Biclustering methods: biological relevance and application in gene expression analysis von Oghabian, Ali, Kilpinen, Sami, Hautaniemi, Sampsa, Czeizler, Elena

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Range of chromatin accessibility configurations are permissive of GABAergic fate acquisition in developing mouse brain von Kilpinen, Sami, Heliölä, Heidi, Achim, Kaia

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LGI2 truncation causes a remitting focal epilepsy in dogs von Seppälä, Eija H, Jokinen, Tarja S, Fukata, Masaki, Fukata, Yuko, Webster, Matthew T, Karlsson, Elinor K, Kilpinen, Sami K, Steffen, Frank, Dietschi, Elisabeth, Leeb, Tosso, Eklund, Ranja, Zhao, Xiaochu, Rilstone, Jennifer J, Lindblad-Toh, Kerstin, Minassian, Berge A, Lohi, Hannes

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Transcriptomic analyses reveal three distinct molecular subgroups of Merkel cell carcinoma with differing prognoses von Sundqvist, Benjamin Z., Kilpinen, Sami K., Böhling, Tom O., Koljonen, Virve S. K., Sihto, Harri J.

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Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome von Kilpinen, Sami, Ojala, Kalle, Kallioniemi, Olli

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Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues von Kilpinen, Sami, Autio, Reija, Ojala, Kalle, Iljin, Kristiina, Bucher, Elmar, Sara, Henri, Pisto, Tommi, Saarela, Matti, Skotheim, Rolf I, Björkman, Mari, Mpindi, John-Patrick, Haapa-Paananen, Saija, Vainio, Paula, Edgren, Henrik, Wolf, Maija, Astola, Jaakko, Nees, Matthias, Hautaniemi, Sampsa, Kallioniemi, Olli

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Facilitates Chromatin Transcription Complex Is an “Accelerator” of Tumor Transformation and Potential Marker and Target of Aggressive Cancers von Garcia, Henry, Miecznikowski, Jeffrey C., Safina, Alfiya, Commane, Mairead, Ruusulehto, Anja, Kilpinen, Sami, Leach, Robert W., Attwood, Kristopher, Li, Yan, Degan, Seamus, Omilian, Angela R., Guryanova, Olga, Papantonopoulou, Olympia, Wang, Jianmin, Buck, Michael, Liu, Song, Morrison, Carl, Gurova, Katerina V.

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Application of Active and Kinase-Deficient Kinome Collection for Identification of Kinases Regulating Hedgehog Signaling von Varjosalo, Markku, Björklund, Mikael, Cheng, Fang, Syvänen, Heidi, Kivioja, Teemu, Kilpinen, Sami, Sun, Zairen, Kallioniemi, Olli, Stunnenberg, Hendrik G., He, Wei-Wu, Ojala, Päivi, Taipale, Jussi

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Extracellular membrane vesicles from umbilical cord blood-derived MSC protect against ischemic acute kidney injury, a feature that is lost after inflammatory conditioning von Kilpinen, Lotta, Impola, Ulla, Sankkila, Lotta, Ritamo, Ilja, Aatonen, Maria, Kilpinen, Sami, Tuimala, Jarno, Valmu, Leena, Levijoki, Jouko, Finckenberg, Piet, Siljander, Pia, Kankuri, Esko, Mervaala, Eero, Laitinen, Saara

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First Analysis of a Bacterial Collagen-Binding Protein with Collagen Toolkits: Promiscuous Binding of YadA to Collagens May Explain How YadA Interferes with Host Processes von Leo, Jack C, Elovaara, Heli, Bihan, Dominique, Pugh, Nicholas, Kilpinen, Sami K, Raynal, Nicolas, Skurnik, Mikael, Farndale, Richard W, Goldman, Adrian

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Fibroblast Growth Factor Receptor 4 Regulates Tumor Invasion by Coupling Fibroblast Growth Factor Signaling to Extracellular Matrix Degradation von SUGIYAMA, Nami, VARJOSALO, Markku, ALITALO, Kari, KESKI-OJA, Jorma, LEHTI, Kaisa, MELLER, Pipsa, LOHI, Jouko, HYYTIÄINEN, Marko, KILPINEN, Sami, KALLIONIEMI, Olli, INGVARSEN, Signe, ENGELHOLM, Lars H, TAIPALE, Jussi

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The transcription factor Sox11 is a prognostic factor for improved recurrence-free survival in epithelial ovarian cancer von Brennan, Donal J, Ek, Sara, Doyle, Emma, Drew, Thomas, Foley, Michael, Flannelly, Grainne, O’Connor, Darran P, Gallagher, William M, Kilpinen, Sami, Kallioniemi, Olli-Pekka, Jirstrom, Karin, O’Herlihy, Colm, Borrebaeck, Carl A.K

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Integrative Functional Genomics Analysis of Sustained Polyploidy Phenotypes in Breast Cancer Cells Identifies an Oncogenic Profile for GINS2 von Rantala, Juha K., Edgren, Henrik, Lehtinen, Laura, Wolf, Maija, Kleivi, Kristine, Vollan, Hans Kristian Moen, Aaltola, Anna-Riina, Laasola, Petra, Kilpinen, Sami, Saviranta, Petri, Iljin, Kristiina, Kallioniemi, Olli

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GTI: a novel algorithm for identifying outlier gene expression profiles from integrated microarray datasets von Mpindi, John Patrick, Sara, Henri, Haapa-Paananen, Saija, Kilpinen, Sami, Pisto, Tommi, Bucher, Elmar, Ojala, Kalle, Iljin, Kristiina, Vainio, Paula, Björkman, Mari, Gupta, Santosh, Kohonen, Pekka, Nees, Matthias, Kallioniemi, Olli

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Characterization of non-specific cytotoxic cell receptor protein 1: a new member of the lectin-type subfamily of F-box proteins von Kallio, Heini, Tolvanen, Martti, Jänis, Janne, Pan, Pei-wen, Laurila, Eeva, Kallioniemi, Anne, Kilpinen, Sami, Tuominen, Vilppu J, Isola, Jorma, Valjakka, Jarkko, Pastorekova, Silvia, Pastorek, Jaromir, Parkkila, Seppo

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Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implication von Wolf, Maija, Korja, Miikka, Karhu, Ritva, Edgren, Henrik, Kilpinen, Sami, Ojala, Kalle, Mousses, Spyro, Kallioniemi, Anne, Haapasalo, Hannu

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Classification of unknown primary tumors with a data-driven method based on a large microarray reference database von Ojala, Kalle A, Kilpinen, Sami K, Kallioniemi, Olli P

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Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data von Kilpinen, Sami K, Ojala, Kalle A, Kallioniemi, Olli P

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Correction: GTI: A Novel Algorithm for Identifying Outlier Gene Expression Profiles from Integrated Microarray Datasets von Mpindi, John Patrick, Sara, Henri, Haapa-Paananen, Saija, Kilpinen, Sami, Pisto, Tommi, Bucher, Elmar, Ojala, Kalle, Iljin, Kristiina, Vainio, Paula, Björkman, Mari, Gupta, Santosh, Kohonen, Pekka, Nees, Matthias, Kallioniemi, Olli

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IPDE3A/I Is a Highly Expressed Therapy Target in Myxoid Liposarcoma von Toivanen, Kirsi, Kilpinen, Sami, Ojala, Kalle, Merikoski, Nanna, Salmikangas, Sami, Sampo, Mika, Böhling, Tom, Sihto, Harri

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