Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. 2019
  2. Published

    L1000 viewer: A search engine and Web interface for the LINCS data repository

    Musa, A., Tripathi, S., Dehmer, M. & Emmert-Streib, F., 2019, In : Frontiers in Genetics. 10, JUN, 557.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Published

    Prostate cancer gene regulatory network inferred from RNA-seq data

    Moore, D., Simoes, R. D. M., Dehmer, M. & Emmert-Streib, F., 2019, In : CURRENT GENOMICS. 20, 1, p. 38-48 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. 2018
  5. Published

    In a quest for engineering acidophiles for biomining applications: Challenges and opportunities

    Gumulya, Y., Boxall, N. J., Khaleque, H. N., Santala, V., Carlson, R. P. & Kaksonen, A. H., 21 Feb 2018, In : Genes. 9, 2, 116.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  6. 2017
  7. Published

    Lessons from the human genome project: Modesty, honesty, and realism

    Emmert-Streib, F., Dehmer, M. & Yli-Harja, O., 23 Nov 2017, In : Frontiers in Genetics. 8, NOV, 184.

    Research output: Contribution to journalComment/debateScientificpeer-review

  8. 2016
  9. Published

    Against dataism and for data sharing of big biomedical and clinical data with research parasites

    Emmert-Streib, F., Dehmer, M. & Yli-Harja, O., 31 Aug 2016, In : Frontiers in Genetics. 7, AUG, 154.

    Research output: Contribution to journalComment/debateScientificpeer-review

  10. Published

    The need for formally defining "modern medicine" by means of experimental design

    Emmert-Streib, F., Tuomisto, L. & Yli-Harja, O., 20 Apr 2016, In : Frontiers in Genetics. 7, APR, 60.

    Research output: Contribution to journalArticleScientificpeer-review

  11. 2015
  12. Published

    Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

    Al Olama, A. A., Dadaev, T., Hazelett, D. J., Li, Q., Leongamornlert, D., Saunders, E. J., Stephens, S., Cieza-Borrella, C., Whitmore, I., Garcia, S. B., Giles, G. G., Southey, M. C., Fitzgerald, L., Gronberg, H., Wiklund, F., Aly, M., Henderson, B. E., Schumacher, F., Haiman, C. A., Schleutker, J., Wahlfors, T., Tammela, T. L., Nordestgaard, B. G., Key, T. J., Travis, R. C., Neal, D. E., Donovan, J. L., Hamdy, F. C., Pharoah, P., Pashayan, N., Khaw, K. T., Stanford, J. L., Thibodeau, S. N., Mcdonnell, S. K., Schaid, D. J., Maier, C., Vogel, W., Luedeke, M., Herkommer, K., Kibel, A. S., Cybulski, C., Wokolorczyk, D., Kluzniak, W., Cannon-Albright, L., Brenner, H., Butterbach, K., Arndt, V., Park, J. Y., Sellers, T., Lin, H. Y., Slavov, C., Kaneva, R., Mitev, V., Batra, J., Clements, J. A., Spurdle, A., Teixeira, M. R., Paulo, P., Maia, S., Pandha, H., Michael, A., Kierzek, A., Govindasami, K., Guy, M., Lophatonanon, A., Muir, K., Viñuela, A., Brown, A. A., Freedman, M., Conti, D. V., Easton, D., Coetzee, G. A., Eeles, R. A. & Kote-Jarai, Z., 1 Oct 2015, In : HUMAN MOLECULAR GENETICS. 24, 19, p. 5589-5602 14 p., ddv203.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Published

    A genome-wide expression quantitative trait loci analysis of proprotein convertase subtilisin/kexin enzymes identifies a novel regulatory gene variant for FURIN expression and blood pressure

    Turpeinen, H., Seppälä, I., Lyytikäinen, L. P., Raitoharju, E., Hutri-Kähönen, N., Levula, M., Oksala, N., Waldenberger, M., Klopp, N., Illig, T., Mononen, N., Laaksonen, R., Raitakari, O., Kähönen, M., Lehtimäki, T. & Pesu, M., 1 Jun 2015, In : HUMAN GENETICS. 134, 6, p. 627-636 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  14. 2014
  15. Published

    Association analysis of 9,560 prostate cancer cases from the International Consortium of Prostate Cancer Genetics confirms the role of reported prostate cancer associated SNPs for familial disease

    Teerlink, C. C., Thibodeau, S. N., McDonnell, S. K., Schaid, D. J., Rinckleb, A., Maier, C., Vogel, W., Cancel-Tassin, G., Egrot, C., Cussenot, O., Foulkes, W. D., Giles, G. G., Hopper, J. L., Severi, G., Eeles, R., Easton, D., Kote-Jarai, Z., Guy, M., Cooney, K. A., Ray, A. M., Zuhlke, K. A., Lange, E. M., Fitzgerald, L. M., Stanford, J. L., Ostrander, E. A., Wiley, K. E., Isaacs, S. D., Walsh, P. C., Isaacs, W. B., Wahlfors, T., Tammela, T., Schleutker, J., Wiklund, F., Grönberg, H., Emanuelsson, M., Carpten, J., Bailey-Wilson, J., Whittemore, A. S., Oakley-Girvan, I., Hsieh, C. L., Catalona, W. J., Zheng, S. L., Jin, G., Lu, L., Xu, J., Camp, N. J. & Cannon-Albright, L. A., Mar 2014, In : HUMAN GENETICS. 133, 3, p. 347-356 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  16. Published

    A Novel MMP12 Locus Is Associated with Large Artery Atherosclerotic Stroke Using a Genome-Wide Age-at-Onset Informed Approach

    Traylor, M., Mäkelä, K. M., Kilarski, L. L., Holliday, E. G., Devan, W. J., Nalls, M. A., Wiggins, K. L., Zhao, W., Cheng, Y. C., Achterberg, S., Malik, R., Sudlow, C., Bevan, S., Raitoharju, E., Oksala, N., Thijs, V., Lemmens, R., Lindgren, A., Slowik, A., Maguire, J. M., Walters, M., Algra, A., Sharma, P., Attia, J. R., Boncoraglio, G. B., Rothwell, P. M., de Bakker, P. I. W., Bis, J. C., Saleheen, D., Kittner, S. J., Mitchell, B. D., Rosand, J., Meschia, J. F., Levi, C., Dichgans, M., Lehtimäki, T., Lewis, C. M. & Markus, H. S., 2014, In : PLOS GENETICS. 10, 7, e1004469.

    Research output: Contribution to journalArticleScientificpeer-review

  17. Enhancing our understanding of ways to analyze metagenomes

    Emmert-Streib, F., 2014, In : Frontiers in Genetics. 5, APR, Article 108.

    Research output: Contribution to journalArticleScientificpeer-review

  18. Published

    Relevance of different prior knowledge sources for inferring gene interaction networks

    Olsen, C., Bontempi, G., Emmert-Streib, F., Quackenbush, J. & Haibe-Kains, B., 2014, In : Frontiers in Genetics. 5, JUN, Article 177.

    Research output: Contribution to journalArticleScientificpeer-review

  19. Published

    The gene regulatory network for breast cancer: Integrated regulatory landscape of cancer hallmarks

    Emmert-Streib, F., Simoes, R. D. M., Mullan, P., Haibe-Kains, B. & Dehmer, M., 2014, In : Frontiers in Genetics. 5, FEB, Article 15.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    Untangling statistical and biological models to understand network inference: The need for a genomics network ontology

    Emmert-Streib, F., Dehmer, M. & Haibe-Kains, B., 2014, In : Frontiers in Genetics. 5, AUG, article 229.

    Research output: Contribution to journalArticleScientificpeer-review

  21. 2013
  22. Published

    Association of neuroimmune guidance cue netrin-1 and its chemorepulsive receptor UNC5B with atherosclerotic plaque expression signatures and stability in human(s) Tampere Vascular Study (TVS)

    Oksala, N., Pärssinen, J., Seppälä, I., Raitoharju, E., Ivana, K., Hernesniemi, J., Lyytikäinen, L. P., Levula, M., Mäkelä, K. M., Sioris, T., Kähönen, M., Laaksonen, R., Hytönen, V. & Lehtimäki, T., Dec 2013, In : Circulation: Cardiovascular Genetics. 6, 6, p. 579-587 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. Published

    Genome-wide association study identifies 3 genomic loci significantly associated with serum levels of homoarginine: The atheroremo consortium

    Kleber, M. E., Seppälä, I., Pilz, S., Hoffmann, M. M., Tomaschitz, A., Oksala, N., Raitoharju, E., Lyytikäinen, L. P., Mäkelä, K. M., Laaksonen, R., Kähönen, M., Raitakari, O. T., Huang, J., Kienreich, K., Fahrleitner-Pammer, A., Drechsler, C., Krane, V., Boehm, B. O., Koenig, W., Wanner, C., Lehtimäki, T., März, W. & Meinitzer, A., Oct 2013, In : Circulation: Cardiovascular Genetics. 6, 5, p. 505-513 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  24. Published

    Somatic alterations contributing to metastasis of a castration-resistant prostate cancer

    Nickerson, M. L., Im, K. M., Misner, K. J., Tan, W., Lou, H., Gold, B., Wells, D. W., Bravo, H. C., Fredrikson, K. M., Harkins, T. T., Milos, P., Zbar, B., Linehan, W. M., Yeager, M., Andresson, T., Dean, M. & Bova, G. S., Sep 2013, In : HUMAN MUTATION. 34, 9, p. 1231-1241 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    Genetic heterogeneity in Finnish hereditary prostate cancer using ordered subset analysis

    Simpson, C. L., Cropp, C. D., Wahlfors, T., George, A., Jones, M. S., Harper, U., Ponciano-Jackson, D., Tammela, T., Schleutker, J. & Bailey-Wilson, J. E., Apr 2013, In : EUROPEAN JOURNAL OF HUMAN GENETICS. 21, 4, p. 437-443 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  26. Published

    A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease

    Al Olama, A. A., Kote-Jarai, Z., Schumacher, F. R., Wiklund, F., Berndt, S. I., Benlloch, S., Giles, G. G., Severi, G., Neal, D. E., Hamdy, F. C., Donovan, J. L., Hunter, D. J., Henderson, B. E., Thun, M. J., Gaziano, M., Giovannucci, E. L., Siddiq, A., Travis, R. C., Cox, D. G., Canzian, F., Riboli, E., Key, T. J., Andriole, G., Albanes, D., Hayes, R. B., Schleutker, J., Auvinen, A., Tammela, T. L. J., Weischer, M., Stanford, J. L., Ostrander, E. A., Cybulski, C., Lubinski, J., Thibodeau, S. N., Schaid, D. J., Sorensen, K. D., Batra, J., Clements, J. A., Chambers, S., Aitken, J., Gardiner, R. A., Maier, C., Vogel, W., Dörk, T., Brenner, H., Habuchi, T., Ingles, S., John, E. M., Dickinson, J. L., Cannon-Albright, L., Teixeira, M. R., Kaneva, R., Zhang, H. W., Lu, Y. J., Park, J. Y., Cooney, K. A., Muir, K. R., Leongamornlert, D. A., Saunders, E., Tymrakiewicz, M., Mahmud, N., Guy, M., Govindasami, K., O'Brien, L. T., Wilkinson, R. A., Hall, A. L., Sawyer, E. J., Dadaev, T., Morrison, J., Dearnaley, D. P., Horwich, A., Huddart, R. A., Khoo, V. S., Parker, C. C., Van As, N., Woodhouse, C. J., Thompson, A., Dudderidge, T., Ogden, C., Cooper, C. S., Lophatonanon, A., Southey, M. C., Hopper, J. L., English, D., Virtamo, J., Marchand, L. L., Campa, D., Kaaks, R., Lindstrom, S., Diver, W. R., Gapstur, S., Yeager, M., Cox, A., Stern, M. C., Corral, R., Aly, M., Isaacs, W., Adolfsson, J., Xu, J., Zheng, S. L., Wahlfors, T., Taari, K., Kujala, P., Klarskov, P., Nordestgaard, B. G., Røder, M. A., Frikke-Schmidt, R., Bojesen, S. E., FitzGerald, L. M., Kolb, S., Kwon, E. M., Karyadi, D. M., Orntoft, T. F., Borre, M., Rinckleb, A., Luedeke, M., Herkommer, K., Meyer, A., Serth, J. R., Marthick, J. R., Patterson, B., Wokolorczyk, D., Spurdle, A., Lose, F., McDonnell, S. K., Joshi, A. D., Shahabi, A., Pinto, P., Santos, J., Ray, A., Sellers, T. A., Lin, H. Y., Stephenson, R. A., Teerlink, C., Muller, H., Rothenbacher, D., Tsuchiya, N., Narita, S., Cao, G. W., Slavov, C., Mitev, V., Chanock, S., Gronberg, H., Haiman, C. A., Kraft, P., Easton, D. F. & Eeles, R. A., Jan 2013, In : HUMAN MOLECULAR GENETICS. 22, 2, p. 408-415 8 p., dds425.

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

    HOXB13 is a susceptibility gene for prostate cancer: Results from the International Consortium for Prostate Cancer Genetics (ICPCG)

    Xu, J., Lange, E. M., Lu, L., Zheng, S. L., Wang, Z., Thibodeau, S. N., Cannon-Albright, L. A., Teerlink, C. C., Camp, N. J., Johnson, A. M., Zuhlke, K. A., Stanford, J. L., Ostrander, E. A., Wiley, K. E., Isaacs, S. D., Walsh, P. C., Maier, C., Luedeke, M., Vogel, W., Schleutker, J., Wahlfors, T., Tammela, T., Schaid, D., McDonnell, S. K., Derycke, M. S., Cancel-Tassin, G., Cussenot, O., Wiklund, F., Grönberg, H., Eeles, R., Easton, D., Kote-Jarai, Z., Whittemore, A. S., Hsieh, C. L., Giles, G. G., Hopper, J. L., Severi, G., Catalona, W. J., Mandal, D., Ledet, E., Foulkes, W. D., Hamel, N., Mahle, L., Moller, P., Powell, I., Bailey-Wilson, J. E., Carpten, J. D., Seminara, D., Cooney, K. A. & Isaacs, W. B., Jan 2013, In : HUMAN GENETICS. 132, 1, p. 5-14 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    B-cell lymphoma gene regulatory networks: Biological consistency among inference methods

    Simoes, R. D. M., Dehmer, M. & Emmert-Streib, F., 2013, In : Frontiers in Genetics. 4, DEC, 00281.

    Research output: Contribution to journalArticleScientificpeer-review

  29. Personalized medicine: Has it started yet? A reconstruction of the early history

    Emmert-Streib, F., 2013, In : Frontiers in Genetics. 3, JAN, Article 313.

    Research output: Contribution to journalArticleScientificpeer-review

  30. 2012
  31. Published

    Loss of SUFU function in familial multiple meningioma

    Aavikko, M., Li, S. P., Saarinen, S., Alhopuro, P., Kaasinen, E., Morgunova, E., Li, Y., Vesanen, K., Smith, M. J., Evans, D. G. R., Pöyhönen, M., Kiuru, A., Auvinen, A., Aaltonen, L. A., Taipale, J. & Vahteristo, P., 7 Sep 2012, In : AMERICAN JOURNAL OF HUMAN GENETICS. 91, 3, p. 520-526 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis

    Inouye, M., Ripatti, S., Kettunen, J., Lyytikäinen, L. P., Oksala, N., Laurila, P. P., Kangas, A. J., Soininen, P., Savolainen, M. J., Viikari, J., Kähönen, M., Perola, M., Salomaa, V., Raitakari, O., Lehtimäki, T., Taskinen, M. R., Järvelin, M. R., Ala-Korpela, M., Palotie, A. & de Bakker, P. I. W., Aug 2012, In : PLOS GENETICS. 8, 8, e1002907.

    Research output: Contribution to journalArticleScientificpeer-review

  33. Published

    Validation of prostate cancer risk-related loci identified from genome-wide association studies using family-based association analysis: Evidence from the International Consortium for Prostate Cancer Genetics (ICPCG)

    Jin, G., Lu, L., Cooney, K. A., Ray, A. M., Zuhlke, K. A., Lange, E. M., Cannon-Albright, L. A., Camp, N. J., Teerlink, C. C., Fitzgerald, L. M., Stanford, J. L., Wiley, K. E., Isaacs, S. D., Walsh, P. C., Foulkes, W. D., Giles, G. G., Hopper, J. L., Severi, G., Eeles, R., Easton, D., Kote-Jarai, Z., Guy, M., Rinckleb, A., Maier, C., Vogel, W., Cancel-Tassin, G., Egrot, C., Cussenot, O., Thibodeau, S. N., McDonnell, S. K., Schaid, D. J., Wiklund, F., Grönberg, H., Emanuelsson, M., Whittemore, A. S., Oakley-Girvan, I., Hsieh, C. L., Wahlfors, T., Tammela, T., Schleutker, J., Catalona, W. J., Zheng, S. L., Ostrander, E. A., Isaacs, W. B. & Xu, J., Jul 2012, In : HUMAN GENETICS. 131, 7, p. 1095-1103 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  34. Published

    Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families

    Bailey-Wilson, J. E., Childs, E. J., Cropp, C. D., Schaid, D. J., Xu, J., Camp, N. J., Cannon-Albright, L. A., Farnham, J. M., George, A., Powell, I., Carpten, J. D., Giles, G. G., Hopper, J. L., Severi, G., English, D. R., Foulkes, W. D., Mæhle, L., Møller, P., Eeles, R., Easton, D., Guy, M., Edwards, S., Badzioch, M. D., Whittemore, A. S., Oakley-Girvan, I., Hsieh, C. L., Dimitrov, L., Stanford, J. L., Karyadi, D. M., Deutsch, K., McIntosh, L., Ostrander, E. A., Wiley, K. E., Isaacs, S. D., Walsh, P. C., Thibodeau, S. N., McDonnell, S. K., Hebbring, S., Lange, E. M., Cooney, K. A., Tammela, T. L. J., Schleutker, J., Maier, C., Bochum, S., Hoegel, J., Grönberg, H., Wiklund, F., Emanuelsson, M., Cancel-Tassin, G., Valeri, A., Cussenot, O. & Isaacs, W. B., 19 Jun 2012, In : BMC MEDICAL GENETICS. 13, 46.

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

    Baculovirus-mediated vascular endothelial growth factor-DΔNΔC gene transfer induces angiogenesis in rabbit skeletal muscle

    Heikura, T., Nieminen, T., Roschier, M. M., Karvinen, H., Kaikkonen, M. U., Mähönen, A. J., Lesch, H. P., Rissanen, T. T., Laitinen, O. H., Airenne, K. J. & Ylä-Herttuala, S., Jan 2012, In : JOURNAL OF GENE MEDICINE. 14, 1, p. 35-43 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  36. Published

    Statistical inference and reverse engineering of gene regulatory networks from observational expression data

    Emmert-Streib, F., Glazko, G. V., Altay, G. & Simoes, R. D. M., 2012, In : Frontiers in Genetics. 3, FEB, Article 8.

    Research output: Contribution to journalArticleScientificpeer-review

  37. 2011
  38. Published

    Ras regulates interleukin-1β-induced HIF-1α transcriptional activity in glioblastoma

    Sharma, V., Dixit, D., Koul, N., Mehta, V. S. & Sen, E., Feb 2011, In : JOURNAL OF MOLECULAR MEDICINE: JMM. 89, 2, p. 123-136 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  39. 2000
  40. Mutation spectra of the drinking water mutagen 3-chloro-4-methyl-5- hydroxy-2(5H)-furanone (MCF) in Salmonella TA100 and TA104: Comparison to MX

    Shaughnessy, D. T., Ohe, T., Landi, S., Warren, S. H., Richard, A. M., Munter, T., Franzén, R., Kronberg, L. & DeMarini, D. M., 2000, In : Environmental and Molecular Mutagenesis. 35, 2, p. 106-113 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  41. 1994
  42. Induction of genotoxic effects by chlorohydroxyfuranones, byproducts of water disinfection, in E. coli K-12 cells recovered from various organs of mice

    Fekadu, K., Parzefall, W., Kronberg, L., Franzen, R., Schulte-Hermann, R. & Knasmüller, S., 1994, In : Environmental and Molecular Mutagenesis. 24, 4, p. 317-324 8 p.

    Research output: Contribution to journalArticleScientificpeer-review