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Publications 2003 2019

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2019

Exome and immune cell score analyses reveal great variation within synchronous primary colorectal cancers

Hanninen, U. A., Wirta, E-V., Katainen, R., Tanskanen, T., Hamberg, J., Taipale, M., Böhm, J., Renkonen-Sinisalo, L., Lepistö, A., Forsström, L. M., Pitkänen, E., Palin, K., Seppälä, T. T., Mäkinen, N., Mecklin, J-P. & Aaltonen, L. A., 30 Apr 2019, In : British Journal of Cancer. 120, 9, p. 922-930 9 p.

Research output: Contribution to journalArticleScientificpeer-review

2018

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 othersRenkonen-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

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Contribution of allelic imbalance to colorectal cancer

Palin, K., Pitkänen, E., Turunen, M., Sahu, B., Pihlajamaa, P., Kivioja, T., Kaasinen, E., Välimäki, N., Hänninen, U. A., Cajuso, T., Aavikko, M., Tuupanen, S., Kilpivaara, O., van den Berg, L., Kondelin, J., Tanskanen, T., Katainen, R., Grau, M., Rauanheimo, H., Plaketti, R-M. & 20 othersTaira, A., Sulo, P., Hartonen, T., Dave, K., Schmierer, B., Botla, S., Sokolova, M., Vähärautio, A., Gladysz, K., Ongen, H., Dermitzakis, E., Bramsen, J. B., Orntoft, T. F., Andersen, C. L., Ristimäki, A., Lepistö, A., Renkonen-Sinisalo, L., Mecklin, J-P., Taipale, J. & Aaltonen, L. A., 10 Sep 2018, In : Nature Communications. 9, 9 p., 3664.

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Exome-wide somatic mutation characterization of small bowel adenocarcinoma

Hänninen, U. A., Katainen, R., Tanskanen, T., Plaketti, R-M., Laine, R., Hamberg, J., Ristimäki, A., Pukkala, E., Taipale, M., Mecklin, J-P., Forsström, L. M., Pitkänen, E., Palin, K., Välimäki, N., Mäkinen, N. & Aaltonen, L. A., Mar 2018, In : PLoS Genetics. 14, 3, 23 p., 1007200.

Research output: Contribution to journalArticleScientificpeer-review

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2017

Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Kondelin, J., Gylfe, A. E., Lundgren, S., Tanskanen, T., Hamberg, J., Aavikko, M., Palin, K., Ristolainen, H., Katainen, R., Kaasinen, E., Taipale, M., Taipale, J., Renkonen-Sinisalo, L., Jarvinen, H., Bohm, J., Mecklin, J-P., Vahteristo, P., Tuupanen, S., Aaltonen, L. A. & Pitkanen, E., 1 Aug 2017, In : Cancer Research. 77, 15, p. 4078-4088 11 p.

Research output: Contribution to journalArticleScientificpeer-review

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Global metabolomic profiling of uterine leiomyomas

Heinonen, H-R., Mehine, M., Mäkinen, N., Pasanen, A., Pitkänen, E., Karhu, A., Sarvilinna, N. S., Sjöberg, J., Heikinheimo, O., Bützow, R., Aaltonen, L. A. & Kaasinen, E., 5 Dec 2017, In : British Journal of Cancer. 117, 12, p. 1855-1864 10 p.

Research output: Contribution to journalArticleScientificpeer-review

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Multiple clinical characteristics separate MED12-mutation-positive and -negative uterine leiomyomas

Heinonen, H-R., Pasanen, A., Heikinheimo, O., Tanskanen, T., Palin, K., Tolvanen, J., Vahteristo, P., Sjoberg, J., Pitkänen, E., Butzow, R., Makinen, N. & Aaltonen, L. A., 21 Apr 2017, In : Scientific Reports. 7, 7 p., 1015.

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Somatic MED12 Nonsense Mutation Escapes mRNA Decay and Reveals a Motif Required for Nuclear Entry

Heikkinen, T., Kämpjärvi, K., Keskitalo, S., von Nandelstadh, P., Liu, X., Rantanen, V., Pitkänen, E., Kinnunen, M., Kuusanmäki, H., Kontro, M., Turunen, M., Mäkinen, N., Taipale, J., Heckman, C., Lehti, K., Mustjoki, S., Varjosalo, M. & Vahteristo, P., Mar 2017, In : Human Mutation. 38, 3, p. 269-274 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Whole-exome sequencing identifies novel candidate predisposition genes for familial polycythemia vera

Hirvonen, E. A. M., Pitkanen, E., Hemminki, K., Aaltonen, L. A. & Kilpivaara, O., 20 Apr 2017, In : Human Genomics. 11, 6 p., 6.

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2016
Open Access

MED12 mutations and FH inactivation are mutually exclusive in uterine leiomyomas

Kampjarvi, K., Makinen, N., Mehine, M., Valipakka, S., Uimari, O., Pitkanen, E., Heinonen, H-R., Heikkinen, T., Tolvanen, J., Ahtikoski, A., Frizzell, N., Sarvilinna, N., Sjoberg, J., Butzow, R., Aaltonen, L. A. & Vahteristo, P., 14 Jun 2016, In : British Journal of Cancer. 114, 12, p. 1405-1411 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Castillo, S., Barth, D., Arvas, M., Pakula, T. M., Pitkänen, E., Blomberg, P., Seppanen-Laakso, T., Nygren, H., Sivasiddarthan, D., Penttila, M. & Oja, M., 21 Nov 2016, In : Biotechnology for Biofuels. 9, 20 p., 252.

Research output: Contribution to journalArticleScientificpeer-review

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2015

3 '-UTR poly(T/U) repeat of EWSR1 is altered in microsatellite unstable colorectal cancer with nearly perfect sensitivity

Kondelin, J., Tuupanen, S., Gylfe, A. E., Aavikko, M., Renkonen-Sinisalo, L., Järvinen, H., Bohm, J., Mecklin, J-P., Andersen, C. L., Vahteristo, P., Pitkanen, E. & Aaltonen, L. A., Sep 2015, In : Familial Cancer. 14, 3, p. 449-453 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Clonally related uterine leiomyomas are common and display branched tumor evolution

Mehine, M., Heinonen, H-R., Sarvilinna, N., Pitkanen, E., Makinen, N., Katainen, R., Tuupanen, S., Butzow, R., Sjoberg, J. & Aaltonen, L. A., 1 Aug 2015, In : Human Molecular Genetics. 24, 15, p. 4407-4416 10 p.

Research output: Contribution to journalArticleScientificpeer-review

CTCF/cohesin-binding sites are frequently mutated in cancer

Katainen, R., Dave, K., Pitkänen, E., Palin, K., Kivioja, T., Valimaki, N., Gylfe, A. E., Ristolainen, H., Hanninen, U. A., Cajuso, T., Kondelin, J., Tanskanen, T., Mecklin, J-P., Järvinen, H., Renkonen-Sinisalo, L., Lepisto, A., Kaasinen, E., Kilpivaara, O., Tuupanen, S., Enge, M. & 2 othersTaipale, J. & Aaltonen, L. A., 1 Jul 2015, In : Nature Genetics. 47, 7, p. 818-+

Research output: Contribution to journalArticleScientificpeer-review

Service Outsourcing with Process Views

Eshuis, R., Norta, A., Kopp, O. & Pitkanen, E., 2015, In : IEEE Transactions on Services Computing. 8, 1, p. 136-154 19 p.

Research output: Contribution to journalArticleScientificpeer-review

Systematic search for rare variants in Finnish early-onset colorectal cancer patients

Tanskanen, T., Gylfe, A. E., Katainen, R., Taipale, M., Renkonen-Sinisalo, L., Järvinen, H., Mecklin, J-P., Bohm, J., Kilpivaara, O., Pitkanen, E., Palin, K., Vahteristo, P., Tuupanen, S. & Aaltonen, L. A., 2015, In : Cancer Genetics. 208, 1-2, p. 35-U100 7 p.

Research output: Contribution to journalArticleScientificpeer-review

2014

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. & Arvas, M., Feb 2014, In : PLoS Computational Biology. 10, 2, p. e1003465 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer

Cajuso Pons, T., Hänninen, U. A., Kondelin, J., Gylfe, A. E., Tanskanen, T., Katainen, R., Pitkanen, E., Ristolainen, H., Kaasinen, E., Taipale, M., Taipale, J., Bohm, J., Renkonen-Sinisalo, L., Mecklin, J-P., Jarvinen, H., Tuupanen, S., Kilpivaara, O. & Vahteristo, P., 1 Aug 2014, In : International Journal of Cancer. 135, 3, p. 611-623 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer

Pitkanen, E., Cajuso Pons, T., Katainen, R., Kaasinen, E., Valimaki, N., Palin, K., Taipale, J., Aaltonen, L. A. & Kilpivaara, O., 2014, In : Oncotarget. 5, 3, p. 853-859 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Identification of 33 candidate oncogenes by screening for base-specific mutations

Tuupanen, S., Hanninen, U. A., Kondelin, J., von Nandelstadh, P., Cajuso, T., Gylfe, A. E., Katainen, R., Tanskanen, T., Ristolainen, H., Bohm, J., Mecklin, J-P., Järvinen, H., Renkonen-Sinisalo, L., Andersen, C. L., Taipale, M., Taipale, J., Vahteristo, P., Lehti, K., Pitkanen, E. & Aaltonen, L. A., 14 Oct 2014, In : British Journal of Cancer. 111, 8, p. 1657-1662 6 p.

Research output: Contribution to journalArticleScientificpeer-review

MED12 mutation frequency in unselected sporadic uterine leiomyomas

Heinonen, H-R., Sarvilinna, N. S., Sjoberg, J., Kampjarvi, K., Pitkanen, E., Vahteristo, P., Makinen, N. & Aaltonen, L. A., Oct 2014, In : Fertility and Sterility : official journal of the American Fertility Society . 102, 4, p. 1137-1142 6 p.

Research output: Contribution to journalArticleScientificpeer-review

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Valimaki, N., Paulin, L., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E. A., Ferguson, L. C., Luo, S., Cao, Z., de Jong, M. A., Duplouy, A., Smolander, O-P., Vogel, H., McCoy, R. C. & 27 othersQian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J. K., Joshi, A., Salojarvi, J., Wheat, C. W., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkanen, E., Ylinen, J., Waterhouse, R. M., Turunen, M., Vaharautio, A., Ojanen, S. P., Schulman, A. H., Taipale, M., Lawson, D., Ukkonen, E., Makinen, V., Goldsmith, M. R., Holm, L., Auvinen, P., Frilander, M. J. & Hanski, I., Sep 2014, In : Nature Communications. 5, 9 p., 4737.

Research output: Contribution to journalArticleScientificpeer-review

2013

Characterization of Uterine Leiomyomas by Whole-Genome Sequencing

Mehine, M., Kaasinen, E., Mäkinen, N., Katainen, R., Kämpjärvi, K., Pitkänen, E., Heinonen, H-R., Butzow, R., Kilpivaara, O., Kuosmanen, A., Ristolainen, H., Gentile, M., Sjöberg, J., Vahteristo, P. & Aaltonen, L. A., 4 Jul 2013, In : New England Journal of Medicine. 369, 1, p. 43-53 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer

Gylfe, A. E., Katainen, R., Kondelin, J., Tanskanen, T., Cajuso Pons, T., Hänninen, U., Taipale, J., Taipale, M., Renkonen-Sinisalo, L., Järvinen, H., Mecklin, J-P., Kilpivaara, O., Pitkänen, E., Vahteristo, P., Tuupanen, S., Karhu, A. & Aaltonen, L. A., 18 Oct 2013, In : PLoS Genetics. 9, 10, 8 p., e1003876.

Research output: Contribution to journalArticleScientificpeer-review

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Identification of Candidate Oncogenes in Human Colorectal Cancers With Microsatellite Instability

Gylfe, A. E., 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., Bohm, J., Mecklin, J-P., Ristimäki, A., Kilpivaara, O. & 4 othersTuupanen, S., Karhu, A., Vahteristo, P. & Aaltonen, L. A., Sep 2013, In : Gastroenterology. 145, 3, p. 540-+ 26 p.

Research output: Contribution to journalArticleScientificpeer-review

Nationwide Registry-Based Analysis of Cancer Clustering Detects Strong Familial Occurrence of Kaposi Sarcoma

Kaasinen, E., Aavikko, M., Vahteristo, P., Patama, T., Li, Y., Saarinen, S., Kilpivaara, O., Pitkänen, E., Knekt, P., Laaksonen, M., Lehtonen, R., Artama, M., Aaltonen, L. A. & Pukkala, E., 24 Jan 2013, In : PLoS One. 8, 1, p. Article Number: e55209 7 p.

Research output: Contribution to journalArticleScientificpeer-review

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2010

Computational methods for metabolic reconstruction

Pitkänen, E., Rousu, J. & Ukkonen, E., 2010, In : Current Opinion in Biotechnology. 21, 1, p. 70-77 8 p.

Research output: Contribution to journalArticleScientificpeer-review

2009

13C-metabolic flux ratio and carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose

Jouhten, P., Pitkänen, E., Pakula, T., Saloheimo, M., Penttilä, M. & Maaheimo, H., 2009, In : BMC Systems Biology. 3, 104, 16 s

Research output: Contribution to journalArticleScientificpeer-review

C-13-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose

Jouhten, P., Pitkanen, E., Pakula, T., Saloheimo, M., Penttila, M. & Maaheimo, H., 29 Oct 2009, In : BMC Systems Biology. 3, 16 p., 104.

Research output: Contribution to journalArticleScientificpeer-review

Inferring branching pathways in genome-scale metabolic networks

Pitkänen, E., Jouhten, P. & Rousu, J., 29 Oct 2009, In : BMC Systems Biology. 3, 22 p., 103.

Research output: Contribution to journalArticleScientificpeer-review

2008

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis

Pitkänen, E., Åkerlund, A., Rantanen, A., Jouhten, P. & Ukkonen, E., 2008, In : Journal of Integrative Bioinformatics : JIB. 5, 102, 13 s

Research output: Contribution to journalArticleScientificpeer-review

Towards structured output prediction of enzyme function

Astikainen, K., Holm, L., Pitkänen, E., Szedmak, S. & Rousu, J., 2008, In : BMC proceedings. 2(Suppl 4), S2, 10 s

Research output: Contribution to journalArticleScientificpeer-review