • Kilpinen S, Autio R, Ojala K, Iljin K, Bucher E, Sara H, Pisto T, Saarela M, Skotheim RI, Björkman M, Mpindi JP, Edgren H, Wolf M, Astola J, Nees M, Hautaniemi S, Kallioniemi O.
    Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
    Genome Biology, 2008 Sep 9:R139.
    [link to pdf] [web site]

  • Nieminen H, Nieminen A, Saarela M, Kallioniemi A, Klefström J, Hautaniemi S, Monni O.
    Deciphering downstream gene targets of PI3K/mTOR/p70S6 pathway in breast cancer
    BMC Genomics, 2008 Jul 24;9(1):348.
    [link to pdf]

  • Tuupanen S, Niittymäki I, Nousiainen K, Vanharanta S, Mecklin JP, Nuorva K, Järvinen H, Hautaniemi S, Karhu A, Aaltonen LA.
    Allelic imbalance at rs6983267 suggests selection of the risk allele in somatic CRC tumor evolution
    Cancer Research, 2008 Jan 1;68(1):14-7.
    [link to pdf]

2007

2006

  • Hemmoranta H, Hautaniemi S, Niemi J, Nicorici D, Laine J, Yli-Harja O, Partanen J, Jaatinen T.
    Transcriptional profiling reflects shared and unique characters for CD34+ and CD133+ cells
    Stem Cells and Development, 2006 Dec;15(6):839-51.
    [link to pdf]

  • Hautaniemi S, Vallenius T, Mäkelä T.
    Systems biology in cancer research
    Duodecim, 2006 Nov;122(20):2484-90.
    [link to pdf] (in Finnish)

  • Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova V, Lauffenburger DA, White FM.
    Effects of HER2-overexpression on cell signaling networks governing proliferation and migration
    Molecular Systems Biology, 2006 Oct;2:54.
    [link to pdf]

  • Hua F, Hautaniemi S, Yokoo R, Lauffenburger DA.
    Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways
    Journal of the Royal Society Interface, 2006 Aug 22;3(9):515-26.
    [link to pdf]

  • Harjunpää A, Taskinen M, Nykter M, Karjalainen-Lindsberg ML, Nyman H, Monni O, Hemmer S, Yli-Harja O, Hautaniemi S, Meri S, Leppä S.
    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, 2006 Oct;135(1):33-42.
    [link to pdf]

  • Lähdesmäki H, Hautaniemi S, Shmulevich I, Yli-Harja O.
    Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks
    Signal Processing, 2006 Apr;86:814-834.
    [link to pdf]

  • Jaatinen T, Hemmoranta H, Hautaniemi S, Niemi J, Nicorici D, Laine J, Yli-Harja O, Partanen J.
    Global gene expression profile of human cord blood-derived CD133+ cells
    Stem Cells, 2006 Mar;24(3):631-41.
    [link to pdf]

  • Berger JA, Hautaniemi S, Mitra SK, Astola J.
    Jointly analyzing gene expression and copy number data in breast cancer using data reduction models
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2006 Jan;3(1):2-16.
    [link to pdf]

2005

  • Arango D, Laiho P, Kokko A, Alhopuro P, Sammalkorpi H, Salovaara R, Nicorici D, Hautaniemi S, Alazzouzi H, Mecklin JP, Järvinen H, Hemminki A, Astola J, Schwartz S Jr, Aaltonen LA.
    Gene expression profiling predicts recurrence in Dukes' C colorectal cancer
    Gastroenterology, 2005 Sep;129(3):874-884.
    [link to pdf]

  • Hautaniemi S, Kharait S, Iwabu A, Wells A, Lauffenburger DA.
    Modeling of signal-response cascades using decision tree analysis
    Bioinformatics, 2005 May;21(9):2027-2035.
    [link to pdf]

  • Liang WS, Maddukuri A, Teslovich TM, de la Fuente C, Agbottah E, Dadgar S, Kehn K, Hautaniemi S, Pumfery A, Stephan DA, Kashanchi F.
    Therapeutic targets for HIV-1 infection in the host proteome
    Retrovirology, 2005 Mar 21;2(1):20.
    [link to pdf]

2004

  • Berger JA, Hautaniemi S, Järvinen AK, Edgren H, Mitra SK, Astola J.
    Optimized LOWESS normalization parameter selection for DNA microarray data
    BMC Bioinformatics, 2004 Dec 9;5(1):194.
    [link to pdf]

  • Mahlamäki EH, Kauraniemi P, Monni O, Wolf M, Hautaniemi S, Kallioniemi A.
    High-resolution genomic and expression profiling reveals 105 putative amplification target genes in pancreatic cancer
    Neoplasia, 2004 Sep-Oct;6(5):432-439.
    [link to pdf]

  • Huusko P, Ponciano-Jackson D, Wolf M, Kiefer JA, Azorsa DO, Tuzmen S, Weaver D, Robbins C, Moses T, Allinen M, Hautaniemi S, Chen Y, Elkahloun A, Basik M, Bova GS, Bubendorf L, Lugli A, Sauter G, Schleutker J, Ozcelik H, Elowe S, Pawson T, Trent JM, Carpten JD, Kallioniemi OP, Mousses S.
    Nonsense-mediated decay microarray analysis reveals mutations of EphB2 in human prostate cancer
    Nature Genetics, 2004 Sep;36(9):979-983.
    [link to pdf]

  • Wolf M, Mousses S, Hautaniemi S, Karhu R, Huusko P, Allinen M, Elkahloun A, Monni O, Chen Y, Kallioniemi A, Kallioniemi OP.
    High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: Impact of copy number on gene expression
    Neoplasia, 2004 May-Jun;6(3):240-247.
    [link to pdf]

  • Järvinen AK, Hautaniemi S, Edgren H, Auvinen P, Saarela J, Kallioniemi OP, Monni O.
    Are data from different cDNA and oligonucleotide microarray platforms comparable?
    Genomics, 2004 Jun;84(6):1164-1168.
    [link to pdf]

  • Hautaniemi S, Ringnér M, Kauraniemi P, Autio R, Edgren H, Yli-Harja O, Astola J, Kallioniemi A, Kallioniemi OP.
    A strategy for identifying putative causes of gene expression variation in human cancers
    Journal of the Franklin Institute, 2004 Jan-Mar;341(1-2):77-88.
    [link to pdf]

  • Kauraniemi P, Hautaniemi S, Autio R, Astola J, Monni O, Elkahloun A, Kallioniemi A.
    Effects of Herceptin treatment on global gene expression patterns in HER2 amplified and nonamplified breast cancer cell lines
    Oncogene, 2004 Jan;23(4):1010-1013.
    [link to pdf]

2003

  • Hautaniemi S, Edgren H, Vesanen P, Wolf M, Järvinen AK, Yli-Harja O, Astola J, Kallioniemi O, Monni O.
    A novel strategy for microarray quality control using Bayesian networks
    Bioinformatics, 2003 Nov;19(16):2031-2038.
    [link to pdf]

  • Mousses S, Caplen NJ, Cornelison R, Weaver D, Basik M, Hautaniemi S, Elkahloun AG, Lotufo RA, Choudary A, Dougherty ER, Suh E, Kallioniemi O.
    RNAi microarray analysis in cultured mammalian cells
    Genome Research, 2003 Oct;13(10):2341-2347.
    [link to pdf]

  • Autio R, Hautaniemi S, Kauraniemi P, Yli-Harja O, Astola J, Wolf M, Kallioniemi A.
    CGH-Plotter: MATLAB toolbox for CGH-data analysis
    Bioinformatics, 2003 Sep;19(13):1714-1715.
    [link to pdf]

  • Hautaniemi S, Yli-Harja O, Astola J, Kauraniemi P, Kallioniemi A, Wolf M, Ruiz J, Mousses S, Kallioniemi OP.
    Analysis and visualization of gene expression microarray data in human cancer using self-organizing maps
    Machine Learning, 2003 Jul;52(1-2):45-66.
    [link to pdf]

2002

  • Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, Ringnér M, Sauter G, Monni O, Elkahloun A, Kallioniemi OP, Kallioniemi A.
    Impact of DNA amplification on gene expression patterns in breast cancer
    Cancer Research, 2002 Nov;62(21):6240-6245.
    [link to pdf]

  • Monni O, Hautaniemi S, Kallioniemi OP.
    Gene chip technique and associated bioinformatics
    Duodecim, 2002 Jun;118(11):1157-1166.
    [link to pdf] (In Finnish only)