Andreas Hildebrandt 0001Johannes Gutenberg University Mainz, GermanySaarland University, Saarbrücken, Germanyhttps://www.bio.informatik.uni-mainz.de/andreas-hildebrandt/https://www.linkedin.com/in/andreas-hildebrandt-53b38073https://orcid.org/0000-0003-2180-6516https://www.wikidata.org/entity/Q30347641https://www.scopus.com/authid/detail.uri?authorId=12238853600Andreas HildebrandtAndreas Hildebrandt 0002Pepperl+Fuchs GmbH, Mannheim, GermanyDavid TeschnerDavid Gomez-ZepedaArthur DeclercqMateusz K. LackiSeymen AvciKonstantin BobUte DistlerThomas MichnaLennart MartensStefan TenzerAndreas Hildebrandt 0001Ionmob: a Python package for prediction of peptide collisional cross-section values.2023September39Bioinform.9https://doi.org/10.1093/bioinformatics/btad486db/journals/bioinformatics/bioinformatics39.html#TeschnerGDLABDMMTH23Thomas KemmerSebastian HackBertil SchmidtAndreas Hildebrandt 0001CUDA-accelerated protein electrostatics in linear space.1020222023June70J. Comput. Sci.https://doi.org/10.1016/j.jocs.2023.102022db/journals/jocs/jocs70.html#KemmerHSH23Konstantin BobDavid TeschnerThomas KemmerDavid Gomez-ZepedaStefan TenzerBertil SchmidtAndreas Hildebrandt 0001Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data.287202223BMC Bioinform.1https://doi.org/10.1186/s12859-022-04833-5db/journals/bmcbi/bmcbi23.html#BobTKGTSH22Felix KallenbornAndreas Hildebrandt 0001Bertil SchmidtCARE: context-aware sequencing read error correction.889-895202137Bioinform.7https://doi.org/10.1093/bioinformatics/btaa738https://www.wikidata.org/entity/Q98578502db/journals/bioinformatics/bioinformatics37.html#KallenbornHS21Lucas GrulichRalf WeigelAndreas Hildebrandt 0001Michael Wand 0001Peter SpichtingerAutomatic shape detection of ice crystals.101429202154J. Comput. Sci.https://doi.org/10.1016/j.jocs.2021.101429db/journals/jocs/jocs54.html#GrulichWHWS21Ernst AlthausAndreas Hildebrandt 0001Domenico MoscaLearning Molecular Classes from Small Numbers of Positive Examples Using Graph Grammars.3-152021AlCoBhttps://doi.org/10.1007/978-3-030-74432-8_1conf/alcob/2021db/conf/alcob/alcob2021.html#Althaus0M21Anna Katharina HildebrandtErnst AlthausAndreas Hildebrandt 0001Privately Querying Privacy: Privacy Estimation with Guaranteed Privacy of User and Database Party.56-722021ALGOCLOUDhttps://doi.org/10.1007/978-3-030-93043-1_4conf/algocloud/2021db/conf/algocloud/algocloud2021.html#HildebrandtAH21Robin KobusJosé Manuel AbuínAndré MüllerSören Lukas HellmannJuan Carlos PichelTomás F. PenaAndreas Hildebrandt 0001Thomas HankelnBertil SchmidtA big data approach to metagenomics for all-food-sequencing.102202021BMC Bioinform.1https://doi.org/10.1186/s12859-020-3429-6https://www.wikidata.org/entity/Q90273062db/journals/bmcbi/bmcbi21.html#KobusAMHPPHHS20André MüllerBertil SchmidtAndreas Hildebrandt 0001Richard MembarthRoland LeißaMatthis KruseSebastian HackAnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation.1030-10402020IPDPShttps://doi.org/10.1109/IPDPS47924.2020.00109conf/ipps/2020db/conf/ipps/ipdps2020.html#MullerS0MLKH20André MüllerBertil SchmidtAndreas Hildebrandt 0001Richard MembarthRoland LeißaMatthis KruseSebastian HackAnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation.2020abs/2002.04561CoRRhttps://arxiv.org/abs/2002.04561db/journals/corr/corr2002.html#abs-2002-04561Bertil SchmidtAndreas Hildebrandt 0001Dedicated Bioinformatics Analysis Hardware.1142-11502019Encyclopedia of Bioinformatics and Computational Biology (2)https://doi.org/10.1016/b978-0-12-809633-8.20186-6reference/bioinf/2019-2db/reference/bioinf/ebcb2019-2.html#Schmidt019Thomas KemmerSergej RjasanowAndreas Hildebrandt 0001NESSie.jl - Efficient and intuitive finite element and boundary element methods for nonlocal protein electrostatics in the Julia language.193-203201828J. Comput. Sci.https://doi.org/10.1016/j.jocs.2018.08.008db/journals/jocs/jocs28.html#KemmerRH18André MüllerChristian Hundt 0002Andreas Hildebrandt 0001Thomas HankelnBertil SchmidtMetaCache: context-aware classification of metagenomic reads using minhashing.3740-3748201733Bioinform.23https://doi.org/10.1093/bioinformatics/btx520https://www.wikidata.org/entity/Q42694050db/journals/bioinformatics/bioinformatics33.html#MullerHHHS17Ernst AlthausAndreas Hildebrandt 0001Domenico MoscaGraph Rewriting Based Search for Molecular Structures: Definitions, Algorithms, Hardness.43-592017STAF Workshopshttps://doi.org/10.1007/978-3-319-74730-9_5conf/staf/2017wdb/conf/staf/staf2017w.html#Althaus0M17Christian Hundt 0002Andreas Hildebrandt 0001Bertil SchmidtrapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs.394201617BMC Bioinform.https://doi.org/10.1186/s12859-016-1244-xhttps://www.wikidata.org/entity/Q36143391db/journals/bmcbi/bmcbi17.html#HundtHS16Hoang-Vu DangBertil SchmidtAndreas Hildebrandt 0001Tuan Tu TranAnna Katharina HildebrandtCUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm.200-211201630Int. J. High Perform. Comput. Appl.2https://doi.org/10.1177/1094342015597988https://www.wikidata.org/entity/Q57011939db/journals/ijhpca/ijhpca30.html#DangSHTH16Anna Katharina HildebrandtDaniel StöckelNina M. FischerLuis de la GarzaJens Krüger 0002Stefan NickelsMarc RöttigCharlotta SchärfeMarcel SchumannPhilipp ThielHans-Peter LenhofOliver KohlbacherAndreas Hildebrandt 0001ballaxy: web services for structural bioinformatics.121-122201531Bioinform.1https://doi.org/10.1093/bioinformatics/btu574https://www.wikidata.org/entity/Q28247170db/journals/bioinformatics/bioinformatics31.html#HildebrandtSFG0NRSSTLKH15Tim SeifertAndreas Lund 0001Benny KneisslSabine C. MuellerChristofer S. TautermannAndreas Hildebrandt 0001SKINK: a web server for string kernel based kink prediction in α-helices.1769-1770201430Bioinform.12https://doi.org/10.1093/bioinformatics/btu096https://www.wikidata.org/entity/Q47798710db/journals/bioinformatics/bioinformatics30.html#SeifertLKMTH14Anna Katharina HildebrandtMatthias DietzenThomas LengauerHans-Peter LenhofErnst AlthausAndreas Hildebrandt 0001Efficient computation of root mean square deviations under rigid transformations.765-771201435J. Comput. Chem.10https://doi.org/10.1002/jcc.23513https://www.wikidata.org/entity/Q44359041db/journals/jcc/jcc35.html#HildebrandtDLLAH14Matthias DietzenElena ZotenkoAndreas Hildebrandt 0001Thomas LengauerCorrection to On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking.3453201454J. Chem. Inf. Model.12https://doi.org/10.1021/ci5006788https://www.wikidata.org/entity/Q57011951db/journals/jcisd/jcisd54.html#DietzenZHL14Ernst AlthausAndreas Hildebrandt 0001Anna Katharina HildebrandtA Greedy Algorithm for Hierarchical Complete Linkage Clustering.25-342014AlCoBhttps://doi.org/10.1007/978-3-319-07953-0_2https://www.wikidata.org/entity/Q57011943conf/alcob/2014db/conf/alcob/alcob2014.html#AlthausHH14Ernst AlthausMarkus BlumenstockAlexej DisterhoftAndreas Hildebrandt 0001Markus KruppAlgorithms for the Maximum Weight Connected k -Induced Subgraph Problem.268-2822014COCOAhttps://doi.org/10.1007/978-3-319-12691-3_21conf/cocoa/2014db/conf/cocoa/cocoa2014.html#AlthausBDHK14Hoang-Vu DangBertil SchmidtAndreas Hildebrandt 0001Anna Katharina HildebrandtParallelized Clustering of Protein Structures on CUDA-Enabled GPUs.1-82014PDPhttps://doi.org/10.1109/PDP.2014.9https://doi.ieeecomputersociety.org/10.1109/PDP.2014.9https://www.wikidata.org/entity/Q57011953conf/pdp/2014db/conf/pdp/pdp2014.html#DangSHH14Anna Katharina DehofSimon LoewHans-Peter LenhofAndreas Hildebrandt 0001NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction.98201314BMC Bioinform.https://doi.org/10.1186/1471-2105-14-98https://www.wikidata.org/entity/Q34621976db/journals/bmcbi/bmcbi14.html#DehofLLH13Markus KruppTimo ItzelThorsten MaassAndreas Hildebrandt 0001Peter R. GalleAndreas TeufelCellLineNavigator: a workbench for cancer cell line analysis.942-948201341Nucleic Acids Res.Database-Issuehttps://doi.org/10.1093/nar/gks1012https://www.wikidata.org/entity/Q36491193db/journals/nar/nar41.html#KruppIMHGT13Stefan NickelsDaniel StöckelSabine C. MuellerHans-Peter LenhofAndreas Hildebrandt 0001Anna Katharina DehofPresentaBALL - A powerful package for presentations and lessons in structural biology.33-402013BioVishttps://doi.org/10.1109/BioVis.2013.6664344https://doi.ieeecomputersociety.org/10.1109/BioVis.2013.6664344https://www.wikidata.org/entity/Q57011959conf/biovis/2013db/conf/biovis/biovis2013.html#NickelsSMLHD13Anna Katharina HildebrandtErnst AlthausHans-Peter LenhofChien-Wen HungAndreas TholeyAndreas Hildebrandt 0001Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics.56-672013GCBhttps://doi.org/10.4230/OASIcs.GCB.2013.56conf/gcb/2013db/conf/gcb/gcb2013.html#HildebrandtALHTH13Martin SlawskiRene HussongAndreas TholeyThomas JakobyBarbara GregoriusAndreas Hildebrandt 0001Matthias Hein 0001Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching.291201213BMC Bioinform.https://doi.org/10.1186/1471-2105-13-291https://www.wikidata.org/entity/Q30538058db/journals/bmcbi/bmcbi13.html#SlawskiHTJGHH12Matthias DietzenElena ZotenkoAndreas Hildebrandt 0001Thomas LengauerOn the Applicability of Elastic Network Normal Modes in Small-Molecule Docking.844-856201252J. Chem. Inf. Model.3https://doi.org/10.1021/ci2004847https://www.wikidata.org/entity/Q34154973db/journals/jcisd/jcisd52.html#DietzenZHL12Stefan NickelsHienke SminiaSabine C. MuellerBas KoolsAnna Katharina DehofHans-Peter LenhofAndreas Hildebrandt 0001ProteinScanAR - An Augmented Reality Web Application for High School Education in Biomolecular Life Sciences.578-5832012IVhttps://doi.org/10.1109/IV.2012.97https://doi.ieeecomputersociety.org/10.1109/IV.2012.97https://www.wikidata.org/entity/Q57011971conf/iv/2012db/conf/iv/iv2012.html#NickelsSMKDLH12Florian BenzAndreas Hildebrandt 0001Sebastian HackA dynamic program analysis to find floating-point accuracy problems.453-4622012PLDIhttps://doi.org/10.1145/2254064.2254118https://doi.org/10.1145/2345156.2254118https://www.wikidata.org/entity/Q57011960conf/pldi/2012db/conf/pldi/pldi2012.html#BenzHH12Anna Katharina DehofAlexander RurainskiQuang Bao Anh BuiSebastian BöckerHans-Peter LenhofAndreas Hildebrandt 0001Automated bond order assignment as an optimization problem.619-625201127Bioinform.5https://doi.org/10.1093/bioinformatics/btq718https://www.wikidata.org/entity/Q33796206db/journals/bioinformatics/bioinformatics27.html#DehofRBBLH11Benny KneisslSabine C. MuellerChristofer S. TautermannAndreas Hildebrandt 0001String Kernels and High-Quality Data Set for Improved Prediction of Kinked Helices in α-Helical Membrane Proteins.3017-3025201151J. Chem. Inf. Model.11https://doi.org/10.1021/ci200278whttps://www.wikidata.org/entity/Q34043738db/journals/jcisd/jcisd51.html#KneisslMTH11Jaydeep P. BardhanAndreas Hildebrandt 0001A fast solver for nonlocal electrostatic theory in biomolecular science and engineering.801-8052011DAChttps://doi.org/10.1145/2024724.2024904conf/dac/2011db/conf/dac/dac2011.html#BardhanH11Andreas Hildebrandt 0001Anna Katharina DehofAlexander RurainskiAndreas BertschMarcel SchumannNora C. ToussaintAndreas MollDaniel StöckelStefan NickelsSabine C. MuellerHans-Peter LenhofOliver KohlbacherBALL - biochemical algorithms library 1.3.531201011BMC Bioinform.https://doi.org/10.1186/1471-2105-11-531https://www.wikidata.org/entity/Q21284344db/journals/bmcbi/bmcbi11.html#HildebrandtDRBSTMSNMLK10Sophie WegglerV. RutkaAndreas Hildebrandt 0001A new numerical method for nonlocal electrostatics in biomolecular simulations.4059-40742010229J. Comput. Phys.11https://doi.org/10.1016/j.jcp.2010.01.040https://www.wikidata.org/entity/Q57011975db/journals/jcphy/jcphy229.html#WegglerRH10Mike PhillipsIliyan GeorgievAnna Katharina DehofStefan NickelsLukas MarsalekHans-Peter LenhofAndreas Hildebrandt 0001Philipp SlusallekMeasuring properties of molecular surfaces using ray casting.1-72010IPDPS Workshopshttps://doi.org/10.1109/IPDPSW.2010.5470898https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2010.5470898https://www.wikidata.org/entity/Q57011983conf/ipps/2010wdb/conf/ipps/ipdps2010w.html#PhillipsGDNMLHS10Lukas MarsalekAnna Katharina DehofIliyan GeorgievHans-Peter LenhofPhilipp SlusallekAndreas Hildebrandt 0001Real-Time Ray Tracing of Complex Molecular Scenes.239-2452010IVhttps://doi.org/10.1109/IV.2010.43https://doi.ieeecomputersociety.org/10.1109/IV.2010.43https://www.wikidata.org/entity/Q57011987conf/iv/2010db/conf/iv/iv2010.html#MarsalekDGLSH10Kugamoorthy GajanananArturo NakasoneAndreas Hildebrandt 0001Helmut PrendingerA Novel Three-Dimensional Collaborative Online Platform for Bio-molecular Modeling.44-552010Smart Graphicshttps://doi.org/10.1007/978-3-642-13544-6_5https://dl.acm.org/doi/10.5555/1894345.1894352https://www.wikidata.org/entity/Q57011979conf/sg/2010db/conf/sg/sg2010.html#GajanananNHP10Rene HussongAndreas Hildebrandt 0001Signal Processing in Proteomics.145-1612010Proteome Bioinformaticshttps://doi.org/10.1007/978-1-60761-444-9_11https://www.wikidata.org/entity/Q46004870books/daglib/0032063db/books/collections/HJ2010.html#HussongH10Rene HussongBarbara GregoriusAndreas TholeyAndreas Hildebrandt 0001Highly accelerated feature detection in proteomics data sets using modern graphics processing units.1937-1943200925Bioinform.15https://doi.org/10.1093/bioinformatics/btp294https://www.wikidata.org/entity/Q33446179db/journals/bioinformatics/bioinformatics25.html#HussongGTH09Alexander RurainskiAndreas Hildebrandt 0001Hans-Peter LenhofA consensus line search algorithm for molecular potential energy functions.1499-1509200930J. Comput. Chem.9https://doi.org/10.1002/jcc.21175https://www.wikidata.org/entity/Q51859953db/journals/jcc/jcc30.html#RurainskiHL09Anna Katharina DehofAlexander RurainskiHans-Peter LenhofAndreas Hildebrandt 0001Automated Bond Order Assignment as an Optimization Problem.201-2092009GCBconf/gcb/2009db/conf/gcb/gcb2009.html#DehofRLH09https://dl.gi.de/handle/20.500.12116/20304http://subs.emis.de/LNI/Proceedings/Proceedings157/article5376.htmlMarc SturmAndreas BertschClemens GröplAndreas Hildebrandt 0001Rene HussongEva LangeNico PfeiferOle Schulz-TrieglaffAlexandra ZerckKnut ReinertOliver KohlbacherOpenMS - An open-source software framework for mass spectrometry.20089BMC Bioinform.https://doi.org/10.1186/1471-2105-9-163https://www.wikidata.org/entity/Q21284208db/journals/bmcbi/bmcbi9.html#SturmBGHHLPSZRK08Ole Schulz-TrieglaffRene HussongClemens GröplAndreas LeinenbachAndreas Hildebrandt 0001Christian G. HuberKnut ReinertComputational Quantification of Peptides from LC-MS Data.685-704200815J. Comput. Biol.7https://doi.org/10.1089/cmb.2007.0117https://www.wikidata.org/entity/Q31171881db/journals/jcb/jcb15.html#Schulz-TrieglaffHGLHHR08Andreas Hildebrandt 0001Ralf BlosseySergej RjasanowOliver KohlbacherHans-Peter LenhofElectrostatic potentials of proteins in water: a structured continuum approach.99-103200723Bioinform.2https://doi.org/10.1093/bioinformatics/btl312https://www.wikidata.org/entity/Q51627987db/journals/bioinformatics/bioinformatics23.html#HildebrandtBRKL07Ole Schulz-TrieglaffRene HussongClemens GröplAndreas Hildebrandt 0001Knut ReinertA Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data.473-4872007conf/recomb/2007RECOMBhttps://doi.org/10.1007/978-3-540-71681-5_33db/conf/recomb/recomb2007.html#Schulz-TrieglaffHGHR07Andreas MollAndreas Hildebrandt 0001Hans-Peter LenhofOliver KohlbacherBALLView: a tool for research and education in molecular modeling.365-366200622Bioinform.3https://doi.org/10.1093/bioinformatics/bti818https://www.wikidata.org/entity/Q28285390db/journals/bioinformatics/bioinformatics22.html#MollHLK06Andreas KellerNicole Ludwig 0001Nicole ComtesseAndreas Hildebrandt 0001Eckart MeeseHans-Peter LenhofA minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors.53920067BMC Bioinform.https://doi.org/10.1186/1471-2105-7-539https://www.wikidata.org/entity/Q33267383db/journals/bmcbi/bmcbi7.html#KellerLCHML06Jan KüntzerTorsten BlumAndreas GeraschChristina BackesAndreas Hildebrandt 0001Michael Kaufmann 0001Oliver KohlbacherHans-Peter LenhofBN++ - A Biological Information System.20063J. Integr. Bioinform.2https://doi.org/10.2390/biecoll-jib-2006-34db/journals/jib/jib3.html#KuntzerBGBHKKL06Eva LangeClemens GröplKnut ReinertOliver KohlbacherAndreas Hildebrandt 0001High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques.243-2542006conf/psb/2006Pacific Symposium on Biocomputinghttp://psb.stanford.edu/psb-online/proceedings/psb06/lange.pdfdb/conf/psb/psb2006.html#LangeGRKH06Andreas MollAndreas Hildebrandt 0001Hans-Peter LenhofOliver KohlbacherBALLView: An object-oriented molecular visualization and modeling framework.791-800200519J. Comput. Aided Mol. Des.11https://doi.org/10.1007/s10822-005-9027-xhttps://www.wikidata.org/entity/Q28296578db/journals/jcamd/jcamd19.html#MollHLK05Eva LangeClemens GröplOliver KohlbacherAndreas Hildebrandt 0001High-accuracy peak picking of proteomics data.2005conf/dagstuhl/2005P5471Computational Proteomicshttp://drops.dagstuhl.de/opus/volltexte/2006/535db/conf/dagstuhl/P5471.html#LangeGKH05Hansjörg TollPeter BergerAndreas HofmannAndreas Hildebrandt 0001Herbert OberacherHans-Peter LenhofChristian G. HuberGlycosylation Patterns of Proteins Studied by Liquid Chromatography-Mass Spectrometry and Bioinformatic Tools.2005conf/dagstuhl/2005P5471Computational Proteomicshttp://drops.dagstuhl.de/opus/volltexte/2006/543db/conf/dagstuhl/P5471.html#TollBHHOLH05Oliver KohlbacherAndreas BurchardtAndreas MollAndreas Hildebrandt 0001Peter BayerHans-Peter LenhofA NMR-spectra-based scoring function for protein docking.184-1922001conf/recomb/2001RECOMBhttps://doi.org/10.1145/369133.369194db/conf/recomb/recomb2001.html#KohlbacherBMHBL01José Manuel AbuínErnst AlthausSeymen AvciChristina BackesJaydeep P. BardhanPeter BayerFlorian BenzPeter BergerAndreas BertschRalf BlosseyTorsten BlumMarkus BlumenstockKonstantin BobSebastian BöckerQuang Bao Anh BuiAndreas BurchardtNicole ComtesseHoang-Vu DangArthur DeclercqMatthias DietzenAlexej DisterhoftUte DistlerNina M. FischerKugamoorthy GajanananPeter R. GalleLuis de la GarzaIliyan GeorgievAndreas GeraschDavid Gomez-ZepedaBarbara GregoriusClemens GröplLucas GrulichSebastian HackThomas HankelnMatthias Hein 0001Sören Lukas HellmannAnna Katharina HildebrandtAnna Katharina DehofAndreas HofmannChristian G. HuberChristian Hundt 0002Chien-Wen HungRene HussongTimo ItzelThomas JakobyFelix KallenbornMichael Kaufmann 0001Andreas KellerThomas KemmerBenny KneisslRobin KobusOliver KohlbacherBas KoolsJens Krüger 0002Markus KruppMatthis KruseJan KüntzerMateusz K. LackiEva LangeAndreas LeinenbachRoland LeißaThomas LengauerHans-Peter LenhofSimon LoewNicole Ludwig 0001Andreas Lund 0001Thorsten MaassLukas MarsalekLennart MartensEckart MeeseRichard MembarthThomas MichnaAndreas MollDomenico MoscaSabine C. MuellerAndré MüllerArturo NakasoneStefan NickelsHerbert OberacherTomás F. PenaNico PfeiferMike PhillipsJuan Carlos PichelHelmut PrendingerKnut ReinertSergej RjasanowMarc RöttigAlexander RurainskiV. RutkaCharlotta SchärfeBertil SchmidtOle Schulz-TrieglaffMarcel SchumannTim SeifertMartin SlawskiPhilipp SlusallekHienke SminiaPeter SpichtingerDaniel StöckelMarc SturmChristofer S. TautermannStefan TenzerDavid TeschnerAndreas TeufelPhilipp ThielAndreas TholeyHansjörg TollNora C. ToussaintTuan Tu TranMichael Wand 0001Sophie WegglerRalf WeigelAlexandra ZerckElena Zotenko