Publications

2017

Journal

  • Neumann U, Genze N, Heider D: EFS: An Ensemble Feature Selection Tool implemented as R-package and Web-Application. BioData Mining 2017, in press. (Link)
  • Elands, R. J. J., Simons, C. C. J. M., Riemenschneider, M., Isaacs, A., Schouten, L. J., Verhage, B. A., … Weijenberg, M. P. (2017). A systematic SNP selection approach to identify mechanisms underlying disease aetiology: linking height to post-menopausal breast and colorectal cancer risk. Scientific Reports, 7, 41034. (Link)
  • Anastasiou O, Kälsch J, Hakmouni M, Kucukoglu O, Heider D, Korth J, Manka P, Sowa J-P, Bechmann L, Saner F, Paul A, Gerken G, Baba H, Canbay A: Low transferrin and high ferritin concentrations are associated with worse outcome in acute liver failure. Liver International 2017, in press. (Link)

2016

Journal

  • Rühle F, Witten A, Barysenka A, Huge A, Arning A, Heller C, Krümpel A, Mester R, Franke A, Lieb W, Riemenschneider M, Hiersche M,  Limperger V, Nowak-Göttl U, Stoll M: Rare genetic variants in SMAP1, B3GAT2 and RIMS1 contribute to pediatric venous thromboemolism. Blood 2016. (Link)
  • Best J, Bilgi H, Heider D, Schotten C, Manka P, Bedreli S, Gorray M, Ertle J, van Grunsven LA, Dechêne A: The GALAD scoring algorithm based on AFP, AFP-L3, and DCP significantly improves detection of BCLC early stage hepatocellular carcinoma. Zeitschrift für Gastroenterologie 2016, 54(12):1296-1305. (Link)
  • Neumann U, Riemenschneider M, Sowa J-P, Baars T, Kälsch J, Canbay A, Heider D: Compensation of feature selection biases accompanied with improved predictive performance for binary classification by using a novel ensemble feature selection approach. BioData Mining 2016, 9(1):36. (Link)
  • Canbay A, Leven A-S, Fingas C, Heider D: Non-alcoholic fatty liver disease (NAFLD): can simple laboratory diagnostics assess progression of NAFLD? LaboratoriumsMedizin 2016, 40(6):367-372. (Link)
  • Riemenschneider M, Hummel T, Heider D: SHIVA – a web application for drug resistance and tropism testing in HIV. BMC Bioinformatics 2016, 17:314. (Link)
  • Emberger-Klein A, Menrad K, Heider D: Determinants of Consumers’ Willingness-to-pay for Fairly-produced, Locally Grown Dairy Products. German Journal of Agricultural Economics 2016, 65(2):94-111. (Link)
  • Riemenschneider M, Cashin KY, Budeus B, Sierra S, Shirvani-Dastgerdi E, Bayanolhag S, Kaiser R, Gorry PR, Heider D: Genotypic Prediction of Co-receptor Tropism of HIV-1 Subtypes A and C. Nature Scientific Reports 2016, 6:24883. (Link)
  • Riemenschneider M, Heider D: Current Approaches in Computational Drug Resistance Prediction in HIV. Current HIV Research 2016, 14(4):307-315. (Link)
  • Riemenschneider M, Senge R, Neumann U, Hüllermeier E, Heider D: Exploiting HIV-1 protease and reverse transcriptase cross-resistance information for improved drug resistance prediction by means of multi-label classification. BioData Mining 2016, 9:10. (Link)
  • Baars T, Neumann U, Jinawy M, Hendricks S, Sowa JP, Kälsch J, Riemenschneider M, Gerken G, Erbel R, Heider D, Canbay A: In Acute Myocardial Infarction Liver Parameters Are Associated With Stenosis Diameter. Medicine 2016, 95(6):e2807. (Link)
  • Grossmann L, Jensen M, Heider D, Jost S, Glücksman E, Hartikainen H, Mahamdallie SS, Gardner M, Hoffmann D, Bass D, Boenigk J: Protistan community analysis: key findings of a large-scale molecular sampling. ISME J. 2016, 10(9):2269-79. (Link)
  • Schmid J, Heider D, Wendel NJ, Sperl N, Sieber V: Bacterial Glycosyltransferases: Challenges and opportunities of a highly diverse enzyme class toward tailoring natural products. Front. Microbiol. 2016, 7:182. (Link)
  • Stenzig  J, Hirt MN, Löser A, Bartholdt LM, Hensel JT, Werner TR, Riemenschneider M, Indenbirken D, Guenther T, Müller C, Hübner N, Stoll M, Eschenhagen T: DNA methylation in an engineered heart tissue model of cardiac hypertrophy: common signatures and effects of DNA methylation inhibitors. Basic Res Cardiol. 2016, 111(1):9.

2015

Journal

  • Lange A, Jost S, Heider D, Bock C, Budeus B, Schilling E, Strittmatter A, Boenigk J, Hoffmann D: AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities. PLoS ONE 2015, 10(11): e0141590. (Link)
  • Kälsch J, Bechmann LP, Heider D, Best J, Manka P, Kälsch H, Sowa JP, Moebus S, Slomiany U, Jöckel KH, Erbel R, Gerken G, Canbay A: Normal liver enzymes are correlated with severity of metabolic syndrome in a large population based cohort. Nature Scientific Reports 2015, 5:13058. (Link)
  • Sierra S, Dybowski JN, Pironti A, Heider D, Güney L, Thielen A, Reuter S, Esser S, Fätkenheuer G, Lengauer T, Hoffmann D, Pfister H, Jensen B, Kaiser R: Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc. PLoS One 2015, 10(5):e0125502. (Link)
  • Grabowski K*, Riemenschneider M*, Schulte L, Witten A, Schulz A, et al. Fetal-Adult Cardiac Transcriptome Analysis in Rats with Contrasting Left Ventricular Mass Reveals New Candidates for Cardiac Hypertrophy. PLoS One 2015, 10(2):e0116807. doi:10.1371/journal.pone.0116807
    *authors contributed equally

Conferences

  • A systematic SNP selection approach for studying gene-environment interactions in cancer epidemiology. Elands R, Riemenschneider M, Simons C, Schouten L, Verhage B, van Steen K, Godschalk R, van den Brandt P, Stoll M, Weijenberg M. Healthy Living: The European Congress of Epidemiology, 2015.

 

2014

Journal

  • Olejnik M, Steuwer M, Gorlatch S, Heider D: gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing. Bioinformatics 2014, 30(22):3272-3273. (Link)
  • Fassl S K, Austermann J, Papantonopoulou O, Riemenschneider M, Xue J, Bertheloot D, Freise N, Spiekermann C, Witten A, Viemann D, Kirschnek S, Stoll M, Latz E, Schultze J L, Roth J, Vogl T: Transcriptome Assessment Reveals a Dominant Role for TLR4 in the Activation of Human Monocytes by the Alarmin MRP8. The Journal of Immunology. DOI: 10.4049/jimmunol.1401085
  • Heider D, Dybowski JN, Wilms C, Hoffmann D: A simple structure-based model for the prediction of HIV-1 co-receptor tropism. BioData Mining 2014, 7:14. (Link)
  • Sowa JP, Atmaca Ö, Kahraman A, Schlattjan M, Lindner M, Sydor S, Scherbaum N, Lackner K, Gerken G, Heider D, Arteel GE, Erim Y, Canbay A: Non-invasive separation of alcoholic and non-alcoholic liver disease with predictive modeling. PLoS One 2014, 9(7):e101444. (Link)
  • Dechêne A, Jochum C, Fingas C, Paul A, Heider D, Syn WK, Gerken G, Canbay A, Zöpf T: Endoscopic management is the treatment of choice for bile leaks after liver resection. Gastrointest Endosc. 2014, 80(4):626-633. (Link)
  • Grotegerd D, Redlich R, Almeida J R C, Riemenschneider M, Kugel H, Arolt V: MANIA-A Pattern Classification Toolbox for Neuroimaging Data. Neuroinformatics 2014. DOI: 10.1007/s12021-014-9223-8

Conferences

  • Heider D, Bartenhagen C, Dybowski JN, Hauke S, Pyka M, Hoffmann D: Unsupervised dimension reduction methods for protein sequence classification, Data Analysis, Machine Learning and Knowledge Discovery 2014, 295-302. (Link)

 

2013

Journal

  • Heider D, Senge R, Cheng W, Hüllermeier E: Multilabel classification for exploiting cross-resistance information in HIV-1 drug resistance prediction. Bioinformatics 2013, 29(16):1946-52. (Link)
  • Grum D, Franke S, Kraff O, Heider D, Schramm A, Hoffmann D, Bayer P: Design of a modular protein-based MRI contrast agent for targeted application. PLoS One 2013, 8(6):e65346. (Link)
  • Sowa JP, Heider D, Bechmann LP, Gerken G, Hoffmann D, Canbay A: Novel algorithm for non-invasive assessment of fibrosis in NAFLD. PLoS One 2013, 8(4):e62439. (Link)
  • Pyka M, Hahn T, Heider D, Krug A, Sommer J, Kircher T, Jansen A: Baseline activity predicts working memory load of preceding task condition. Hum Brain Mapp. 2013, 34(11):3010-22.
  • Wang Y, Rawi R, Wilms C, Heider D, Yang R, Hoffmann D: A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes. PLoS One 2013, 8(3):e58804. (Link)
  • Ertle JM, Heider D, Wichert M, Keller B, Kueper R, Hilgard P, Gerken G, Schlaak JF: A combination of α-fetoprotein and des-γ-carboxy prothrombin is superior in detection of hepatocellular carcinoma. Digestion 2013, 87(2):121-31 (Link)
  • Jiang QQ, Bartsch L, Sicking W, Wich PR, Heider D, Hoffmann D, Schmuck C: A new approach to inhibit human β-tryptase by protein surface binding of four-armed peptide ligands with two different sets of arms. Org Biomol Chem. 2013, 11(10):1631-9. (Link)

Conferences

  • Hauke S, Biedermann S, Mühlhäuser M, Heider D: On the Application of Supervised Machine Learning to Trustworthiness Assessment, Proc. 12th International Conference on Trust, Security and Privacy in Computing and Communications 2013, Melbourne, Australia, 525-534.

2012

Journal

  • Wünsch D, Fetz V, Heider D, Tenzer S, Bier C, Kunst L, Knauer S, Stauber R: Chemico-genetic strategies to inhibit the leukemic potential of threonine aspartase-1. Blood Cancer J. 2012, 2(6):e77. (Link)
  • Kessler D, Gruen GC, Heider D, Morgner J, Reis H, Schmid KW, Jendrossek V: The action of small GTPases Rab11 and Rab25 in vesicle trafficking during cell migration. Cell Physiol Biochem. 2012, 29(5-6):647-56. (Link)
  • Riemenschneider M, Preuss C, Stoll M: Genetics of complex diseases: An evolutionary perspective. Current Topics in Genetics 2012, 5:113-121.
  • van den Boom J, Heider D, Martin SR, Pastore A, Mueller JW: 3′-Phosphoadenosine 5′-phosphosulfate (PAPS) synthases, naturally fragile enzymes specifically stabilized by nucleotide binding. J Biol Chem. 2012, 287(21):17645-55. (Link)
  • Preuss C, Riemenschneider M, Wiedmann D, Stoll M: Evolutionary Dynamics of Co-Segregating Gene Clusters Associated with Complex Diseases. PLoS ONE 2012, 7(5).

Conferences

  • Pyka M, Kircher T, Hauke S, Heider D: The Brain in a box: an encoding scheme for natural neural networks, Proceedings of the 4th International Joint Conference on Computational Intelligence 2012, Barcelona, Spain, 196-201.

2011

Journal

  • Dybowski JN, Riemenschneider M, Hauke S, Pyka M, Verheyen J, Hoffmann D, Heider D: Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers. BioData Mining 2011, 4:26. (Link)
  • Lederer C, Heider D, van den Boom J, Hoffmann D, Mueller JW, Bayer P: Single-domain parvulins constitute a specific marker for recently proposed deep-branching archaeal subgroups. Evol Bioinform Online 2011, 7:135-48 (Link)
  • Winkler J, Armano G, Dybowski JN, Kuhn O, Ledda F, Heider D: Computational Design of a DNA- and Fc-Binding Fusion Protein. Adv Bioinformatics 2011, 2011:457578. (Link)
  • Heider D, Hoffmann D: Interpol: An R package for preprocessing of protein sequences. BioData Mining 2011, 4:16. (Link)
  • Pyka M, Heider D, Hauke S, Kircher T, Jansen A: Dynamic causal modeling with genetic algorithms. J Neurosci Methods 2011, 194(2):402-406. (Link)
  • Heider D, Verheyen J, Hoffmann D: Machine learning on normalized protein sequences. BMC Res Notes 2011, 4:94. (Link)
  • Heider D, Barnekow A: DNA Watermarking: Challenging Perspectives for Biotechnological Applications. Current Bioinformatics 2011, 6(3): 375-382. (Link)

Conferences

  • Driver J, Heider D, Hauke S, Borschbach M, Pyka M: Hierarchical Text Clustering Based on Independent Component Analysis, Proceedings of the Computational Linguistics-Applications Conference 2011, Warsaw, Poland, ISBN: 978-83-60810-47-7, 17-21.
  • Hauke S, Pyka M, Heider D: Group-Agreement as a Reliability Measure for Witness Recommendations in Reputation-based Trust Protocols, Transactions on Computational Science XII, Lecture Notes in Computer Science 2011, 6670:231-255.

2010

Journal

  • Dybowski JN, Heider D, Hoffmann D: Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism. AIDS Res Ther. 2010, 7:41. (Link)
  • Dybowski JN, Heider D, Hoffmann D: Prediction of co-receptor usage of HIV-1 from genotype. PLoS Comput Biol. 2010, 6(4):e1000743. (Link)
  • Heider D, Verheyen J, Hoffmann D: Predicting Bevirimat resistance of HIV-1 from genotype. BMC Bioinformatics 2010, 11:37. (Link)
  • Heider D, Hauke S, Pyka M, Kessler D: Insights into the classification of small GTPases. Adv Appl Bioinform Chem. 2010, 3:15-24. (Link)
  • Pyka M, Hertog M, Fernandez R, Hauke S, Heider D, Dannlowski U, Konrad C: fMRI data visualization with BrainBlend and Blender. Neuroinformatics 2010, 8(1):21-31. (Link)

Conferences

  • Hauke S, Pyka M, Borschbach M, Heider D: Harnessing Recommendations from Weakly Linked Neighbors in Reputation-Based Trust Formation, International Conference on Cyberworlds 2010, 163-170.
  • Hauke S, Pyka M, Heider D: Towards Improved Trust Diffusion Through Active Recommender Propagation, Systemics and InformaticsWorld Network 2010, 10:121-129.
  • Hauke S, Pyka M, Borschbach M, Heider D: Augmenting Reputation-based Trust Metrics with Rumor-like Dissemination of Reputation Information, IFIP Advances in Information and Communication Technology 2010, 330:136-147.
  • Winkler J, Hauke S, Pyka M, Heider D: JACVANN: A Java Framework For Complex Valued Artificial Neural Networks, Systemics and Informatics World Network 2010, 10:48-55.

Book Chapter

  • Hauke S, Pyka M, Borschbach M, Heider D: Reputation-Based Trust Diffusion in Complex Socio-Economic Networks, Information Retrieval and Mining in Distributed Environments, Studies in Computational Intelligence 2010, Springer-Verlag, ISBN 978-3-642-16088-2, 21-40.

2009

Journal

  • Pyka M, Beckmann CF, Schöning S, Hauke S, Heider D, Kugel H, Arolt V, Konrad C: Impact of working memory load on FMRI resting state pattern in subsequent resting phases. PLoS One 2009, 4(9):e7198. (Link)
  • Heider D, Appelmann J, Bayro T, Dreckmann W, Held A, Winkler J, Barnekow A, Borschbach M: A computational approach for the identification of small GTPases based on preprocessed amino acid sequences. Technol Cancer Res Treat. 2009, 8(5):333-41. (Link)
  • Heider D, Pyka M, Barnekow A: DNA watermarks in non-coding regulatory sequences. BMC Res Notes 2009, 2:125. (Link)

Conferences

  • Hauke S, Pyka M, Heider D, Borschbach M: A reputation-based trust framework leveraging the dynamics of complex socio-economic networks for information dissemination, Communications of SIWN 2009, 7:53-58.
  • Borschbach M, Hauke S, Pyka M, Heider D: Opportunities and limitations of a principal component analysis optimized machine learning approach for the identification and classification of cancer involved proteins, Communications of SIWN 2009, 6:85-89.

2008

Journal

  • Heider D, Kessler D, Barnekow A: Watermarking sexually reproducing diploid organisms. Bioinformatics 2008, 24(17):1961-2. (Link)
  • Heider D, Barnekow A: DNA watermarks: a proof of concept. BMC Mol Biol. 2008, 9:40. (Link)

2007

Journal

  • Heider D, Barnekow A: DNA-based watermarks using the DNA-Crypt algorithm, BMC Bioinformatics 2007, 8:176. (Link)
FacebookTwitterGoogle+