Myself.

Lukas Folkman
Research Fellow
bioinformatics | computational biology | data science | machine learning

Coastal and Marine Research Centre &
Institute for Integrated and Intelligent Systems
Griffith University, Australia



Curriculum vitae Contact Research & profiles Tools & downloads Publications




About me

I am a computer scientist with research interests in bioinformatics and developing machine learning methods for the life sciences. I earned my PhD from the Institute for Integrated and Intelligent Systems, Griffith University (Australia) in 2015, with a thesis on the prediction of stability and functional changes caused by genomic variants. Following this, I moved to Switzerland to continue my training as a postdoctoral fellow at ETH Zurich in the Machine Learning & Computational Biology Lab. There, my research focused on machine learning methods for precision medicine. In 2018, I moved to Austria to join CeMM Research Center for Molecular Medicine to develop machine learning methods for single-cell RNA-seq data analysis, for which I received European Commission's Marie Skล‚odowska-Curie Actions Postdoctoral Fellowship. While at CeMM, and later at the Institute of Artificial Intelligence, Medical University of Vienna, I was also the lead bioinformatician and data scientist for a project exploring epigenetic-immunological interplay and developed graph neural networks for virtual screening of small molecules. In 2022, I returned to Griffith University, where my research focuses on computer vision methods for marine wildlife monitoring and precision aquaculture at the Coastal and Marine Research Centre.


Contact

  • E-mail.


Research

  • bioinformatics and biomedical data science
  • machine learning for the life sciences
  • computer vision for precision aquaculture and ecology

Profiles

Tools & downloads

300BCG:
  Multi-omics analysis of innate and adaptive responses to BCG vaccination
300BCG
Source code on GitHub      Website

KRL:
  Kernelized rank learning for personalized drug recommendation

DDIG:
  Prediction of disease-causing genetic variants (indels, nonsense, and synonymous)

EASE-MM:
  Prediction of protein stability changes (ฮ”ฮ”G) induced by protein mutations
KRL
KRL
KRL
Source code on GitHub      Datasets Web server      Singularity container Web server      Singularity container


Publications

# denotes equal contributions

  • Moorlag# SJCFM, Folkman# L, ter Horst# R, Krausgruber# T, Barreca B, Schuster LC, Fife V, Matzaraki V, Li W, Reichl S, Mourits VP, Koeken VACM, de Bree LCJ, Dijkstra H, Lemmers H, van Cranenbroek B, van Rijssen E, Koenen HJPM, Joosten I, Xu C,Li Y, Joosten LAB, van Crevel R, Netea* MG & Bock* C (2024)
    Multi-omics analysis of innate and adaptive responses to BCG vaccination reveals epigenetic cell states that predict trained immunity
    Immunity 57(1), 171โ€“187
    ๐Ÿ“„ [Open access] [PubMed] [Press release] [Website] [GitHub]
    โ˜… Selected for Nature Research Highlights
  • Teufel LU, Matzaraki V, Folkman L, ter Horst R, Moorlag SJCFM, Mulders-Manders CM, Netea MG, Krausgruber T, Joosten LAB, Arts RJW (2024)
    Insights into the multifaceted role of interleukin-37 on human immune cell regulation
    Clinical Immunology 268(1), 110368
    ๐Ÿ“„ [Open access] [PubMed]
  • The Critical Assessment of Genome Interpretation Consortium (2024)
    CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
    Genome Biology 25, 53
    ๐Ÿ“„ [Open access] [PubMed]
  • de Bree LCJ, Mourits VP, Koeken VACM, Moorlag SJCFM, Janssen R, Folkman L, Barreca D, Krausgruber T, Fife-Gernedl V, Novakovic B, Arts RJW, Dijkstra H, Lemmers H, Bock C, Joosten LAB, van Crevel R, Benn CS & Netea MG (2020)
    Circadian rhythm influences induction of trained immunity by BCG vaccination
    The Journal of Clinical Investigation 130(10), 5603โ€“5617
    ๐Ÿ“„ [Open access] [PubMed]
  • Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, Pal LR, Savojardo C, Yin Y, Zhou Y, Radivojac P & Bromberg Y (2019)
    Assessment of methods for predicting the effects of PTEN and TPMT protein variants
    Human Mutation 40(9), 1495โ€“1506
    ๐Ÿ“„ [Article] [Open access via PMC] [PubMed] [CAGI5]
  • Savojardo C, Petrosino M, Babbi G, Bovo S, Corbiโ€Verge C, Casadio R, Fariselli P, Folkman L, Garg A, Karimi M, Katsonis P, Kim PM, Lichtarge O, Martelli PL, Pasquo A, Pal D, Shen Y, Strokach AV, Turina P, Zhou Y, Andreoletti G, Brenner S, Chiaraluce R, Consalvi V & Capriotti E (2019)
    Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge
    Human Mutation 40(9), 1392โ€“1399
    ๐Ÿ“„ [Article] [Open access via PMC] [PubMed] [CAGI5]
  • Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Nodzak C, Pal LR, Radivojac P, Savojardo C, Shi X, Zhou Y, Uppal A, Xu Q, Yin Y, Pejaver V, Wang M, Wei L, Moult J, Yu GK, Brenner SE & LeBowitz JH (2019)
    Assessment of predicted enzymatic activity of alphaโ€Nโ€acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016
    Human Mutation 40(9), 1519โ€“1529
    ๐Ÿ“„ [Article] [Open access via PMC] [PubMed] [CAGI4]
  • He# X, Folkman# L & Borgwardt K (2018)
    Kernelized rank learning for personalized drug recommendation
    Bioinformatics 34(16), 2808โ€“2816
    ๐Ÿ“„ [Open access] [Poster] [PubMed] [GitHub] [Datasets]
    โ˜… ISMB/ECCB 2017 and [BC]2 2017 best poster awards
  • Livingstone# M, Folkman# L, Yang Y, Zhang P, Mort M, Cooper DN, Liu Y, Stantic B & Zhou Y (2017)
    Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants
    Human Mutation 38(10), 1336โ€“1347
    ๐Ÿ“„ [Article] [Preprint] [PubMed] [Web server and datasets] [Singularity container]
  • Folkman L, Stantic B, Sattar A & Zhou Y (2016)
    EASE-MM: sequence-based prediction of mutation-induced stability changes with feature-based multiple models
    Journal of Molecular Biology, 428(6), 1394โ€“1405
    ๐Ÿ“„ [Article] [Preprint] [PubMed] [Web server and datasets] [Singularity container]
    โ˜… Ranked 3rd in the frataxin stability prediction during the Critical Assessment of Genome Interpretation 2018 competition
  • Folkman L, Yang Y, Li Z, Stantic B, Sattar B, Mort M, Cooper DN, Liu Y & Zhou Y (2015)
    DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations by sequence and structural properties at nucleotide and protein levels
    Bioinformatics 31(10), 1599โ€“1606
    ๐Ÿ“„ [Open access] [PubMed] [Web server and datasets] [Singularity container]
    โ˜… Winner of the Three Minutes Thesis Competition 2014 at the School of Information and Communication Technology, Griffith University
  • Folkman L, Stantic B & Sattar A (2014)
    Feature-based multiple models improve classification of mutation-induced stability changes
    BMC Genomics 15(Suppl 4), S6
    ๐Ÿ“„ [Open access] [PubMed]
  • Folkman L, Stantic B & Sattar A (2014)
    Towards sequence-based prediction of mutation-induced stability changes in unseen non-homologous proteins
    BMC Genomics 15(Suppl 1), S4
    ๐Ÿ“„ [Open access] [PubMed]
  • Folkman L, Stantic B & Sattar A (2013)
    Sequence-only evolutionary and predicted structural features for the prediction of stability changes in protein mutants
    BMC Bioinformatics 14(Suppl 2), S6
    ๐Ÿ“„ [Open access] [PubMed]
  • Higgs T, Folkman L & Stantic B (2013)
    Combining protein fragment feature-based resampling and local optimisation
    inย โ€˜IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB)โ€™, Vol. 7986 of LNCS, pp. 114โ€“125, Springer
    ๐Ÿ“„ [Article]
  • Folkman L, Pullan W & Stantic B (2011)
    Generic parallel genetic algorithm framework for protein optimisation
    inย โ€˜Algorithms and architectures for parallel processing (ICA3PP)โ€™, Vol. 7017 of LNCS, pp. 64โ€“73, Springer
    ๐Ÿ“„ [Article]
  • Stetsko A, Folkman L, & Matyas V (2010)
    Neighbor-based intrusion detection in wireless sensor networks
    inย โ€˜Wireless and Mobile Communications (ICWMC)โ€™, pp. 420โ€“42, IEEE
    ๐Ÿ“„ [Article]