• PL 20 (Tukholmankatu 8)

    00014

    Finland

20032019
If you made any changes in Pure these will be visible here soon.

Publications 2003 2019

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

Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival

Cajuso, T., Sulo, P., Tanskanen, T., Katainen, R., Taira, A., Hanninen, U. A., Kondelin, J., Forsstrom, L., Valimaki, N., Aavikko, M., Kaasinen, E., Ristimaki, A., Koskensalo, S., Lepisto, A., Renkonen-Sinisalo, L., Seppala, T., Kuopio, T., Bohm, J., Mecklin, J-P., Kilpivaara, O. & 3 othersPitkanen, E., Palin, K. & Aaltonen, L. A., 6 Sep 2019, In : Nature Communications. 10, 9 p., 4022.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
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

Open Access
File

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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

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

Open Access
File
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

Open Access
File
Open Access
File

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

Open Access
File
Open Access

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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
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

Open Access
File
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

Open Access
File

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

Open Access
File

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

Open Access
File
2011

Minimum mutation algorithm for gapless metabolic network evolution

Pitkänen, E., Arvas, M. & Rousu, J., 2011, Bioinformatics 2011: International Conference of Bioinformatics Models, Methods and Algorithms. Insticc Press

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels

Astikainen, K., Holm, L., Pitkänen, E., Szedmak, S. & Rousu, J., 28 Feb 2011, Biomedical Engineering Systems and Technologies: Third International Joint Conference, BIOSTEC 2010, Valencia, Spain, January 20-23, 2010, Revised Selected Papers. Fred, A., Filipe, J. & Gamboa, H. (eds.). Springer, p. 367-379 13 p. (Communications of Computer and Information Science; vol. 127).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

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

Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks

Pitkänen, E., 2010, Helsinki: Yliopistopaino. 204 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Reaction Kernels: Structured Output Prediction Approaches for Novel Enzyme Function

Astikainen, K., Pitkänen, E., Rousu, J., Holm, L. & Szedmak, S., 20 Jan 2010, Proceedings of the First International Conference on Bioinformatics. Fred, A., Filipe, J. & Gamboa, H. (eds.). The Institute for Systems and Technologies of Information, Control and Communication, p. 48-55

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-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

Reaction kernels: predicting enzyme functions you have never seen before

Astikainen, K., Holm, L. U. T., Pitkänen, E. & Rousu, J., 2009, Helsinki: Helsingin yliopisto, tietojenkäsittelytieteen laitos. 13 p.

Research output: Book/ReportBookScientificpeer-review

2008

A computational method for reconstructing gapless metabolic networks

Pitkänen, E., Rantanen, A., Rousu, J. & Ukkonen, E., 2008, Bioinformatics Research and Development: proceedings. p. 288-302 15 p. (Communications in computer and information science; vol. 13).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

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

2007

Towards structured output prediction of enzyme function (extended abstract)

Astikainen, K., Holm, L., Pitkänen, E., Szedmak, S. & Rousu, J., 2007, Proceedings of the International Workshop on Machine Learning in Systems Biology 2007, MLSB'07, September 24-25, 2007, Evry, France: Universite d'Evry-Val d'Essonne 2007. p. 27-32 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2006

Ab initio prediction of molecular fragments from tandem mass spectrometry data

Heinonen, M., Rantanen, A., Mielikäinen, T., Pitkänen, E., Kokkonen, J. & Rousu, J., 2006, German Conference on Bioinformatics, GCB 2006, Tubingen, Germany, September 19-22, 2006. p. 40-53 14 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation

Rantanen, A., Maaheimo, H., Pitkänen, E., Rousu, J. & Ukkonen, E., 2006, Transactions on computational systems biology VI. Berlin: Springer, p. 198-220 23 p. ( LECTURE NOTES IN COMPUTER SCIENCE; vol. 4220).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Pathway assistant: a web portal for metabolic modelling

Parikka, P., Pitkänen, E., Rantanen, A., Åkerlund, A. & Ukkonen, E., 2006, NETTAB 2006: Sixth International Workshop on Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics, July, 10th-13th, 2006, Santa Margherita di Pula, Cagliari, Italy : 2006. p. 90-96 7 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2005

Finding feasible pathways in metabolic networks

Pitkänen, E., Rantanen, A., Rousu, J. H. & Ukkonen, E., 2005, Proceedings of the Panhellenic Conference on Informatics. Springer-Verlag, p. 123-133 11 p. (Lecture Notes in Computer Science; vol. 3746).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Flow analysis of metabolite fragments for flux estimation

Rantanen, A., Rousu, J., Pitkänen, E., Maaheimo, H. & Ukkonen, E., 2005, Third international workshop on computational methods in systems biology: 2005. p. 242-255 14 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review