Harri Lähdesmäki

Peer-reviewed scientific articles

Journal article-refereed, Original research

mGPfusion: Predicting protein stability changes upon single and multiple mutations with Gaussian processes and data fusion

Jokinen, Emmi; Heinonen, Markus; Lähdesmäki, Harri

2017 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA⁺ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells

Lund, Riikka J.; Rahkonen, Nelly; Malonzo, Maia; Kauko, Leni; Emani, Maheswara Reddy; Kivinen, Virpi; Närvä, Elisa; Kemppainen, Esko; Laiho, Asta; Skottman, Heli; Hovatta, Outi; Rasool, Omid; Nykter, Matti; Lähdesmäki, Harri; Lahesmaa, Riitta

2017 in Stem Cell Reports (Cell Press)

ISSN: 2213-6711

Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation

Tripathi, Subhash K.; Chen, Zhi; Larjo, Antti; Kanduri, Kartiek; Nousiainen, Kari; Äijo, Tarmo; Ricaño-Ponce, Isis; Hrdlickova, Barbara; Tuomela, Soile; Laajala, Essi; Salo, Verna; Kumar, Vinod; Wijmenga, Cisca; Lähdesmäki, Harri; Lahesmaa, Riitta

2017 in CELL REPORTS (Elsevier)

ISSN: 2211-1247

TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells

Tsagaratou, Ageliki; González-Avalos, Edahí; Rautio, Sini; Scott-Browne, James P.; Togher, Susan; Pastor, William A.; Rothenberg, Ellen V.; Chavez, Lukas; Lähdesmäki, Harri; Rao, Anjana

2017 in NATURE IMMUNOLOGY (Nature Publishing Group)

ISSN: 1529-2908

A subpopulation model to analyze heterogeneous cell differentiation dynamics

Chan, Yat Hin; Intosalmi, Jukka; Rautio, Sini; Lähdesmäki, Harri

2016 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks

Intosalmi, Jukka; Nousiainen, Kari; Ahlfors, Helena; Lähdesmäki, Harri

2016 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

The landscape of copy number variations in Finnish families with autism spectrum disorders

Kanduri, Chakravarthi; Kantojärvi, Katri; Salo, Paula M.; Vanhala, Raija; Buck, Gemma; Blancher, Christine; Lähdesmäki, Harri; Järvelä, Irma

2016 in AUTISM RESEARCH (John Wiley and Sons Inc.)

ISSN: 1939-3792

Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells

Konki, Mikko; Pasumarthy, Kalyan; Malonzo, Maia; Sainio, Annele; Valensisi, Cristina; Söderström, Mirva; Emani, Maheswara Reddy; Stubb, Aki; Närvä, Elisa; Ghimire, Bishwa; Laiho, Asta; Järveläinen, Hannu; Lahesmaa, Riitta; Lähdesmäki, Harri; Hawkins, R. David; Lund, Riikka J.

2016 in SCIENTIFIC REPORTS (NATURE PUBLISHING GROUP)

ISSN: 2045-2322

Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells

Rahkonen, Nelly; Stubb, Aki; Malonzo, Maia; Edelman, Sanna; Emani, Maheswara Reddy; Närvä, Elisa; Lähdesmäki, Harri; Ruohola-Baker, Hannele; Lahesmaa, Riitta; Lund, Riikka

2016 in STEM CELL RESEARCH (Elsevier)

ISSN: 1873-5061

Synthetic transcription amplifier system for orthogonal control of gene expression in saccharomyces cerevisiae

Rantasalo, Anssi; Czeizler, Elena; Virtanen, Riitta; Rousu, Juho; Lähdesmäki, Harri; Penttilä, Merja; Jäntti, Jussi; Mojzita, Dominik

2016 in PLOS ONE (PUBLIC LIBRARY SCIENCE)

ISSN: 1932-6203

Comparative analysis of human and mouse transcriptomes of Th17 cell priming

Tuomela, Soile; Rautio, Sini; Ahlfors, Helena; Öling, Viveka; Salo, Verna; Ullah, Ubaid; Chen, Zhi; Hämälistö, Saara; Tripathi, Subhash K.; Äijö, Tarmo; Rasool, Omid; Soueidan, Hayssam; Wessels, Lodewyk; Stockinger, Brigitta; Lähdesmäki, Harri; Lahesmaa, Riitta

2016 in ONCOTARGET (IMPACT JOURNALS LLC)

ISSN: 1949-2553

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

Vatanen, Tommi; Kostic, Aleksandar D.; D'Hennezel, Eva; Siljander, Heli; Franzosa, Eric A.; Yassour, Moran; Kolde, Raivo; Vlamakis, Hera; Arthur, Timothy D.; Hämäläinen, Anu Maaria; Peet, Aleksandr; Tillmann, Vallo; Uibo, Raivo; Mokurov, Sergei; Dorshakova, Natalya; Ilonen, Jorma; Virtanen, Suvi M.; Szabo, Susanne J.; Porter, Jeffrey A.; Lähdesmäki, Harri; Huttenhower, Curtis; Gevers, Dirk; Cullen, Thomas W.; Knip, Mikael; Xavier, Ramnik J.

2016 in CELL (Cell Press)

ISSN: 0092-8674

Control of Foxp3 stability through modulation of TET activity

Yue, Xiaojing; Trifari, Sara; Äijö, Tarmo; Tsagaratou, Ageliki; Pastor, William A.; Zepeda-Martínez, Jorge A.; Lio, Chan Wang J; Li, Xiang; Huang, Yun; Vijayanand, Pandurangan; Lähdesmäki, Harri; Rao, Anjana

2016 in JOURNAL OF EXPERIMENTAL MEDICINE (Rockefeller University Press)

ISSN: 0022-1007

LuxGLM A probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs

Äijö, Tarmo; Yue, Xiaojing; Rao, Anjana; Lähdesmäki, Harri

2016 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways

Äijö, Tarmo; Huang, Yun; Mannerström, Henrik; Chavez, Lukas; Tsagaratou, Ageliki; Rao, Anjana; Lähdesmäki, Harri

2016 in GENOME BIOLOGY (BioMed Central)

ISSN: 1474-7596

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

Balasubramani, Anand; Larjo, Antti; Chang, Xing; Hastie, Ryan B.; Togher, Susan; Bassein, Jed A.; Lähdesmäki, Harri; Rao, Anjana

2015 in NATURE COMMUNICATIONS (NATURE PUBLISHING GROUP)

ISSN: 2041-1723

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

Heinonen, Mirkka T.; Laine, Antti-Pekka; Soderhall, Cilla; Gruzieva, Olena; Rautio, Sini; Melen, Erik; Pershagen, Goran; Lahdesmaki, Harri J.; Knip, Mikael; Ilonen, Jorma; Henttinen, Tiina A.; Kere, Juha; Lahesmaa, Riitta

2015 in JOURNAL OF IMMUNOLOGY (American Association of Immunologists)

ISSN: 0022-1767

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

Heinonen, Mirkka T.; Kanduri, Kartiek; Lahdesmaki, Harri J.; Lahesmaa, Riitta; Henttinen, Tiina A.

2015 in IMMUNOLOGY AND CELL BIOLOGY (Nature Publishing Group)

ISSN: 0818-9641

Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data

Intosalmi, Jukka; Ahlfors, Helena; Rautio, Sini; Mannerström, Henrik; Chen, Zhi; Lahesmaa, Riitta; Stockinger, Birgitta; Lähdesmäki, Harri

2015 in BMC SYSTEMS BIOLOGY (BIOMED CENTRAL LTD)

The effect of music performance on the transcriptome of professional musicians

Kanduri, Chakravarthi; Kuusi, Tuire; Ahvenainen, Minna; Philips, Anju K.; Lähdesmäki, Harri; Järvelä, I.

2015 in SCIENTIFIC REPORTS (NATURE PUBLISHING GROUP)

ISSN: 2045-2322

Identification of global regulators of T-helper cell lineage specification

Kanduri, Kartiek; Tripathi, Subhash; Larjo, Antti; Mannerström, Henrik; Ullah, Ubaid; Lund, Riikka; Hawkins, David; Ren, Bing; Lähdesmäki, Harri; Lahesmaa, Riitta

2015 in GENOME MEDICINE (BIOMED CENTRAL LTD)

The effect of listening to music on human transcriptome

Kanduri, Chakravarthi; Raijas, Pirre; Ahvenainen, Minna; Philips, Anju K.; Ukkola-Vuoti, Liisa; Lahdesmaki, Harri; Jarvela, Irma

2015 in PeerJ Computer Science (BIOMED CENTRAL LTD)

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

Kostic, Aleksandar D.; Gevers, Dirk; Siljander, Heli; Vatanen, Tommi; Hyotylainen, Tuulia; Hamalainen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Poho, Paivi; Mattila, Ismo; Lahdesmaki, Harri; Franzosa, Eric A.; Vaarala, Outi; de Goffau, Marcus; Harmsen, Hermie; Ilonen, Jorma; Virtanen, Suvi M.; Clish, Clary B.; Oresic, Matej; Huttenhower, Curtis; Knip, Mikael; Xavier, Ramnik J.

2015 in CELL HOST AND MICROBE (Cell Press)

ISSN: 1931-3128

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

Kumar, Vinod; Gutierrez-Achury, Javier; Kanduri, Kartiek; Almeida, Rodrigo; Hrdlickova, Barbara; Zhernakova, Daria V.; Westra, Harm-Jan; Karjalainen, Juha; Ricano-Ponce, Isis; Li, Yang; Stachurska, Anna; Tigchelaar, Ettje F.; Abdulahad, Wayel H.; Lahdesmaki, Harri; Hofker, Marten H.; Zhernakova, Alexandra; Franke, Lude; Lahesmaa, Riitta; Wijmenga, Cisca; Withoff, Sebo

2015 in HUMAN MOLECULAR GENETICS (Oxford University Press)

ISSN: 0964-6906

BinDNase: A discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

Kähärä, Juhani; Lähdesmäki, Harri

2015 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

Using multi-step proposal distribution for improved MCMC convergence in Bayesian network structure learning

Larjo, Antti; Lähdesmäki, Harri

2015 in EURASIP JOURNAL ON BIOINFORMATICS AND SYSTEMS BIOLOGY (Springer Publishing Company)

ISSN: 1687-4145

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

Martinez, Gustavo J.; Pereira, Renata M.; Äijö, Tarmo; Kim, Edward Y.; Marangoni, Francesco; Pipkin, Matthew E.; Togher, Susan; Heissmeyer, Vigo; Zhang, Yi Chen; Crotty, Shane; Lamperti, Edward D.; Ansel, K.Mark; Mempel, Thorsten R.; Lähdesmäki, Harri; Hogan, Patrick G.; Rao, Anjana

2015 in IMMUNITY (Cell Press)

ISSN: 1074-7613

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

Moulder, Robert; Bhosale, Santosh D.; Erkkila, Timo; Laajala, Essi; Salmi, Jussi; Nguyen, Elizabeth V.; Kallionpaa, Henna; Mykkanen, Juha; Vaha-Makila, Mari; Hyoty, Heikki; Veijola, Riitta; Ilonen, Jorma; Simell, Tuula; Toppari, Jorma; Knip, Mikael; Goodlett, David R.; Lahdesmaki, Harri; Simell, Olli; Lahesmaa, Riitta

2015 in DIABETES (American Diabetes Association Inc.)

ISSN: 0012-1797

MixChIP a probabilistic method for cell type specific protein-DNA binding analysis

Rautio, Sini; Lähdesmäki, Harri

2015 in BMC BIOINFORMATICS (BioMed Central)

ISSN: 1471-2105

Self-organization and missing values in SOM and GTM

Vatanen, T.; Osmala, M.; Raiko, T.; Lagus, K.; Sysi-Aho, M.; Orešič, M.; Honkela, T.; Lähdesmäki, H.

2015 in NEUROCOMPUTING (Elsevier Science B.V.)

ISSN: 0925-2312

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, Juha; Lund, Riikka J.; Li, Y.; Ullah, U.; Modderman, R.; Abdulahad, W.; Lähdesmäki, Harri; Franke, L.; Lahesmaa, Riitta; Wijmenga, C.; Withoff, S.

2014 in GENOME MEDICINE (BIOMED CENTRAL LTD)

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.; Simell, T.; Wijmenga, C.; Knip, M.; Lähdesmäki, H.; Simell, O.; Lahesmaa, R.

2014 in DIABETES (American Diabetes Association Inc.)

ISSN: 0012-1797

Standard of hygiene and immune adaptation in newborn infants

Kallionpää, Henna; Laajala, Essi; Öling, Viveka; Härkönen, Taina; Tillmann, Vallo; Dorshakova, Natalya V.; Ilonen, Jorma; Lähdesmäki, Harri; Knip, Mikael; Lahesmaa, Riitta

2014 in CLINICAL IMMUNOLOGY (Academic Press Inc.)

ISSN: 1521-6616

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

Laurila, Kirsti; Autio, Reija; Kong, Lingjia; Närvä, Elisa; Hussein, Samer; Otonkoski, Timo; Lahesmaa, Riitta; Lähdesmäki, Harri

2014 in BIODATA MINING (BIOMED CENTRAL LTD)

ISSN: 1756-0381

Notch signaling regulates neural crest differentiation from human pluripotent stem cells

Noisa, P; Lund, C; Kanduri, Kartiek; Lund, Riikka; Lähdesmäki, Harri; Lahesmaa, Riitta; Lundin, K; Chokechuwattanalert, H; Otonkoski, Timo; Tuuri, T; Raivio, T

2014 in JOURNAL OF CELL SCIENCE (Company of Biologists Ltd)

ISSN: 0021-9533

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

Närvä, Elisa; Pursiheimo, Juha-Pekka; Laiho, Asta; Rahkonen, Nelly; Reddy Emani, Maheswara; Viitala, Miro; Laurila, Kirsti; Sahla, Roosa; Lund, Riikka; Lähdesmäki, Harri; Jaakkola, Panu; Lahesmaa, Riitta

2014 in PLOS ONE (PUBLIC LIBRARY SCIENCE)

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; Lahesmaa, R; Yamasaki, S; Malissen, M; Aebersold, R; Gstaiger, M; Malissen, B

2014 in NATURE IMMUNOLOGY (Nature Publishing Group)

ISSN: 1529-2908

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 (NATL ACAD SCIENCES)

ISSN: 0027-8424

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

Äijö, Tarmo; Butty, V.; Chen, JZ.; Salo, V.; Tripathi, S.; Burge, C.B.; Lahesmaa, R.; Lähdesmäki, H.

2014 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

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

Hawkins, R.David; Larjo, Antti; Tripathi, Subhash K.; Wagner, Ulrich; Luu, Ying; Lönnberg, Tapio; Raghav, Suni K.; Lee, Leonard K.; Lund, Riikka; Lähdesmäki, Harri; Bing, Ren; Lahesmaa, Riitta

2013 in IMMUNITY (Cell Press)

ISSN: 1074-7613

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 (Nature Publishing Group)

ISSN: 1018-4813

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

Ko, Myunggon; An, Jungeun; Bandukwala, Hozefa S.; Chavez, Lukas; Äijö, Tarmo; Pastor, William A.; Segal, Matthew F.; Li, Huiming; Koh, Kian Peng; Lähdesmäki, Harri; Hogan, Patrick G.; Aravind, L.; Rao, Anjana

2013 in NATURE (NATURE PUBLISHING GROUP)

ISSN: 0028-0836

Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data

Kähärä, J.; Lähdesmäki, H.

2013 in BMC BIOINFORMATICS (BioMed Central)

Goserelin and bicalutamide treatments alter the expression of microRNAs in 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 (Wiley-Liss Inc.)

ISSN: 0270-4137

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; Lähdesmäki, Harri; Lahesmaa, R.R.

2013 in JOURNAL OF BIOLOGICAL CHEMISTRY (AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC)

ISSN: 0021-9258

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, Harri; Järvelä, I.

2013 in PLOS ONE (PUBLIC LIBRARY SCIENCE)

Evaluation of methods for modeling transcription factor sequence specificity

Weirauch, M.T.; Cote, A.; Norel, R.; Annala, M.; Zhao, Y.; Riley, T.J.; Saez-Rodriguez, J.; Cokelaer, T.; Vedenko, A.; Talukder, S.; consortium, DREAM5; Bussemaker, H.J.; Morris, Q.D.; Bulyk, M.L.; Stolovitzky, G.; Hughes, T.R; Lähdesmäki, Harri; Laurila, Kirsti; ,

2013 in NATURE BIOTECHNOLOGY (NATURE PUBLISHING GROUP)

ISSN: 1087-0156

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

Äijö, Tarmo; Granberg, Kirsi; Lähdesmäki, Harri

2013 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

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, Tarmo; Chang, X.; Gagnon, J.; Pape, U.J.; Anantharaman, V.; Aravind, L.; Pursiheimo, J-P.; Oberdoerffer, S.; Liu, X.S.; Lahesmaa, R.; Lähdesmäki, Harri; Rao, A.

2012 in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (NATL ACAD SCIENCES)

ISSN: 0027-8424

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, Harri

2012 in ONCOGENE (Nature Publishing Group)

ISSN: 0950-9232

Chemical castration and antiandrogens 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, Harri; Kaipia, A.; Tammela, T.L.J.; Visakorpi, T.

2012 in JOURNAL OF PATHOLOGY (John Wiley and Sons Ltd)

ISSN: 0022-3417

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, Harri; Rao, A.; Lahesmaa, R.

2012 in STEM CELLS (AlphaMed Press)

ISSN: 1066-5099

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, Harri; Lahesmaa, R.

2012 in BLOOD (American Society of Hematology)

ISSN: 0006-4971

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, Harri; Jänne, O.A; Visakorpi, T.

2012 in ONCOGENE (Nature Publishing Group)

ISSN: 0950-9232

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 (BIOMED CENTRAL LTD)

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

Annala, Matti; Laurila, Kirsti; Lähdesmäki, Harri; Nykter, Matti

2011 in PLOS ONE (PUBLIC LIBRARY SCIENCE)

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, Harri; Weerden, W.M. van; Wolf, M.; Kallioniemi, O.P.; Jenster, G.; Visakorpi, T.

2011 in GENES CHROMOSOMES AND CANCER (Wiley-Liss Inc.)

ISSN: 1045-2257

Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network

Aho, Tommi; Almusa, Henrikki; Matilainen, Jukka; Larjo, Antti; Ruusuvuori, Pekka; Aho, Kaisa-Leena; Wilhelm, Thomas; Lähdesmäki, Harri; Beyer, Andreas; Harju, Manu; Chowdhury, Sharif; Leinonen, Kalle; Roos, Christophe; Yli-Harja, Olli

2010 in PLOS ONE (PUBLIC LIBRARY SCIENCE)

Novel data fusion method and exploration of multiple information sources for transcription factor target gene prediction

Dai, Xiaofeng; Lähdesmäki, Harri

2010 in EURASIP JOURNAL ON ADVANCES IN SIGNAL PROCESSING (Springer Publishing Company)

ISSN: 1687-6172

Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming

Elo, Laura L.; Järvenpää, Henna; Tuomela, Soile; Raghav, Sunil; Ahlfors, Helena; Laurila, Kirsti; Gupta, Bhawna; Lund, Riikka J.; Tahvanainen, Johanna; Hawkins, R.David; Oresic, Matej; Lähdesmäki, Harri; Rasool, Omid; Rao, Kanury V.; Aittokallio, Tero; Lahesmaa, Riitta

2010 in IMMUNITY (Cell Press)

ISSN: 1074-7613

Probabilistic analysis of gene expression measurements from heterogeneous tissues

Erkkilä, Timo; Lehmusvaara, Saara; Ruusuvuori, Pekka; Visakorpi, Tapio; Shmulevich, Ilya; Lähdesmäki, Harri

2010 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding

Laurila, Kirsti; Lähdesmäki, Harri

2009 in IN SILICO BIOLOGY (IOS Press)

Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics

Äijö, Tarmo; Lähdesmäki, Harri

2009 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

Conference proceedings

Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo

Heinonen, Markus; Mannerström, Henrik; Rousu, Juho; Kaski, Samuel; Lähdesmäki, Harri

2016 in JMLR: Workshop and Conference Proceedings (JMLR)

ISSN: 1938-7228

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

Larjo, A.; Lähdesmäki, H.

2013

A unified probabilistic framework for clustering genes from gene expression and protein-protein interaction data

Dai, Xiaofeng; Lähdesmäki, Harri

2009

A probabilistic model for competitive binding of transcription factors

Laurila, Kirsti; Lähdesmäki, Harri

2009

Decomposing gene expression into regulatory and differential parts with Bayesian data fusion

Nikkilä, Janne; Erkkilä, Timo; Lähdesmäki, Harri

2008

Non-refereed scientific articles

Unrefereed journal articles

Selected proceedings of Machine Learning in Systems Biology MLSB 2016

van Dijk, Aalt D J; Lähdesmäki, Harri; de Ridder, Dick; Rousu, Juho

2016 in BMC BIOINFORMATICS (BioMed Central)

ISSN: 1471-2105

Book section

Structure learning for Bayesian networks as models of biological networks

Larjo, A.; Shmulevich, I.; Lähdesmäki, Harri

2012

ISBN: 978-1-62703-106-6

ISSN: 1064-3745

Scientific books (monographs)

Book (editor)

Selected proceedings of Machine Learning in Systems Biology MLSB 2016

van Dijk, Aalt D J; Lähdesmäki, Harri; de Ridder, Dick; Rousu, Juho

2016 in BMC BIOINFORMATICS (BioMed Central)

ISSN: 1471-2105

Publications intended for professional communities

Article in professional conference proceedings

A probabilistic method for quantifying chromatin interactions

Halla-Aho, Viivi; Mannerström, Henrik; Lähdesmäki, Harri

2015

Integrated views into cancer regulomes reveal regulatory hot spots

Erkkilä, Timo; Kreisberg, Richard; Reynolds, Sheila; Thorsson, Vesteinn; Lin, Jake; Torkkola, Kari; Bressler, Ryan; Bernard, Brady; Ruusuvuori, Pekka; Annala, Matti; Leinonen, Kalle; Ylipää, Antti; Yli-Harja, Olli; Boyle, John; Nykter, Matti; Lähdesmäki, Harri; Shmulevich, Ilya

2011

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, Olli; Boyle, J.; Nykter, M.; Lähdesmäki, Harri; Shmulevich, I.

2011

RF-ACE for uncovering nonlinear associations from heterogeneous cancer data

Erkkilä, Timo; Reynolds, Sheila; Torkkola, Kari; Lin, Jake; May, Patrick; Sorsa, Saija; Bernard, Brady; Norberg, Adam; Robinson, Thomas; Eakin, Andrea; Bressler, Ryan; Kreisberg, Richard; Leinonen, Kalle; Rovira, Hector; Thorsson, Vesteinn; Yli-Harja, Olli; Lähdesmäki, Harri; Shmulevich, Ilya

2011

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

Laurila, Kirsti; Närvä, Elisa; Hussein, Samer; Otonkoski, Timo; Lahesmaa, Riitta; Lähdesmäki, Harri

2011

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

Annala, Matti; Laurila, Kirsti; Nykter, Matti; Lähdesmäki, Harri

2010

Inferring genetic regulatory interactions from time-collapsed Boolean summary variables

Erkkilä, Timo; Thorsson, Vesteinn; Lähdesmäki, Harri; Shmulevich, Ilya

2010

Efficient learning of signaling network model structures using Bayesian networks

Larjo, Antti; Lähdesmäki, Harri

2010

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

Laurila, Kirsti; Vahedi, Golnaz; Kanno, Yuka; Lahesmaa, Riitta; OShea, John J.; Lähdesmäki, Harri

2010

Effects of endocrine therapy on mRNA and microRNA expression profiles in prostate cancer

Lehmusvaara, Saara; Erkkilä, Timo; Lähdesmäki, Harri; Kujala, P.; Tammela, Teuvo L.J.; Visakorpi, Tapio

2010

The effect of AR expression level on the chromatin binding of the receptor

Urbanucci, A.; Sahu, B.; Seppälä, J.; Kukkola, S.; Waltering, K.; Lähdesmäki, H.; Jänne, O.; Visakorpi, T.

2010

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

Äijö, Tarmo; Lönnberg, Tapio; Edelman, Sanna; Tuomela, Soile; Järvenpää, Henna; Lahesmaa, Riitta; Lähdesmäki, Harri

2010

Learning gene regulatory networks with delayed ODEs and continuous-time expression representation

Äijö, Tarmo; Yli-Harja, Olli; Lähdesmäki, Harri

2010

Published development or research report

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

Battle, Stephanie L.; Larjo, Antti; Liao, Joling; Lahdesmaki, Harri; Lieber, Andre; Hawkins, R.David

2015

Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network

Aho, Tommi; Almusa, Henrikka; Matilainen, Jukka; Larjo, Antti; Ruusuvuori, Pekka; Aho, Kaisa-Leena; Wilhelm, Thomas; Lähdesmäki, Harri; Beyer, Andreas; Harju, Manu; Chowdhury, Sharif; Leinonen, Kalle; Roos, Christophe; Yli-Harja, Olli

2009

Incorporating spatial information of heterogeneous cell populations into Bayesian mRNA- and miRNA-expression analysis

Erkkilä, Timo; Ruusuvuori, Pekka; Lehmusvaara, Saara; Visakorpi, Tapio; Shmulevich, Ilya; Lähdesmäki, Harri

2009

A probabilistic model for competitive binding of transcription factors

Laurila, Kirsti; Lähdesmäki, Harri

2009

Protein-protein interactions improve multiple transcription factor binding site prediction

Laurila, Kirsti; Pukkila, Heidi; Yli-Harja, Olli; Lähdesmäki, Harri

2009

Learning the structure of a gene regulatory network from gene expression measurements using non-parametric molecular kinetics

Äijö, Tarmo; Lähdesmäki, Harri

2009

Learning gene regulatory networks with delayed ODEs and continuous-time expression representation

Äijö, Tarmo; Lähdesmäki, Harri

2009

Patents and invention disclosures

Patent

Generating data to improve protein stability prediction

Heinonen, Markus; Jokinen, Emmi; Kaski, Samuel; Rousu, Juho; Lähdesmäki, Harri

2016

Identification of global regulators of T-helper cell lineage specification

Kanduri, Kartiek; Tripathi, Subhash; Larjo, Antti; Mannerström, Henrik; Ullah, Ubaid; Lund, Riikka; Hawkins, R. David; Ren, Bing; Lähdesmäki, Harri; Lahesmaa, Riitta

2016 in SCANDINAVIAN JOURNAL OF IMMUNOLOGY (WILEY-BLACKWELL)

ISSN: 0300-9475

Enterovirus-associated changes in plasma proteome of children with genetic susceptibility to type 1 diabetes

Lietzen, Niina; Cheng, Lu; Oikarinen, Sami; Goo, Young Ah; Goodlett, David; Toppari, Jorma; Ilonen, Jorma; Veijola, Riitta; Knip, Mikael; Lähdesmäki, Harri; Hyöty, Heikki; Lahesmaa, Riitta

2016 in SCANDINAVIAN JOURNAL OF IMMUNOLOGY (WILEY-BLACKWELL)

ISSN: 0300-9475

Comparative analysis of human and mouse transcriptomes of Th17 cell priming

Tuomela, Soile; Rautio, Sini; Ahlfors, Helena; Oling, Viveka; Salo, Verna; Ullah, Ubaid; Chen, Zhi; Hämälistö, Saara; Tripathi, Subhash; Äijö, Tarmo; Rasool, Omid; Soueidan, Hayssam; Wessels, Lodewyk; Stockinger, Brigitta; Lähdesmäki, Harri; Lahesmaa, Riitta

2016 in SCANDINAVIAN JOURNAL OF IMMUNOLOGY (WILEY-BLACKWELL)

ISSN: 0300-9475