3. Publications

Publications

2024

  • Pott H, Weckler B, Gaffron S, Martin R, Maier D, Alter P, Biertz F, Speicher T, Bertrams W, Jung AL, Laakmann K, Heider D, Wouters M, Vogelmeier CF, Schmeck B: Diffusion capacity and static hyperinflation as markers of disease progression predict 3-year mortality in COPD: Results from COSYCONET. Respiratory Research 2024; 1-13 (Link)
  • Tajabadi M, Heider D: Fair Swarm Learning: Improving Incentives for Collaboration by a Fair Reward Mechanism. Knowledge-Based Systems 2024, 304:112451 (Link)
  • Tajabadi M, Martin R, Heider D: Privacy-Preserving Decentralized Learning Methods for Biomedical Applications. Computational and Structural Biotechnology Journal 23(2024):3281-3287 (Link)
  • Leite JMRS, Ribeiro A, Pereira JL, Alves de Souza C, Heider D, Pavan Soler JM, Mingroni-Netto RC, Fisberg RM, Rogero MM, Sarti FM: Missense genetic variants in major bitter taste receptors are associated with diet quality and food intake in a highly admixed underrepresented population. Clinical Nutrition ESPEN 2024, in press. (Link)
  • Welzel M, Dressler H, Heider D: Turbo autoencoders for the DNA data storage channel with Autoturbo-DNA. iScience 2024, 27(5):109575. (Link)
  • Ren Y, Li C, Sapugahawatte DN, Zhu C, Spänig S, Jamrozy D, Rothen J, Daubenberger CA, Bentley SD, Ip M, Heider D: Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning. Computers in Biology and Medicine 2024, 171:108185. (Link)
  • Heider D, Henning Stetefeld, Andreas Meisel, Julian Bösel, Marie Artho, Ralf Linker, Klemens Angstwurm, Bernhard Neumann: POLAR: prediction of prolonged mechanical ventilation in patients with myasthenic crisis. Journal of Neurology 2024, in press. (Link)
  • Mengel N, Welzel M, Niedenthal W, Stein M, Heider D, Chatterjee S: Inkjet-printed quantum dots on paper as concept towards high-density long-term data storage. Journal of Physics Communications 2024, 8(2):025005. (Link)
  • Sarumi OA, Hahn M, Heider D: NeuralBeds: Neural Embeddings for Efficient DNA Data Compression and Optimized Similarity Search. Computational and Structural Biotechnology Journal 2024, 23:732-741. (Link)

2023

  • Pfeifer B, Chereda H, Martin R, Saranti A, Clemens S, Hauschild AC, Beissbarth T, Holzinger A, Heider D: Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification. Bioinformatics 2023, 39(11): btad703 (Link)
  • Arabi F, Javadi-Zarnaghi F, Löchel HF, Martin R, Heider D: LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens. Infection 2023, 51:1809-1818. (Link)
  • Anžel A, Heider D, Hattab G: Interactive polar diagrams for model comparison. Computer Methods and Programs in Biomedicine 2023, 242:107843. (Link)
  • Schwarz PM, Welzel M, Heider D, Freisleben B: RepairNatrix – a Snakemake workflow for processing DNA sequencing data for DNA storage. Bioinformatics Advances 2023, in press. (Link)
  • Deep A, Bludau D, Welzel M, Clemens S, Heider D, Boenigk J, Beisser D: Natrix2–Improved amplicon workflow with novel Oxford Nanopore Technologies support and enhancements in clustering, classification and taxonomic databases. MBMG Metabarcoding and Metagenomics 2023, 7: 263–271. (Link)
  • Holzinger A, Saranti A, Hauschild AC, Beinecke J, Heider D, Roettger R, Mueller H, Baumbach J, Pfeifer B: Human-in-the-Loop Integration with Domain-Knowledge Graphs for Explainable Federated Deep Learning. International Cross-Domain Conference for Machine Learning and Knowledge Extraction 2023, 45-64. (Link)
  • Tajabadi M, Grabenhenrich, Riberio A, Leyer M, Heider D: Sharing Data With Shared Benefits: Artificial Intelligence Perspective. Journal of Medical Internet Research 2023, 25:e47540 (Link)
  • Klau JH, Maj C, Klinkhammer H, Krawitz PM, Mayer A, Hillmer AM, Schumacher J, Heider D: AI-based multi-PRS models outperform classical single-PRS models. Frontiers in Genetics 2023, 14:1217860 (Link)
  • Matschinske J, Späth J, Bakhtiari M, Probul N, Kazemi Majdabadi MM, Nasirigerdeh R, Torkzadehmahani R, Hartebrodt A, Orban B-A, Fejér S-J, Zolotareva O, Das S, Baumbach L, Pauling JK, Tomašević O, Bihari B, Bloice M, Donner NC, Fdhila W, Frisch T, Hauschild A-C, Heider D, Holzinger A, Hötzendorfer W, Hospes J, Kacprowski T, Kastelitz M, List M, Mayer R, Moga M, Müller H, Pustozerova A, Röttger R, Saak CC, Saranti A, Schmidt HHHW, Tschohl C, Wenke NK, Baumbach J: The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach. Journal of Medical Internet Research 2023, 25:e42621-e42621. (Link)
  • Waechter C, Fehse L, Welzel M, Heider D, Babalija L, Cheko J, Mueller J, Pöling J, Braun T, Pankuweit S, Weihe E, Kinscherf R, Schieffer B, Luesebrink U, Soufi M, Ruppert V: Comparative analysis of full-length 16s ribosomal RNA genome sequencing in human fecal samples using primer sets with different degrees of degeneracy. Frontiers in Genetics 2023, 14:1213829. (Link)
  • Jung AL, Han M, Griss K, Bertrams W, Nell C, Greulich T, Klemmer A, Pott H, Heider D, Vogelmeier CF, Hippenstiel S, Suttorp NW, Schmeck BT: Novel protein biomarkers for pneumonia and acute exacerbations in COPD: a pilot study. Frontiers in Medicine 2023, 10:1180746. (Link)
  • Hess T, Maj C, Gehlen J, Borisov O, Haas SL, Gockel I, et al.: Dissecting the genetic heterogeneity of gastric cancer. EBioMedicine 2023, 92:104616. (Link)
  • Müller P, Velazquez Camacho O, Yazbeck AM, Wölwer C, Zhai W, Schumacher J, Heider D, Buettner R, Quaas A, Hillmer AM: Why loss of Y? A pan-cancer genome analysis of tumors with loss of Y chromosome. Computational and Structural Biotechnology Journal 2023, 21:1573-1583. (Link)
  • Spänig S, Michel A, Heider D: Unsupervised encoding selection through ensemble pruning for biomedical classification. BioData Mining 2023. (Link)
  • Jung AL, Møller Jørgensen M, Bæk R, Artho M, Griss K, Han M, Bertrams W, Greulich T, Koczulla R, Hippenstiel S, Heider D, Suttorp N, Schmeck B: Surface proteome of plasma extracellular vesicles as mechanistic and clinical biomarkers for malaria. Infection 2023, in press. (Link)
  • Martin R, Nguyen MK, Lowack N, Heider D: ODNA: Identification of Organellar DNA by Machine Learning. Bioinformatics 2023, 39(5). (Link)
  • Ezekannagha C, Welzel M, Heider D, Hattab G: DNAsmart: Multiple Attribute Ranking Tool for DNA Data Storage Systems Author links open overlay panel. Computational and Structural Biotechnology Journal 2023, 1448-1460 (Link)
  • Welzel M, Schwarz PM, Löchel HF, Kabdullayeva T, Clemens S, Becker A, Freisleben B, Heider D. DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage. Nature communications 2023, 14:628 (Link)
  • Näher AF, Vorisek CN, Klopfenstein SAI, Lehne M, Thun S, Alsalamah S, Pujari S, Heider D, Ahrens W, Pigeot I, Marckmann G, Jenny MA, Renard BY, von Kleist M, Wieler LH, Balzer F, Grabenhenrich L. Secondary data for global health digitalisation. Lancet Digital Health 2023, 5(2):e93-e101. (Link)
  • Namba S, Saito Y, Kogure Y, Masuda T, Bondy ML, Gharahkhani P, Gockel I, Heider D, Hillmer A, Jankowski J, MacGregor S, Maj C, Melin B, Ostrom QT, Palles C, Schumacher J, Tomlinson I, Whiteman DC, Okada Y, Kataoka K: Common Germline Risk Variants Impact Somatic Alterations and Clinical Features across Cancers. Cancer Research 2023, 83(1):20-27. (Link)
  • Hattab G, Anžel A, Spänig S, Neumann N, Heider D: A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification. NAR Genomics and Bioinformatics 2023, 5(1): lqac103. (Link)

2022

  • Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Schwengers O, Heider D. Deep Transfer Learning Enables Robust Prediction of Antimicrobial Resistance for Novel Antibiotics. Antibiotics 2022. 11;1611. (Link)
  • Hauschild AC, Martin R, Holst SC, Wienbeck J, Heider D. Guideline for Software Life Cycle in Health Informatics. iScience 2022. 25(12):105534 (Link)
  • Leyh C, Heucke N, Schotten C, Büchter M, Bechmann LP, Wichert M, Dechêne A, Herrmann K, Heider D, Sydor S, Lemmer P, Ludwig JM, Pospiech J, Theysohn J, Damm R, March C, Powerski M, Pech M, Özcürümez M, Weigt J, Keitel V, Lange CM, Schmidt H, Canbay A, Best J, Gerken G, Manka PP: LiMAx Prior to Radioembolization for Hepatocellular Carcinoma as an Additional Tool for Patient Selection in Patients with Liver Cirrhosis. Cancers 2022, 14(19):4584. (Link)
  • Schröder J, Chegwidden L, Maj C, Gehlen J, Speller J, Böhmer AC, Borisov O, Hess T, Kreuser N, Venerito M, Alakus H, May A, Gerges C, Schmidt T, Thieme R, Heider D, Hillmer AM, Reingruber J, Lyros O, Dietrich A, Hoffmeister A, Mehdorn M, Lordick F, Stocker G, Hohaus M, Reim D, Kandler J, Müller M, Ebigbo A, Fuchs C, Bruns CJ, Hölscher AH, Lang H, Grimminger PP, Dakkak D, Vashist Y, May S, Görg S, Franke A, Ellinghaus D, Galavotti S, Veits L, Weismüller J, Dommermuth J, Benner U, Rösch T, Messmann H, Schumacher B, Neuhaus H, Schmidt C, Wissinowski TT, Nöthen MM, Wellcome Trust Case Control Consortium 2 (WTCCC2), Esophageal Adenocarcinoma Genetics Consortium (EAGLE), Barrett’s and Esophageal Adenocarcinoma Consortium (BEACON), Dong J, Ong J-S, Buas MF, Thrift AP, Vaughan TL, Tomlinson I, Whiteman DC, Fitzgerald RC, Jankowski J, Vieth M, Mayr A, Gharahkhani P, MacGregor S, Gockel I, Palles C, Schumacher J: GWAS meta-analysis of 16 790 patients with Barrett’s oesophagus and oesophageal adenocarcinoma identifies 16 novel genetic risk loci and provides insights into disease aetiology beyond the single marker level, Gut 2022, in press. (Link)
  • Schulte C, Solda A, Spänig S, Adams N, Bekic I, Streicher W, Heider D, Strasser R, Maric HM: Multivalent binding kinetics resolved by fluorescence proximity sensing, Communications Biology 2022, 5:1070. (Link)
  • Sperlea T, Heider D, Hattab G: A theoretical basis for bioindication in complex ecosystems. Ecologial Indicators 2022, 140:109050. (Link)
  • Ezekannagha C, Becker A, Heider D, Hattab G: Design considerations for advancing data storage with synthetic DNA for long-term archiving. Materials Today Bio 2022, in press. (Link)
  • Kaya G, Ezekannagha C, Heider D, Hattab G: Context-Aware Phylogenetic Trees for Phylogeny-Based Taxonomy Visualization. Frontiers in Genetics 2022. 13:891240. (Link)
  • Löchel HF, Welzel M, Hattab G, Hauschild AC, Heider D: Fractal construction of constrained code words for DNA storage systems. Nucleic Acids Research 2022, in press. (Link)
  • Roberts JM, Heider D, Bergman L, Thornburg KL: Vision for Improving Pregnancy Health: Innovation and the Future of Pregnancy Research, Reproductive Sciences 2022, in press. (Link)
  • Jahn M, Özcürümez MK, Dolff S, Rohn H, Heider D, Dechene A, Canbay A, Rath PM, Katsounas A: A Multipathogen Bile Sample-based PCR Assay Can Guide Empirical Antimicrobial Strategies in Cholestatic Liver Diseases, Journal of Clinical and Translational Hepatology 2022, in press. (Link)
  • Anžel A, Heider D, Hattab G: MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks. Computational and Structural Biotechnology Journal 2022, 20, 1044–1055. (Link)
  • Nasirigerdeh R, Torkzadehmahani R, Matschinske J, Frisch T, List M, Späth J, Weiss S, Völker U, Pitkänen E, Heider D, Wenke NK, Kaissis G, Rueckert D, Kacprowski T, Baumbach J: sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies. Genome Biology 2022, 23:32 (Link)
  • Stroth S, Tauscher J, Wolff N, Küpper C, Poustka L, Roepke S, Roessner V, Heider D, Kamp‐Becker I: Phenotypic differences between female and male individuals with suspicion of autism spectrum disorder. Molecular Autism 2022, 13:11. (Link)
  • Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Schwengers O, Heider D: Multi-label classification for multi-drug resistance prediction of Escherichia coli. Computational and Structural Biotechnology Journal 2022, 20:1264-1270. (Link)
  • Hauschild AC, Lemanczyk M, Matschinske J, Frisch T, Zolotareva O, Holzinger A, Baumbach J, Heider D: Federated Random Forests can improve local performance of predictive models for various health care applications. Bioinformatics 2022, 38(8):2278-2286 (Link)
  • Sperlea T, Schenk JP, Dreßler H, Beisser D, Hattab G, Boenigk J, Heider D. The relationship between land cover and microbial community composition in European lakes. Science of The Total Environment 2022, 825:153732 (Link)
  • Beinecke JM, Anders P, Schurrat T, Heider D, Luster M, Librizzi D, Hauschild AC: Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records. Computers in Biology and Medicine 2022, 143:105263 (Link)
  • Manka P, Sydor S, Schänzer-Ocklenburg JM, Brandenburg M, Best J, Vilchez-Vargas R, Link A, Heider D, Brodesser S, Figge A, Jähnert A, Coombes JD, Cubero FJ, Kahraman A, Kim M-S, Kälsch J, Kinner S, Faber KN, Moshage H, Gerken G, Syn W-K, Canbay A, Bechmann LP: A Potential Role for Bile Acid Signaling in Celiac Disease-Associated Fatty Liver. Metabolites 2022, 12(2):130. (Link)
  • El-Shaikh A, Welzel M, Heider D, Seeger B: High-scale random access on DNA storage systems. NAR Genomics and Bioinformatics 2022, 4(1):lqab126. (Link)

2021

Journal

  • Park Y, Hauschild AC, Heider D: Transfer learning compensates limited data, batch effects and technological heterogeneity in single-cell sequencing. NAR Genomics and Bioinformatics 2021, 3(4):lqab104. (Link)
  • Beinecke J, Heider D: Gaussian noise up-sampling is better suited than SMOTE and ADASYN for clinical decision making. BioData Mining 2021, 14:49 (Link)
  • Löchel HF, Heider D: Chaos Game Representation and its applications in Bioinformatics. Computational and Structural Biotechnology Journal. 2021. (Link)
  • Gandouz M, Holzmann H, Heider D: Machine learning with asymmetric abstention for biomedical decision-making. BMC Medical Informatics and Decision Making 2021, 21:294. (Link)
  • Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Hauschild A-C, Schwengers O, Heider D: Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Bioinformatics 2021, in press. (Link)
  • Martin R, Dressler H, Hattab G, Hackl T, Fischer MG, Heider D: MOSGA 2: Comparative genomics and validation tools. Computational and Structural Biotechnology Journal. 2021, 19:5504-5509. (Link)
  • Lemmer P, Selbach N, Baars T, Porsch-Özcürümez M, Heider D, Canbay A, Sowa J-P: Transaminase concentrations cannot separate NAFL and NASH in morbidly obese patients irrespective of histological algorithm. Digestive Diseases 2021, in press. (Link)
  • Anžel A, Heider D, Hattab G. The Visual Story of Data Storage: From Storage Properties to User Interfaces. Computational and Structural Biotechnology Journal. 2021 Aug 24. (Link)
  • Stroth S, Tauscher J, Wolff N, Küpper C, Poustka L, Roepke S, Roessner V, Heider D, Kamp-Becker I: Is the combination of ADOS and ADI-R necessary to classify ASD? Rethinking the “gold standard” in diagnosing ASD. Frontiers in Psychiatry 2021, 12:727308. (Link)
  • Spänig S, Eick L, Nuy JK, Beisser D, Ip M, Heider D*, Boenigk J*: A multi-omics study on quantifying antimicrobial resistance in European freshwater lakes. Environment International 2021, 157: 106821. *shared last & corresponding authors (Link)
  • Spänig S, Mohsen S, Hattab G, Hauschild AC, Heider D: A large-scale comparative study on peptide encodings for biomedical classification. NAR Genomics and Bioinformatics 2021, 3(2): lqab039. (Link)
  • Stroth S, Tauscher J, Wolff N, Küpper C, Poustka L, Roepke S, Roessner V, Heider D, Kamp‐Becker I: Identification of the most indicative and discriminative features from diagnostic instruments for children with autism. JCPP Advances 2021, 1(2): e12023. (Link)
  • Hauschild AC, Eick L, Wienbeck J, Heider D: Fostering reproducibility, reusability, and technology transfer in health informatics. iScience 2021, 24(7): 102803. (Link)
  • Park Y, Heider D, Hauschild A.C.: Integrative Analysis of Next-Generation Sequencing for Next-Generation Cancer Research toward Artificial Intelligence. Cancers 2021, 13(13), 3148. (Link)
  • Sperlea T, Kreuder N, Beisser D, Hattab G, Boenigk J, Heider D: Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework. Molecular Ecology 2021, 30(9): 2131-2144. (Link)
  • Wagner D, Heider D, Hattab G: Mushroom data creation, curation, and simulation to support classification tasks. Scientific Reports 2021, 11(1): 1-12 (Link)
  • Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O’Toole AN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M: Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics 2021, 22(2): 642-663. (Link)

2020

Journal

  • Martin R, Hackl T, Hattab G, Fischer MG, Heider D: MOSGA: Modular Open-Source Genome Annotator. Bioinformatics 2020, 36(22): 5514–5515 (Link).
  • Welzel M, Lange A, Heider D, Schwarz M, Freisleben B, Jensen M, Boenigk J, Beisser D: Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads. BMC Bioinformatics 2020, 21:526 (Link).
  • Hattab G, Rhyne TM, Heider D: Ten simple rules to colorize biological data visualization. PLoS Comput Biol. 2020, 16(10): e1008259. (Link)
  • Martin R, Löchel HF, Welzel M, Hattab G, Hauschild AC, Heider D: CORDITE: the curated CORona Drug InTERactions database for SARS-CoV-2. Cell iScience 2020, 23:7 (Link).
  • Sperlea T, Muth L, Martin R, Weigel C, Waldminghaus T, Heider D: gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning. Scientific Reports 2020, 10:6727 (Link)
  • Löchel HF, Heider D: Comparative analyses of error handling strategies for next-generation sequencing in precision medicine. Scientific Reports 2020, 10:5750. (Link)
  • Schwarz M, Welzel M, Kabdullayeva T, Becker A, Freisleben B, Heider D: MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing, and PCR errors. Bioinformatics 2020, 36(11): 3322-3326. (Link)
  • Hackl T, Martin R, Barenhoff K, Duponchel S, Heider D, Fischer MG: Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis. Scientific Data 2020, 7:29. (Link)
  • Löchel HF, Eger D, Sperlea T, Heider D: Deep Learning on Chaos Game Representation for Proteins. Bioinformatics 2020, 36(1): 272–279. (Link)

2019

Journal

  • Schwarz J, Heider D: GUESS: Projecting Machine Learning Scores to Well-Calibrated Probability Estimates for Clinical Decision Making. Bioinformatics 2019, 35(14): 2458–2465 (Link)
  • Best J, Bechmann LP, Sowa LP, Sydor S, Dechêne A, Pflanz K, Bedreli S, Schotten C, Geier A, Berg T, Fischer J, Vogel A, Bantel H, Weinmann A, Schattenberg JM, Huber Y, Wege H, von Felden J, Schulze K, Bettinger D, Thimme R, Sinner F, Schütte K, Weiss KH, Toyoda H, Yasuda S, Kumada T, Berhane S, Wichert M, Heider D, Gerken G, Johnson P, Canbay A: GALAD Score Detects Early Hepatocellular Carcinoma in an International Cohort of Patients With Nonalcoholic Steatohepatitis, Clinical Gastroenterology and Hepatology 2019, 18(3):728-735. (Link)
  • Martin R, Heider D: ContraDRG: Automatic partial charge prediction by Machine Learning, Frontiers in Genetics 2019, 10:990. (Link)
  • Spänig S, Emberger-Klein A, Sowa JP, Canbay A, Menrad K, Heider D: The Virtual Doctor: An Interactive Clinical-Decision-Support System based on Deep Learning for Non-Invasive Prediction of Diabetes, Artificial Intelligence in Medicine 2019, 100:101706. (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, 8:491–504. (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)

Conferences

  • Pfannschmidt L, Göpfert C, Neumann U, Heider D, Hammer B: FRI – Feature Relevance Intervals for Interpretable and Interactive Data Exploration. 16th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology, Certosa di Pontignano, Siena – Tuscany, Italy.

2018

Journal

  • 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 2020, 16(1):71-80. (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)
  • 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

  • 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)

 

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)

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)
  • 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)

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)
  • 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)

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)