Publications

2019

Journal

  • Löchel HF, Eger D, Sperlea T, Heider D: Deep Learning on Chaos Game Representation for Proteins. Bioinformatics 2019, in press. (Link)
  • Schotten C, Bechmann LP, Manka P, Theysohn J, Dechêne A, El Fouly A, Barbato F, Neumann U, Radünz S,  Sydor S, Heider D, Venerito M, Canbay A, Gerken G, Herrmann K, Wedemeyer H, Best J: NAFLD-associated comorbidities in advanced stage HCC do not alter the safety and efficacy of Y 90 radioembolization. Liver Cancer 2019, in press. (Link)
  • Canbay A, Kälsch J, Neumann U, Rau M, Hohenester S, Strucksberg K-H, Baba HA, Rust C, Bantel H, Geier A, Heider D, Sowa J-P: Non-invasive assessment of NAFLD as systemic disease – a machine learning perspective. PLoS One 2019, 14(3):e0214436. (Link)
  • Spänig S, Heider D: Encodings and models for antimicrobial peptide classification for multi-resistant pathogens. BioData Mining 2019, 12:7. (Link)

2018

Journal

  • Schwarz J and Heider D: GUESS: Projecting Machine Learning Scores to Well-Calibrated Probability Estimates for Clinical Decision Making. Bioinformatics 2018, in press. (Link)
  • Sperlea T, Füser S, Boenigk J, Heider D: SEDE-GPS: socio-economic data enrichment based on GPS information. BMC Bioinformatics 2018, 19(Suppl 15):440. (Link)
  • Löchel HF, Riemenschneider M, Frishman D, Heider D: SCOTCH: Subtype A Coreceptor Tropism Classification in HIV-1. Bioinformatics 2018, 34(15): 2575–2580. (Link)
  • Riemenschneider M, Wienbeck J, Scherag A, Heider D: Data Science for MDx Applications: From Academia to Clinic to Industry. Systems Medicine 2018, in press. (Link)
  • Baars T, Sowa J-P, Neumann U, Hendricks S, Jinawy M, Kälsch J, Gerken G, Rassaf T, Heider D, Canbay A: Liver parameters as part of a non-invasive model for prediction of all-cause mortality after myocardial infarction. Archives of Medical Science 2018, in press. (Link)
  • Armano G, Giuliani A, Neumann U, Rothe N, Heider D: Phi-Delta-Diagrams: Software Implementation of a Visual Tool for Assessing Classifier and Feature Performance. Mach. Learn. Knowl. Extr. 2018, 1(1):7 (Link)

2017

Journal

  • Riemenschneider M, Herbst A, Rasch A, Gorlatch S, Heider D: eccCL: Parallelized GPU implementation of Ensemble Classifier Chains. BMC Bioinformatics 2017, 18:371. (Link)
  • Neumann U, Genze N, Heider D: EFS: An Ensemble Feature Selection Tool implemented as R-package and Web-Application. BioData Mining 2017, 10:21. (Link)
  • Elands RJJ, Simons CCJM, Riemenschneider M, Isaacs A, Schouten LJ, Verhage BA, … Weijenberg MP: A systematic SNP selection approach to identify mechanisms underlying disease aetiology: linking height to post-menopausal breast and colorectal cancer risk. Scientific Reports 2017, 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, 37(7):1032-1041. (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)