Myself.

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

Institute for Artificial Intelligence, Medical University of Vienna, Austria
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences



Curriculum vitae Contact Research & profiles Tools & downloads Publications




Contact

  • E-mail.

Research

  • machine learning, data science, computational biology
  • explainable deep learning for single-cell transcriptomics
  • graph neural networks for molecular property prediction
  • in silico drug recommendation and precision medicine
  • prediction of disease-causing and functionally-relevant genomic variants
  • integrative statistical analysis of high-dimensional datasets

Profiles


Tools & downloads
KRL
KRL
KRL

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
Source code on GitHub      Datasets Web server      Singularity container Web server      Singularity container


Publications

# denotes equal contributions

  • 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]