Paweł Widera

School of Computing
Newcastle University
1 Science Square
Newcastle, NE4 5TG, UK

Office: 5.014
E-mail: name.surname@ncl.ac.uk
GPG key: 4096R/BBCFE170

Lecturer

PhD - Univerisity of Nottingham, UK
MSc, BSc - Poznań University of Technology, Poland

Research Interests

bioinformatics, evolutionary algorithms, heuristics and metaheuristics, interactive data visualisation, machine learning

Publications

Current

• DOI BibTeX
  P. Widera, P.M. Welsing, S.O. Danso, S. Peelen, M. Kloppenburg, M. Loef, A.C. Marijnissen, E.M. van Helvoort, F.J. Blanco, J. Magalhães, F. Berenbaum, I.K. Haugen, A. Bay-Jensen, A. Mobasheri, C. Ladel, J. Loughlin, F.P. Lafeber, A. Lalande, J. Larkin, H. Weinans, J. Bacardit
  Development and validation of a machine learning-supported strategy of patient selection for osteoarthritis clinical trials: the IMI-APPROACH study
  in Osteoarthritis and Cartilage Open, 5(4):100406, December 2023

  @ARTICLE{Widera2023,
    author = {Widera, Paweł and Welsing, Paco M. J. and Danso, Samuel O. and Peelen, Sjaak and Kloppenburg, Margreet and Loef, Marieke and Marijnissen, Anne C. and van Helvoort, Eefje M. and Blanco, Francisco J. and Magalhães, Joana and Berenbaum, Francis and Haugen, Ida K. and Bay-Jensen, Anne-Christine and Mobasheri, Ali and Ladel, Christoph and Loughlin, John and Lafeber, Floris P. J. G. and Lalande, Agnès and Larkin, Jonathan and Weinans, Harrie and Bacardit, Jaume},
    title = {{D}evelopment and validation of a machine learning-supported strategy of patient selection for osteoarthritis clinical trials: the {IMI-APPROACH} study},
    year = 2023,
    month = dec,
    doi = {10.1016/j.ocarto.2023.100406},
    journal = {Osteoarthritis and Cartilage Open},
    volume = {5},
    number = {4},
    pages = {100406}
  }
  

• DOI BibTeX
  F. Angelini, P. Widera, A. Mobasheri, J. Blair, A. Struglics, M. Uebelhoer, Y. Henrotin, A.C. Marijnissen, M. Kloppenburg, F. Blanco, I.K. Haugen, F. Berenbaum, C. Ladel, J. Larkin, A. Bay-Jensen, J. Bacardit
  Osteoarthritis endotype discovery via clustering of biochemical marker data
  in Annals of the Rheumatic Diseases, 81(5):666–675, March 2022

  @ARTICLE{Angelini2022,
    author = {Angelini, Federico and Widera, Pawe{\l} and Mobasheri, Ali and Blair, Joseph and Struglics, Andr{\'{e}} and Uebelhoer, Melanie and Henrotin, Yves and Marijnissen, Anne CA and Kloppenburg, Margreet and Blanco, Francisco and Haugen, Ida K and Berenbaum, Francis and Ladel, Christoph and Larkin, Jonathan and Bay-Jensen, Anne and Bacardit, Jaume},
    title = {{O}steoarthritis endotype discovery via clustering of biochemical marker data},
    year = 2022,
    month = mar,
    doi = {10.1136/annrheumdis-2021-221763},
    journal = {Annals of the Rheumatic Diseases},
    volume = {81},
    number = {5},
    pages = {666--675}
  }
  

• DOI BibTeX
  E.M. van Helvoort, C. Ladel, S. Mastbergen, M. Kloppenburg, F.J. Blanco, I.K. Haugen, F. Berenbaum, J. Bacardit, P. Widera, P.M. Welsing, F. Lafeber
  Baseline clinical characteristics of predicted structural and pain progressors in the IMI-APPROACH knee OA cohort
  in RMD Open, 7(3), August 2021

  @ARTICLE{Helvoort2021,
    author = {van Helvoort, Eefje Martine and Ladel, Christoph and Mastbergen, Simon and Kloppenburg, Margreet and Blanco, Francisco J. and Haugen, Ida K. and Berenbaum, Francis and Bacardit, Jaume and Widera, Paweł and Welsing, Paco M.J. and Lafeber, Floris},
    title = {{B}aseline clinical characteristics of predicted structural and pain progressors in the {IMI}-{APPROACH} knee {OA} cohort},
    year = 2021,
    month = aug,
    doi = {10.1136/rmdopen-2021-001759},
    journal = {RMD Open},
    volume = {7},
    number = {3}
  }
  

• DOI eprint data BibTeX
  P. Widera, P.M. Welsing, C. Ladel, J. Loughlin, F.P. Lafeber, F. Petit Dop, J. Larkin, H. Weinans, A. Mobasheri, J. Bacardit
  Multi-classifier prediction of knee osteoarthritis progression from incomplete imbalanced longitudinal data
  in Scientific Reports, 10(1), May 2020

  @ARTICLE{Widera2020,
    author = {Widera, Paweł and Welsing, Paco M. J. and Ladel, Christoph and Loughlin, John and Lafeber, Floris P. J. G. and Petit Dop, Florence and Larkin, Jonathan and Weinans, Harrie and Mobasheri, Ali and Bacardit, Jaume},
    title = {{M}ulti-classifier prediction of knee osteoarthritis progression from incomplete imbalanced longitudinal data},
    year = 2020,
    month = may,
    doi = {10.1038/s41598-020-64643-8},
    journal = {Scientific Reports},
    volume = {10},
    number = {1}
  }
  

• DOI BibTeX
  J. Tellechea-Luzardo, C. Winterhalter, P. Widera, J. Kozyra, V. de Lorenzo, N. Krasnogor
  Linking engineered cells to their digital twins: a version control system for strain engineering
  in ACS Synthetic Biology, 9(3):536–545, February 2020

  @ARTICLE{Tellechea-Luzardo2020,
    author = {Tellechea-Luzardo, Jonathan and Winterhalter, Charles and Widera, Pawe{\l} and Kozyra, Jerzy and de Lorenzo, V{\'{\i}}ctor and Krasnogor, Natalio},
    title = {{L}inking engineered cells to their digital twins: a version control system for strain engineering},
    year = 2020,
    month = feb,
    doi = {10.1021/acssynbio.9b00400},
    journal = {ACS Synthetic Biology},
    volume = {9},
    number = {3},
    pages = {536--545}
  }
  

• DOI eprint code BibTeX
  N. Lazzarini, P. Widera, S. Williamson, R. Heer, N. Krasnogor, J. Bacardit
  Functional networks inference from rule-based machine learning models
  in BioData Mining, 9(1), December 2016

  @ARTICLE{Lazzarini2016,
    author = {Lazzarini, Nicola and Widera, Paweł and Williamson, Stuart and Heer, Rakesh and Krasnogor, Natalio and Bacardit, Jaume},
    title = {{F}unctional networks inference from rule-based machine learning models},
    year = 2016,
    month = dec,
    doi = {10.1186/s13040-016-0106-4},
    journal = {BioData Mining},
    volume = {9},
    number = {1}
  }
  

• DOI eprint code BibTeX
  D. Sanassy, P. Widera, N. Krasnogor
  Meta-stochastic simulation of biochemical models for Systems and Synthetic Biology
  in ACS Synthetic Biology, 4(1):39–47, January 2015

  @ARTICLE{Sanassy2015,
    author = {Sanassy, Daven and Widera, Paweł and Krasnogor, Natalio},
    title = {{M}eta-stochastic simulation of biochemical models for {S}ystems and {S}ynthetic {B}iology},
    year = 2015,
    month = jan,
    doi = {10.1021/sb5001406},
    journal = {ACS Synthetic Biology},
    volume = {4},
    number = {1},
    pages = {39--47}
  }
  

• DOI code BibTeX
  J. Blakes, O. Raz, U. Feige, J. Bacardit, P. Widera, T. Ben-Yehezkel, E. Shapiro, N. Krasnogor
  A heuristic for maximizing DNA reuse in synthetic DNA library assembly
  in ACS Synthetic Biology, 3(8):529–542, August 2014

  @ARTICLE{Blakes2014,
    author = {Blakes, Jonathan and Raz, Ofir and Feige, Uriel and Bacardit, Jaume and Widera, Paweł and Ben-Yehezkel, Tuval and Shapiro, Ehud and Krasnogor, Natalio},
    title = {{A} heuristic for maximizing {DNA} reuse in synthetic {DNA} library assembly},
    year = 2014,
    month = aug,
    doi = {10.1021/sb400161v},
    journal = {ACS Synthetic Biology},
    volume = {3},
    number = {8},
    pages = {529--542}
  }
  

• DOI eprint code BibTeX
  C. Winterhalter, P. Widera, N. Krasnogor
  JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks
  in Bioinformatics, 30(7):1029–1030, April 2014

  @ARTICLE{Winterhalter2014,
    author = {Winterhalter, Charles and Widera, Paweł and Krasnogor, Natalio},
    title = {{JEPETTO}: a {C}ytoscape plugin for gene set enrichment and topological analysis based on interaction networks},
    year = 2014,
    month = apr,
    doi = {10.1093/bioinformatics/btt732},
    journal = {Bioinformatics},
    volume = {30},
    number = {7},
    pages = {1029--1030}
  }
  

• DOI BibTeX
  B.J. Dekkers, S. Pearce, R.P. van Bolderen-Veldkamp, A. Marshall, P. Widera, J. Gilbert, H. Drost, G.W. Bassel, K. Müller, J.R. King, A.T. Wood, I. Grosse, M. Quint, N. Krasnogor, G. Leubner-Metzger, M.J. Holdsworth, L. Bentsink
  Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination
  in Plant Physiology, 163(1):205–215, September 2013

  @ARTICLE{Dekkers2013,
    author = {Dekkers, Bas J. W. and Pearce, Simon and van Bolderen-Veldkamp, R. P. and Marshall, Alex and Widera, Paweł and Gilbert, James and Drost, Hajk-Georg and Bassel, George W. and Müller, Kerstin and King, John R. and Wood, Andrew T. A. and Grosse, Ivo and Quint, Marcel and Krasnogor, Natalio and Leubner-Metzger, Gerhard and Holdsworth, Michael J. and Bentsink, Leónie},
    title = {{T}ranscriptional dynamics of two seed compartments with opposing roles in {A}rabidopsis seed germination},
    year = 2013,
    month = sep,
    doi = {10.1104/pp.113.223511},
    journal = {Plant Physiology},
    volume = {163},
    number = {1},
    pages = {205--215}
  }
  

• DOI eprint BibTeX
  J. Bacardit, P. Widera, A. Marquez-Chamorro, F. Divina, J.S. Aguilar-Ruiz, N. Krasnogor
  Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features
  in Bioinformatics, 28(19):2441–2448, October 2012

  @ARTICLE{Bacardit2012,
    author = {Bacardit, Jaume and Widera, Paweł and Marquez-Chamorro, A. and Divina, F. and Aguilar-Ruiz, J. S. and Krasnogor, Natalio},
    title = {{C}ontact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features},
    year = 2012,
    month = oct,
    doi = {10.1093/bioinformatics/bts472},
    journal = {Bioinformatics},
    volume = {28},
    number = {19},
    pages = {2441--2448}
  }
  

• DOI eprint code BibTeX
  P. Widera, N. Krasnogor
  Protein Models Comparator: scalable bioinformatics computing on the Google App Engine platform
  in Computing Research Repository, arXiv:1102.4293v2, July 2011

  @ARTICLE{Widera2011,
    author = {Widera, Paweł and Krasnogor, Natalio},
    title = {{P}rotein {M}odels {C}omparator: scalable bioinformatics computing on the {G}oogle {A}pp {E}ngine platform},
    year = 2011,
    month = jul,
    doi = {10.48550/arXiv.1102.4293},
    journal = {Computing Research Repository},
    volume = {arXiv:1102.4293v2}
  }
  

• DOI eprint BibTeX
  P. Widera, J. Bacardit, N. Krasnogor, C. García-Martínez, M. Lozano
  Evolutionary symbolic discovery for bioinformatics, systems and synthetic biology
  in Proceedings of the 12th Annual Conference Companion on Genetic and Evolutionary Computation, p.1991–1998, Portland, USA, July 2010

  @INPROCEEDINGS{Widera2010a,
    author = {Widera, Paweł and Bacardit, Jaume and Krasnogor, Natalio and García-Martínez, Carlos and Lozano, Manuel},
    title = {{E}volutionary symbolic discovery for bioinformatics, systems and synthetic biology},
    year = 2010,
    month = jul,
    doi = {10.1145/1830761.1830842},
    booktitle = {Proceedings of the 12th Annual Conference Companion on Genetic and Evolutionary Computation},
    pages = {1991--1998},
    address = {Portland, USA}
  }
  

• DOI eprint data BibTeX
  P. Widera, J.M. Garibaldi, N. Krasnogor
  GP challenge: evolving energy function for protein structure prediction
  in Genetic Programming and Evolvable Machines, 11(1):61–88, March 2010

  @ARTICLE{Widera2010,
    author = {Widera, Paweł and Garibaldi, Jonathan M. and Krasnogor, Natalio},
    title = {{GP} challenge: evolving energy function for protein structure prediction},
    year = 2010,
    month = mar,
    doi = {10.1007/s10710-009-9087-0},
    journal = {Genetic Programming and Evolvable Machines},
    volume = {11},
    number = {1},
    pages = {61--88}
  }
  

• DOI eprint BibTeX
  P. Widera, J.M. Garibaldi, N. Krasnogor
  Evolutionary design of the energy function for protein structure prediction
  in 2009 IEEE Congress on Evolutionary Computation, p.1305–1312, Trondheim, Norway, May 2009

  @INPROCEEDINGS{Widera2009,
    author = {Widera, Paweł and Garibaldi, Jonathan M. and Krasnogor, Natalio},
    title = {{E}volutionary design of the energy function for protein structure prediction},
    year = 2009,
    month = may,
    doi = {10.1109/CEC.2009.4983095},
    booktitle = {2009 IEEE Congress on Evolutionary Computation},
    pages = {1305--1312},
    address = {Trondheim, Norway}
  }
  

Past

• DOI eprint BibTeX
  J. Błażewicz, M. Figlerowicz, P. Formanowicz, M. Kasprzak, B. Nowierski, R. Styszyński, Ł. Szajkowski, P. Widera, M. Wiktorczyk
  Assembling the SARS-CoV genome — new method based on graph theoretical approach
  in Acta Biochimica Polonica, 51(4):983-993, October 2004

  @ARTICLE{Blazewicz2004b,
    author = {Błażewicz, Jacek and Figlerowicz, Marek and Formanowicz, Piotr and Kasprzak, Marta and Nowierski, Bartosz and Styszyński, Rafał and Szajkowski, Łukasz and Widera, Paweł and Wiktorczyk, Mariusz},
    title = {{A}ssembling the {SARS}-{C}o{V} genome --- new method based on graph theoretical approach},
    year = 2004,
    month = oct,
    doi = {10.18388/abp.2004_3531},
    journal = {Acta Biochimica Polonica},
    volume = {51},
    number = {4},
    pages = {983-993}
  }
  

• DOI eprint BibTeX
  J. Błażewicz, M. Figlerowicz, P. Jackowiak, D. Janny, D. Jarczyński, M. Kasprzak, M. Nalewaj, B. Nowierski, R. Styszyński, Ł. Szajkowski, P. Widera
  Parallel DNA sequence assembly
  in 5th Mexican International Conference on Computer Science (ENC 2004), p.378–382, Colima, Mexico, September 2004
  Parallel Computing Systems conference

  @INPROCEEDINGS{Blazewicz2004a,
    author = {Błażewicz, Jacek and Figlerowicz, Marek and Jackowiak, Przemysław and Janny, Dariusz and Jarczyński, Dariusz and Kasprzak, Marta and Nalewaj, Maciej and Nowierski, Bartosz and Styszyński, Rafał and Szajkowski, Łukasz and Widera, Paweł},
    title = {{P}arallel {DNA} sequence assembly},
    year = 2004,
    month = sep,
    doi = {10.1109/ENC.2004.1342630},
    booktitle = {5th Mexican International Conference on Computer Science (ENC 2004)},
    pages = {378--382},
    address = {Colima, Mexico}
  }
  

• eprint BibTeX
  J. Błażewicz, M. Kasprzak, P. Jackowiak, D. Janny, D. Jarczyński, M. Nalewaj, B. Nowierski, R. Styszyński, S. Łukasz, W. Paweł
  ASM — DNA assembly application
  Poznań Supercomputing and Networking Center technical report, RA-001/2004, March 2004

  @TECHREPORT{Blazewicz2004,
    author = {Błażewicz, Jacek and Kasprzak, Marta and Jackowiak, Przemysław and Janny, Dariusz and Jarczyński, Dariusz and Nalewaj, Maciej and Nowierski, Bartosz and Styszyński, Rafał and Łukasz, Szajkowski and Paweł, Widera},
    title = {{ASM} --- {DNA} assembly application},
    year = 2004,
    month = mar,
    institution = {Poznań Supercomputing and Networking Center},
    number = {RA-001/2004}
  }
  

• BibTeX
  J. Błażewicz, M. Kasprzak, T. Redliński, R. Styszyński, M. Werla, P. Widera
  Bioportal – the DNA sequence assembly algorithms
  Poznań Supercomputing and Networking Center technical report, RA-003/2002, November 2002
  (in Polish, a summary of my B.Sc. thesis)

  @TECHREPORT{Blazewicz2002,
    author = {Błażewicz, Jacek and Kasprzak, Marta and Redliński, Tomasz and Styszyński, Rafał and Werla, Marcin and Widera, Paweł},
    title = {{B}ioportal – the {DNA} sequence assembly algorithms},
    year = 2002,
    month = nov,
    institution = {Poznań Supercomputing and Networking Center},
    number = {RA-003/2002}
  }