Publications

@ARTICLE{schreiner2023cmdc39203932,
  author = {Schreiner, W.~ and Karch, R.~ and Cibena, M.~ and Tomasiak, L.~ and Kenn, M.~ and Pfeiler, G.~},
  title = {Clustering Molecular Dynamics Conformations of the CC’-Loop of the PD-1 Immuno-Checkpoint Receptor.},
  journal = {Computational and Structural Biotechnology Journal},
  year = {2023},
  volume = {21},
  pages = {3920--3932},
  doi = {10.1016/j.csbj.2023.07.004}
}

@ARTICLE{kenn2023frec119,
  author = {Kenn, M.~ and Karch, R.~ and Singer, C.F.~ and Dorffner, G.~ and Schreiner, W.~},
  title = {Flexible Risk Evidence Combination Rules in Breast Cancer Precision Therapy.},
  journal = {Journal of Personalized Medicine},
  year = {2023},
  volume = {13},
  number = {1},
  pages = {119},
  issn = {2075-4426},
  doi = {10.3390/jpm13010119},
  keywords = {precision medicine;personalized medicine;data science;breast cancer;mathematical oncology;Dempster-Shafer theory;evidence theory;hormone receptor status;theory of belief functions}
}

@INCOLLECTION{schreiner2022pupl35693573,
  author = {Schreiner, W.~ and Karch, R.~ and Cibena, M.~ and Tomasiak, L.~ and Kenn, M.~ and Pfeiler, G.~},
  title = {The Performance of UMAP Plus Linkage Compared with Daura-Clustering of Molecular Dynamics of the PD-1 Checkpoint Receptor.},
  booktitle = {Proceedings 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Las Vegas, USA \& Changsha, China, 6–8 December 2022},
  publisher = {Institute of Electrical and Electronics Engineers (IEEE)},
  year = {2022},
  editor = {Adjeroh,D.;Long,Q.;Shi,X.;Guo,F.;Hu,X.;Aluru,S.;Narasimhan,G.;Wang,J.;Kang,M.;Mondal,A.M.;Liu,J.},
  pages = {3569--3573},
  address = {Piscataway, NJ},
  month = {dec},
  url = {https://www.doi.org/10.1109/BIBM55620.2022.9995272}
}

@ARTICLE{kenn2022mdis838129,
  author = {Kenn, M.~ and Karch, R.~ and Tomasiak, L.~ and Cibena, M.~ and Pfeiler, G.~ and Koelbl, H.~ and Schreiner, W.~},
  title = {Molecular Dynamics Identifies Semi-Rigid Domains in the PD-1 Checkpoint Receptor Bound to Its Natural Ligand PD-L1.},
  journal = {Frontiers in Bioengineering and Biotechnology},
  year = {2022},
  volume = {10},
  pages = {838129},
  issn = {2296-4185},
  doi = {10.3389/fbioe.2022.838129},
  keywords = {molecular dynamics;oncology;checkpoint inhibitor;cluster analysis;drug design;immune therapy}
}

@ARTICLE{koller2022seia946348,
  author = {Koller, S.~ and Kendler, J.~ and Karacs, J.~ and Wolf, A.~ and Kreuzinger, C.~ and Von Der Decken, I.~ and Mungenast, F.~ and Mechtcheriakova, D.~ and Schreiner, W.~ and Gleiss, A.~ and J{\"a}ger, W.~ and Cacsire Castillo-Tong, D.~ and Thalhammer, T.~},
  title = {SLCO4A1 Expression Is Associated with Activated Inflammatory Pathways in High-Grade Serous Ovarian Cancer.},
  journal = {Frontiers in Pharmacology},
  year = {2022},
  volume = {13},
  pages = {946348},
  issn = {1663-9812},
  doi = {10.3389/fphar.2022.946348},
  keywords = {high-grade serous ovarian cancer;ABCC3;inflammatory signaling pathways;NF-kB;OATP4A1;SLCO4A1;SLCO4A1-AS1}
}

@ARTICLE{tomasiak2022cfaf36,
  author = {Tomasiak, L.~ and Karch, R.~ and Schreiner, W.~},
  title = {Conformational Flexibility of a Free and TCR-Bound pMHC-I Protein Investigated by Long-Term Molecular Dynamics Simulations.},
  journal = {BMC Immunology},
  year = {2022},
  volume = {23},
  number = {Suppl 1: Selected Papers 4th International Workshop on Computational Methods for the Immune System Function (CMISF 2020): Immunology, Virtual, 16–19 December 2020},
  pages = {36},
  doi = {10.1186/s12865-022-00510-7}
}

@ARTICLE{kenn2022dtvc570,
  author = {Kenn, M.~ and Karch, R.~ and Cacsire Castillo-Tong, D.~ and Singer, C.F.~ and Koelbl, H.~ and Schreiner, W.~},
  title = {Decision Theory versus Conventional Statistics for Personalized Therapy of Breast Cancer.},
  journal = {Journal of Personalized Medicine},
  year = {2022},
  volume = {12},
  number = {4},
  pages = {570},
  issn = {2075-4426},
  doi = {10.3390/jpm12040570},
  keywords = {precision medicine;biomarkers;personalized medicine;data science;breast cancer;gene expression;mathematical oncology;receptor status;decision theory}
}

@ARTICLE{pichler2022gnog139151,
  author = {Pichler, K.M.~ and Fischer, A.~ and Alphonsus, J.~ and Chiari, C.~ and Schmidt, S.~ and Kenn, M.~ and Schreiner, W.~ and Weinmann, D.~ and Rothbauer, M.~ and Windhager, R.~ and Gabius, H.-J.~ and Toegel, S.~},
  title = {Galectin Network in Osteoarthritis: Galectin-4 Programs a Pathogenic Signature of Gene and Effector Expression in Human Chondrocytes in Vitro.},
  journal = {Histochemistry and Cell Biology},
  year = {2022},
  volume = {157},
  number = {2},
  pages = {139--151},
  issn = {1432-119X 0948-6143},
  doi = {10.1007/s00418-021-02053-1},
  keywords = {Inflammation;Lectin;NF-κB;3D spheres;Cartilage;Primary cells}
}

@ARTICLE{roither2021mac9092,
  author = {Roither, B.~ and Oostenbrink, C.~ and Pfeiler, G.~ and K{\"o}lbl, H.~ and Schreiner, W.~},
  title = {Molekulardynamik am Checkpoint.},
  journal = {Spectrum Onkologie},
  year = {2021},
  volume = {3/2021},
  pages = {90--92},
  issn = {2223-0645},
  url = {https://www.medmedia.at/apps/download/download_pdf.php?file=wp-content/uploads/2021/06/so-2021-03-lr.pdf#page=90}
}

@ARTICLE{kenn2021eswe7072,
  author = {Kenn, M~ and Cacsire Castillo-Tong, D.~ and Singer, C.F.~ and Karch, R.~ and Cibena, M.~ and K{\"o}lbl, H.~ and Schreiner, W.~},
  title = {Evidenz statt Wahrscheinlichkeiten: Entscheidungstheorie f{\"u}r die Pr{\"a}zisionsmedizin.},
  journal = {Spectrum Onkologie},
  year = {2021},
  volume = {2/2021},
  pages = {70--72},
  url = {https://www.medmedia.at/apps/download/download_pdf.php?file=wp-content/uploads/2021/04/so-2021-02-lr.pdf#page=70}
}

@ARTICLE{kenn2021dtpt4233,
  author = {Kenn, M.~ and Cacsire Castillo-Tong, D.~ and Singer, C.F.~ and Karch, R.~ and Cibena, M.~ and Koelbl, H.~ and Schreiner, W.~},
  title = {Decision Theory for Precision Therapy of Breast Cancer.},
  journal = {Scientific Reports},
  year = {2021},
  volume = {11},
  pages = {4233},
  issn = {2045-2322},
  doi = {10.1038/s41598-021-82418-7}
}

@ARTICLE{roither2021piuc5,
  author = {Roither, B.~ and Oostenbrink, C.~ and Pfeiler, G.~ and Koelbl, H.~ and Schreiner, W.~},
  title = {Pembrolizumab Induces an Unexpected Conformational Change in the CC’-Loop of PD-1.},
  journal = {Cancers},
  year = {2021},
  volume = {13},
  number = {1},
  pages = {5},
  issn = {2072-6694},
  doi = {10.3390/cancers13010005},
  keywords = {immunotherapy;antibodies;checkpoint inhibitors;molecular conformation;molecular dynamics simulation}
}

@ARTICLE{roither2020mdic557,
  author = {Roither, B.~ and Oostenbrink, C.~ and Schreiner, W.~},
  title = {Molecular Dynamics of the Immune Checkpoint Programmed Cell Death Protein I, PD-1: Conformational Changes of the BC-Loop upon Binding of the Ligand PD-L1 and the Monoclonal Antibody Nivolumab.},
  journal = {BMC Bioinformatics},
  year = {2020},
  volume = {21},
  number = {Suppl 17: Selected papers from the 3rd International Workshop on Computational Methods for the Immune System Function (CMISF 2019), San Diego, CA, USA, 18–21 November 2019},
  pages = {557},
  issn = {1471-2105},
  doi = {10.1186/s12859-020-03904-9},
  keywords = {Humans;Antibodies;Monoclonal/immunology;PD-1;PD-L1;Protein Binding;Cluster Analysis;Mathematical oncology;*Molecular Dynamics Simulation;Nivolumab;Ligands;B7-H1 Antigen/*chemistry/metabolism;BC-loop;Hydrogen Bonding;Molecular dynamics;Nivolumab/*immunology;Programmed Cell Death 1 Receptor/*chemistry/immunology/metabolism;Protein Domains}
}

@INPROCEEDINGS{tomasiak2020lmds12951302,
  author = {Tomasiak, L.~ and Karch, R.~ and Schreiner, W.~},
  title = {Long-Term Molecular Dynamics Simulations Reveal Flexibility Properties of a Free and TCR-Bound pMHC-I System.},
  booktitle = {Proceedings 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Seoul, Korea, 16–19 December 2020},
  year = {2020},
  editor = {Park,T.;Cho,Y.-R.;Hu,X.;Yoo,I.;Woo,H.G.;Wang,J.;Facelli,J.;Nam,S.;Kang,M.},
  pages = {1295--1302},
  address = {Piscataway, NJ},
  publisher = {IEEE},
  doi = {10.1109/BIBM49941.2020.9313545},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100345478\&doi=10.1109%2fBIBM49941.2020.9313545\&partnerID=40\&md5=2948b457d9ecfeba2799c184a625635b}
}

@ARTICLE{kenn2020mnrr1363827,
  author = {Kenn, M.~ and Cacsire Castillo-Tong, D.~ and Singer, C.F.~ and Cibena, M.~ and K{\"o}lbl, H.~ and Schreiner, W.~},
  title = {Microarray Normalization Revisited for Reproducible Breast Cancer Biomarkers.},
  journal = {BioMed Research International},
  year = {2020},
  volume = {2020},
  pages = {1363827},
  issn = {2314-6141 2314-6133},
  doi = {10.1155/2020/1363827}
}

@ARTICLE{toegel2020gtdms94s94,
  author = {Toegel, S.~ and Pichler, K.M.~ and Weinmann, D.~ and Fiebrich, J.~ and Kenn, M.~ and Schreiner, W.~ and Lass, R.~ and Windhager, R.~ and Gabius, H.-J.~},
  title = {Galectin-4 Triggers Disease Markers in Osteoarthritic Chondrocytes via NF-κB.},
  journal = {Osteoarthritis and Cartilage},
  year = {2020},
  volume = {28},
  number = {Suppl 1: Abstracts 2020 OARSI World Congress on Osteoarthritis Promoting Clinical and Basic Research in Osteoarthritis, Vienna, Austria, 30 April–3 May 2020},
  pages = {S94},
  issn = {1063-4584},
  doi = {10.1016/j.joca.2020.02.144},
  url = {https://www.sciencedirect.com/science/article/pii/S1063458420302119}
}

@INPROCEEDINGS{roither2019mdic21922196,
  author = {Roither, B.~ and Oostenbrink, C.~ and Schreiner, W.~},
  title = {Molecular Dynamics of the Immune Checkpoint Programmed Cell Death Protein I, PD-1: Conformational Changes of the BC-Loop upon Binding of the Ligand PD-L1 and the Monoclonal Antibody Nivolumab.},
  booktitle = {Proceedings 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), San Diego, CA, USA, 18–21 November 2019},
  year = {2019},
  editor = {Yoo,I.;Bi,J.;Hu,X.},
  pages = {2192--2196},
  address = {Piscataway, NJ},
  month = {nov},
  publisher = {IEEE},
  doi = {10.1109/BIBM47256.2019.8983404},
  keywords = {apoptosis;cancer;PD-1;PD-L1;immunotherapy;proteins;antigen-specific T cells;autoimmunity;BC-Loop;BC-loop conformations;biochemistry;cellular biophysics;clinically used blocking antibody nivolumab;complete extracellular domain;conformational selection model;drug delivery systems;drug target;drugs;immune checkpoint programmed cell death protein;immune system;immunosuppressive interaction;Mathematical Oncology;molecular biophysics;molecular configurations;Molecular Dynamics;molecular dynamics method;molecular dynamics simulations;nanomedicine;Nivolumab;patient diagnosis;programmed cell death protein ligand;programmed cell death protein ligand I;signal transduction;tumor-specific CD8+ T cells;tumours}
}

@ARTICLE{gruber2019oaia1357,
  author = {Gruber, E.S.~ and Oberhuber, G.~ and Birner, P.~ and Schlederer, M.~ and Kenn, M.~ and Schreiner, W.~ and Jomrich, G.~ and Schoppmann, S.F.~ and Gnant, M.~ and Tse, W.~ and Kenner, L.~},
  title = {The Oncogene AF1Q is Associated with WNT and STAT Signaling and Offers a Novel Independent Prognostic Marker in Patients with Resectable Esophageal Cancer.},
  journal = {Cells},
  year = {2019},
  volume = {8},
  number = {11},
  pages = {1357},
  note = {
[Erratum: Gruber E.S., Oberhuber G., Birner P., Schlederer M., Kenn M., Schreiner W., Jomrich G., Schoppmann S.F., Gnant M., Tse W., Kenner L. Erratum: Gruber, E.S.; et al. The Oncogene AF1Q is Associated with WNT and STAT Signaling and Offers a Novel Independent Prognostic Marker in Patients with Resectable Esophageal Cancer. Cells 2019, 8, 1357. Cells 9(12):2724, (2020)]},
  issn = {2073-4409 2073-4409},
  doi = {10.3390/cells8111357},
  keywords = {*prognosis;*AF1Q;*esophageal cancer;*MLLT11;*STAT;*WNT}
}

@ARTICLE{karch2019idmf720,
  author = {Karch, R.~ and Stocsits, C.~ and Ilieva, N.~ and Schreiner, W.~},
  title = {Intramolecular Domain Movements of Free and Bound pMHC and TCR Proteins: A Molecular Dynamics Simulation Study.},
  journal = {Cells},
  year = {2019},
  volume = {8},
  number = {7},
  pages = {720},
  issn = {2073-4409 2073-4409},
  doi = {10.3390/cells8070720},
  keywords = {Humans;*antigen;*domain movements;*major histocompatibility complex;*Major Histocompatibility Complex;*molecular dynamics simulation;*T-cell receptor;Binding Sites;Molecular Dynamics Simulation;Peptides/*chemistry;Protein Binding;Protein Conformation;Receptors;Antigen;T-Cell;alpha-beta/*chemistry}
}

@ARTICLE{kinslechner2019cagas197s198,
  author = {Kinslechner, K.~ and Kenn, M.~ and Weinmann, D.~ and Walzer, S.M.~ and Windhager, R.~ and Schreiner, W.~ and Gabius, H.-J.~ and Toegel, S.~},
  title = {Combined Activity of Galectin-1,-3, and-8 Drives Functional Disease Markers in Osteoarthritic Chondrocytes via NF-KB.},
  journal = {Osteoarthritis and Cartilage},
  year = {2019},
  volume = {27},
  number = {Suppl 1: Abstracts 2019 OARSI World Congress on Osteoarthritis. Promoting Clinical and Basic Research in Osteoarthritis, Toronto, Canada, 2–5 May 2019},
  pages = {S197--S198},
  issn = {1063-4584},
  doi = {10.1016/j.joca.2019.02.305}
}

@ARTICLE{haider2019tgfa222236,
  author = {Haider, C.~ and Hnat, J.~ and Wagner, R.~ and Huber, H.~ and Timelthaler, G.~ and Grubinger, M.~ and Coulouarn, C.~ and Schreiner, W.~ and Schlangen, K.~ and Sieghart, W.~ and Peck-Radosavljevic, M.~ and Mikulits, W.~},
  title = {Transforming Growth Factor-β and Axl Induce CXCL5 and Neutrophil Recruitment in Hepatocellular Carcinoma.},
  journal = {Hepatology},
  year = {2019},
  volume = {69},
  number = {1},
  pages = {222--236},
  doi = {10.1002/hep.30166},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85058848183\&doi=10.1002%2fhep.30166\&partnerID=40\&md5=ad92ca02750a75135d3187c196e5dbab}
}

@ARTICLE{kenn2018cgep313326,
  author = {Kenn, M.~ and Cacsire Castillo-Tong, D.~ and Singer, C.F.~ and Cibena, M.~ and K{\"o}lbl, H.~ and Schreiner, W.~},
  title = {Co-Expressed Genes Enhance Precision of Receptor Status Identification in Breast Cancer Patients.},
  journal = {Breast Cancer Research and Treatment},
  year = {2018},
  volume = {172},
  number = {2},
  pages = {313--326},
  issn = {1573-7217 0167-6806},
  doi = {10.1007/s10549-018-4920-x},
  keywords = {Female;Humans;Disease-Free Survival;Breast cancer;Biomarkers;Tumor/genetics;Precision Medicine;Gene Expression Regulation;Neoplastic;Data science;Gene expression;Mathematical oncology;Precision medicine;Receptor status;Breast Neoplasms/classification/*genetics/pathology;Estrogen Receptor alpha/*genetics;Receptor;ErbB-2/*genetics;Receptors;Cell Surface;Receptors;Progesterone/*genetics}
}

@ARTICLE{weinmann2018gifd41874205,
  author = {Weinmann, D.~ and Kenn, M.~ and Schmidt, S.~ and Schmidt, K.~ and Walzer, S.M.~ and Kubista, B.~ and Windhager, R.~ and Schreiner, W.~ and Toegel, S.~ and Gabius, H.-J.~},
  title = {Galectin-8 Induces Functional Disease Markers in Human Osteoarthritis and Cooperates with Galectins-1 and -3.},
  journal = {Cellular and Molecular Life Sciences},
  year = {2018},
  volume = {75},
  number = {22},
  pages = {4187--4205},
  issn = {1420-9071 1420-682X},
  doi = {10.1007/s00018-018-2856-2},
  keywords = {Female;Humans;Male;Aged;Middle Aged;Aged;80 and over;Polymorphism;Single Nucleotide;Inflammation;Biomarkers/metabolism;Disease Progression;RNA;Messenger/metabolism;Cells;Cultured;Interleukin;Chondrocytes/metabolism;Gene Expression;Chondrocytes;Galectin 1/metabolism;Galectin 3/metabolism;Galectins/genetics/*metabolism;Lectin;NF-kappa B/metabolism;NF-kappaB;Osteoarthritis/*genetics/metabolism/pathology}
}

@ARTICLE{toegel2018fcgws21s22,
  author = {Toegel, S.~ and Weinmann, D.~ and Kenn, M.~ and Schreiner, W.~ and Walzer, S.~ and Gabius, H.-J.~ and Windhager, R.~},
  title = {Functional Cooperation of Galectin-8 with Galectin-1 and-3 in Triggering Disease Markers of Human Osteoarthritis.},
  journal = {Osteoarthritis and Cartilage},
  year = {2018},
  volume = {26},
  number = {Suppl 1: Abstracts OARSI World Congress on Osteoarthritis: Promoting Clinical and Basic Research in Osteoarthritis, Liverpool, UK, 26–29 April 2018},
  pages = {S21--S22},
  issn = {1063-4584},
  doi = {10.1016/j.joca.2018.02.059},
  url = {https://www.oarsijournal.com/issue/S1063-4584(18)X0004-1}
}

@ARTICLE{bolomsky2018melz325335,
  author = {Bolomsky, A.~ and Heusschen, R.~ and Schlangen, K.~ and Stangelberger, K.~ and Muller, J.~ and Schreiner, W.~ and Zojer, N.~ and Caers, J.~ and Ludwig, H.~},
  title = {Maternal Embryonic Leucine Zipper Kinase Is a Novel Target for Proliferation-Associated High-Risk Myeloma.},
  journal = {Haematologica},
  year = {2018},
  volume = {103},
  number = {2},
  pages = {325--335},
  issn = {1592-8721 0390-6078},
  doi = {10.3324/haematol.2017.172973},
  keywords = {Animals;Humans;Prognosis;Mice;Apoptosis/drug effects;Cell Cycle/drug effects;Cell Line;Tumor;Risk Assessment;Cell Proliferation/*drug effects;Multiple Myeloma/*drug therapy/pathology;Naphthyridines/pharmacology;Protein-Serine-Threonine Kinases/*antagonists \& inhibitors/metabolism}
}

@ARTICLE{kenn2017geii7734177359,
  author = {Kenn, M.~ and Schlangen, K.~ and Cacsire Castillo-Tong, D.~ and Singer, C.F.~ and Cibena, M.~ and Koelbl, H.~ and Schreiner, W.~},
  title = {Gene Expression Information Improves Reliability of Receptor Status in Breast Cancer Patients.},
  journal = {Oncotarget},
  year = {2017},
  volume = {8},
  number = {44},
  pages = {77341--77359},
  issn = {1949-2553 1949-2553},
  doi = {10.18632/oncotarget.20474},
  keywords = {data science;breast cancer;gene expression;mathematical oncology;receptor status}
}

@ARTICLE{bolomsky2016melzabstract 309,
  author = {Bolomsky, A.~ and Heusschen, R.~ and Schlangen, K.~ and Sch{\"o}nfelder, K.~ and Muller, J.~ and Schreiner, W.~ and Zojer, N.~ and Caers, J.~ and Ludwig, H.~},
  title = {Maternal Embryonic Leucine Zipper Kinase (MELK) Drives a High-Risk Gene Network and Represents an Attractive Novel Drug Target in Multiple Myeloma.},
  journal = {Blood},
  year = {2016},
  volume = {128},
  number = {22: Abstracts 58th American Society of Hematology (ASH) Annual Meeting, San Diego, CA, USA, 3–6 December 2016},
  pages = {Abstract 309},
  issn = {0006-4971},
  doi = {10.1182/blood.V128.22.309.309}
}

@ARTICLE{bolomsky2016tbwp251252,
  author = {Bolomsky, A.~ and Schlangen, K.~ and Schreiner, W.~ and Zojer, N.~ and Ludwig, H.~},
  title = {Targeting of BMI-1 with PTC-209 Affects Myeloma Cell Growth \& Survival and Impairs the Tumour Microenvironment.},
  journal = {Haematologica},
  year = {2016},
  volume = {101},
  number = {Suppl 1: Abstract Book 21st Congress of the European Hematology Association, Copenhagen, Denmark, 9–12 June 2016},
  pages = {251--252},
  issn = {0390-6078},
  url = {http://www.haematologica.org/content/101/s1}
}

@ARTICLE{kenn2016smcc16001614,
  author = {Kenn, M.~ and Ribarics, R.~ and Ilieva, N.~ and Cibena, M.~ and Karch, R.~ and Schreiner, W.~},
  title = {Spatiotemporal Multistage Consensus Clustering in Molecular Dynamics Studies of Large Proteins.},
  journal = {Molecular BioSystems},
  year = {2016},
  volume = {12},
  number = {5},
  pages = {1600--1614},
  issn = {1742-2051 1742-2051},
  doi = {10.1039/c5mb00879d},
  keywords = {Algorithms;Protein Conformation;*Cluster Analysis;*Molecular Dynamics Simulation;CD8 Antigens/chemistry/metabolism;Major Histocompatibility Complex;Models;Molecular;Multiprotein Complexes/chemistry;Protein Interaction Domains and Motifs;Proteins/*chemistry/metabolism;Receptors;Antigen;T-Cell/chemistry/metabolism}
}

@ARTICLE{bolomsky2016tbwp17,
  author = {Bolomsky, A.~ and Schlangen, K.~ and Schreiner, W.~ and Zojer, N.~ and Ludwig, H.~},
  title = {Targeting of BMI-1 with PTC-209 Shows Potent Anti-Myeloma Activity and Impairs the Tumour Microenvironment.},
  journal = {Journal of Hematology \& Oncology},
  year = {2016},
  volume = {9},
  pages = {17},
  issn = {1756-8722},
  doi = {10.1186/s13045-016-0247-4},
  keywords = {Multiple myeloma;expression;cells;poor-prognosis;bmi-1;bone-marrow microenvironment;inhibitor;Microenvironment;molecular marker;noxa;protein bmi-1;ptc-209;side population;wnt}
}

@ARTICLE{schreiner2015rmdl210675,
  author = {Schreiner, W.~ and Karch, R.~ and Ribarics, R.~ and Cibena, M.~ and Ilieva, N.~},
  title = {Relative Movements of Domains in Large Molecules of the Immune System.},
  journal = {Journal of Immunology Research},
  year = {2015},
  volume = {2015},
  pages = {210675},
  issn = {2314-7156 2314-8861 2314-7156},
  doi = {10.1155/2015/210675},
  keywords = {Humans;Mutation;Binding Sites;Protein Binding;*Molecular Dynamics Simulation;Protein Interaction Domains and Motifs;beta 2-Microglobulin/*chemistry/immunology;CD8 Antigens/*chemistry/immunology;HLA-B27 Antigen/*chemistry/immunology;Immunological Synapses/chemistry/immunology;Least-Squares Analysis;Peptides/*chemistry/immunology;Protein Structure;Secondary;Receptors;Antigen;T-Cell;alpha-beta/*chemistry/immunology;Structural Homology;Protein}
}

@ARTICLE{ribarics2015gdhd173593,
  author = {Ribarics, R.~ and Kenn, M.~ and Karch, R.~ and Ilieva, N.~ and Schreiner, W.~},
  title = {Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes.},
  journal = {Journal of Immunology Research},
  year = {2015},
  volume = {2015},
  pages = {173593},
  issn = {2314-7156 2314-8861 2314-7156},
  doi = {10.1155/2015/173593},
  keywords = {Humans;Mutation;Binding Sites;Protein Binding;*Molecular Dynamics Simulation;Protein Interaction Domains and Motifs;HLA-B27 Antigen/*chemistry/immunology;Immunological Synapses/chemistry/immunology;Least-Squares Analysis;Peptides/*chemistry/immunology;Protein Structure;Secondary;Receptors;Antigen;T-Cell/*chemistry/immunology}
}

@INCOLLECTION{schreiner2014sveu153179,
  author = {Schreiner, W.~},
  title = {Sch{\"o}pfung via Evolution – und m{\"o}gliche Implikationen: Evolutionstheologie.},
  booktitle = {Glaube und Denken. Jahrbuch der Karl-Heim-Gesellschaft},
  publisher = {Peter Lang},
  year = {2014},
  editor = {Rothgangel,M.;Beuttler,U.},
  number = {27},
  pages = {153--179},
  address = {Frankfurt am Main},
  url = {https://doi.org/10.3726/978-3-653-05022-6}
}

@ARTICLE{schwaiger2014shct78287842,
  author = {Schwaiger, J.~ and Aberle, J.H.~ and Stiasny, K.~ and Knapp, B.~ and Schreiner, W.~ and Fae, I.~ and Fischer, G.~ and Scheinost, O.~ and Chmelik, V.~ and Heinz, F.X.~},
  title = {Specificities of Human CD4+ T Cell Responses to an Inactivated Flavivirus Vaccine and Infection: Correlation with Structure and Epitope Prediction.},
  journal = {Journal of Virology},
  year = {2014},
  volume = {88},
  number = {14},
  pages = {7828--7842},
  issn = {1098-5514 0022-538X 0022-538X},
  doi = {10.1128/JVI.00196-14},
  keywords = {Adolescent;Adult;Female;Humans;Male;Young Adult;Aged;Middle Aged;Aged;80 and over;CD4-Positive T-Lymphocytes/*immunology;Protein Conformation;Antigens;Viral/*chemistry/*immunology;Encephalitis Viruses;Tick-Borne/*immunology;Encephalitis;Tick-Borne/*immunology;Enzyme-Linked Immunospot Assay;Epitopes/*immunology;Interleukin-2/metabolism;Vaccines;Inactivated/administration \& dosage/immunology;Viral Vaccines/administration \& dosage/*immunology}
}

@ARTICLE{ribarics2014gaah943186,
  author = {Ribarics, R.~ and Karch, R.~ and Ilieva, N.~ and Schreiner, W.~},
  title = {Geometric Analysis of Alloreactive HLA α-Helices.},
  journal = {BioMed Research International},
  year = {2014},
  volume = {2014},
  pages = {943186},
  issn = {2314-6141 2314-6133},
  doi = {10.1155/2014/943186},
  keywords = {Humans;*Molecular Dynamics Simulation;Protein Structure;Secondary;HLA Antigens/*chemistry}
}

@ARTICLE{kenn2014fsdb731325,
  author = {Kenn, M.~ and Ribarics, R.~ and Ilieva, N.~ and Schreiner, W.~},
  title = {Finding Semirigid Domains in Biomolecules by Clustering Pair-Distance Variations.},
  journal = {BioMed Research International},
  year = {2014},
  volume = {2014},
  pages = {731325},
  issn = {2314-6141 2314-6133},
  doi = {10.1155/2014/731325},
  keywords = {Algorithms;Models;Theoretical;Gene Expression Profiling;Oligonucleotide Array Sequence Analysis;Pattern Recognition;Automated;Signal Transduction;Molecular Dynamics Simulation;*Fuzzy Logic;*Cluster Analysis;*Computational Biology;Gene Expression Regulation/genetics/*immunology}
}

@ARTICLE{boucheron2014ctcl439448,
  author = {Boucheron, N.~ and Tschismarov, R.~ and Goeschl, L.~ and Moser, M.A.~ and Lagger, S.~ and Sakaguchi, S.~ and Winter, M.~ and Lenz, F.~ and Vitko, D.~ and Breitwieser, F.P.~ and M{\"u}ller, L.~ and Hassan, H.~ and Bennett, K.L.~ and Colinge, J.~ and Schreiner, W.~ and Egawa, T.~ and Taniuchi, I.~ and Matthias, P.~ and Seiser, C.~ and Ellmeier, W.~},
  title = {CD4+ T Cell Lineage Integrity Is Controlled by the Histone Deacetylases HDAC1 and HDAC2.},
  journal = {Nature Immunology},
  year = {2014},
  volume = {15},
  number = {5},
  pages = {439--448},
  note = {
[Erratum: Nature Immunology 15(9), 894, (2014)]},
  issn = {1529-2916 1529-2908 1529-2908},
  doi = {10.1038/ni.2864},
  keywords = {Animals;Mice;Cells;Cultured;Mice;Inbred C57BL;Mice;Knockout;CD4-Positive T-Lymphocytes/*immunology;Protein Binding;Cytokines/metabolism;CD8-Positive T-Lymphocytes/*immunology;Cell Differentiation/genetics;Cell Lineage/genetics;Core Binding Factor alpha Subunits/metabolism;Core Binding Factor beta Subunit/metabolism;Cytotoxicity;Immunologic/genetics;Histocompatibility Antigens Class II/genetics/metabolism;Histone Deacetylase 1/genetics/*metabolism;Histone Deacetylase 2/genetics/*metabolism;Th1 Cells/*immunology}
}

@ARTICLE{mertz2014miam3465,
  author = {Mertz, K.D.~ and Pathria, G.~ and Wagner, C.~ and Saarikangas, J.~ and Sboner, A.~ and Romanov, J.~ and Gschaider, M.~ and Lenz, F.~ and Neumann, F.~ and Schreiner, W.~ and Nemethova, M.~ and Glassmann, A.~ and Lappalainen, P.~ and Stingl, G.~ and Small, J.V.~ and Fink, D.~ and Chin, L.~ and Wagner, S.N.~},
  title = {MTSS1 Is a Metastasis Driver in a Subset of Human Melanomas.},
  journal = {Nature Communications},
  year = {2014},
  volume = {5},
  pages = {3465},
  issn = {2041-1723 2041-1723},
  doi = {10.1038/ncomms4465},
  keywords = {Animals;Female;Humans;Cell Line;Tumor;Gene Expression Regulation;Neoplastic;*Neoplasm Metastasis;Melanoma/genetics/*metabolism/pathology;Mice;Nude;Microfilament Proteins/genetics/*metabolism;Neoplasm Proteins/genetics/*metabolism}
}

@ARTICLE{hischenhuber2013dgaa18621879,
  author = {Hischenhuber, B.~ and Havlicek, H.~ and Todoric, J.~ and H{\"o}llrigl-Binder, S.~ and Schreiner, W.~ and Knapp, B.~},
  title = {Differential Geometric Analysis of Alterations in MH α-Helices.},
  journal = {Journal of Computational Chemistry},
  year = {2013},
  volume = {34},
  number = {21},
  pages = {1862--1879},
  note = {[Erratum: Journal of Computational Chemistry 34(32), 2834, (2013)]},
  issn = {1096-987X 0192-8651 0192-8651},
  doi = {10.1002/jcc.23328},
  keywords = {Crystallography;X-Ray;*Major Histocompatibility Complex;Protein Structure;Secondary;Receptors;Antigen;T-Cell/*chemistry}
}

@ARTICLE{knapp2013erdle64464,
  author = {Knapp, B.~ and Dorffner, G.~ and Schreiner, W.~},
  title = {Early Relaxation Dynamics in the LC 13 T Cell Receptor in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study.},
  journal = {PLoS One},
  year = {2013},
  volume = {8},
  number = {6},
  pages = {e64464},
  issn = {1932-6203 1932-6203},
  doi = {10.1371/journal.pone.0064464},
  keywords = {Humans;Binding Sites;Protein Binding;*Molecular Dynamics Simulation;Peptides/*chemistry/immunology;Receptors;Antigen;T-Cell/*chemistry/immunology;Ligands;Major Histocompatibility Complex/*immunology;Molecular Docking Simulation;Thermodynamics}
}

@ARTICLE{gschaider2012aaame49865,
  author = {Gschaider, M.~ and Neumann, F.~ and Peters, B.~ and Lenz, F.~ and Cibena, M.~ and Goiser, M.~ and Wolf, I.~ and Wenzel, J.~ and Mauch, C.~ and Schreiner, W.~ and Wagner, S.N.~},
  title = {An Attempt at a Molecular Prediction of Metastasis in Patients with Primary Cutaneous Melanoma.},
  journal = {PLoS One},
  year = {2012},
  volume = {7},
  number = {11},
  pages = {e49865},
  issn = {1932-6203 1932-6203},
  doi = {10.1371/journal.pone.0049865},
  keywords = {Humans;Predictive Value of Tests;Prognosis;Proportional Hazards Models;Gene Expression Profiling;Regression Analysis;Skin Neoplasms/*pathology;Gene Expression Regulation;Neoplastic/*physiology;Medical Oncology/methods;Melanoma/metabolism/*secondary;Neoplasm Metastasis/*diagnosis}
}

@ARTICLE{schreiner2012rerm173521,
  author = {Schreiner, W.~ and Karch, R.~ and Knapp, B.~ and Ilieva, N.~},
  title = {Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations.},
  journal = {Computational and Mathematical Methods in Medicine},
  year = {2012},
  volume = {2012},
  pages = {173521},
  issn = {1748-6718 1748-670X 1748-670X},
  doi = {10.1155/2012/173521},
  keywords = {Algorithms;Animals;Humans;Time Factors;Reproducibility of Results;Models;Statistical;Models;Theoretical;Computer Simulation;Computational Biology/*methods;*Molecular Dynamics Simulation;Models;Molecular;Immune System/chemistry;Molecular Conformation;Proteins/chemistry;Receptors;Antigen;T-Cell/chemistry}
}

@ARTICLE{knapp2012ahwa43,
  author = {Knapp, B.~ and Fischer, G.~ and Van Hemelen, D.~ and Fae, I.~ and Maillere, B.~ and Ebner, C.~ and Schreiner, W.~ and Bohle, B.~ and Jahn-Schmid, B.~},
  title = {Association of HLA-DR1 with the Allergic Response to the Major Mugwort Pollen Allergen: Molecular Background.},
  journal = {BMC Immunology},
  year = {2012},
  volume = {13},
  pages = {43},
  issn = {1471-2172 1471-2172},
  doi = {10.1186/1471-2172-13-43},
  keywords = {Humans;Computer Simulation;Molecular Sequence Data;Amino Acid Sequence;Hypersensitivity/*immunology;Models;Molecular;Allergens/chemistry/*immunology;Antigen Presentation/immunology;Antigen-Presenting Cells/immunology;Antigens;Plant/chemistry/*immunology;Artemisia/*chemistry;Epitopes;T-Lymphocyte/chemistry/immunology;HLA-DR1 Antigen/*immunology;HLA-DR4 Antigen/*immunology;Mutation/genetics;Peptides/chemistry/immunology;Plant Proteins/chemistry/*immunology;Pollen/*immunology;Protein Binding/immunology}
}

@ARTICLE{hischenhuber2012mcmh14811490,
  author = {Hischenhuber, B.~ and Frommlet, F.~ and Schreiner, W.~ and Knapp, B.~},
  title = {MH2c: Characterization of Major Histocompatibility Alpha-Helices – An Information Criterion Approach.},
  journal = {Computer Physics Communications},
  year = {2012},
  volume = {183},
  number = {7},
  pages = {1481--1490},
  issn = {0010-4655 0010-4655},
  doi = {10.1016/j.cpc.2012.02.008},
  keywords = {Akaike Information Criterion;Conformational changes;Helix;MH;MHC;Minimization and fitting;Molecular dynamics simulation;Proteins;Secondary structure;Structure and properties;Utility;AIC;Akaike Information Criterion;cAIC;corrected Akaike Information Criterion;CDR;complementarity determining region;G;binding groove;IMGT(R);the international ImMunoGeneTics information system(R);MD;Molecular Dynamics;MH;major histocompatibility;MH1;major histocompatibility class I;MH2;major histocompatibility class II;MH2c;MH helix curves (name of software);p;peptide;PC;principal component;PCA;Principal Component Analysis;PDB;Protein Data Bank;Theory;modeling;and computer simulation;TR;T cell receptor;VMD;Visual Molecular Dynamics}
}

@ARTICLE{knapp2011iicd9971005,
  author = {Knapp, B.~ and Frantal, S.~ and Cibena, M.~ and Schreiner, W.~ and Bauer, P.~},
  title = {Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?},
  journal = {Journal of Computational Biology},
  year = {2011},
  volume = {18},
  number = {8},
  pages = {997--1005},
  issn = {1557-8666 1066-5277},
  doi = {10.1089/cmb.2010.0237},
  keywords = {Algorithms;Humans;Observer Variation;Data Collection;Bias;*Models;Statistical;*Computational Biology/methods/statistics \& numerical data;Molecular Dynamics Simulation/*standards/statistics \& numerical data}
}

@ARTICLE{knapp2011puga241,
  author = {Knapp, B.~ and Giczi, V.~ and Ribarics, R.~ and Schreiner, W.~},
  title = {PeptX: Using Genetic Algorithms to Optimize Peptides for MHC Binding.},
  journal = {BMC Bioinformatics},
  year = {2011},
  volume = {12},
  pages = {241},
  issn = {1471-2105 1471-2105},
  doi = {10.1186/1471-2105-12-241},
  keywords = {Animals;Humans;*Algorithms;*Major Histocompatibility Complex;Protein Binding;Artificial Intelligence;Genes;MHC Class I;Peptides/chemistry/immunology/*metabolism}
}

@ARTICLE{knapp2010vapr28682873,
  author = {Knapp, B.~ and Lederer, N.~ and Omasits, U.~ and Schreiner, W.~},
  title = {vmdICE: A Plug-in for Rapid Evaluation of Molecular Dynamics Simulations Using VMD.},
  journal = {Journal of Computational Chemistry},
  year = {2010},
  volume = {31},
  number = {16},
  pages = {2868--2873},
  issn = {1096-987X 0192-8651},
  doi = {10.1002/jcc.21581},
  keywords = {*Software;Peptides/*chemistry;*Molecular Dynamics Simulation;Models;Molecular}
}

@ARTICLE{knapp2010acale11653,
  author = {Knapp, B.~ and Omasits, U.~ and Schreiner, W.~ and Epstein, M.M.~},
  title = {A Comparative Approach Linking Molecular Dynamics of Altered Peptide Ligands and MHC with in Vivo Immune Responses.},
  journal = {PLoS One},
  year = {2010},
  volume = {5},
  number = {7},
  pages = {e11653},
  issn = {1932-6203 1932-6203},
  doi = {10.1371/journal.pone.0011653},
  keywords = {Animals;Female;Mice;Molecular Dynamics Simulation;Protein Binding;*Ligands;CD4-Positive T-Lymphocytes/immunology;Encephalomyelitis;Autoimmune;Experimental/chemically induced;Histocompatibility Antigens Class II/*chemistry/*metabolism;Myelin Basic Protein/chemistry;Peptides/chemistry/genetics/*immunology/*metabolism;Protein Conformation/drug effects}
}

@ARTICLE{roopra2009jgaj24122417,
  author = {Roopra, S.~ and Knapp, B.~ and Omasits, U.~ and Schreiner, W.~},
  title = {jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability.},
  journal = {Journal of Chemical Information and Modeling},
  year = {2009},
  volume = {49},
  number = {10},
  pages = {2412--2417},
  issn = {1549-960X 1549-9596},
  doi = {10.1021/ci900248f},
  keywords = {*Software;Computer Graphics;*Molecular Dynamics Simulation;User-Computer Interface}
}

@ARTICLE{knapp2009guim103107,
  author = {Knapp, B.~ and Schreiner, W.~},
  title = {Graphical User Interfaces for Molecular Dynamics—Quo Vadis?},
  journal = {Bioinformatics and Biology Insights},
  year = {2009},
  volume = {3},
  pages = {103--107},
  issn = {1177-9322 1177-9322},
  doi = {10.4137/BBI.S3332},
  url = {https://doi.org/10.4137%2FBBI.S3332},
  keywords = {graphical user interface;molecular dynamics}
}

@ARTICLE{knapp2009acch301307,
  author = {Knapp, B.~ and Omasits, U.~ and Frantal, S.~ and Schreiner, W.~},
  title = {A Critical Cross-Validation of High Throughput Structural Binding Prediction Methods for pMHC.},
  journal = {Journal of Computer-Aided Molecular Design},
  year = {2009},
  volume = {23},
  number = {5},
  pages = {301--307},
  doi = {10.1007/s10822-009-9259-2},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-65049084476\&doi=10.1007%2fs10822-009-9259-2\&partnerID=40\&md5=1a3139d9b7eafe54c519130cbef0c680}
}

@ARTICLE{knapp20093api18391844,
  author = {Knapp, B.~ and Omasits, U.~ and Bohle, B.~ and Maillere, B.~ and Ebner, C.~ and Schreiner, W.~ and Jahn-Schmid, B.~},
  title = {3-Layer-Based Analysis of Peptide-MHC Interaction: In Silico Prediction, Peptide Binding Affinity and T Cell Activation in a Relevant Allergen-Specific Model.},
  journal = {Molecular Immunology},
  year = {2009},
  volume = {46},
  number = {8-9},
  pages = {1839--1844},
  issn = {1872-9142 0161-5890},
  doi = {10.1016/j.molimm.2009.01.009},
  keywords = {Humans;Computer Simulation;Amino Acid Sequence;Allergens/immunology;Imaging;Three-Dimensional/methods;Protein Binding;Protein Conformation;Forecasting;Models;Molecular;Peptides/chemistry/immunology/*metabolism;Antigen Presentation/immunology;Amino Acid Substitution;Epitope Mapping/methods;HLA-DR Antigens/chemistry/genetics/immunology/*metabolism;HLA-DRB1 Chains;Lymphocyte Activation/*immunology;Major Histocompatibility Complex/immunology;Substrate Specificity;T-Lymphocytes/*immunology/metabolism}
}

@ARTICLE{omasits2008akpm781793,
  author = {Omasits, U.~ and Knapp, B.~ and Neumann, M.~ and Steinhauser, O.~ and Stockinger, H.~ and Kobler, R.~ and Schreiner, W.~},
  title = {Analysis of Key Parameters for Molecular Dynamics of pMHC Molecules.},
  journal = {Molecular Simulation},
  year = {2008},
  volume = {34},
  number = {8},
  pages = {781--793},
  doi = {10.1080/08927020802256298},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-49649086640\&doi=10.1080%2f08927020802256298\&partnerID=40\&md5=0c7717506a724a6cba36da40b979ca5c}
}

@ARTICLE{knapp2008scsb977982,
  author = {Knapp, B.~ and Omasits, U.~ and Schreiner, W.~},
  title = {Side Chain Substitution Benchmark for Peptide/MHC Interaction.},
  journal = {Protein Science},
  year = {2008},
  volume = {17},
  number = {6},
  pages = {977--982},
  issn = {1469-896X 0961-8368 0961-8368},
  doi = {10.1110/ps.073402508},
  keywords = {Reproducibility of Results;*Major Histocompatibility Complex;Protein Binding;Protein Conformation;Peptides/*chemistry/metabolism}
}

@INCOLLECTION{kobler2007imds443447,
  author = {Kobler, R.~ and K{\"o}ckerbauer, T.~ and Omasits, U.~ and Neumann, M.~ and Schreiner, W.~ and Volkert, J.~},
  title = {Interactive Molecular Dynamics Simulations on the Grid.},
  booktitle = {Computer Aided Systems Theory – EUROCAST 2007. 11th International Conference on Computer Aided Systems Theory, EUROCAST 2007, Las Palmas de Gran Canaria, Spain, 12–16 February 2007, Revised Selected Papers},
  publisher = {Springer},
  year = {2007},
  editor = {Moreno Díaz,R.;Pichler,F.;Quesada Arencibia,A.},
  number = {4739},
  series = {Lecture Notes in Computer Science},
  pages = {443--447},
  address = {Berlin},
  doi = {10.1007/978-3-540-75867-9_56},
  url = {https://doi.org/10.1007/978-3-540-75867-9_56}
}

@ARTICLE{karch2006agpf599611,
  author = {Karch, R.~ and Neumann, M.~ and Neumann, F.~ and Ullrich, R.~ and Neum{\"u}ller, J.~ and Schreiner, W.~},
  title = {A Gibbs Point Field Model for the Spatial Pattern of Coronary Capillaries.},
  journal = {Physica A: Statistical Mechanics and Its Applications},
  year = {2006},
  volume = {369},
  number = {2},
  pages = {599--611},
  doi = {10.1016/j.physa.2006.02.018},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33745684691\&doi=10.1016%2fj.physa.2006.02.018\&partnerID=40\&md5=19f138af2cd4898b0e087e4e80702df6}
}

@ARTICLE{schreiner2006oats416429,
  author = {Schreiner, W.~ and Karch, R.~ and Neumann, M.~ and Neumann, F.~ and Szawlowski, P.~ and Roedler, S.~},
  title = {Optimized Arterial Trees Supplying Hollow Organs.},
  journal = {Medical Engineering \& Physics},
  year = {2006},
  volume = {28},
  number = {5},
  pages = {416--429},
  issn = {1350-4533 1350-4533},
  doi = {10.1016/j.medengphy.2005.07.019},
  keywords = {Humans;*Algorithms;Computer Simulation;Blood Flow Velocity;Blood Pressure;*Models;Cardiovascular;*Ventricular Function;Arteries/*physiology;Coronary Circulation/*physiology;Viscera/*blood supply/*physiology}
}

@ARTICLE{nadler2005eegd829844,
  author = {Nadler, B.A.~ and Karch, R.~ and Neumann, M.~ and Neumann, F.~ and Aharinejad, S.~ and Schreiner, W.~},
  title = {Error Estimation of Geometrical Data Obtained by Histomorphometry of Oblique Vessel Sections: A Computer Model Study.},
  journal = {Computers in Biology and Medicine},
  year = {2005},
  volume = {35},
  number = {9},
  pages = {829--844},
  issn = {0010-4825 0010-4825},
  doi = {10.1016/j.compbiomed.2004.07.003},
  keywords = {Animals;Swine;*Computer Simulation;Blood Vessels/*anatomy \& histology}
}

@ARTICLE{karch2005spcc135144,
  author = {Karch, R.~ and Neumann, F.~ and Ullrich, R.~ and Neum{\"u}ller, J.~ and Podesser, B.K.~ and Neumann, M.~ and Schreiner, W.~},
  title = {The Spatial Pattern of Coronary Capillaries in Patients with Dilated, Ischemic, or Inflammatory Cardiomyopathy.},
  journal = {Cardiovascular Pathology},
  year = {2005},
  volume = {14},
  number = {3},
  pages = {135--144},
  issn = {1054-8807 1054-8807},
  doi = {10.1016/j.carpath.2005.03.003},
  keywords = {Adult;Female;Humans;Male;Retrospective Studies;Aged;Middle Aged;Models;Biological;Computer Simulation;Capillaries;*Coronary Circulation;Cardiomyopathy;Dilated/*pathology/surgery;Coronary Vessels/*pathology;Heart Failure/pathology/surgery;Heart Transplantation;Myocardial Ischemia/*pathology/surgery;Myocarditis/*pathology/surgery}
}

@ARTICLE{karch2003fpph307321,
  author = {Karch, R.~ and Neumann, F.~ and Podesser, B.K.~ and Neumann, M.~ and Szawlowski, P.~ and Schreiner, W.~},
  title = {Fractal Properties of Perfusion Heterogeneity in Optimized Arterial Trees: A Model Study.},
  journal = {Journal of General Physiology},
  year = {2003},
  volume = {122},
  number = {3},
  pages = {307--321},
  issn = {0022-1295 1540-7748 0022-1295},
  doi = {10.1085/jgp.200208747},
  keywords = {Animals;Computer Simulation;Regional Blood Flow;*Models;Cardiovascular;Arteries/*physiology;*Fractals}
}

@ARTICLE{karch2003vpao548563,
  author = {Karch, R.~ and Neumann, F.~ and Neumann, M.~ and Szawlowski, P.~ and Schreiner, W.~},
  title = {Voronoi Polyhedra Analysis of Optimized Arterial Tree Models.},
  journal = {Annals of Biomedical Engineering},
  year = {2003},
  volume = {31},
  number = {5},
  pages = {548--563},
  issn = {0090-6964 0090-6964},
  doi = {10.1114/1.1566444},
  keywords = {Humans;*Algorithms;Models;Statistical;Computer Simulation;Quality Control;Regional Blood Flow/physiology;Retina;*Models;Anatomic;*Models;Cardiovascular;Anatomy;Cross-Sectional/methods;Arteries/*anatomy \& histology/*growth \& development/physiology;Retinal Vessels/physiology}
}

@ARTICLE{schreiner2003hpia285301,
  author = {Schreiner, W.~ and Karch, R.~ and Neumann, M.~ and Neumann, F.~ and Roedler, S.M.~ and Heinze, G.~},
  title = {Heterogeneous Perfusion Is a Consequence of Uniform Shear Stress in Optimized Arterial Tree Models.},
  journal = {Journal of Theoretical Biology},
  year = {2003},
  volume = {220},
  number = {3},
  pages = {285--301},
  issn = {0022-5193 0022-5193},
  doi = {10.1006/jtbi.2003.3136},
  keywords = {Humans;Stress;Mechanical;Blood Pressure/physiology;*Computer Simulation;*Hemorheology;*Models;Cardiovascular;Arteries/*physiology}
}

@ARTICLE{karch2000fcoa250264,
  author = {Karch, R.~ and Neumann, F.~ and Neumann, M.~ and Schreiner, W.~},
  title = {Functional Characteristics of Optimized Arterial Tree Models Perfusing Volumes of Different Thickness and Shape.},
  journal = {Journal of Vascular Research},
  year = {2000},
  volume = {37},
  number = {4},
  pages = {250--264},
  issn = {1018-1172 1018-1172},
  doi = {10.1159/000025739},
  keywords = {Computer Simulation;*Models;Cardiovascular;*Blood Circulation;*Blood Volume;Arteries/*anatomy \& histology/*physiology}
}

@ARTICLE{karch2000sgoa495511,
  author = {Karch, R.~ and Neumann, F.~ and Neumann, M.~ and Schreiner, W.~},
  title = {Staged Growth of Optimized Arterial Model Trees.},
  journal = {Annals of Biomedical Engineering},
  year = {2000},
  volume = {28},
  number = {5},
  pages = {495--511},
  issn = {0090-6964 0090-6964},
  doi = {10.1114/1.290},
  keywords = {Algorithms;Humans;Models;Anatomic;*Models;Cardiovascular;Arteries/*anatomy \& histology/*growth \& development/physiology;Biomedical Engineering;Coronary Vessels/anatomy \& histology/growth \& development/physiology;Heart/anatomy \& histology/growth \& development/physiology}
}

@ARTICLE{schreiner1999ssda2745,
  author = {Schreiner, W.~ and Neumann, F.~ and Karch, R.~ and Neumann, M.~ and Roedler, S.M.~ and End, A.~},
  title = {Shear Stress Distribution in Arterial Tree Models, Generated by Constrained Constructive Optimization.},
  journal = {Journal of Theoretical Biology},
  year = {1999},
  volume = {198},
  number = {1},
  pages = {27--45},
  issn = {0022-5193 0022-5193},
  doi = {10.1006/jtbi.1999.0898},
  keywords = {Humans;*Computer Simulation;*Stress;Mechanical;*Models;Cardiovascular;Arteries/*anatomy \& histology;Blood Viscosity/physiology}
}

@ARTICLE{karch1999atma1938,
  author = {Karch, R.~ and Neumann, F.~ and Neumann, M.~ and Schreiner, W.~},
  title = {A Three-Dimensional Model for Arterial Tree Representation, Generated by Constrained Constructive Optimization.},
  journal = {Computers in Biology and Medicine},
  year = {1999},
  volume = {29},
  number = {1},
  pages = {19--38},
  issn = {0010-4825 0010-4825},
  doi = {10.1016/s0010-4825(98)00045-6},
  keywords = {Algorithms;Humans;*Models;Biological;Blood Pressure/physiology;Regional Blood Flow/physiology;*Computer Simulation;Hemodynamics/physiology;Vasoconstriction/physiology;Vascular Resistance/physiology;Vasodilation/physiology;Blood Viscosity/physiology;Arteries/anatomy \& histology/*physiology;Blood Volume/physiology;Microcirculation/physiology;Neovascularization;Physiologic;Stochastic Processes}
}

@ARTICLE{podesser1998ortr6368,
  author = {Podesser, B.K.~ and Neumann, F.~ and Neumann, M.~ and Schreiner, W.~ and Wollenek, G.~ and Mallinger, R.~},
  title = {Outer Radius-Wall Thickness Ratio, a Postmortem Quantitative Histology in Human Coronary Arteries.},
  journal = {Acta Anatomica},
  year = {1998},
  volume = {163},
  number = {2},
  pages = {63--68},
  issn = {0001-5180 0001-5180},
  doi = {10.1159/000046485},
  keywords = {Adult;Humans;Male;Image Processing;Computer-Assisted;Coronary Vessels/*anatomy \& histology}
}

@ARTICLE{aharinejad1998mhca5059,
  author = {Aharinejad, S.~ and Schreiner, W.~ and Neumann, F.~},
  title = {Morphometry of Human Coronary Arterial Trees.},
  journal = {Anatomical Record},
  year = {1998},
  volume = {251},
  number = {1},
  pages = {50--59},
  issn = {0003-276X 0003-276X},
  doi = {10.1002/(SICI)1097-0185(199805)251:1<50::AID-AR9>3.0.CO;2-I},
  keywords = {Female;Humans;Male;Middle Aged;Computer Simulation;Cadaver;Microscopy;Electron;Scanning;Anthropometry;Models;Anatomic;Blood Pressure/physiology;Coronary Circulation/physiology;Coronary Vessels/*anatomy \& histology/ultrastructure;Heart/anatomy \& histology;Models;Cardiovascular}
}

@INCOLLECTION{schreiner1997gtot371380,
  author = {Schreiner, W.~ and Neumann, F.~ and Karch, R.~ and Neumann, M.~ and End, A.~ and Roedler, S.M.~},
  title = {Geometrical and Topological Optimization and Their Relation to the Bifurcation Laws in Optimized Arterial Tree Models.},
  booktitle = {Computer Aided Optimum Design of Structures V. Proceedings of the Fifth International Conference on Computer Aided Optimum Design of Structures (OPTI 97), Rome, Italy, 8–10 September 1997},
  publisher = {Wit Press},
  year = {1997},
  editor = {Hernandez,S.;Brebbia,C.A.},
  number = {31},
  series = {WIT Transactions on the Built Environment},
  pages = {371--380},
  address = {Southampton},
  url = {https://www.witpress.com/elibrary/wit-transactions-on-the-built-environment/31/8234}
}

@ARTICLE{mueller1997vprt10031007,
  author = {Mueller, M.R.~ and Salat, A.~ and Stangl, P.~ and Murabito, M.~ and Pulaki, S.~ and Boehm, D.~ and Koppensteiner, R.~ and Ergun, E.~ and Mittlboeck, M.~ and Schreiner, W.~ and Losert, U.~ and Wolner, E.~},
  title = {Variable Platelet Response to Low-Dose ASA and the Risk of Limb Deterioration in Patients Submitted to Peripheral Arterial Angioplasty.},
  journal = {Thrombosis and Haemostasis},
  year = {1997},
  volume = {78},
  number = {3},
  pages = {1003--1007},
  issn = {0340-6245 0340-6245},
  doi = {10.1055/s-0038-1657677},
  keywords = {Female;Humans;Male;Risk Factors;Aged;Middle Aged;Administration;Oral;Leg/*blood supply;Blood Platelets/*drug effects;*Angioplasty;Balloon;Arterial Occlusive Diseases/*therapy;Aspirin/administration \& dosage/*therapeutic use;Intermittent Claudication/*therapy;Platelet Aggregation Inhibitors/administration \& dosage/*therapeutic use;Platelet Aggregation/drug effects;Smoking}
}

@ARTICLE{neumann1997csca353357,
  author = {Neumann, F.~ and Schreiner, W.~ and Neumann, M.~},
  title = {Computer Simulation of Coronary Arterial Trees.},
  journal = {Advances in Engineering Software},
  year = {1997},
  volume = {28},
  number = {6},
  pages = {353--357},
  doi = {10.1016/S0965-9978(97)00021-5},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031195594\&doi=10.1016%2fS0965-9978%2897%2900021-5\&partnerID=40\&md5=b82896f45269514ac7de442b98f306cf}
}

@ARTICLE{schreiner1997avfa147158,
  author = {Schreiner, W.~ and Neumann, F.~ and Neumann, M.~ and End, A.~ and Roedler, S.M.~},
  title = {Anatomical Variability and Functional Ability of Vascular Trees Modeled by Constrained Constructive Optimization.},
  journal = {Journal of Theoretical Biology},
  year = {1997},
  volume = {187},
  number = {2},
  pages = {147--158},
  issn = {0022-5193 0022-5193},
  doi = {10.1006/jtbi.1997.0413},
  keywords = {Humans;*Computer Simulation;*Models;Cardiovascular;Coronary Circulation/*physiology;Coronary Vessels/*anatomy \& histology}
}

@INCOLLECTION{karch1997toat312,
  author = {Karch, R.~ and Schreiner, W.~ and Neumann, M.~ and Neumann, F.~},
  title = {Three-Dimensional Optimization of Arterial Tree Models.},
  booktitle = {Simulations in Biomedicine IV. Proceedings of the Fourth International Conference on Computers in Biomedicine (BIOMED), Umbria, Italy, 9–11 June 1997},
  publisher = {Wit Press},
  year = {1997},
  editor = {Power,H.;Brebbia,C.H.;Kenny,J.},
  number = {4},
  series = {WIT Transactions on Biomedicine and Health},
  pages = {3--12},
  address = {Southampton},
  url = {https://www.witpress.com/Secure/elibrary/papers/BIO97/BIO97001FU.pdf}
}

@INCOLLECTION{neumann1997sdes2335,
  author = {Neumann, M.~ and Neumann, F.~ and Karch, R.~ and Schreiner, W.~},
  title = {Size and Discretization Effects in Simulations of Coronary Hemodynamics.},
  booktitle = {Simulations in Biomedicine IV. Proceedings of the Fourth International Conference on Computers in Biomedicine (BIOMED), Umbria, Italy, 9–11 June 1997},
  publisher = {Wit Press},
  year = {1997},
  editor = {Power,H.;Brebbia,C.H.;Kenny,J.},
  number = {4},
  series = {WIT Transactions on Biomedicine and Health},
  pages = {23--35},
  address = {Southampton},
  url = {https://www.witpress.com/Secure/elibrary/papers/BIO97/BIO97003FU.pdf}
}

@INCOLLECTION{neumann1997scat3746,
  author = {Neumann, M.~ and Schreiner, W.~ and Karch, R.~ and Neumann, F.~},
  title = {Structure of Computer-Generated Arterial Trees with Different Optimization Target Functions.},
  booktitle = {Simulations in Biomedicine IV. Proceedings of the Fourth International Conference on Computers in Biomedicine (BIOMED), Umbria, Italy, 9–11 June 1997},
  publisher = {Wit Press},
  year = {1997},
  editor = {Power,H.;Brebbia,C.H.;Kenny,J.},
  number = {4},
  series = {WIT Transactions on Biomedicine and Health},
  pages = {37--46},
  address = {Southampton},
  url = {https://www.witpress.com/Secure/elibrary/papers/BIO97/BIO97004FU.pdf}
}

@INCOLLECTION{schreiner1997lsgs125134,
  author = {Schreiner, W.~ and Neumann, F.~ and Neumann, M.~ and Karch, R.~},
  title = {Local Symmetry and Global Structure of Coronary Arterial Tree Models Generated by Constrained Constructive Optimization.},
  booktitle = {Simulations in Biomedicine IV. Proceedings of the Fourth International Conference on Computers in Biomedicine (BIOMED), Umbria, Italy, 9–11 June 1997},
  publisher = {Wit Press},
  year = {1997},
  editor = {Power,H.;Brebbia,C.H.;Kenny,J.},
  number = {4},
  series = {WIT Transactions on Biomedicine and Health},
  pages = {125--134},
  address = {Southampton},
  url = {https://www.witpress.com/Secure/elibrary/papers/BIO97/BIO97012FU.pdf}
}

@ARTICLE{roedler1997ffah10181025,
  author = {R{\"o}dler, S.M.~ and Moritz, A.~ and Schreiner, W.~ and End, A.~ and Dubsky, P.~ and Wolner, E.~},
  title = {Five-Year Follow-Up after Heart Valve Replacement with the Carbomedics Bileaflet Prosthesis.},
  journal = {Annals of Thoracic Surgery},
  year = {1997},
  volume = {63},
  number = {4},
  pages = {1018--1025},
  doi = {10.1016/S0003-4975(97)00174-4},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0342276117\&doi=10.1016%2fS0003-4975%2897%2900174-4\&partnerID=40\&md5=8a0f0280428a41998bfcf18da5d215bb}
}

@ARTICLE{vankan1997feab375385,
  author = {Vankan, W.J.~ and Huyghe, J.M.~ and Janssen, J.D.~ and Huson, A.~ and Hacking, W.J.G.~ and Schreiner, W.~},
  title = {Finite Element Analysis of Blood Flow through Biological Tissue.},
  journal = {International Journal of Engineering Science},
  year = {1997},
  volume = {35},
  number = {4},
  pages = {375--385},
  issn = {0020-7225},
  doi = {10.1016/S0020-7225(96)00108-5},
  url = {http://www.sciencedirect.com/science/article/pii/S0020722596001085}
}

@ARTICLE{schreiner1997lbac129140,
  author = {Schreiner, W.~ and Neumann, F.~ and Neumann, M.~ and Karch, R.~ and End, A.~ and Roedler, S.M.~},
  title = {Limited Bifurcation Asymmetry in Coronary Arterial Tree Models Generated by Constrained Constructive Optimization.},
  journal = {Journal of General Physiology},
  year = {1997},
  volume = {109},
  number = {2},
  pages = {129--140},
  issn = {0022-1295 1540-7748 0022-1295},
  doi = {10.1085/jgp.109.2.129},
  keywords = {Algorithms;Linear Models;Computer Simulation;Regression Analysis;Models;Anatomic;Blood Pressure/physiology;Coronary Circulation/physiology;Coronary Vessels/*anatomy \& histology/physiology;Viscosity}
}

@INCOLLECTION{neumann1996vcam259268,
  author = {Neumann, F.~ and Neumann, M.~ and Karch, R.~ and Schreiner, W.~},
  title = {Visualization of Computer-Generated Arterial Model Trees.},
  booktitle = {Simulation Modelling in Bioengineering. Proceedings of the First International BIOSIM ’96 Conference, Mérida, Venezuela, 23–25 October 1996},
  publisher = {WIT Press},
  year = {1996},
  editor = {Cerrolaza,M.;Jugo,D.;Brebbia,C.A.},
  number = {3},
  series = {WIT Transactions on Biomedicine and Health},
  pages = {259--268},
  address = {Southampton},
  url = {https://www.witpress.com/Secure/elibrary/papers/BSIM96/BSIM96024FU.pdf}
}

@INCOLLECTION{neumann1996srsc3951,
  author = {Neumann, M.~ and Neumann, F.~ and Karch, R.~ and Schreiner, W.~},
  title = {Spatially Resolved Simulation of Coronary Hemodynamics.},
  booktitle = {Simulation Modelling in Bioengineering. Proceedings of the First International BIOSIM ’96 Conference, Mérida, Venezuela, 23–25 October 1996},
  publisher = {WIT Press},
  year = {1996},
  editor = {Cerrolaza,M.;Jugo,D.;Brebbia,C.A.},
  number = {3},
  series = {WIT Transactions on Biomedicine and Health},
  pages = {39--51},
  address = {Southampton},
  url = {https://www.witpress.com/Secure/elibrary/papers/BSIM96/BSIM96004FU.pdf}
}

@ARTICLE{grimm1996cmai13391345,
  author = {Grimm, M.~ and Yeganehfar, W.~ and Laufer, G.~ and Madl, C.~ and Kramer, L.~ and Eisenhuber, E.~ and Simon, P.~ and Kupilik, N.~ and Schreiner, W.~ and Pacher, R.~ and Bunzel, B.~ and Wolner, E.~ and Grimm, G.~},
  title = {Cyclosporine May Affect Improvement of Cognitive Brain Function after Successful Cardiac Transplantation.},
  journal = {Circulation},
  year = {1996},
  volume = {94},
  number = {6},
  pages = {1339--1345},
  issn = {0009-7322 0009-7322},
  doi = {10.1161/01.cir.94.6.1339},
  keywords = {Female;Humans;Male;Middle Aged;Quality of Life;Reaction Time;Cognition/*drug effects;*Heart Transplantation;Psychometrics/methods;Forecasting;*Postoperative Care;Affect;Brain/*physiopathology;Cyclosporine/*adverse effects;Evoked Potentials;Auditory}
}

@ARTICLE{schreiner1996sqbs161174,
  author = {Schreiner, W.~ and Neumann, F.~ and Neumann, M.~ and End, A.~ and M{\"u}ller, M.R.~},
  title = {Structural Quantification and Bifurcation Symmetry in Arterial Tree Models Generated by Constrained Constructive Optimization.},
  journal = {Journal of Theoretical Biology},
  year = {1996},
  volume = {180},
  number = {2},
  pages = {161--174},
  issn = {0022-5193 0022-5193},
  doi = {10.1006/jtbi.1996.0092},
  keywords = {Algorithms;Animals;Regional Blood Flow;*Computer Simulation;*Models;Cardiovascular;*Arteries}
}

@ARTICLE{end1995aell12451251,
  author = {End, A.~ and Stift, A.~ and Wieselthaler, G.~ and Griesmacher, A.~ and Schlechta, B.~ and Koppensteiner, R.~ and Schreiner, W.~ and Geissler, K.~ and Stockenhuber, F.~ and Klepetko, W.~},
  title = {Anemia and Erythropoietin Levels in Lung Transplant Recipients.},
  journal = {Transplantation},
  year = {1995},
  volume = {60},
  number = {11},
  pages = {1245--1251},
  issn = {0041-1337},
  keywords = {Adult;Female;Humans;Male;Retrospective Studies;Risk Factors;Aged;Middle Aged;Prognosis;Survival Analysis;Lung Transplantation/*adverse effects;Anemia/etiology/*physiopathology;Erythropoiesis;Erythropoietin/*blood}
}

@ARTICLE{schreiner1995iots583599,
  author = {Schreiner, W.~ and Neumann, F.~ and Neumann, M.~ and End, A.~ and Roedler, S.M.~ and Aharinejad, S.~},
  title = {The Influence of Optimization Target Selection on the Structure of Arterial Tree Models Generated by Constrained Constructive Optimization.},
  journal = {Journal of General Physiology},
  year = {1995},
  volume = {106},
  number = {4},
  pages = {583--599},
  issn = {0022-1295 1540-7748 0022-1295},
  doi = {10.1085/jgp.106.4.583},
  keywords = {Animals;Humans;Middle Aged;Computer Simulation;Blood Pressure;*Models;Cardiovascular;Arteries/*anatomy \& histology/physiology}
}

@ARTICLE{grimm1995itss916920,
  author = {Grimm, M.~ and Grimm, G.~ and Zuckermann, A.~ and Wieselthaler, G.~ and Feuerstein, M.~ and Daneschvar, H.~ and Schmiedinger, H.~ and Schreiner, W.~ and Wolner, E.~ and Laufer, G.~},
  title = {ICD Therapy in Survivors of Sudden Cardiac Death Awaiting Heart Transplantation.},
  journal = {Annals of Thoracic Surgery},
  year = {1995},
  volume = {59},
  number = {4},
  pages = {916--920},
  issn = {0003-4975 0003-4975},
  doi = {10.1016/0003-4975(95)00013-b},
  keywords = {Female;Humans;Male;Retrospective Studies;Middle Aged;*Heart Transplantation;*Defibrillators;Implantable;*Waiting Lists;Death;Sudden;Cardiac/*prevention \& control;Tachycardia;Ventricular/mortality/surgery/*therapy}
}