Department of Computer Science

  • Finland

Publications 1977 2109

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2020

High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study

Pensar, J., Xu, Y., Puranen, S., Pesonen, M., Kabashima, Y. & Corander, J., Jan 2020, In : Computational Statistics & Data Analysis. 141, p. 62-76 15 p.

Research output: Contribution to journalArticleScientificpeer-review

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2019

Accurate Calibration Scheme for a Multi-Camera Mobile Mapping System

Khoramshahi, E., Campos, M. B., Tommaselli, A. M. G., Vilijanen, N., Mielonen, T., Kaartinen, H., Kukko, A. & Honkavaara, E., 25 Nov 2019, In : Remote Sensing. 11, 23, 22 p., 2778.

Research output: Contribution to journalArticleScientificpeer-review

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A Constrained Randomization Approach to Interactive Visual Data Exploration with Subjective Feedback

Kang, B., Puolamäki, K., Lijffijt, J. & Bie, T. D., 18 Apr 2019, In : IEEE Transactions on Knowledge and Data Engineering. 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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Action-Oriented Programming Model: Collective Executions and Interactions in the Fog

Mäkitalo, N., Aaltonen, T., Raatikainen, M., Ometov, A., Andreev, S., Koucheryavy, Y. & Mikkonen, T., Nov 2019, In : The Journal of Systems and Software. 157, 25 p., 110391.

Research output: Contribution to journalArticleScientificpeer-review

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Additive multivariate Gaussian processes for joint species distribution modeling with heterogeneous data

Vanhatalo, J. P., Hartmann, M. & Veneranta, L., 2019, In : Bayesian analysis.

Research output: Contribution to journalArticleScientificpeer-review

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A Faster Tree-Decomposition Based Algorithm for Counting Linear Extensions

Kangas, K., Koivisto, M. & Salonen, S., 3 Oct 2019, In : Algorithmica. 18 p.

Research output: Contribution to journalArticleScientificpeer-review

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A framework for space-efficient variable-order Markov models

Cunial, F., Alanko, J. & Belazzougui, D., 2019, In : Bioinformatics. 35, 22, p. 4607-4616 10 p.

Research output: Contribution to journalArticleScientificpeer-review

A Humboldtian approach to life and climate of the geological past: Estimating palaeotemperature from dental traits of mammalian communities

Oksanen, O., Zliobaite, I., Saarinen, J., Lawing, A. M. & Fortelius, M., Aug 2019, In : Journal of Biogeography. 46, 8, p. 1760-1776 17 p.

Research output: Contribution to journalArticleScientificpeer-review

ALDH1A1-related stemness in high-grade serous ovarian cancer is a negative prognostic indicator but potentially targetable by EGFR/mTOR-PI3K/aurora kinase inhibitors

Kaipio, K., Chen, P., Roering, P., Huhtinen, K., Mikkonen, P., Östling, P., Lehtinen, L., Mansuri, N., Korpela, T., Potdar, S., Hynninen, J., Auranen, A., Grénman, S., Wennerberg, K., Hautaniemi, S. & Carpén, O., 3 Dec 2019, In : Journal of Pathology. 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Algebraic methods in the congested clique

Censor-Hillel, K., Kaski, P., Korhonen, J. H., Lenzen, C., Paz, A. & Suomela, J., Dec 2019, In : Distributed Computing. 32, 6, p. 461-478 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Algorithms for learning parsimonious context trees

Eggeling, R., Grosse, I. & Koivisto, M., Jun 2019, In : Machine Learning. 108, 6, p. 879-911 33 p.

Research output: Contribution to journalArticleScientificpeer-review

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Aligning optical maps to de Bruijn graphs

Mukherjee, K., Alipanahi, B., Kahveci, T., Salmela, L. & Boucher, C., 15 Sep 2019, In : Bioinformatics. 35, 18, p. 3250-3256 7 p.

Research output: Contribution to journalArticleScientificpeer-review

A Logical Approach to Context-Specific Independence

Corander, J., Hyttinen, A., Kontinen, J., Pensar, J. & Väänänen, J., Sep 2019, In : Annals of Pure and Applied Logic. 170, 9, p. 975-992 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Anagrelide for Gastrointestinal Stromal Tumor

Pulkka, O-P., Gebreyohannes, Y. K., Wozniak, A., Mpindi, J-P., Tynninen, O., Icay, K., Cervera, A., Keskitalo, S., Murumägi, A., Kulesskiy, E., Laaksonen, M., Wennerberg, K., Varjosalo, M., Laakkonen, P., Lehtonen, R., Hautaniemi, S., Kallioniemi, O., Schöffski, P., Sihto, H. & Joensuu, H., 1 Mar 2019, In : Clinical Cancer Research. 25, 5, p. 1676-1687 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Anduril 2: Upgraded large-scale data integration framework

Cervera, A., Rantanen, V., Ovaska, K., Laakso, M., Nuñez-Fontarnau, J., Alkodsi, A., Casado, J., Facciotto, C., Häkkinen, A., Louhimo, R., Karinen, S., Zhang, K., Lavikka, K., Lyly, L., Pal Singh, M. & Hautaniemi, S., 2019, In : Bioinformatics. 35, 19, p. 3815-3817 3 p.

Research output: Contribution to journalArticleScientificpeer-review

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An Integrated Hardware/Software Design Methodology for Signal Processing Systems

Li, L., Sau, C., Fanni, T., Li, J., Viitanen, T., Christophe, F., Palumbo, F., Raffo, L., Huttunen, H., Takala, J. & Bhattacharyya, S. S., Feb 2019, In : Journal of Systems Architecture. 93, p. 1-19 19 p.

Research output: Contribution to journalArticleScientificpeer-review

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An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph

Cairo, M., Medvedev, P., Acosta, N. O., Rizzi, R. & Tomescu, A. I., Oct 2019, In : ACM Transactions on Algorithms. 15, 4, 17 p., 48.

Research output: Contribution to journalArticleScientificpeer-review

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An SDN Perspective on Multi-connectivity and Seamless Flow Migration

Hätönen, S., Huque, T. I. U., Rao, A., Jourjon, G., Gramoli, V. & Tarkoma, S., 2019, In : IEEE Networking Letters.

Research output: Contribution to journalArticleScientificpeer-review

Applying the Positional Burrows–Wheeler Transform to All-Pairs Hamming distance

Mäkinen, V. & Norri, T., Jun 2019, In : Information Processing Letters. 146, p. 17-19 3 p.

Research output: Contribution to journalArticleScientificpeer-review

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Bayesian meta-analysis across genome-wide association studies of diverse phenotypes

Trochet, H., Pirinen, M., Band, G., Jostins, L., McVean, G. & Spencer, C. C. A., Jul 2019, In : Genetic Epidemiology. 43, 5, p. 532-547 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Bit-parallel sequence-to-graph alignment

Rautiainen, M., Mäkinen, V. & Marschall, T., 1 Oct 2019, In : Bioinformatics. 35, 19, p. 3599-3607 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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Brand as a cognitive mediator: investigating the effect of media brands as a structural feature of textual news messages

Laaksonen, S-M., Falco, A., Salminen, M., Aula, P. S. & Ravaja, N., 8 Mar 2019, In : Journal of Product and Brand Management. 28, 1, p. 1-14 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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Breakthrough percepts of famous faces

Alsufyani, A., Hajilou, O., Zoumpoulaki, A., Filetti, M., Alsufyani, H., Solomon, C. J., Gibson, S. J., Alroobaea, R. & Bowman, H., Jan 2019, In : Psychophysiology. 56, 1, 20 p., 13279.

Research output: Contribution to journalArticleScientificpeer-review

Burst statistics in an early biofilm quorum sensing model: the role of spatial colony-growth heterogeneity

Kindler, O., Pulkkinen, O., Cherstvy, A. G. & Metzler, R., 19 Aug 2019, In : Scientific Reports. 9, 19 p., 12077.

Research output: Contribution to journalArticleScientificpeer-review

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Chemogenomic Analysis of the Druggable Kinome and Its Application to Repositioning and Lead Identification Studies

Ravikumar, B., Timonen, S., Alam, Z., Parri, E., Wennerberg, K. & Aittokallio, T., 21 Nov 2019, In : Cell chemical biology. 26, 11, p. 1608-1622 21 p.

Research output: Contribution to journalArticleScientificpeer-review

Cognitive ergonomics for data analysis. Experimental study of cognitive limitations in a data-based judgement task

Kalakoski, V., Henelius, A., Oikarinen, E., Ukkonen, A. & Puolamäki, K., 3 Oct 2019, In : Behaviour & Information Technology. 38, 10, p. 1038-1047 10 p.

Research output: Contribution to journalArticleScientificpeer-review

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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Menden, M. P., Wang, D., Mason, M. J., Szalai, B., Bulusu, K. C., Guan, Y., Yu, T., Kang, J., Jeon, M., Wolfinger, R., Nguyen, T., Zaslavskiy, M., Abante, J., Abecassis, B. S., Aben, N., Aghamirzaie, D., Aittokallio, T., Akhtari, F. S., Al-lazikani, B., Alam, T. & 280 others, Allam, A., Allen, C., de Almeida, M. P., Altarawy, D., Alves, V., Amadoz, A., Anchang, B., Antolin, A. A., Ash, J. R., Aznar, V. R., Ba-alawi, W., Bagheri, M., Bajic, V., Ball, G., Ballester, P. J., Baptista, D., Bare, C., Bateson, M., Bender, A., Bertrand, D., Wijayawardena, B., Boroevich, K. A., Bosdriesz, E., Bougouffa, S., Bounova, G., Brouwer, T., Bryant, B., Calaza, M., Calderone, A., Calza, S., Capuzzi, S., Carbonell-Caballero, J., Carlin, D., Carter, H., Castagnoli, L., Celebi, R., Cesareni, G., Chang, H., Chen, G., Chen, H., Chen, H., Cheng, L., Chernomoretz, A., Chicco, D., Cho, K-H., Cho, S., Choi, D., Choi, J., Choi, K., Choi, M., Cock, M. D., Coker, E., Cortes-Ciriano, I., Cserzö, M., Cubuk, C., Curtis, C., Daele, D. V., Dang, C. C., Dijkstra, T., Dopazo, J., Draghici, S., Drosou, A., Dumontier, M., Ehrhart, F., Eid, F-E., ElHefnawi, M., Elmarakeby, H., van Engelen, B., Engin, H. B., de Esch, I., Evelo, C., Falcao, A. O., Farag, S., Fernandez-Lozano, C., Fisch, K., Flobak, A., Fornari, C., Foroushani, A. B. K., Fotso, D. C., Fourches, D., Friend, S., Frigessi, A., Gao, F., Gao, X., Gerold, J. M., Gestraud, P., Ghosh, S., Gillberg, J., Godoy-Lorite, A., Godynyuk, L., Godzik, A., Goldenberg, A., Gomez-Cabrero, D., Gonen, M., de Graaf, C., Gray, H., Grechkin, M., Guimera, R., Guney, E., Haibe-Kains, B., Han, Y., Hase, T., He, D., He, L., Heath, L. S., Hellton, K. H., Helmer-Citterich, M., Hidalgo, M. R., Hidru, D., Hill, S. M., Hochreiter, S., Hong, S., Hovig, E., Hsueh, Y-C., Hu, Z., Huang, J. K., Huang, R. S., Hunyady, L., Hwang, J., Hwang, T. H., Hwang, W., Hwang, Y., Isayev, O., Don’t Walk, O. B., Jack, J., Jahandideh, S., Ji, J., Jo, Y., Kamola, P. J., Kanev, G. K., Karacosta, L., Karimi, M., Kaski, S., Kazanov, M., Khamis, A. M., Khan, S. A., Kiani, N. A., Kim, A., Kim, J., Kim, J., Kim, K., Kim, K., Kim, S., Kim, Y., Kim, Y., Kirk, P. D. W., Kitano, H., Klambauer, G., Knowles, D., Ko, M., Kohn-Luque, A., Kooistra, A. J., Kuenemann, M. A., Kuiper, M., Kurz, C., Kwon, M., van Laarhoven, T., Laegreid, A., Lederer, S., Lee, H., Lee, J., Lee, Y. W., Lepp_aho, E., Lewis, R., Li, J., Li, L., Liley, J., Lim, W. K., Lin, C., Liu, Y., Lopez, Y., Low, J., Lysenko, A., Machado, D., Madhukar, N., Maeyer, D. D., Malpartida, A. B., Mamitsuka, H., Marabita, F., Marchal, K., Marttinen, P., Mason, D., Mazaheri, A., Mehmood, A., Mehreen, A., Michaut, M., Miller, R. A., Mitsopoulos, C., Modos, D., Moerbeke, M. V., Moo, K., Motsinger-Reif, A., Movva, R., Muraru, S., Muratov, E., Mushthofa, M., Nagarajan, N., Nakken, S., Nath, A., Neuvial, P., Newton, R., Ning, Z., Niz, C. D., Oliva, B., Olsen, C., Palmeri, A., Panesar, B., Papadopoulos, S., Park, J., Park, S., Park, S., Pawitan, Y., Peluso, D., Pendyala, S., Peng, J., Perfetto, L., Pirro, S., Plevritis, S., Politi, R., Poon, H., Porta, E., Prellner, I., Preuer, K., Pujana, M. A., Ramnarine, R., Reid, J. E., Reyal, F., Richardson, S., Ricketts, C., Rieswijk, L., Rocha, M., Rodriguez-Gonzalvez, C., Roell, K., Rotroff, D., de Ruiter, J. R., Rukawa, P., Sadacca, B., Safikhani, Z., Safitri, F., Sales-Pardo, M., Sauer, S., Schlichting, M., Seoane, J. A., Serra, J., Shang, M-M., Sharma, A., Sharma, H., Shen, Y., Shiga, M., Shin, M., Shkedy, Z., Shopsowitz, K., Sinai, S., Skola, D., Smirnov, P., Soerensen, I. F., Soerensen, P., Song, J-H., Song, S. O., Soufan, O., Spitzmueller, A., Steipe, B., Suphavilai, C., Tamayo, S. P., Tamborero, D., Tang, J., Tanoli, Z-R., Tarres-Deulofeu, M., Tegner, J., Thommesen, L., Tonekaboni, S. A. M., Tran, H., Troyer, E. D., Truong, A., Tsunoda, T., Turu, G., Tzeng, G-Y., Verbeke, L., Videla, S. & Consortium, A-S. D. C. DREAM., 17 Jun 2019, In : Nature Communications. 10, 1, 17 p., 2674.

Research output: Contribution to journalArticleScientificpeer-review

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Computational Creativity Infrastructure for Online Software Composition: A Conceptual Blending Use Case

Martins, P., Goncalo Oliveira, H., Carlos Gonçalves, J., Cruz, A., Cardoso, A., Žnidaršič, M., Lavrač, N., Linkola, S., Toivonen, H., Hervás, R., Méndez, G. & Gervás, P., 8 Feb 2019, In : IBM Journal of Research and Development. 63, 1, p. 9:1-9:17 17 p., 9.

Research output: Contribution to journalArticleScientificpeer-review

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Concept drift over geological times: predictive modeling baselines for analyzing the mammalian fossil record

Žliobaite, I., May 2019, In : Data Mining and Knowledge Discovery. 33, 3, p. 773-803 31 p.

Research output: Contribution to journalArticleScientificpeer-review

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Conceptual Representations for Computational Concept Creation

Xiao, P., Toivonen, H., Gross, O., Cardoso, A., Correia, J., Machado, P., Martins, P., Goncalo Oliveira, H., Sharma, R., Pinto, A. M., Diaz, A., Francisco, V., Gervás, P., Hervas, R., León, C., Forth, J., Purver, M., Wiggins, G. A., Miljkovic, D., Podpecan, V. & 8 others, Pollak, S., Kralj, J., Znidarsic, M., Bohanec, M., Lavrač, N., Urbancic, T., Van Der Velde, F. & Battersby, S., Feb 2019, In : ACM Computing Surveys. 52, 1, 33 p., 9.

Research output: Contribution to journalArticleScientificpeer-review

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Cost-effective survival prediction for patients with advanced prostate cancer using clinical trial and real-world hospital registry datasets

Murtojärvi, M., Halkola, A. S., Airola, A., Laajala, T. D., Mirtti, T., Aittokallio, T. & Pahikkala, T., 17 Nov 2019, In : International Journal of Medical Informatics. 133

Research output: Contribution to journalArticleScientificpeer-review

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Counting graded lattices of rank 3 that have few coatoms

Kohonen, J., Jun 2019, In : International Journal of Algebra and Computation. 29, 4, p. 663-680 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Counting Linear Extensions: Parameterizations by Treewidth

Eiben, E., Ganian, R., Kangas, K. & Ordyniak, S., Apr 2019, In : Algorithmica. 81, 4, p. 1657-1683 27 p.

Research output: Contribution to journalArticleScientificpeer-review

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Crowd Replication: Sensing-Assisted Quantification of Human Behaviour in Public Spaces

Hemminki, J. J. S., Nurmi, P. T., Tarkoma, S. A. O., Konomi, SI. & KURIBAYASHI, K., 2019, (Accepted/In press) In : ACM transactions on spatial algorithms and systems.

Research output: Contribution to journalArticleScientificpeer-review

DALI and the persistence of protein shape

Holm, L., 13 Nov 2019, In : Protein Science. 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Dandelion: A Unified Code Offloading System for Wearable Computing

Golkarifard, M., Yang, J., Huang, Z., Movaghar, A. & Hui, P., 1 Mar 2019, In : IEEE Transactions on Mobile Computing. 18, 3, p. 546-559 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Decoding attentional states for neurofeedback: Mindfulness vs. wandering thoughts

Zhigalov, A., Heinilä, E., Parviainen, T., Parkkonen, L. & Hyvärinen, A., 15 Jan 2019, In : NeuroImage. 185, p. 565-574 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Density-Friendly Graph Decomposition

Tatti, N., Oct 2019, In : ACM Transactions on Knowledge Discovery from Data. 13, 5, 29 p., 54.

Research output: Contribution to journalArticleScientificpeer-review

Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.

Merla, C., Rodrigues, C., Passet, V., Corbella, M., Thorpe, H. A., Kallonen, T. V. S., Zong, Z., Marone, P., Bandi, C., Sassera, D., Corander, J., Feil, E. J. & Brisse, S., 25 Oct 2019, In : Frontiers in Microbiology. 10, 9 p., 2360.

Research output: Contribution to journalArticleScientificpeer-review

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Developing hand-worn input and haptic support for real-world target finding

Hsieh, Y-T., Jylhä, A., Orso, V., Andolina, S., Hoggan, E., Gamberini, L. & Jacucci, G., Feb 2019, In : Personal and Ubiquitous Computing. 23, 1, p. 117-132 16 p.

Research output: Contribution to journalArticleScientificpeer-review

DevOps in practice: A multiple case study of five companies

Lwakatare, L. E., Kilamo, T., Karvonen, T., Sauvola, T., Heikkilä, V., Itkonen, J., Kuvaja, P., Mikkonen, T., Oivo, M. & Lassenius, C., Oct 2019, In : Information and Software Technology. 114, p. 217-230 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Diet and brood size in rural and urban Northern Goshawks Accipiter gentilis in southern Finland

Solonen, T., Lokki, H. & Sulkava, S., Feb 2019, In : Avian Biology Research. 12, 1, p. 3-9 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Distinct subtypes of diffuse large B-cell lymphoma defined by hypermutated genes

Alkodsi, A., Cervera, A., Zhang, K., Louhimo, R., Meriranta, L., Pasanen, A., Leivonen, S-K., Holte, H., Leppä, S., Lehtonen, R. & Hautaniemi, S., Nov 2019, In : Leukemia. 33, 11, p. 2662-2672 11 p.

Research output: Contribution to journalArticleScientificpeer-review

DNMT Inhibitors Increase Methylation in the Cancer Genome

Giri, A. K. & Aittokallio, T., 24 Apr 2019, In : Frontiers in Pharmacology. 10, 11 p., 385.

Research output: Contribution to journalArticleScientificpeer-review

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Dominant TOM1 mutation associated with combined immunodeficiency and autoimmune disease

Keskitalo, S., Haapaniemi, E. M., Glumoff, V., Liu, X., Lehtinen, V., Fogarty, C., Rajala, H., Chiang, S. C., Mustjoki, S., Kovanen, P., Lohi, J., Bryceson, Y. T., Seppänen, M., Kere, J., Heiskanen, K. & Varjosalo, M., 27 Jun 2019, In : Npj genomic medicine. 4, 7 p., 14.

Research output: Contribution to journalArticleScientificpeer-review

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Doubly Stochastic Neighbor Embedding on Spheres

Lu, Y., Corander, J. & Yang, Z., 1 Dec 2019, In : Pattern Recognition Letters. 128, p. 100-106 7 p.

Research output: Contribution to journalArticleScientificpeer-review

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Effects of live music therapy on heart rate variability and self-reported stress and anxiety among hospitalized pregnant women: A randomized controlled trial

Teckenberg-Jansson, P., Turunen, S., Pölkki, T., Lauri-Haikala, M-J., Lipsanen, J., Henelius, A., Aitokallio-Tallberg, A., Pakarinen, S., Leinikka, M. & Huotilainen, M., 2019, In : Nordic Journal of Music Therapy. 28, 1, p. 7-26 20 p.

Research output: Contribution to journalArticleScientificpeer-review

Energy-Efficient Power Control of Train-Ground mmWave Communication for High-Speed Trains

Wang, L., Ai, B., Niu, Y., Chen, X. & Hui, P., Aug 2019, In : IEEE Transactions on Vehicular Technology. 68, 8, p. 7704-7714 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Evoking Physiological Synchrony and Empathy Using Social VR with Biofeedback

Salminen, M., Järvelä, S., Ruonala, A., Harjunen, V. J., Jacucci, G., Hamari, J. & Ravaja, N., 9 Dec 2019, In : IEEE Transactions on Affective Computing. 1949-3045.

Research output: Contribution to journalArticleScientificpeer-review

Evolutionary Hysteresis and Ratchets in the Evolution of Periodical Cicadas

Toivonen, J. & Fromhage, L., 1 Jul 2019, In : American Naturalist. 194, 1, p. 38-46 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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