Hautaniemi Lab

Publications

All articles are available directly or upon request.

Articles from work at University of Helsinki (Spring 2006 -- )

2013

• 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, Choromosomes and Cancer, 2013 Feb;52(2):191-201.
  [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]
  
  
• 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, 2012 Dec 26, E-pub ahead of print.
  [pdf] [Anduril report]
  
  
• 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, 2012 Dec 28, E-pub ahead of print.
  [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, 2012 Oct 4, E-pub ahead of print.
  [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, in press.
  
  
• 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.
  [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.
  [pdf]
  
  
• Hu Y, Ylivinkka I, Chen P, Li L, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M.
  Netrin-4 promotes glioblastoma cell proliferation via integrin beta-4 signaling
  Neoplasia, 2012 Mar; 14(3): 219-227.
  [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.
  [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.
  [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.
  [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.
  [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.
  [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.
  [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.
  [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.
  [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, and 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.
  [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.
  [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.
  [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.
  [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.
  [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.
  [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
  EMBO Journal,2011 Sep 13;30(19):3962-76.
  [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.
  [pdf]
  
  
• Chen P, Lepikhova T, Hu YZ, Monni O and Hautaniemi S.
  Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants
  Nucleic Acids Research, 2011 Oct;39(18):e123.
  [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.
  [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).
  [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.
  [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.
  [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.
  [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.
  [pdf] [website] [results website] [commentary]
  
  
• 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.
  [pdf]
  
  
• Laakso M, Hautaniemi S.
  Integrative platform to translate gene sets to networks
  Bioinformatics, 2010 Jul 15;26(14):1802-3.
  [pdf] [download]
  
  
• 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.
  [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.
  [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.
  [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.
  [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.
  [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.
  [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.
  [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.
  [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.
  [pdf]

2008

• Ovaska K, Laakso M, Hautaniemi S.
  Fast Gene Ontology based clustering for microarray experiments
  BioData Mining 2008 Nov 21;1(1):11.
  [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 17330 human genes across 9783 samples from 175 types of healthy and pathological tissues
  Genome Biology 2008 Sep 9:R139.
  [pdf] [web site]


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

2007

• Laakso M, Tuupanen S, Karhu A, Lehtonen R, Aaltonen LA, Hautaniemi S.
  Computational identification of candidate loci for recessively inherited mutation using high throughput SNP arrays
  Bioinformatics 2007 Aug 1;23(15):1952-61.
  [pdf] [download]


• Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM.
  Multiple reaction monitoring for robust quantitative analysis of cellular signaling networks
  Proc Natl Acad Sci U S A 2007 Apr;104(14):5860-65.
  [pdf]


• Kharait S, Hautaniemi S, Wu S, Iwabu A, Lauffenburger DA, Wells A.
  Decision tree analysis predicts quantitative effects of contractility signaling on cell motility
  BMC Systems Biology 2007 Jan;1:9.
  [pdf]

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.
  [pdf]


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

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


• 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.
  [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.
  [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.
  [pdf]


• 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.
  [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.
  [pdf] [supplementary page]
  


• 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.
  NMD microarray analysis reveals mutations of the EphB2 gene in human prostate cancer
  Nature Genetics 2004 Sep;36(9):979-983.
  [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 on gene expression
  Neoplasia 2004 May-Jun;6(3):240-247.
  [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.
  [pdf] [supplementary page]
  


• 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.
  [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 non-amplified breast cancer cell lines
  Oncogene 2004 Jan;23(4):1010-1013.
  [pdf]
  


• 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.
  [pdf] [supplementary page]
  


• 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.
  [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.
  [pdf] [supplementary page]
  


• 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.
  [pdf]
  


• 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.
  [pdf]
  


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