̽»¨¾«Ñ¡

Mattias Rantalainen

Mattias Rantalainen

Senior Lecturer | Docent
Telephone: +46852482465
Visiting address: ,
Postal address: C8 Medicinsk epidemiologi och biostatistik, C8 MEB II Rantalainen, 171 77 Stockholm
Part of:

About me

  • The Predictive Medicine group focus on ̽»¨¾«Ñ¡ research that is driven by statistical machine learning, artificial intelligence and big data. Currently our main focus is on computational pathology. I am an associate professor (docent) at the Department of Medical Epidemiology and Biostatistics where I lead the Predictive Medicine group. 


  • I was previously a research fellow (2009-2013) with a joint affiliation at the Department of Statistics (University of Oxford) and at the Wellcome Trust Centre for Human Genetics (University of Oxford) where I worked with Professor Chris Holmes and Dr. Cecilia Lindgren. I was awarded a MRC Centenary Early Career Award (2012-2013) and a Medical Research Council (MRC) Special Training Fellowship in Bio̽»¨¾«Ñ¡ Informatics (2009-2012). I had a postdoctoral position working on the data analysis work package for the MolPAGE consortium in Prof Chris Holmes’ group at the Department of Statistics in Oxford (2008). I completed my PhD at Imperial College London where I developed novel multivariate pattern 
  • recognition methods with applications in metabonomics, working together with Professor Elaine Holmes and Professor Jeremy Nicholson. I have an undergraduate degree in
    Engineering Biology (combined BSc/MSc) from Umeå University in Sweden.

Research

  • The Predictive Medicine group focus on ̽»¨¾«Ñ¡ research that is driven by statistical machine learning, artificial intelligence (AI) and large population representative data sets. Currently our research is centered on projects in the computational pathology domain. 


  • We develop and apply statistical and machine learning methodologies for predictive modelling in bio̽»¨¾«Ñ¡ applications with a particular interest in precision medicine and cancer research. Our mission is to drive the development and application of data-driven approaches in cancer precision medicine and to develop and validate novel patient stratification models, including prognostic and treatment predictive applications. To achieve this we develop methods and models that allow us to transform large bio̽»¨¾«Ñ¡ data into clinically relevant predictions at the individual level. Some of our research is focused on clinical translation and implementation. Our research is based on large datasets (big-data) across multiple modalities including comprehensive molecular profiling (e.g. DNA- and RNA-sequencing), clinical information and ̽»¨¾«Ñ¡ imaging data (histopathology).

     

  • MAIN RESEARCH AREAS 


  • Computational pathology: AI (deep learning) driven research focusing on developing and validating models in the domain of cancer histopathology. The research is based on large population representative studies (we have >
  • 70, 000 WSIs collected in-house). The main focus is on breast, prostate and colorectal cancer (www.chimestudy.se &
  • www.abcap.org). I coordinate the Swedish AI Precision Pathology (SwAIPP) consortium, focusing on translation and implementation of AI-based pathology (www.swaipp.org) Cancer precision medicine:* Development and validation of predictive models for improved patient stratification, based on comprehensive molecular phenotyping data (e.g. DNA- and RNA-sequencing) 

  •  

  • CURRENT RESEARCH GRANTS (as PI)
    Our work is supported by Swedish Research Council (VR), Swedish Cancer Society, ERA PerMed, MEDTECHLABS, VINNOVA, SWElife, SeRC and ̽»¨¾«Ñ¡.

     

  • SUPERVISION OF PHD STUDENTS
    * Philippe Weitz (main supervisor)
    * Abhinav Sharma (main supervisor)
    * Dusan Rasic (co-supervisor)
    * Sandra Kristiane Sinius Pouplier (co-supervisor)
    * Tewodros Yalew (co-supervisor)
    * Quang Thinh Trac (co-supervisor)
    * Venkatesh Chellappa Patel (co-supervisor)
    * Xiaoyang Du (co-supervisor)

     

  • OTHER GROUP MEMBERS
    * Yanbo Feng (Postdoc)
    * Leslie Solorzano Vargas (Postdoc)
    * Bojing Liu (Postdoc)
    * Constance Boissin (Postdoc)
    * Duong Tran (Project assistant)
    * Yujie Xiang (Research assistant)
    * Ariane Buckenmeyer (Research technician)
    * Viktoria Sartor (MSc student)


    FORMER GROUP MEMBERS/SUPERVISED STUDENTS
    * Yinxi Wang (PhD student, main supervisor)
    * Peter Ström (PhD student, co-supervisor)
    * Pablo Gonzalez Ginestet (PhD student, co-supervisor)
    * Charlotte Von Heijne Widlund (visiting scientist)
    * Mei Wang (Postdoc

  • currently Research Assistant Professor, School of life science, Peking University, China)
    * Arvind Mer (Postdoc, currently Assistant Professor, University of Ottawa, Canada)
    * Nghia Vu (Postdoc
  • currently Assistant Professor, ̽»¨¾«Ñ¡, MEB)
    * Daniel Garcia León (Postdoc)
    * Astrid Helzen (Technician)
    * Balasz Acs (Associated postdoc)
    * Kajsa Ledesma Eriksson (MSc student)
    * Sandy Kang Lövgren (MSc student)
    * Anton Normelius (MSc student)
    * Boxi Zhang (MSc student)
    * Youcheng Zhang (MSc student)

     

  • SELECTED PUBLICATIONS
    Wang Y, Acs B, Robertson S, Liu B, Solorzano L, Wählby C, Hartman J, *Rantalainen M.* Improved breast cancer histological grading using deep
    learning, Annals of Oncology. 2022 33 (1), 89-98

    Wang Y, Kartasalo K, Valkonen M, Larsson C, Ruusuvuori P, Hartman J,  

  • *Rantalainen M.* Predicting molecular phenotypes from histopathology images: a transcriptome-wide expression-morphology analysis in breast cancer. Cancer Research. 2021 81 (19), 5115-5126
    Weitz P, Wang Y, Hartman J, *Rantalainen M*. An investigation of attention mechanisms in histopathology whole-slide-image analysis for regression
    objectives. In Proceedings of the IEEE/CVF International Conference on Computer Vision 2021 (pp. 611-619).
    Acs B, *Rantalainen M*, Hartman J., Artificial intelligence as the next step towards precision pathology. Journal of Internal Medicine. 2020 Mar 3.

    Liu B, Wang Y, Weitz P, Lindberg J, Egevad L, Grönberg H, Eklund M, *Rantalainen M.* Using deep learning to detect patients at risk for prostate cancer despite benign biopsies. iScience. 2022 25 (7) 104663

    Weitz P, Wang Y, Kartasalo K, Egevad L, Lindberg J, Grönberg H, Eklund M, *Rantalainen M.* Transcriptome-wide prediction of prostate cancer gene
    expression from histopathology images using co-expression based convolutional neural networks. Bioinformatics. 2022 38 (13), 3462-3469
    Ström, P., Kartasalo, K., Olsson, H., Solorzano, L., Delahunt, B., Berney, D.M., Bostwick, D.G., Evans, A.J., Grignon, D.J., Humphrey, P.A., Iczkowski, K.A.. Kench, J.G., Kristiansen, G., van der Kwast, T.H., Leite, K.R.M.,  

  • McKenneym, J.K., Oxley, J., Pan, C.C., Samaratunga, H., Srigley, J.R., Takahashi, H., Tsuzuki, T., Varma, M., Zhou, M., Lindberg, J., Lindeskog, C., Ruusuvuori, P, Wählby, C., Grönberg, H., *Rantalainen, M.*, Egevad,  
  • L., Eklund, M., Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study. /The Lancet Oncology/. 2020 Jan 8.
    Wang, M., Lindberg, J., Klevebring, D., Nilsson, C., Lehmann, S., Grönberg, H., *Rantalainen, M.*, Development and validation of a novel RNA sequencing-based prognostic score for acute myeloid leukemia, J Natl Cancer Inst, 2018 Mar 18 

  • Vu, T.N., Wills, Q.F., Kalari, K.R., Niu, N., Wang, L., Pawitan, Y., *Rantalainen M.*, Isoform-level gene expression patterns in single-cell RNA-sequencing data, Bioinformatics, 2018 Feb 1

    Wang, M., Klevebring, D., Lindberg, K., Czene, K., Grönberg, H., *Rantalainen M.*

  • Determining breast cancer histological grade from RNA 
  • sequencing data. Breast Cancer Research, 2016, 18(1). 

  • Vu, N.T., Wills, Q.F., Kalari, K.R., Niu, N., Wang, L., *Rantalainen M.*§, Pawitan Y.§. Beta-Poisson model for single-cell RNA-seq data analyses. Bioinformatics, 2016, btw202.

Teaching

  • Course director: "Multivariate prediction modelling with applications in precision medicine" ().

Articles

  • Journal article: BMC CANCER. 2024;24(1):1510
    Ekholm A; Wang Y; Vallon-Christersson J; Boissin C; Rantalainen M
  • Journal article: MEDICAL IMAGE ANALYSIS. 2024;97:103257
    Weitz P; Valkonen M; Solorzano L; Carr C; Kartasalo K; Boissin C; Koivukoski S; Kuusela A; Rasic D; Feng Y; Pouplier SS; Sharma A; Eriksson KL; Robertson S; Marzahl C; Gatenbee CD; Anderson ARA; Wodzinski M; Jurgas A; Marini N; Atzori M; Müller H; Budelmann D; Weiss N; Heldmann S; Lotz J; Wolterink JM; De Santi B; Patil A; Sethi A; Kondo S; Kasai S; Hirasawa K; Farrokh M; Kumar N; Greiner R; Latonen L; Laenkholm A-V; Hartman J; Ruusuvuori P; Rantalainen M
  • Journal article: BREAST CANCER RESEARCH. 2024;26(1):123
    Sharma A; Lovgren SK; Eriksson KL; Wang Y; Robertson S; Hartman J; Rantalainen M
  • Article: BREAST CANCER RESEARCH AND TREATMENT. 2024;206(1):163-175
    Wang Y; Sun W; Karlsson E; Lovgren SK; Acs B; Rantalainen M; Robertson S; Hartman J
  • Journal article: BREAST CANCER RESEARCH. 2024;26(1):90
    Boissin C; Wang Y; Sharma A; Weitz P; Karlsson E; Robertson S; Hartman J; Rantalainen M
  • Article: BREAST CANCER RESEARCH. 2024;26(1):17
    Sharma A; Weitz P; Wang Y; Liu B; Vallon-Christersson J; Hartman J; Rantalainen M
  • Article: EUROPEAN JOURNAL OF CANCER. 2023;191:112953
    Wang Y; Ali MA; Vallon-Christersson J; Humphreys K; Hartman J; Rantalainen M
  • Article: SCIENTIFIC DATA. 2023;10(1):562
    Weitz P; Valkonen M; Solorzano L; Carr C; Kartasalo K; Boissin C; Koivukoski S; Kuusela A; Rasic D; Feng Y; Pouplier SS; Sharma A; Eriksson KL; Latonen L; Laenkholm A-V; Hartman J; Ruusuvuori P; Rantalainen M
  • Article: NPJ PRECISION ONCOLOGY. 2023;7(1):32
    Trac QT; Pawitan Y; Mou T; Erkers T; Ostling P; Bohlin A; Osterroos A; Vesterlund M; Jafari R; Siavelis I; Backvall H; Kiviluoto S; Orre LM; Rantalainen M; Lehtio J; Lehmann S; Kallioniemi O; Vu TN
  • Article: ISCIENCE. 2022;25(7):104663
    Liu B; Wang Y; Weitz P; Lindberg J; Hartman J; Wang W; Egevad L; Gronberg H; Eklund M; Rantalainen M
  • Article: BIOINFORMATICS. 2022;38(13):3462-3469
    Weitz P; Wang Y; Kartasalo K; Egevad L; Lindberg J; Gronberg H; Eklund M; Rantalainen M
  • Article: ANNALS OF ONCOLOGY. 2022;33(1):89-98
    Wang Y; Acs B; Robertson S; Liu B; Solorzano L; Wahlby C; Hartman J; Rantalainen M
  • Article: CANCER RESEARCH. 2021;81(19):5115-5126
    Wang Y; Kartasalo K; Weitz P; Acs B; Valkonen M; Larsson C; Ruusuvuori P; Hartman J; Rantalainen M
  • Article: BLOOD ADVANCES. 2021;5(4):1003-1016
    Mareschal S; Palau A; Lindberg J; Ruminy P; Nilsson C; Bengtzen S; Engvall M; Eriksson A; Neddermeyer A; Marchand V; Jansson M; Bjorklund M; Jardin F; Rantalainen M; Lennartsson A; Cavelier L; Gronberg H; Lehmann S
  • Article: NATURE COMMUNICATIONS. 2021;12(1):1054
    Mer AS; Heath EM; Tonekaboni SAM; Dogan-Artun N; Nair SK; Murison A; Garcia-Prat L; Shlush L; Hurren R; Voisin V; Bader GD; Nislow C; Rantalainen M; Lehmann S; Gower M; Guidos CJ; Lupien M; Dick JE; Minden MD; Schimmer AD; Haibe-Kains B
  • Article: BLOOD CANCER JOURNAL. 2020;10(6):67
    Osterroos A; Bjorklund M; Eriksson A; Lindberg J; Nilsson C; Mareschal S; Rantalainen M; Gronberg H; Lehmann S
  • Article: THE LANCET ONCOLOGY. 2020;21(2):222-232
    Strom P; Kartasalo K; Olsson H; Solorzano L; Delahunt B; Berney DM; Bostwick DG; Evans AJ; Grignon DJ; Humphrey PA; Iczkowski KA; Kench JG; Kristiansen G; van der Kwast TH; Leite KRM; McKenney JK; Oxley J; Pan C-C; Samaratunga H; Srigley JR; Takahashi H; Tsuzuki T; Varma M; Zhou M; Lindberg J; Lindskog C; Ruusuvuori P; Wahlby C; Gronberg H; Rantalainen M; Egevad L; Eklund M
  • Article: CLINICAL CANCER RESEARCH. 2019;25(6):1766-1773
    De Laere B; Oeyen S; Mayrhofer M; Whitington T; van Dam P-J; Van Oyen P; Ghysel C; Ampe J; Ost P; Demey W; Hoekx L; Schrijvers D; Brouwers B; Lybaert W; Everaert EG; De Maeseneer D; Strijbos M; Bols A; Fransis K; Beije N; de Kruijff IE; van Dam V; Brouwer A; Goossens D; Heyrman L; Van den Eynden GG; Rutten A; Del Favero J; Rantalainen M; Rajan P; Sleijfer S; Ullen A; Yachnin J; Gronberg H; Van Laere SJ; Lindberg J; Dirix LY
  • Article: GENOME MEDICINE. 2018;10(1):85
    Mayrhofer M; De Laere B; Whitington T; Van Oyen P; Ghysel C; Ampe J; Ost P; Demey W; Hoekx L; Schrijvers D; Brouwers B; Lybaert W; Everaert E; De Maeseneer D; Strijbos M; Bols A; Fransis K; Oeyen S; van Dam P-J; Van den Eynden G; Rutten A; Aly M; Nordstrom T; Van Laere S; Rantalainen M; Rajan P; Egevad L; Ullen A; Yachnin J; Dirix L; Gronberg H; Lindberg J
  • Article: JOURNAL OF THE NATIONAL CANCER INSTITUTE. 2018;110(10):1094-1101
    Wang M; Lindberg J; Klevebring D; Nilsson C; Lehmann S; Gronberg H; Rantalainen M
  • Show more

All other publications

  • Review: EUROPEAN UROLOGY FOCUS. 2021;7(4):687-691
    Kartasalo K; Bulten W; Delahunt B; Chen P-HC; Pinckaers H; Olsson H; Ji X; Mulliqi N; Samaratunga H; Tsuzuki T; Lindberg J; Rantalainen M; Wahlby C; Litjens G; Ruusuvuori P; Egevad L; Eklund M
  • Review: JOURNAL OF INTERNAL MEDICINE. 2020;288(1):62-81
    Acs B; Rantalainen M; Hartman J
  • Letter: JAMA ONCOLOGY. 2019;5(7):1060-1062
    De Laere B; Rajan P; Gronberg H; Dirix L; Lindberg J; Mayrhofer M; Whitington T; van Dam P-J; Van Oyen P; Ghysel C; Ampe J; Ost P; Demey W; Hoela L; Schrijvers D; Brouwers B; Lybaert W; Everaert E; De Maeseneer D; Strijbos M; Bols A; Fransis K; Beije N; de Kruijff I; van Dam V; Brouwer A; Goossens D; Heyrman L; Van den Eynden G; Rutten A; Del Favero J; Rantalainen M; Sleijfer S; Ullen A; Yachnin J; Van Laere S; De laere L; Develter T; Vantieghem S; Herman S; Coifs G; Lamotte V; Boumans A; Baitar A; Haeck R; Wallays G

Employments

  • Senior Lecturer, Department of Medical Epidemiology and Biostatistics, ̽»¨¾«Ñ¡, 2020-

Degrees and Education

  • Docent, ̽»¨¾«Ñ¡, 2020

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