Marcin J. Skwark

PhD, Postdoctoral Researcher

Office:

Aalto Science Institute Room 3170 in TUAS Building,
Otaniementie 17, Otaniemi campus area, Espoo

Postal Address:

Aalto University School of Science,
Department of Information and Computer Science,
P.O. Box 15400, FI-00076 Aalto, Finland

Telephone:

+358 40 93 23023

Email:

firstname.lastname@aalto.fi

About Me

I'm a postdoctoral researcher in The Finnish Centre of Excellence in Computational Inference Research (COIN), working with Prof. Erik Aurell. My research interest include computational structural biology and inference on large, fuzzy data sets of biological relevance.

Curriculum Vitae

• CV (public version, full version available upon request)

Publications

2014

• Feinauer Christoph, Skwark Marcin J., Pagnani Andrea, Aurell Erik. Improving Contact Prediction along Three Dimensions. PLoS Comput Biol, 10(10):e1003847, 2014. [More info] [BibTeX]
Preferred BibTeX:


@article{
    10.1371/journal.pcbi.1003847,
    author = "Feinauer, Christoph and Skwark, Marcin J. and Pagnani, Andrea and Aurell, Erik",
    publisher = "Public Library of Science",
    doi = "10.1371/journal.pcbi.1003847",
    responsibleauthor = "Skwark, Marcin and Aurell, Erik",
    language = "eng",
    title = "Improving Contact Prediction along Three Dimensions",
    url = "http://dx.doi.org/10.1371%2Fjournal.pcbi.1003847",
    journal = "PLoS Comput Biol",
    issn = "1553-734X",
    number = "10",
    month = "10",
    volume = "10",
    juforank = "3",
    il = "yes",
    year = "2014",
    unitcode = "T306-100",
    kay = "A, C",
    impactfactor = "A1",
    pages = "e1003847"
}

• Ge Changrong, Gomez-Llobregat Jordi, Skwark Marcin J., Ruysschaert Jean-Marie, Wieslander Ake, Linden Martin. Membrane remodeling capacity of a vesicle-inducing glycosyltransferase. FEBS Journal, 281(16):3667-3684, 2014. [BibTeX]
Preferred BibTeX:


@article{
    ge2014membrane,
    author = "Ge, Changrong and Gomez-Llobregat, Jordi and Skwark, Marcin J. and Ruysschaert, Jean-Marie and Wieslander, Ake and Linden, Martin",
    publisher = "Wiley Online Library",
    responsibleauthor = "Skwark, Marcin",
    language = "eng",
    title = "Membrane remodeling capacity of a vesicle-inducing glycosyltransferase",
    journal = "FEBS Journal",
    issn = "742-4658",
    number = "16",
    volume = "281",
    juforank = "2",
    il = "yes",
    year = "2014",
    unitcode = "T306-100",
    kay = "A,C",
    impactfactor = "A1",
    pages = "3667-3684"
}

• Michel Mirco, Hayat Sikander, Skwark Marcin J., Sander Chris, Marks Debora S., Elofsson Arne. PconsFold: improved contact predictions improve protein models. Bioinformatics, 30(17):i482-i488, 2014. [BibTeX]
Preferred BibTeX:


@article{
    michel2014pconsfold,
    author = "Michel, Mirco and Hayat, Sikander and Skwark, Marcin J. and Sander, Chris and Marks, Debora S. and Elofsson, Arne",
    juforank = "3",
    issn = "1460-2059",
    responsibleauthor = "Skwark, Marcin",
    language = "eng",
    title = "PconsFold: improved contact predictions improve protein models",
    journal = "Bioinformatics",
    publisher = "Oxford Univ Press",
    number = "17",
    volume = "30",
    il = "yes",
    year = "2014",
    unitcode = "T306-100",
    kay = "A,C",
    impactfactor = "A1",
    pages = "i482--i488"
}

2013

• Bendz Maria, Skwark Marcin, Nilsson Daniel, Granholm Viktor, Cristobal Susana, Käll Lukas, Elofsson Arne. Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics, 13(9):1467-1480, 2013. [BibTeX]
Preferred BibTeX:


@article{
    bendz2013membrane,
    author = {Bendz, Maria and Skwark, Marcin and Nilsson, Daniel and Granholm, Viktor and Cristobal, Susana and K{\"a}ll, Lukas and Elofsson, Arne},
    responsibleauthor = "Skwark, Marcin",
    language = "eng",
    title = "Membrane protein shaving with thermolysin can be used to evaluate topology predictors",
    journal = "Proteomics",
    issn = "1615-9861",
    publisher = "Wiley Online Library",
    number = "9",
    volume = "13",
    juforank = "2",
    il = "yes",
    year = "2013",
    unitcode = "T306-100",
    kay = "NA",
    impactfactor = "A1",
    pages = "1467--1480"
}

• Skwark Marcin J.. Ensemble methods for protein structure prediction. 2013. [More info] [BibTeX]
Preferred BibTeX:


@phdthesis{
    SkwarkThesis,
    author = "Skwark, Marcin J.",
    juforank = "NA",
    school = "Stockholm University",
    isbn = "978-91-7447-698-9",
    language = "eng",
    title = "Ensemble methods for protein structure prediction",
    url = "http://www.diva-portal.org/smash/record.jsf?pid=diva2:617433",
    responsibleauthor = "Skwark, Marcin",
    flags = "copy public",
    il = "yes",
    year = "2013",
    unitcode = "T306-100",
    kay = "NA",
    impactfactor = "G5",
    type = "Doctoral dissertation",
    pages = "60"
}

2012

• van Dijl Jan Maarten, Dreisbach Annette, Skwark Marcin J., Sibbald Mark J.J.B., Tjalsma Harold, Zweers Jessica C., Buist Girbe. Ins and Outs of Bacillus subtilis membrane proteome. 2012. [BibTeX]
Preferred BibTeX:


@incollection{
    graumann2012bacillus,
    editor = "Graumann, Peter",
    author = "van Dijl, Jan Maarten and Dreisbach, Annette and Skwark, Marcin J. and Sibbald, Mark J.J.B. and Tjalsma, Harold and Zweers, Jessica C. and Buist, Girbe",
    juforank = "NA",
    isbn = "978-1-904455-97-4",
    language = "eng",
    title = "Ins and Outs of Bacillus subtilis membrane proteome",
    booktitle = "Bacillus: cellular and molecular biology",
    address = "Norfolk, UK",
    publisher = "Caister Academic Press",
    responsibleauthor = "Skwark, Marcin",
    il = "yes",
    year = "2012",
    unitcode = "T306-100",
    kay = "NA",
    impactfactor = "A3"
}

2011

• Larsson Per, Skwark Marcin J., Wallner Björn, Elofsson Arne. Improved predictions by Pcons. net using multiple templates. Bioinformatics, 27(3):426-427, 2011. [BibTeX]
Preferred BibTeX:


@article{
    larsson2011improved,
    author = {Larsson, Per and Skwark, Marcin J. and Wallner, Bj{\"o}rn and Elofsson, Arne},
    responsibleauthor = "Skwark, Marcin",
    language = "eng",
    title = "Improved predictions by Pcons. net using multiple templates",
    journal = "Bioinformatics",
    issn = "1367-4803",
    publisher = "Oxford Univ Press",
    number = "3",
    volume = "27",
    juforank = "3",
    il = "yes",
    year = "2011",
    unitcode = "T306-100",
    kay = "NA",
    impactfactor = "A1",
    pages = "426--427"
}

2009

• Larsson Per, Skwark Marcin J., Wallner Björn, Elofsson Arne. Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins: Structure, Function, and Bioinformatics, 77(S9):167-172, 2009. [BibTeX]
Preferred BibTeX:


@article{
    larsson2009assessment,
    author = {Larsson, Per and Skwark, Marcin J. and Wallner, Bj{\"o}rn and Elofsson, Arne},
    responsibleauthor = "Skwark, Marcin",
    language = "eng",
    title = "Assessment of global and local model quality in CASP8 using Pcons and ProQ",
    journal = "Proteins: Structure, Function, and Bioinformatics",
    publisher = "Wiley Online Library",
    number = "S9",
    volume = "77",
    juforank = "1",
    il = "yes",
    year = "2009",
    unitcode = "T306-100",
    kay = "NA",
    impactfactor = "A1",
    pages = "167--172"
}

2008

• Viklund Håkan, Bernesel Andreas, Skwark Marcin, Elofsson Arne. SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics, 24(24):2928-2929, 2008. [BibTeX]
Preferred BibTeX:


@article{
    viklund2008spoctopus,
    author = "Viklund, H{\aa}kan and Bernesel, Andreas and Skwark, Marcin and Elofsson, Arne",
    juforank = "3",
    responsibleauthor = "Skwark, Marcin",
    language = "eng",
    title = "SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology",
    journal = "Bioinformatics",
    issn = "1367-4803",
    publisher = "Oxford Univ Press",
    number = "24",
    volume = "24",
    il = "yes",
    year = "2008",
    kay = "NA",
    impactfactor = "A1",
    pages = "2928--2929"
}