Merja Heinäniemi

Dynamic evolution of TCF3‐PBX1 leukemias at the single‐cell level under chemotherapy pressure

Kusterer, Mira; Lahnalampi, Mari; Voutilainen, Minna; Brand, Alexandra; Pennisi, Sandra; Norona, Johana; Gentile, Gaia; Herzog, Heike; Greve, Gabriele; Lübbert, Michael; Sipola, Mikko; Kaartinen, Emma; Sankowski, Roman; Prinz, Marco; Killmer, Saskia; Lago, Marilyn S.; Bengsch, Bertram; Cysar, Stepan R.; Aumann, Konrad; Werner, Martin; Duyster, Justus; Lohi, Olli; Heinäniemi, Merja; Duque‐Afonso, Jesús. 2025. HemaSphere. 9: 1-18 A1 Journal article (refereed), original research

An R Approach to Data Cleaning and Wrangling for Education Research

Kopra, Juho; Tikka, Santtu; Heinäniemi, Merja; López-Pernas, Sonsoles; Saqr, Mohammed. Teoksessa: Saqr, Mohammed; López-Pernas, Sonsoles(toim.) , 2024. Learning Analytics Methods and Tutorials: A Practical Guide Using R. s. 95-119. Springer A3 Book section, Chapters in research books

Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Gezelius, Henrik; Enblad, Anna Pia; Lundmark, Anders; Åberg, Martin; Blom, Kristin; Rudfeldt, Jakob; Raine, Amanda; Harila, Arja; Rendo, Verónica; Heinäniemi, Merja; Andersson, Claes; Nordlund, Jessica. 2024. NAR genomics and bioinformatics. 6: . lqae001 A1 Journal article (refereed), original research

Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells in Vitro

Selvarajan, Ilakya; Kiema, Miika; Huang, Ru Ting; Li, Jin; Zhu, Jiayu; Pölönen, Petri; Örd, Tiit; Õunap, Kadri; Godiwala, Mehvash; Golebiewski, Anna Kathryn; Ravindran, Aarthi; Mäklin, Kiira; Toropainen, Anu; Stolze, Lindsey K; Arce, Maximiliano; Magnusson, Peetra U; White, Stephen; Romanoski, Casey E; Heinäniemi, Merja; Laakkonen, Johanna P; Fang, Yun; Kaikkonen, Minna U. 2024. Arteriosclerosis, thrombosis, and vascular biology. 44: 1330-1345 A1 Journal article (refereed), original research

Development of combination therapies with BTK inhibitors and dasatinib to treat CNS-infiltrating E2A-PBX1+/preBCR+ ALL

Gentile, Gaia; Poggio, Teresa; Catalano, Antonella; Voutilainen, Minna; Lahnalampi, Mari; Andrade-Martinez, Marta; Ma, Tobias; Sankowski, Roman; Goncharenko, Lina; Tholen, Stefan; Han, Kyuho; Morgens, David W.; Prinz, Marco; Lübbert, Michael; Engel, Sophia; Hartmann, Tanja Nicole; Cario, Gunnar; Schrappe, Martin; Lenk, Lennart; Stanulla, Martin; Duyster, Justus; Bronsert, Peter; Bassik, Michael C.; Cleary, Michael L.; Schilling, Oliver; Heinäniemi, Merja; Duque-Afonso, Jesús. 2024. Blood advances. 8: 2846-2860 A1 Journal article (refereed), original research

Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia

Malyukova, Alena; Lahnalampi, Mari; Falqués-Costa, Ton; Pölönen, Petri; Sipola, Mikko; Mehtonen, Juha; Teppo, Susanna; Akopyan, Karen; Viiliainen, Johanna; Lohi, Olli; Hagström-Andersson, Anna K; Heinäniemi, Merja; Sangfelt, Olle. 2024. Genome biology. 25: . 143 A1 Journal article (refereed), original research

Visualizing and Reporting Educational Data with R

López-Pernas, Sonsoles; Misiejuk, Kamila; Tikka, Santtu; Kopra, Juho; Heinäniemi, Merja; Saqr, Mohammed. Teoksessa: Saqr, Mohammed; López-Pernas, Sonsoles(toim.) , 2024. Learning Analytics Methods and Tutorials: A Practical Guide Using R. s. 151-194. Springer A3 Book section, Chapters in research books

A pan-cancer analysis shows immunoevasive characteristics in NRF2 hyperactive squamous malignancies

Härkönen, Jouni; Pölönen, Petri; Deen, Ashik Jawahar; Selvarajan, Ilakya; Teppo, Hanna-Riikka; Dimova, Elitsa Y.; Kietzmann, Thomas; Ahtiainen, Maarit; Väyrynen, Juha P.; Väyrynen, Sara A.; Elomaa, Hanna; Tynkkynen, Niko; Eklund, Tiia; Kuopio, Teijo; Talvitie, Eva-Maria; Taimen, Pekka; Kallajoki, Markku; Kaikkonen, Minna U.; Heinäniemi, Merja; Levonen, Anna-Liisa. 2023. Redox biology. 61: A1 Journal article (refereed), original research

Erythroid/megakaryocytic differentiation confers BCL-XL dependency and venetoclax resistance in acute myeloid leukemia

Kuusanmäki, Heikki; Dufva, Olli; Vähä-Koskela, Markus; Leppä, Aino-Maija; Huuhtanen, Jani; Vänttinen, Ida Maria; Nygren, Petra Johanna; Klievink, Jay; Bouhlal, Jonas Otto Vilhelm; Pölönen, Petri; Zhang, Qi; Adnan Awad, Shady; Mancebo-Pérez, Cristina; Saad, Joseph; Miettinen, Juho J.; Javarappa, Komal Kumar; Aakko, Sofia; Ruokoranta, Tanja; Eldfors, Samuli; Heinäniemi, Merja; Theilgaard-Mönch, Kim; Wartiovaara-Kautto, Ulla; Keränen, Mikko A I; Porkka, Kimmo; Konopleva, Marina; Wennerberg, Krister. 2023. Blood. 141: 1610-1625 A1 Journal article (refereed), original research

Generation of a Zebrafish Knock-In Model Recapitulating Childhood ETV6::RUNX1-Positive B-Cell Precursor Acute Lymphoblastic Leukemia

Zapilko, Veronika; Moisio, Sanni; Parikka, Mataleena; Heinäniemi, Merja; Lohi, Olli. 2023. Cancers. 15: A1 Journal article (refereed), original research

Genomic Determinants of Therapy Response in ETV6::RUNX1 Leukemia

Oksa, Laura; Moisio, Sanni; Maqbool, Khurram; Foroughi-Asl, Hassan; Kramer, Roger; Nikkilä, Atte; Vepsäläinen, Kaisa; Duque-Afonso, Jesus; Hauer, Julia; Nordlund, Jessica; Wirta, Valtteri; Lohi, Olli; Heinäniemi, Merja. 2023. Blood abstract

In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution

Fischer, Anja; Lersch, Robert; de Andrade Krätzig, Niklas; Strong, Alexander; Friedrich, Mathias J.; Weber, Julia; Engleitner, Thomas; Öllinger, Rupert; Yen, Hsi-Yu; Kohlhofer, Ursula; Gonzalez-Menendez, Irene; Sailer, David; Kogan, Liz; Lahnalampi, Mari; Laukkanen, Saara; Kaltenbacher, Thorsten; Klement, Christine; Rezaei, Majdaddin; Ammon, Tim; Montero, Juan J.; Schneider, Günter; Mayerle, Julia; Heikenwälder, Mathias; Schmidt-Supprian, Marc; Quintanilla-Martinez, Leticia; Steiger, Katja; Liu,. 2023. Cell genomics. 3: A1 Journal article (refereed), original research

Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

Krali, Olga; Marincevic-Zuniga, Yanara; Arvidsson, Gustav; Enblad, Anna Pia; Lundmark, Anders; Sayyab, Shumaila; Zachariadis, Vasilios; Heinäniemi, Merja; Suhonen, Janne; Oksa, Laura; Vepsäläinen, Kaisa; Öfverholm, Ingegerd; Barbany, Gisela; Nordgren, Ann; Lilljebjörn, Henrik; Fioretos, Thoas; Madsen, Hans O; Marquart, Hanne Vibeke; Flaegstad, Trond; Forestier, Erik; Jónsson, Ólafur G; Kanerva, Jukka; Lohi, Olli; Norén-Nyström, Ulrika; Schmiegelow, Kjeld; Harila, Arja; Heyman, Mats; Lönnerholm, . 2023. npj precision oncology. 7: . 131 A1 Journal article (refereed), original research

Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers

Dufva, Olli; Gandolfi, Sara; Huuhtanen, Jani; Dashevsky, Olga; Duàn, Hanna; Saeed, Khalid; Klievink, Jay; Nygren, Petra; Bouhlal, Jonas; Lahtela, Jenni; Näätänen, Anna; Ghimire, Bishwa R.; Hannunen, Tiina; Ellonen, Pekka; Lähteenmäki, Hanna; Rumm, Pauliina; Theodoropoulos, Jason; Laajala, Essi; Härkönen, Jouni; Pölönen, Petri; Heinäniemi, Merja; Hollmén, Maija; Yamano, Shizuka; Shirasaki, Ryosuke; Barbie, David A.; Roth, Jennifer A.; Romee, Rizwan; Sheffer, Michal; Lähdesmäki, Harri; Lee, Dean A. 2023. Immunity. 56: 2816-2835.e13 A1 Journal article (refereed), original research

Combination therapies to inhibit LCK tyrosine kinase and mTOR signaling in T-cell Acute Lymphoblastic Leukemia

Laukkanen, Saara; Bacquelaine Veloso, Alexandra; Yan, Chuan; Oksa, Laura; Alpert, Eric J.; Do, Daniel; Hyvärinen, Noora; McCarthy, Karin; Adhikari, Abhinav; Yang, Qiqi; Iyer, Sowmya; Garcia, Sara P.; Pello, Annukka; Ruokoranta, Tanja; Moisio, Sanni; Adhikari, Sadiksha; Yoder, Jeffrey A.; Gallagher, Kayleigh Mary; Whelton, Lauren; Allen, James R.; Jin, Alexander Hai; Loontiens, Siebe; Heinäniemi, Merja; Kelliher, Michelle A; Heckman, Caroline A.; Lohi, Olli; Langenau, David M. 2022. Blood. 140: 1891–1906 A1 Journal article (refereed), original research

Recurrent Germline Variant in RAD21 Predisposes Children to Lymphoblastic Leukemia or Lymphoma

Schedel, Anne; Friedrich, Ulrike Anne; Morcos, Mina N. F.; Wagener, Rabea; Mehtonen, Juha; Watrin, Titus; Saitta, Claudia; Brozou, Triantafyllia; Michler, Pia; Walter, Carolin; Försti, Asta; Baksi, Arka; Menzel, Maria; Horak, Peter; Paramasivam, Nagarajan; Fazio, Grazia; Autry, Robert J; Fröhling, Stefan; Suttorp, Meinolf; Gertzen, Christoph; Gohlke, Holger; Bhatia, Sanil; Wadt, Karin; Schmiegelow, Kjeld; Dugas, Martin; Richter, Daniela; Glimm, Hanno; Heinäniemi, Merja; Jessberger, Rolf; Cazzani. 2022. International journal of molecular sciences. 23: A1 Journal article (refereed), original research

Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data

Turunen, Tanja; Hernández de Sande, Ana; Pölönen, Petri; Heinäniemi, Merja. 2021. Computational and Structural Biotechnology Journal. 19: 1944-1955 A1 Journal article (refereed), original research

Immunogenomic Landscape of Hematological Malignancies

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. Cancer cell. 38: 380-399.e13 A1 Journal article (refereed), original research

Signalling input from divergent pathways subverts B cell transformation

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. Nature. 583: 845-851 A1 Journal article (refereed), original research

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

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. Genome medicine. 12: Article number: 99 A1 Journal article (refereed), original research

Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies

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. Cancer research. 79: 2466-2479 A1 Journal article (refereed), original research

Semisupervised Generative Autoencoder for Single-Cell Data

Ngo Trong, Trung; Mehtonen, Juha; González, Geraldo; Kramer, Roger; Hautamäki, Ville; Heinäniemi, Merja. 2019. Journal of computational biology. [Published online: 2 December 2019]: 1-14 A1 Journal article (refereed), original research

Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture

Bouvy-Liivrand Maria, Hernández de Sande Ana, Pölönen Petri, Mehtonen Juha, Vuorenmaa Tapio, Niskanen Henri, Sinkkonen Lasse, Unelma Kaikkonen Minna, Heinäniemi Merja. 2017. Nucleic acids research. 45: 9837-9849 A1 Journal article (refereed), original research

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia

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 research. 26: 1468-1477 A1 Journal article (refereed), original research

Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots

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. eLife. 5: e13087 A1 Journal article (refereed), original research

Gene-pair expression signatures reveal lineage control

Heinäniemi M, Nykter M, Kramer R, Wienecke-Baldacchino A, Sinkkonen L, Zhou JX, Kreisberg R, Kauffman SA, Huang S, Shmulevich I. 2013. Nature methods. 10: 577-583 A1 Journal article (refereed), original research

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Dynamic evolution of TCF3‐PBX1 leukemias at the single‐cell level under chemotherapy pressure

An R Approach to Data Cleaning and Wrangling for Education Research

Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells in Vitro

Development of combination therapies with BTK inhibitors and dasatinib to treat CNS-infiltrating E2A-PBX1+/preBCR+ ALL

ECCB2024: The 23rd European Conference on Computational Biology

Getting Started with R for Education Research

Introductory Statistics with R for Educational Researchers

Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia

Visualizing and Reporting Educational Data with R

A pan-cancer analysis shows immunoevasive characteristics in NRF2 hyperactive squamous malignancies

Erythroid/megakaryocytic differentiation confers BCL-XL dependency and venetoclax resistance in acute myeloid leukemia

Generation of a Zebrafish Knock-In Model Recapitulating Childhood ETV6::RUNX1-Positive B-Cell Precursor Acute Lymphoblastic Leukemia

Genomic Determinants of Therapy Response in ETV6::RUNX1 Leukemia

In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution

Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers

Combination therapies to inhibit LCK tyrosine kinase and mTOR signaling in T-cell Acute Lymphoblastic Leukemia

Recurrent Germline Variant in RAD21 Predisposes Children to Lymphoblastic Leukemia or Lymphoma

Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data

Immunogenomic Landscape of Hematological Malignancies

Signalling input from divergent pathways subverts B cell transformation

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

Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies

Semisupervised Generative Autoencoder for Single-Cell Data

Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia

Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots

Gene-pair expression signatures reveal lineage control