PUBLICATIONS

 

2018

  1. Klukowski, P., Augoff, M., Zieba, M., Drwal, M., Gonczarek, A., and Walczak, M. J. (2018). NMRNet: A deep learning approach to automated peak picking of protein NMR spectra. Bioinformatics.

  2. Klukowski, P. and Schubert, M. (2018). Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics. Bioinformatics.

  3. Klukowski, P., Augoff, M., Zamorski, M., Gonczarek, A., and Walczak, M. J. (2018). Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra. J. Biomol NMR,71(1),11-18.

  4. Zięba, M., Klukowski, P., Gonczarek, A., Nikolaev, Y., and Walczak, M. J. (2018). Gaussian process regression for automated signal tracking in step-wise perturbed nuclear magnetic resonance spectra. Applied Soft Computing, 68, 162-171.

  5. Klukowski, P., Gonczarek, A. (2018). Towards fully automated protein structure elucidation with NMR spectroscopy, The 3rd International workshop on biomedical informatics with optimization and machine learning (BOOM), 55th International Conference on Machine Learning (ICML), Stockholm, Sweden.

2017

  1. Gonczarek, A., Klukowski, P., Drwal, M., Świątek, P. (2017). A Bayesian Framework for Chemical Shift Assignment, Asian Conference on Intelligent Information and Database Systems (ACIIDS), Kanazawa, Japan.

2016

  1. Klukowski, P. , Gonczarek, A. (2016). Deep Structured Models for Protein Structure Studies with Nuclear Magnetic Resonance Spectroscopy, PhD forum, The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Riva del Garda, Italy.

2015

  1. Morales-Navarrete, H., Segovia-Miranda, F., Klukowski, P., Meyer, K., Nonaka, H., Marsico, G., Chernykh, M., Kalaidzidis, A., Zerial, M., and Kalaidzidis, Y. (2015). A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture. Elife.

  2. Klukowski, P., Gonczarek, A., and Walczak, M. J. (2015). A benchmark for automated peak picking of protein NMR spectra, IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB), Niagara Falls, Canada.

  3. Klukowski, P., Walczak, M. J., Gonczarek, A., Boudet, J., and Wider, G. (2015). Computer vision-based automated peak picking applied to protein NMR spectra. Bioinformatics, 31(18), 2981–2988.

 

 

SELECTED PROJECTS

 

Deep convolutional neural network
for an automated signal selection in protein NMR spectra

 

Chemical shift-based identification
of oligosaccharide topology

Image analysis for confocal microscopy in the context of 3D liver tissue architecture studies

Commercial projects

X 2014 - ...

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II 2016 - VI 2018

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VII 2013 - VII 2014

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RECENT WORK

 

2018/6/6

Our manuscript "Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics" has been accepted in Bioinformatics. 

Open access article is available here. The algorithm proposed in the paper is accessible by the web page glyconmrsearch.nmrhub.eu

 

2018/5/28

Our manuscript "Towards fully automated protein structure elucidation with NMR spectroscopy" has been accepted at BOOM workshop (ICML 2018).

 

 

2018/3/4

Our manuscript "NMRNet: A deep learning approach to automated peak picking of protein NMR spectra" has been accepted in Bioinformatics.

 

CONTACT DETAILS

E-mail:
Building C-3, room 121
Department of Computer Science
Wrocław University of Technology
Wybrzeże Stanisława Wyspiańskiego 27
50-370 Wrocław, Poland