Merja Heinäniemi

Absolute copy number aware CNV calling of sub-megabase segments in ultra-low coverage single-cell DNA sequencing data

Kolbeinsdottir, Solrun; Zachariadis, Vasilios; Sommerauer, Christian; Lohi, Olli; Heinäniemi, Merja; Enge, Martin, 2025, Nucleic acids research, 53, 17, gkaf919. A1 Journal article (refereed), original research

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, 2, e70071. A1 Journal article (refereed), original research

Genomic determinants of therapy response in ETV6::RUNX1 leukemia

Oksa, Laura; Moisio, Sanni; Maqbool, Khurram; Kramer, Roger; Nikkilä, Atte; Jayasingha, Buddika; Mäkinen, Artturi; Foroughi-Asl, Hassan; Rounioja, Samuli; Suhonen, Janne; Krali, Olga; Voutilainen, Miikka; Lahnalampi, Mari; Vepsäläinen, Kaisa; Huang, Sui; Duque-Afonso, Jesus; Hauer, Julia; Nordlund, Jessica; Wirta, Valtteri; Lohi, Olli; Heinäniemi, Merja, 2025, Leukemia, 39, 9, 2125-2139. A1 Journal article (refereed), original research

MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution

de Sande, Ana Hernández; Turunen, Tanja; Bouvy-Liivrand, Maria; Örd, Tiit; Palani, Senthil; Lahnalampi, Mari; Tundidor-Centeno, Celia; Liljenbäck, Heidi; Virta, Jenni; Niskanen, Henri; Jayasingha, Buddika; Smålander, Olli-Pekka; Sinkkonen, Lasse; Mikkola, Lea; Sauter, Thomas; Roivainen, Anne; Lönnberg, Tapio; Kaikkonen, Minna U; Heinäniemi, Merja, 2025, Genome medicine, 17, 1, 112. A1 Journal article (refereed), original research

The Frequency but not the Phenotype of Circulating Peripheral T Helper Cells is Increased at Later Stages of Progression to Type 1 Diabetes

Schroderus, Anna Mari; Hanel, Andrea; Vandamme, Céline; Pitkänen, Viola; Rytkönen-Nissinen, Marja; Heinäniemi, Merja; Knip, Mikael; Veijola, Riitta; Toppari, Jorma; Ilonen, Jorma; Lempainen, Johanna; Kinnunen, Tuure, 2025, European journal of immunology, 55, 6, e51704. A1 Journal article (refereed), original research

Trajectories from single-cells to PAX5-driven leukemia reveal PAX5-MYC interplay in vivo

Auer, Franziska; Morcos, Mina N F; Sipola, Mikko; Akhtar, Irfan; Moisio, Sanni; Vogt, Julia; Haag, Rebecca; Lahnalampi, Mari; Tuononen, Tiina J; Hanel, Andrea; Viitasalo, Anna; Friedrich, Ulrike A; Dahl, Andreas; Prexler, Carolin; Pandyra, Aleksandra A; Stepensky, Polina; Takagi, Masatoshi; Borkhardt, Arndt; Heinäniemi, Merja; Hauer, Julia, 2025, Leukemia, 39, 7, 1607-1626. 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, 2024, Saqr, Mohammed; López-Pernas, Sonsoles, Learning Analytics Methods and Tutorials: A Practical Guide Using R, 95-119. 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, 1, 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, 6, 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, 11, 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, 1, 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, 2024, Saqr, Mohammed; López-Pernas, Sonsoles, Learning Analytics Methods and Tutorials: A Practical Guide Using R, 151-194. 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, 102644. 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, 13, 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, 24, 5821. 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, 3, 100276. 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, 1, 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, 12, 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, 17, 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, 9, 5174. 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, 3, 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, 7818, 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, 1, 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, 10, 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, 17, 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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Absolute copy number aware CNV calling of sub-megabase segments in ultra-low coverage single-cell DNA sequencing data

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

Genomic determinants of therapy response in ETV6::RUNX1 leukemia

MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution

The Frequency but not the Phenotype of Circulating Peripheral T Helper Cells is Increased at Later Stages of Progression to Type 1 Diabetes

Trajectories from single-cells to PAX5-driven leukemia reveal PAX5-MYC interplay in vivo

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