Harri Lähdesmäki

Professor (Associate Professor)

Research outputs

  1. 2015
  2. Published
  3. Published

    Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex

    Balasubramani, A., Larjo, A., Chang, X., Hastie, R. B., Togher, S., Bassein, J. A., Lähdesmäki, H. & Rao, A., 2015, In : Nature Communications. 6, p. 1-15 7307.

    Research output: Contribution to journalArticle

  4. Published

    Epigenomic characterization of gene regulatory networks in human ovarian cancer stem cells

    Battle, S. L., Larjo, A., Liao, J., Lahdesmaki, H., Lieber, A. & Hawkins, R. D., 2015, p. S04.

    Research output: Working paperProfessional

  5. Published

    GIMAP GTPase Family Genes: Potential Modifiers in Autoimmune Diabetes, Asthma, and Allergy

    Heinonen, M. T., Laine, A-P., Soderhall, C., Gruzieva, O., Rautio, S., Melen, E., Pershagen, G., Lahdesmaki, H. J., Knip, M., Ilonen, J. & 3 others, Henttinen, T. A., Kere, J. & Lahesmaa, R., 2015, In : JOURNAL OF IMMUNOLOGY. 194, 12, p. 5885-5894

    Research output: Contribution to journalArticle

  6. Published

    Identification of global regulators of T-helper cell lineage specification

    Kanduri, K., Tripathi, S., Larjo, A., Mannerström, H., Ullah, U., Lund, R., Hawkins, D., Ren, B., Lähdesmäki, H. & Lahesmaa, R., 2015, In : GENOME MEDICINE. 7, 122

    Research output: Contribution to journalArticle

  7. Published

    Serum Proteomes Distinguish Children Developing Type 1 Diabetes in a Cohort With HLA-Conferred Susceptibility

    Moulder, R., Bhosale, S. D., Erkkila, T., Laajala, E., Salmi, J., Nguyen, E. V., Kallionpaa, H., Mykkanen, J., Vaha-Makila, M., Hyoty, H. & 9 others, Veijola, R., Ilonen, J., Simell, T., Toppari, J., Knip, M., Goodlett, D. R., Lahdesmaki, H., Simell, O. & Lahesmaa, R., 2015, In : DIABETES. 64, 6, p. 2265-2278

    Research output: Contribution to journalArticle

  8. Published

    Systematic annotation of celiac disease loci refines pathological pathways and suggests a genetic explanation for increased interferon-gamma levels

    Kumar, V., Gutierrez-Achury, J., Kanduri, K., Almeida, R., Hrdlickova, B., Zhernakova, D. V., Westra, H-J., Karjalainen, J., Ricano-Ponce, I., Li, Y. & 10 others, Stachurska, A., Tigchelaar, E. F., Abdulahad, W. H., Lahdesmaki, H., Hofker, M. H., Zhernakova, A., Franke, L., Lahesmaa, R., Wijmenga, C. & Withoff, S., 2015, In : HUMAN MOLECULAR GENETICS. 24, 2, p. 397-409

    Research output: Contribution to journalArticle

  9. Published

    The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

    Kostic, A. D., Gevers, D., Siljander, H., Vatanen, T., Hyotylainen, T., Hamalainen, A-M., Peet, A., Tillmann, V., Poho, P., Mattila, I. & 12 others, Lahdesmaki, H., Franzosa, E. A., Vaarala, O., de Goffau, M., Harmsen, H., Ilonen, J., Virtanen, S. M., Clish, C. B., Oresic, M., Huttenhower, C., Knip, M. & Xavier, R. J., 2015, In : CELL HOST AND MICROBE. 17, 2, p. 260-273

    Research output: Contribution to journalArticle

  10. Published

    The effect of listening to music on human transcriptome

    Kanduri, C., Raijas, P., Ahvenainen, M., Philips, A. K., Ukkola-Vuoti, L., Lahdesmaki, H. & Jarvela, I., 2015, In : PeerJ Computer Science. 3, p. e830

    Research output: Contribution to journalArticle

  11. Published

    The effect of music performance on the transcriptome of professional musicians

    Kanduri, C., Kuusi, T., Ahvenainen, M., Philips, A. K., Lähdesmäki, H. & Järvelä, I., 2015, In : Scientific Reports. 5, p. 1-7 9506.

    Research output: Contribution to journalArticle

  12. Published

    The Transcription Factor NFAT Promotes Exhaustion of Activated CD8+ T Cells

    Martinez, G. J., Pereira, R. M., Äijö, T., Kim, E. Y., Marangoni, F., Pipkin, M. E., Togher, S., Heissmeyer, V., Zhang, Y. C., Crotty, S. & 6 others, Lamperti, E. D., Ansel, K. M., Mempel, T. R., Lähdesmäki, H., Hogan, P. G. & Rao, A., 2015, In : IMMUNITY. 42, 2, p. 265-278

    Research output: Contribution to journalArticle

  13. Published

    Tubulin- and actin-associating GIMAP4 is required for IFN-gamma secretion during Th cell differentiation

    Heinonen, M. T., Kanduri, K., Lahdesmaki, H. J., Lahesmaa, R. & Henttinen, T. A., 2015, In : IMMUNOLOGY AND CELL BIOLOGY. 93, 2, p. 158-166

    Research output: Contribution to journalArticle

  14. Published
  15. 2014
  16. Published

    Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells

    Laurila, K., Autio, R., Kong, L., Närvä, E., Hussein, S., Otonkoski, T., Lahesmaa, R. & Lähdesmäki, H., 13 Dec 2014, In : BIODATA MINING. 7, 16 p., 32.

    Research output: Contribution to journalArticle

  17. Published

    Continuous hypoxic culturing of human embryonic stem cells enhances Ssea-3 and Myc levels

    Närvä, E., Pursiheimo, J-P., Laiho, A., Rahkonen, N., Reddy Emani, M., Viitala, M., Laurila, K., Sahla, R., Lund, R., Lähdesmäki, H. & 2 others, Jaakkola, P. & Lahesmaa, R., 2014, In : PloS one. 8, 11, p. 1-10 e78847.

    Research output: Contribution to journalArticle

  18. Published

    Dissecting the dynamic changes of 5-hydroxymethylcytosine in T cell development and differentiation

    Tsagaratou, A., Äijö, T., Lio, C-W., Yue, X., Huang, Y., Jacobsen, S., Lähdesmäki, H. & Rao, A., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 32, p. pp. E3306-E3315

    Research output: Contribution to journalArticle

  19. Published

    Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell type specificity

    Hrdlickova, B., Kumar, V., Kanduri, K., Zhernakova, D. V., Tripathi, S., Karjalainen, J., Lund, R. J., Li, Y., Ullah, U., Modderman, R. & 6 others, Abdulahad, W., Lähdesmäki, H., Franke, L., Lahesmaa, R., Wijmenga, C. & Withoff, S., 2014, In : GENOME MEDICINE. 6, 88, p. 13

    Research output: Contribution to journalArticle

  20. Published

    Innate immune activity is detected prior to seroconversion in children with HLA-conferred T1D susceptibility

    Kallionpää, H., Elo, LL., Laajala, E., Mykkänen, J., Ricanno-Ponce, I., Vaarma, M., Laajala, TD., Hyöty, H., Ilonen, J., Veijola, R. & 6 others, Simell, T., Wijmenga, C., Knip, M., Lähdesmäki, H., Simell, O. & Lahesmaa, R., 2014, In : DIABETES. 63, 7, p. 2402-2414

    Research output: Contribution to journalArticle

  21. Published

    Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

    Äijö, T., Butty, V., Chen, JZ., Salo, V., Tripathi, S., Burge, C. B., Lahesmaa, R. & Lähdesmäki, H., 2014, In : Bioinformatics. 30, 12, p. pp. i113-i120

    Research output: Contribution to journalArticle

  22. Published

    Notch signaling regulates neural crest differentiation from human pluripotent stem cells

    Noisa, P., Lund, C., Kanduri, K., Lund, R., Lähdesmäki, H., Lahesmaa, R., Lundin, K., Chokechuwattanalert, H., Otonkoski, T., Tuuri, T. & 1 others, Raivio, T., 2014, In : JOURNAL OF CELL SCIENCE. 127, p. 2083-2094

    Research output: Contribution to journalArticle

  23. Published

    Quantitative proteomic analysis of signalosome dynamics in primary T cells identifies the CD6 surface receptor as a LAT-independent TCR signaling hub

    Roncagalli, R., Hauri, S., Fiore, F., Liang, Y., Chen, Z., Kanduri, K., Sansoni, A., Joly, R., Malzac, A., Lähdesmäki, H. & 6 others, Lahesmaa, R., Yamasaki, S., Malissen, M., Aebersold, R., Gstaiger, M. & Malissen, B., 2014, In : NATURE IMMUNOLOGY. 15, 4, p. 384-392

    Research output: Contribution to journalArticle

  24. Published

    Standard of hygiene and immune adaptation in newborn infants

    Kallionpää, H., Laajala, E., Öling, V., Härkönen, T., Tillmann, V., Dorshakova, N. V., Ilonen, J., Lähdesmäki, H., Knip, M. & Lahesmaa, R., 2014, In : CLINICAL IMMUNOLOGY. 155, 1, p. 136-147

    Research output: Contribution to journalArticle

  25. 2013
  26. Published

    Active learning for Bayesian network models of biological networks using structure priors

    Larjo, A. & Lähdesmäki, H., 2013, IEEE International Workshop on Genomic Signal Processing and Statistics, Houston, TX, USA, November 17-19, 2013.

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

  27. Published
  28. Published

    Evaluation of methods for modeling transcription factor sequence specificity

    DREAM5 Consortium, 2013, In : NATURE BIOTECHNOLOGY. 31, 2, p. 126-134

    Research output: Contribution to journalArticle

  29. Published

    Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music

    Ukkola-Vuoti, L., Kanduri, C., Oikkonen, J., Buck, G., Blancher, C., Raijas, P., Karma, K., Lähdesmäki, H. & Järvelä, I., 2013, In : PloS one. 8, 2, p. 1-9 e56356.

    Research output: Contribution to journalArticle

  30. Published

    Global Chromatin State Analysis Reveals Lineage-Specific Enhancers during the Initiation of Human T helper 1 and T helper 2 Cell Polarization

    Hawkins, R. D., Larjo, A., Tripathi, S. K., Wagner, U., Luu, Y., Lönnberg, T., Raghav, S. K., Lee, L. K., Lund, R., Lähdesmäki, H. & 2 others, Bing, R. & Lahesmaa, R., 2013, In : IMMUNITY. 38, 6, p. 1271

    Research output: Contribution to journalArticle

  31. Published

    Goserelin and bicalutamide treatments alter the expression of microRNAs in the prostate

    Lehmusvaara, S., Erkkilä, T., Urbanucci, A., Jalava, S., Seppälä, J., Kaipia, A., Kujala, P., Lähdesmäki, H., Tammela, T. L. J. & Visakorpi, T., 2013, In : PROSTATE. 73, 1, p. 101-112

    Research output: Contribution to journalArticle

  32. Published

    Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX

    Ko, M., An, J., Bandukwala, H. S., Chavez, L., Äijö, T., Pastor, W. A., Segal, M. F., Li, H., Koh, K. P., Lähdesmäki, H. & 3 others, Hogan, P. G., Aravind, L. & Rao, A., 2013, In : Nature. 497, 7447, p. 122-126

    Research output: Contribution to journalArticle

  33. Published

    Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation

    Tahvanainen, J., Kyläniemi, M. K., Gupta, K., Kanduri, B., Lähteenmäki, H., Kallonen, T., Rajavuori, A., Rasool, O., Koskinen, P. J., Rao, K. V. S. & 2 others, Lähdesmäki, H. & Lahesmaa, R. R., 2013, In : Journal of biological chemistry. 288, 5, p. 3048-3058

    Research output: Contribution to journalArticle

  34. Published

    Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements

    Äijö, T., Granberg, K. & Lähdesmäki, H., 2013, In : Bioinformatics. 29, 10, p. 1283-1291

    Research output: Contribution to journalArticle

  35. Published

    The genome wide landscape of copy number variations in the isolated Finnish population: the MUSGEN study provides evidence for a founder effect

    Kanduri, C., Ukkola-Vuoti, L., Oikkonen, J., Buck, G., Blancher, C., Raijas, P., Karma, K., Lähdesmäki, H. & Järvelä, I., 2013, In : European journal of human genetics. 288, 5, p. 3048-3058

    Research output: Contribution to journalArticle

  36. 2012
  37. Published

    Androgen-regulated miR-32 targets BTG2 and is overexpressed in castration-resistant prostate cancer

    Jalava, S. E., Urbanucci, A., Latonen, L. M., Waltering, K. K., Sahu, B., Jänne, O. A., Seppälä, J. & Lähdesmäki, H., 2012, In : Oncogene. 31, 41, p. 4460-4471

    Research output: Contribution to journalArticle

  38. Published

    An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation

    Äijö, T., Edelman, S., Lönnberg, T., Larjo, A., Kallionpää, H., Tuomela, S., Engström, E., Lahesmaa, R. & Lähdesmäki, H., 2012, In : BMC GENOMICS. 13, 1, p. 572

    Research output: Contribution to journalArticle

  39. Published

    Chemical castration and anti-androgens induce differential gene expression in prostate cancer

    Lehmusvaara, S., Erkkilä, T., Urbanucci, A., Waltering, K., Seppälä, J., Larjo, A., Tuominen, V., Isola, J., Kujala, P., Lähdesmäki, H. & 3 others, Kaipia, A., Tammela, T. L. J. & Visakorpi, T., 2012, In : JOURNAL OF PATHOLOGY. 227, 3, p. 336-345

    Research output: Contribution to journalArticle

  40. Published

    Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells

    Benson, M. J., Äijö, T., Chang, X., Gagnon, J., Pape, U. J., Anantharaman, V., Aravind, L., Pursiheimo, J-P., Oberdoerffer, S., Liu, X. S. & 3 others, Lahesmaa, R., Lähdesmäki, H. & Rao, A., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 40, p. 16252-16257

    Research output: Contribution to journalArticle

  41. Published

    Identification of early gene expression changes during human Th17 cell differentiation

    Tuomela, S., Tripathi, V., Salo, S. K., Chen, Z., Laurila, K., Äijö, T., Gupta, B., Oikari, L., Stockinger, B., Lähdesmäki, H. & 1 others, Lahesmaa, R., 2012, In : BLOOD. 119, 23, p. 151-160

    Research output: Contribution to journalArticle

  42. Published

    Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer

    Urbanucci, A., Sahu, B., Seppälä, J., Larjo, A., Latonen, L. M., Waltering, K. K., Tammela, T. L. J., Vessella, R. L., Lähdesmäki, H., Jänne, O. A. & 1 others, Visakorpi, T., 2012, In : Oncogene. 31, 17, p. 2153-2163

    Research output: Contribution to journalArticle

  43. Published

    RNA binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation

    Närvä, E., Rahkonen, N., Emani, M. R., Lund, R., Pursiheimo, J-P., Nästi, J., Autio, R., Rasool, O., Denessiouk, K., Lähdesmäki, H. & 2 others, Rao, A. & Lahesmaa, R., 2012, In : STEM CELLS. 30, 3, p. 452-460

    Research output: Contribution to journalArticle

  44. Published

    Structure learning for Bayesian networks as models of biological networks

    Larjo, A., Shmulevich, I. & Lähdesmäki, H., 2012, Data Mining for Systems Biology, Methods in Molecular Biology. Mamitsuka, H., DeLisi, C. & Kanehisa, M. (eds.). New York: Humana Press, p. 35-45

    Research output: Chapter in Book/Report/Conference proceedingChapterScientific

  45. 2011
  46. Published

    A linear model for transcription factor binding affinity prediction in protein binding microarrays

    Annala, M., Laurila, K., Lähdesmäki, H. & Nykter, M., 2011, In : PloS one. 6, 5, p. 1-13 e20059.

    Research output: Contribution to journalArticle

  47. Published

    Integrated views into cancer regulomes reveal regulatory hot spots

    Erkkilä, T., Kreisberg, R., Reynolds, S., Thorsson, V., Lin, J., Torkkola, K., Bressler, R., Bernard, B., Ruusuvuori, P., Annala, M. & 7 others, Leinonen, K., Ylipää, A., Yli-Harja, O., Boyle, J., Nykter, M., Lähdesmäki, H. & Shmulevich, I., 2011, The 11th SocBiN Conference, Helsinki, Finland.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

  48. Published

    Integrated Views into Cancer Regulomes Reveal Regulatory Hot Spots

    Erkkilä, T., Kreisberg, R., Reynolds, S., Thorsson, V., Bernard, B., Bressler, R., Ruusuvuori, P., Annala, M., Ylipää, A., Yli-Harja, O. & 4 others, Boyle, J., Nykter, M., Lähdesmäki, H. & Shmulevich, I., 2011, Eight International Workshop on Computational Systems Biology, WCSB 2011.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

  49. Published

    RF-ACE for uncovering nonlinear associations from heterogeneous cancer data

    Erkkilä, T., Reynolds, S., Torkkola, K., Lin, J., May, P., Sorsa, S., Bernard, B., Norberg, A., Robinson, T., Eakin, A. & 8 others, Bressler, R., Kreisberg, R., Leinonen, K., Rovira, H., Thorsson, V., Yli-Harja, O., Lähdesmäki, H. & Shmulevich, I., 2011, The Cancer Genome Atlas' 1st Annual Scientific Symposium, Maryland, USA.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

  50. Published

    SNP genotype effects on gene and transcript expression variation in human embryonic and induced pluripotent stem cells

    Laurila, K., Närvä, E., Hussein, S., Otonkoski, T., Lahesmaa, R. & Lähdesmäki, H., 2011, The 11th SocBiN Conference, Helsinki, Finland.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

  51. Published

    The miR-15a-miR-16-1 locus is homozygously deleted in a subset of prostate cancers

    Porkka, K., Ogg, E-L., Saramäki, O. R., Vessella, R. L., Pukkila, H., Lähdesmäki, H., Weerden, W. M. V., Wolf, M., Kallioniemi, O. P., Jenster, G. & 1 others, Visakorpi, T., 2011, In : GENES CHROMOSOMES AND CANCER. 50, 7, p. 499-509

    Research output: Contribution to journalArticle

  52. 2010
  53. Published

    Genomic signal processing

    Braga-Neto, U., Kuang, R., Lähdesmäki, H., Vikalo, H. & Yoon, B. J., 1 Dec 2010, In : Eurasip Journal on Advances in Signal Processing. 2010, 137263.

    Research output: Contribution to journalEditorial

  54. Published

    A linear model for transcription factor binding affinity prediction in PBM microarrays

    Annala, M., Laurila, K., Nykter, M. & Lähdesmäki, H., 2010, RECOMB The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

  55. Published

    Comparing multiple time-course differentiation profiles of human T helper cells using a Bayesian approach

    Äijö, T., Lönnberg, T., Edelman, S., Tuomela, S., Järvenpää, H., Lahesmaa, R. & Lähdesmäki, H., 2010, RECOMB The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

  56. Published

    Cross-species comparison of STAT6 transcription factor regulation in mice and human

    Laurila, K., Vahedi, G., Kanno, Y., Lahesmaa, R., OShea, J. J. & Lähdesmäki, H., 2010, RECOMB The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

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