• A unified framework for analysis of individual-based models in ecology and beyond 

      Cornell, Stephen J; Suprunenko, Yevhen F; Finkelshtein, Dmitri; Somervuo, Panu; Ovaskainen, Otso (Journal article; Peer reviewed, 2019)
      Individual-based models,‘IBMs’, describe naturally the dynamics of interacting organisms orsocial orfinancial agents. They are considered too complex for mathematical analysis, butcomputer simulations of them cannot give ...
    • Domain-specific neural networks improve automated bird sound recognition already with small amount of local data 

      Lauha, Patrik; Somervuo, Panu; Lehikoinen, Petteri; Geres, Lisa; Richter, Tobias; Seibold, Sebastian; Ovaskainen, Otso (Peer reviewed; Journal article, 2022)
      An automatic bird sound recognition system is a useful tool for collecting data of different bird species for ecological analysis. Together with autonomous recording units (ARUs), such a system provides a possibility to ...
    • Ecological signals of arctic plant-microbe associations are consistent across eDNA and vegetation surveys 

      Parisy, Bastien; Schmidt, Niels M.; Wirta, Helena; Stewart, Lærke Søndergaard; Pellissier, Loic; Holben, William E.; Pannoni, Sam; Somervuo, Panu; Jones, Mirkka M.; Siren, Jukka; Vesterinen, Eero; Ovaskainen, Otso Tapio; Roslin, Tomas (Peer reviewed; Journal article, 2023)
      Understanding how different taxa respond to abiotic characteristics of the environment is of key interest for understanding the assembly of communities. Yet, whether eDNA data will suffice to accurately capture environmental ...
    • Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient 

      Abrego, Nerea; Huotari, Tea; Tack, Ayco J.M.; Lindahl, Björn D.; Tikhonov, Gleb; Somervuo, Panu; Schmidt, Niels Martin; Ovaskainen, Otso; Roslin, Tomas (Peer reviewed; Journal article, 2020)
      How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate ...
    • Mathematical and simulation methods for deriving extinction thresholds in spatial and stochastic models of interacting agents 

      Ovaskainen, Otso; Somervuo, Panu; Finkelshtein, Dmitri (Peer reviewed; Journal article, 2021)
      In ecology, one of the most fundamental questions relates to the persistence of populations, or conversely to the probability of their extinction. Deriving extinction thresholds and characterizing other critical phenomena ...
    • A molecular-based identification resource for the arthropods of Finland 

      Roslin, Tomas; Somervuo, Panu; Pentinsaari, Mikko; Hebert, Paul D. N.; Agda, Jireh; Ahlroth, Petri; Anttonen, Perttu; Aspi, Jouni; Blagoev, Gergin; Blanco, Santiago; Chan, Dean; Clayhills, Tom; deWaard, Jeremy; deWaard, Stephanie; Elliot, Tyler; Elo, Riikka; Haapala, Sami; Helve, Eero; Ilmonen, Jari; Hirvonen, Petri; Ho, Chris; Itämies, Juhani; Ivanov, Vladislav; Jakovlev, Jevgeni; Juslén, Aino; Jussila, Reijo; Kahanpää, Jere; Kaila, Lauri; Kaitila, Jari-Pekka; Kakko, Ari; Kakko, Iiro; Karhu, Ali; Karjalainen, Sami; Kjærandsen, Jostein; Koskinen, Janne; Laasonen, Erkki M.; Laasonen, Leena; Laine, Erkka; Lampila, Petri; Levesque-Beaudin, Valerie; Lu, Liuqiong; Lähteenaro, Meri; Majuri, Pekka; Malmberg, Sampsa; Manjunath, Ramya; Martikainen, Petri; Mattila, Jaakko; McKeown, Jaclyn; Metsälä, Petri; Miklasevskaja, Margarita; Miller, Meredith; Miskie, Renee; Muinonen, Arto; Mukkala, Veli-Matti; Naik, Suresh; Nikolova, Nadia; Nupponen, Kari; Ovaskainen, Otso; Österblad, Ika; Paasivirta, Lauri; Pajunen, Timo; Parkko, Petri; Paukkunen, Juho; Penttinen, Ritva; Perez, Kate; Pohjoismäki, Jaakko; Prosser, Sean; Raekunnas, Martti; Rahulan, Miduna; Rannisto, Meeri; Ratnasingham, Sujeevan; Raukko, Pekka; Rinne, Aki; Rintala, Teemu; Miranda Romo, Susana; Salmela, Jukka; Salokannel, Juha; Savolainen, Riitta; Schulman, Leif; Sihvonen, Pasi; Soliman, Dina; Sones, Jayme; Steinke, Claudia; Ståhls, Gunilla; Tabell, Jukka; Tiusanen, Mikko; Várkonyi, Gergely; Vesterinen, Eero J.; Viitanen, Esko; Vikberg, Veli; Viitasaari, Matti; Vilen, Jussi; Warne, Connor; Wei, Catherine; Winqvist, Kaj; Zakharov, Evgeny; Mutanen, Marko (Peer reviewed; Journal article, 2022)
      To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference ...
    • Monitoring Fungal Communities With the Global Spore Sampling Project 

      Ovaskainen, Otso; Abrego, Nerea; Somervuo, Panu; Palorinne, Isabella; Hardwick, Bess; Pitkänen, Juha-Matti; Andrew, Nigel R.; Niklaus, Pascal A.; Schmidt, Niels Martin; Seibold, Sebastian; Vogt, Juliane; Zakharov, Evgeny V.; Hebert, Paul D. N.; Roslin, Tomas; Ivanova, Natalia V. (Peer reviewed; Journal article, 2020)
      The kingdom Fungi is a megadiverse group represented in all ecosystem types. The global diversity and distribution of fungal taxa are poorly known, in part due to the limitations related to traditional fruit-body survey ...
    • PROTAX-Sound: A probabilistic framework for automated animal sound identification 

      De Camargo, Ulisses Moliterno; Somervuo, Panu; Ovaskainen, Otso (Journal article; Peer reviewed, 2017)
      Autonomous audio recording is stimulating new field in bioacoustics, with a great promise for conducting cost-effective species surveys. One major current challenge is the lack of reliable classifiers capable of multi-species ...
    • Spatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems 

      Hamis, Sara; Somervuo, Panu; Ågren, J Arvid; Tadele, Dagim Shiferaw; Kesseli, Juha; Scott, Jacob G.; Nykter, Matti; Gerlee, Philip; Finkelshtein, Dmitri; Ovaskainen, Otso Tapio (Peer reviewed; Journal article, 2023)
      Theoretical and applied cancer studies that use individual-based models (IBMs) have been limited by the lack of a mathematical formulation that enables rigorous analysis of these models. However, spatial cumulant models ...
    • A Successful Crowdsourcing Approach for Bird Sound Classification 

      Lehikoinen, Petteri; Rannisto, Meeri; Camargo, Ulisses; Aintila, Aki; Lauha, Patrik; Piirainen, Esko; Somervuo, Panu; Ovaskainen, Otso Tapio (Peer reviewed; Journal article, 2023)
      Automated recorders are increasingly used in remote sensing of wildlife, yet automated methods of processing the audio remains challenging. Identifying animal sounds with machine learning provides a solution, but optimizing ...