MERJA HEINäNIEMI

Contact info

Teaching Activities

Research groups and research projects

Research groups

• Bioinformatics Center
• Systems Genomics - Heinäniemi lab

Publications

• Turunen, Tanja; Hernández de Sande, Ana; Pölönen, Petri; Heinäniemi, Merja. 2021. Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data Computational and Structural Biotechnology Journal In Press, Journal Pre-proof 15.4.21: 1-34. 2021
• Välimäki, Mika J.; Leigh, Robert S.; Kinnunen, Sini M.; March, Alexander R.; de Sande, Ana Hernández; Kinnunen, Matias; Varjosalo, Markku; Heinäniemi, Merja; Kaynak, Bogac L.; Ruskoaho, Heikki. 2021. GATA-targeted compounds modulate cardiac subtype cell differentiation in dual reporter stem cell line Stem cell research & therapy 12 1: 190. 2021
• Chan, Lai N; Murakami, Mark A; Robinson, Mark E; Caeser, Rebecca; Sadras, Teresa; Lee, Jaewoong; Cosgun, Kadriye Nehir; Kume, Kohei; Khairnar, Vishal; Xiao, Gang; Ahmed, Mohamed A; Aghania, Eamon; Deb, Gauri; Hurtz, Christian; Shojaee, Seyedmehdi; Hong, Chao; Pölönen, Petri; Nix, Matthew A; Chen, Zhengshan; Chen, Chun Wei; Chen, Jianjun. 2020. Signalling input from divergent pathways subverts B cell transformation Nature 583 7818: 845-851. 2020
• Dufva, Olli; Pölönen, Petri; Brück, Oscar; Keränen, Mikko AI; Klievink, Jay; Mehtonen, Juha; Huuhtanen, Jani; Kumar, Ashwini; Malani, Disha; Siitonen, Sanna; Kankainen, Matti; Ghimire, Bishwa; Lahtela, Jenni; Mattila, Pirkko; Vähä-Koskela, Markus; Wennerberg, Krister; Granberg, Kirsi; Leivonen, Suvi-Katri; Meriranta, Leo; Heckman, Caroline; et al. [incl. Heinäniemi, Merja]. 2020. Immunogenomic Landscape of Hematological Malignancies Cancer cell 38 3: 380-399.e13. 2020
• Laukkanen, S; Oksa, L; Nikkilä, A; Lahnalampi, M; Parikka, M; Seki, M; Takita, J; Degerman, S; de Bock, CE; Heinäniemi, M; Lohi, O. 2020. SIX6 is a TAL1-regulated transcription factor in T-ALL and associated with inferior outcome Leukemia & lymphoma 61 13: 3089-3100. 2020
• Loppi, Sanna; Korhonen, Paula; Bouvy-Liivrand, Maria; Cagliola, Simone; Turunen, Tiia A; Turunen, Mikko P; Hernandez de Sande, Ana; Kolosowska, Natalia; Scoyni, Flavia; Rosell, Anna; García-Berrocoso, Teresa; Lemarchant, Sighild; Dhungana, Hiramani; Montaner, Joan; Koistinaho, Jari; Kanninen, Katja M; Kaikkonen, Minna U; Giugno, Rosalba; Heinäniemi, Merja; Malm, Tarja. 2020. Peripheral inflammation preceeding ischemia impairs neuronal survival through mechanisms involving miR-127 in aged animals Aging cell 2021; 20 1: e13287. 2020
• Mehtonen, Juha; Teppo, Susanna; Lahnalampi, Mari; Kokko, Aleksi; Kaukonen, Riina; Oksa, Laura; Bouvy-Liivrand, Maria; Malyukova, Alena; Mäkinen, Artturi; Laukkanen, Saara; Mäkinen, Petri I; Rounioja, Samuli; Ruusuvuori, Pekka; Sangfelt, Olle; Lund, Riikka; Lönnberg, Tapio; Lohi, Olli; Heinäniemi, Merja. 2020. Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities Genome medicine 12 1: Article number: 99. 2020
• Moisio, Olli; Palani, Senthil; Virta, Jenni; Elo, Petri; Liljenbäck, Heidi; Tolvanen, Tuula; Käkelä, Meeri; Miner, Maxwell G; Herre, Erika Atencio; Marjamäki, Päivi; Örd, Tiit; Heinäniemi, Merja; Kaikkonen, Minna U; Zhang, Fenghua; Srinivasarao, Madduri; Knuuti, Juhani; Low, Philip S; Saraste, Antti; Li, Xiang-Guo; Roivainen, Anne. 2020. Radiosynthesis and preclinical evaluation of [ 68 Ga]Ga-NOTA-folate for PET imaging of folate receptor ß-positive macrophages Scientific reports 10 1: 13593. 2020
• Pölönen, P; Mehtonen, J; Lin, J; Liuksiala, T; Häyrynen, S; Teppo, S; Mäkinen, A; Kumar, A; Malani, D; Pohjolainen, V; Porkka, K; Heckman, CA; May, P; Hautamäki, V; Granberg, KJ; Lohi, O; Nykter, M; Heinäniemi, M. 2019. Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies Cancer research 79 10: 2466-2479. 2019
• Pölönen, P; Jawahar Deen, A; Leinonen, HM; Jyrkkänen, HK; Kuosmanen, S; Mononen, M; Jain, A; Tuomainen, T; Pasonen-Seppänen, S; Hartikainen, JM; Mannermaa, A; Nykter, M; Tavi, P; Johansen, T; Heinäniemi, M; Levonen, AL. 2019. Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma Oncogene 38: 7473-7490. 2019
• Ngo Trong, Trung; Mehtonen, Juha; González, Geraldo; Kramer, Roger; Hautamäki, Ville; Heinäniemi, Merja. 2019. Semisupervised Generative Autoencoder for Single-Cell Data Journal of computational biology [Published online: 2 December 2019]: 1-14. 2019
• Mehtonen, J; Pölönen, P; Häyrynen, S; Dufva, O; Lin, J; Liuksiala, T; Granberg, K; Lohi, O; Hautamäki, V; Nykter, M; Heinäniemi, M. 2019. Data-driven characterization of molecular phenotypes across heterogeneous sample collections Nucleic acids research 47 13: e76. 2019
• de Bock, Charles E; Demeyer, Sofie; Degryse, Sandrine; Verbeke, Delphine; Sweron, Bram; Gielen, Olga; Vandepoel, Roel; Vicente, Carmen; Vanden Bempt, Marlies; Dagklis, Antonis; Geerdens, Ellen; Bornschein, Simon; Gijsbers, Rik; Soulier, Jean; Meijerink, Jules P; Heinäniemi, Merja; Teppo, Susanna; Bouvy-Liivrand, Maria; Lohi, Olli; Radaelli Enrico et al.. 2018. HOXA9 cooperates with activated JAK/STAT signaling to drive leukemia development. Cancer Discovery 8 5: 616-631. 2018
• Bouvy-Liivrand Maria, Hernández de Sande Ana, Pölönen Petri, Mehtonen Juha, Vuorenmaa Tapio, Niskanen Henri, Sinkkonen Lasse, Unelma Kaikkonen Minna, Heinäniemi Merja. 2017. Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture. NUCLEIC ACIDS RESEARCH 45 17: 9837-9849. 2017
• Laukkanen, S; Grönroos, T; Pölönen, P; Kuusanmäki, H; Mehtonen, J; Cloos, J; Ossenkoppele, G; Gjertsen, B; Øystein, B; Heckman, C; Heinäniemi, M; Kontro, M; Lohi, O. 2017. In silico and preclinical drug screening identifies dasatinib as a targeted therapy for T-ALL Blood Cancer Journal 7: e604. 2017
• Niskanen, Henri; Tuszynska, Irina; Zaborowski, Rafal; Heinäniemi, Merja; Ylä-Herttuala, Seppo; Wilczynski, Bartek; Kaikkonen, Minna U. 2017. Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions NUCLEIC ACIDS RESEARCH 2018; 46 4: 1724-1740. 2017
• Teppo Susanna, Laukkanen Saara, Liuksiala Thomas, Nordlund Jessica, Oittinen Mikko, Teittinen Kaisa, Grönroos Toni, St-Onge Pascal, Sinnett Daniel, Syvänen Ann-Christine, Nykter Matti, Viiri Keijo, Heinäniemi Merja, Lohi Olli. 2016. Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia. Genome research 26: 1468-1477. 2016
• Heinäniemi Merja, Vuorenmaa Tapio, Teppo Susanna, Kaikkonen Minna U, Bouvy-Liivrand Maria, Mehtonen Juha, Niskanen Henri, Zachariadis Vasilios, Laukkanen Saara, Liuksiala Thomas, Teittinen Kaisa, Lohi Olli. 2016. Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots. Elife 5: e13087. 2016
• Pacheco Maria Pires, John Elisabeth, Kaoma Tony, Heinäniemi Merja, Nicot Nathalie, Vallar Laurent, Bueb Jean-Luc, Sinkkonen Lasse, Sauter Thomas. 2015. Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. BMC GENOMICS [ONLINE:HTTP://WWW.BIOMEDCENTRAL.COM/BMCGENOMICS/] 16:809. 2015
• Bouvy-Liivrand Maria, Heinäniemi Merja, John Elisabeth, Schneider Jochen G, Sauter Thomas, Sinkkonen Lasse. 2014. Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis. RNA Biology 11 1: 76-91. 2014
• Heinäniemi M, Nykter M, Kramer R, Wienecke-Baldacchino A, Sinkkonen L, Zhou JX, Kreisberg R, Kauffman SA, Huang S, Shmulevich I. 2013. Gene-pair expression signatures reveal lineage control. Nature Methods 10: 577-583. 2013
• Galhardo M, Sinkkonen L, Berninger P, Lin J, Sauter T, Heinäniemi M. 2013. Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. NUCLEIC ACIDS RESEARCH 2013 Nov 5. [Epub ahead of print]: --. 2013