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Krumbach, Jan H. ; Bauer, Daniel ; Sharifzadeh, Atiyeh Sadat ; Saponaro, Andrea ; Lautenschläger, Rene ; Lange, Kristina ; Rauh, Oliver ; DiFrancesco, Dario ; Moroni, Anna ; Thiel, Gerhard ; Hamacher, Kay (2023)
Alkali metal cations modulate the geometry of different binding sites in HCN4 selectivity filter for permeation or block.
In: The Journal of general physiology, 155 (10)
doi: 10.1085/jgp.202313364
Artikel, Bibliographie
Kunzmann, Patrick ; Müller, Tom David ; Greil, Maximilian ; Krumbach, Jan Hendrik ; Anter, Jacob Marcel ; Bauer, Daniel ; Islam, Faisal ; Hamacher, Kay (2023)
Biotite: new tools for a versatile Python bioinformatics library.
In: BMC bioinformatics, 24 (1)
doi: 10.1186/s12859-023-05345-6
Artikel, Bibliographie
Wirth, Felix Nikolaus ; Kussel, Tobias ; Müller, Armin ; Hamacher, Kay ; Prasser, Fabian (2022)
EasySMPC: a simple but powerful no-code tool for practical secure multiparty computation.
In: BMC bioinformatics, 23 (1)
doi: 10.1186/s12859-022-05044-8
Artikel, Bibliographie
Kussel, Tobias ; Brenner, Torben ; Tremper, Galina ; Schepers, Josef ; Lablans, Martin ; Hamacher, Kay (2022)
Record linkage based patient intersection cardinality for rare disease studies using Mainzelliste and secure multi-party computation.
In: Journal of translational medicine, 20 (1)
doi: 10.1186/s12967-022-03671-6
Artikel, Bibliographie
Birka, Timm ; Hamacher, Kay ; Kussel, Tobias ; Möllering, Helen ; Schneider, Thomas (2022)
SPIKE: secure and private investigation of the kidney exchange problem.
In: BMC medical informatics and decision making, 22 (1)
doi: 10.1186/s12911-022-01994-4
Artikel, Bibliographie
Wettstein, Reto ; Kussel, Tobias ; Hund, Hauke ; Fegeler, Christian ; Dugas, Martin ; Hamacher, Kay (2022)
Secure Multi-Party Computation Based Distributed Feasibility Queries - A HiGHmed Use Case.
In: Studies in health technology and informatics, 296
doi: 10.3233/shti220802
Artikel, Bibliographie
Keul, Frank ; Hamacher, Kay (2022)
Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure.
In: Entropy (Basel, Switzerland), 24 (4)
doi: 10.3390/e24040505
Artikel, Bibliographie
Kunzmann, Patrick ; Anter, Jacob Marcel ; Hamacher, Kay (2022)
Adding hydrogen atoms to molecular models via fragment superimposition.
In: Algorithms for molecular biology : AMB, 17 (1)
doi: 10.1186/s13015-022-00215-x
Artikel, Bibliographie
Hamacher, Kay ; Kussel, Tobias ; von Landesberger, Tatiana ; Baumgartl, Tom ; Höhn, Markus ; Scheithauer, Simone ; Marschollek, Michael ; Wulffk, Antje (2022)
Fallzahlen, Re-Identifikation und der technische Datenschutz.
In: Datenschutz und Datensicherheit - DuD, 46 (3)
doi: 10.1007/s11623-022-1579-6
Artikel, Bibliographie
Stammler, Sebastian ; Kussel, Tobias ; Schoppmann, Phillipp ; Stampe, Florian ; Tremper, Galina ; Katzenbeisser, Stefan ; Hamacher, Kay ; Lablans, Martin (2022)
Mainzelliste SecureEpiLinker (MainSEL): privacy-preserving record linkage using secure multi-party computation.
In: Bioinformatics (Oxford, England), 38 (6)
doi: 10.1093/bioinformatics/btaa764
Artikel, Bibliographie
Kunzmann, Patrick ; Anter, Jacob Marcel ; Hamacher, Kay (2022)
Adding hydrogen atoms to molecular models via fragment superimposition.
In: Algorithms for Molecular Biology, 2022, 17
doi: 10.26083/tuprints-00021427
Artikel, Zweitveröffentlichung, Verlagsversion
Kunzmann, Patrick ; Hamacher, Kay (2022)
Biotite: a unifying open source computational biology framework in Python.
In: BMC Bioinformatics, 2022, 19
doi: 10.26083/tuprints-00012854
Artikel, Zweitveröffentlichung, Verlagsversion
Keul, Frank ; Hamacher, Kay (2022)
Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure.
In: Entropy, 2022, 24 (4)
doi: 10.26083/tuprints-00021285
Artikel, Zweitveröffentlichung, Verlagsversion
Porro, Alessandro ; Saponaro, Andrea ; Gasparri, Federica ; Bauer, Daniel ; Gross, Christine ; Pisoni, Matteo ; Abbandonato, Gerardo ; Hamacher, Kay ; Santoro, Bina ; Thiel, Gerhard ; Moroni, Anna (2022)
The HCN domain couples voltage gating and cAMP response in hyperpolarization-activated cyclic nucleotide-gated channels.
In: eLife, 2019, 2019
doi: 10.26083/tuprints-00013344
Artikel, Zweitveröffentlichung, Verlagsversion
Bauer, Daniel ; Wissmann, Jan ; Moroni, Anna ; Thiel, Gerhard ; Hamacher, Kay (2022)
Weak Cation Selectivity in HCN Channels Results From K+-Mediated Release of Na+ From Selectivity Filter Binding Sites.
In: Function (Oxford, England), 3 (3)
doi: 10.1093/function/zqac019
Artikel, Bibliographie
Schmidt, Michael ; Hamacher, Kay (2022)
hoDCA: higher order direct-coupling analysis.
In: BMC Bioinformatics, 2018, 19
doi: 10.26083/tuprints-00012863
Artikel, Zweitveröffentlichung, Verlagsversion
Saponaro, Andrea ; Bauer, Daniel ; Giese, M. Hunter ; Swuec, Paolo ; Porro, Alessandro ; Gasparri, Federica ; Sharifzadeh, Atiyeh Sadat ; Chaves-Sanjuan, Antonio ; Alberio, Laura ; Parisi, Giacomo ; Cerutti, Gabriele ; Clarke, Oliver B. ; Hamacher, Kay ; Colecraft, Henry M. ; Mancia, Filippo ; Hendrickson, Wayne A. ; Siegelbaum, Steven A. ; DiFrancesco, Dario ; Bolognesi, Martino ; Thiel, Gerhard ; Santoro, Bina ; Moroni, Anna (2021)
Gating movements and ion permeation in HCN4 pacemaker channels.
In: Molecular cell, 81 (14)
doi: 10.1016/j.molcel.2021.05.033
Artikel, Bibliographie
Schmidt, Michael ; Hamacher, Kay (2021)
Identification of biophysical interaction patterns in direct coupling analysis.
In: Physical review. E, 103 (4)
doi: 10.1103/PhysRevE.103.042418
Artikel, Bibliographie
Schmidt, Michael ; Schroeder, Indra ; Bauer, Daniel ; Thiel, Gerhard ; Hamacher, Kay (2021)
Inferring functional units in ion channel pores via relative entropy.
In: European biophysics journal : EBJ
doi: 10.1007/s00249-020-01480-7
Artikel, Bibliographie
Güllülü, Ömer ; Hehlgans, Stephanie ; Mayer, Benjamin E. ; Gößner, Ines ; Petraki, Chrysi ; Hoffmann, Melanie ; Dombrowsky, Maximilian J. ; Kunzmann, Patrick ; Hamacher, Kay ; Strebhardt, Klaus ; Fokas, Emmanouil ; Rödel, Claus ; Münch, Christian ; Rödel, Franz (2021)
A spatial and functional interaction of a heterotetramer Survivin-DNA-PKcs complex in DNA damage response.
In: Cancer research, 81 (9)
doi: 10.1158/0008-5472.CAN-20-2931
Artikel, Bibliographie
Schmidt, Michael ; Hamacher, Kay ; Reinhardt, Felix ; Lotz, Thea S. ; Groher, Florian ; Suess, Beatrix ; Jager, Sven (2020)
SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures.
In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17 (6)
doi: 10.1109/TCBB.2019.2926711
Artikel, Bibliographie
Kunzmann, Patrick ; Mayer, Benjamin E. ; Hamacher, Kay (2020)
Substitution matrix based color schemes for sequence alignment visualization.
In: BMC bioinformatics, 21 (1)
doi: 10.1186/s12859-020-3526-6
Artikel, Bibliographie
Buchmann, Johannes ; Geihs, Matthias ; Hamacher, Kay ; Katzenbeisser, Stefan ; Stammler, Sebastian (2020)
Long-term integrity protection of genomic data.
In: EURASIP Journal on Information Security, 2019, 2019 (1)
doi: 10.25534/tuprints-00011399
Artikel, Zweitveröffentlichung
Kunzmann, Patrick ; Mayer, Benjamin E. ; Hamacher, Kay (2020)
Substitution matrix based color schemes for sequence alignment visualization.
In: BMC Bioinformatics, 2020, 21 (1)
doi: 10.25534/tuprints-00013521
Artikel, Zweitveröffentlichung
Porro, Alessandro ; Saponaro, Andrea ; Gasparri, Federica ; Bauer, Daniel ; Gross, Christine ; Pisoni, Matteo ; Abbandonato, Gerardo ; Hamacher, Kay ; Santoro, Bina ; Thiel, Gerhard ; Moroni, Anna (2019)
The HCN domain couples voltage gating and cAMP response in Hyperpolarization-activated Cyclic Nucleotide-gated channels.
In: eLife, 8
doi: 10.7554/eLife.49672
Artikel, Bibliographie
Buchmann, Johannes ; Geihs, Matthias ; Hamacher, Kay ; Katzenbeisser, Stefan ; Stammler, Sebastian (2019)
Long-term integrity protection of genomic data.
In: EURASIP Journal on Information Security
doi: 10.1186/s13635-019-0099-x
Artikel, Bibliographie
Boussebayle, Adrien ; Torka, Daniel ; Ollivaud, Sandra ; Braun, Johannes ; Bofill-Bosch, Cristina ; Dombrowski, Max ; Groher, Florian ; Hamacher, Kay ; Suess, Beatrix (2019)
Next-level riboswitch development-implementation of Capture-SELEX facilitates identification of a new synthetic riboswitch.
In: Nucleic acids research, 47 (9)
doi: 10.1093/nar/gkz216
Artikel, Bibliographie
Groher, Ann-Christin ; Jager, Sven ; Schneider, Christopher ; Groher, Florian ; Hamacher, Kay ; Suess, Beatrix (2019)
Tuning the Performance of Synthetic Riboswitches using Machine Learning.
In: ACS Synthetic Biology, 8 (1)
doi: 10.1021/acssynbio.8b00207
Artikel, Bibliographie
Schmidt, Michael ; Hamacher, Kay (2018)
hoDCA: higher order direct-coupling analysis.
In: BMC bioinformatics, 19 (1)
Artikel, Bibliographie
Marini, Carla ; Porro, Alessandro ; Rastetter, Agnès ; Dalle, Carine ; Rivolta, Ilaria ; Bauer, Daniel ; Oegema, Renske ; Nava, Caroline ; Parrini, Elena ; Mei, Davide ; Mercer, Catherine ; Dhamija, Radhika ; Chambers, Chelsea ; Coubes, Christine ; Thévenon, Julien ; Kuentz, Paul ; Julia, Sophie ; Pasquier, Laurent ; Dubourg, Christèle ; Carré, Wilfrid ; Rosati, Anna ; Melani, Federico ; Pisano, Tiziana ; Giardino, Maria ; Innes, A. Micheil ; Alembik, Yves ; Scheidecker, Sophie ; Santos, Manuela ; Figueiroa, Sonia ; Garrido, Cristina ; Fusco, Carlo ; Frattini, Daniele ; Spagnoli, Carlotta ; Binda, Anna ; Granata, Tiziana ; Ragona, Francesca ; Freri, Elena ; Franceschetti, Silvana ; Canafoglia, Laura ; Castellotti, Barbara ; Gellera, Cinzia ; Milanesi, Raffaella ; Mancardi, Maria Margherita ; Clark, Damien R. ; Kok, Fernando ; Helbig, Katherine L. ; Ichikawa, Shoji ; Sadler, Laurie ; Neupauerová, Jana ; Laššuthova, Petra ; Šterbová, Katalin ; Laridon, Annick ; Brilstra, Eva ; Koeleman, Bobby ; Lemke, Johannes R. ; Zara, Federico ; Striano, Pasquale ; Soblet, Julie ; Smits, Guillaume ; Deconinck, Nicolas ; Barbuti, Andrea ; DiFrancesco, Dario ; LeGuern, Eric ; Guerrini, Renzo ; Santoro, Bina ; Hamacher, Kay ; Thiel, Gerhard ; Moroni, Anna ; DiFrancesco, Jacopo C. ; Depienne, Christel (2018)
HCN1 mutation spectrum: from neonatal epileptic encephalopathy to benign generalized epilepsy and beyond.
In: Brain : a journal of neurology, 141 (11)
Artikel, Bibliographie
Kunzmann, Patrick ; Hamacher, Kay (2018)
Biotite: a unifying open source computational biology framework in Python.
In: BMC bioinformatics, 19 (1)
Artikel, Bibliographie
Groß, Christine ; Saponaro, Andrea ; Santoro, Bina ; Moroni, Anna ; Thiel, Gerhard ; Hamacher, Kay (2018)
Mechanical transduction of cytoplasmic-to-transmembrane-domain movements in a hyperpolarization-activated cyclic nucleotide-gated cation channel.
In: The Journal of biological chemistry, 293 (33)
doi: 10.1074/jbc.RA118.002139
Artikel, Bibliographie
Dombrowsky, Maximilian J. ; Jager, Sven ; Schiller, Benjamin ; Mayer, Benjamin E. ; Stammler, Sebastian ; Hamacher, Kay (2018)
StreaMD: Advanced analysis of molecular dynamics using R.
In: Journal of computational chemistry, 39 (21)
Artikel, Bibliographie
Groher, Florian ; Bofill-Bosch, Cristina ; Schneider, Christopher ; Braun, Johannes ; Jager, Sven ; Geißler, Katharina ; Hamacher, Kay ; Suess, Beatrix (2018)
Riboswitching with ciprofloxacin-development and characterization of a novel RNA regulator.
In: Nucleic acids research, 46 (4)
Artikel, Bibliographie
Schmidt, M. ; Hamacher, Kay (2017)
Three-body interactions improve contact prediction within direct-coupling analysis.
In: Physical Review E, 96 (5)
Artikel, Bibliographie
Weißgraeber, Stephanie ; Saponaro, Andrea ; Thiel, Gerhard ; Hamacher, Kay (2017)
A reduced mechanical model for cAMP-modulated gating in HCN channels.
In: Scientific reports, 7
Artikel, Bibliographie
Groß, Christine ; Hamacher, Kay ; Schmitz, Katja ; Jager, Sven (2017)
Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis.
In: Journal of chemical information and modeling, 57 (2)
Artikel, Bibliographie
Keul, Frank ; Hess, Martin ; Goesele, Michael ; Hamacher, Kay (2017)
PFASUM: a substitution matrix from Pfam structural alignments.
In: BMC Bioinformatics, 18 (1)
doi: 10.1186/s12859-017-1703-z
Artikel, Bibliographie
Jager, Sven ; Schiller, Benjamin ; Babel, Philipp ; Blumenroth, Malte ; Strufe, Thorsten ; Hamacher, Kay (2017)
StreAM-Tg: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs.
In: Algorithms for molecular biology : AMB, 12
doi: 10.1186/s13015-017-0105-0
Artikel, Bibliographie
Hess, Martin ; Keul, Frank ; Goesele, Michael ; Hamacher, Kay (2016)
Addressing inaccuracies in BLOSUM computation improves homology search performance.
In: BMC Bioinformatics, 17 (1)
doi: 10.1186/s12859-016-1060-3
Artikel, Bibliographie
Bensinger, Dennis ; Neumann, Theresa ; Scholz, Christoph ; Voss, Constantin ; Knorr, Sabine ; Kuckelkorn, Ulrike ; Hamacher, Kay ; Kloetzel, Peter-Michael ; Schmidt, Boris (2016)
Elastase-like Activity Is Dominant to Chymotrypsin-like Activity in 20S Proteasome's β5 Catalytic Subunit.
In: ACS chemical biology, 11 (7)
Artikel, Bibliographie
Greiner, Timo ; Bolduan, Sebastian ; Hertel, Brigitte ; Groß, Christine ; Hamacher, Kay ; Schubert, Ulrich ; Moroni, Anna ; Thiel, Gerhard (2016)
Ion Channel Activity of Vpu Proteins Is Conserved throughout Evolution of HIV-1 and SIV.
In: Viruses, 8 (12)
Artikel, Bibliographie
Buß, O. ; Jager, S. ; Dold, S.-M. ; Zimmermann, S. ; Hamacher, Kay ; Schmitz, K. ; Rudat, J. (2016)
Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters.
In: PloS one, 11 (1)
Artikel, Bibliographie
Scholz, Christoph ; Knorr, Sabine ; Hamacher, Kay ; Schmidt, Boris (2015)
DOCKTITE-A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in the Molecular Operating Environment.
In: Journal of chemical information and modeling, 55 (2)
Artikel, Bibliographie
Hoffgaard, Franziska ; Kast, S. M. ; Moroni, Anna ; Thiel, Gerhard ; Hamacher, Kay (2015)
Tectonics of a K(+) channel: The importance of the N-terminus for channel gating.
In: Biochimica et biophysica acta, 1848 (12)
Artikel, Bibliographie
Bose, Ranjan ; Thiel, Gerhard ; Hamacher, Kay (2014)
Clustering of Giant Virus-DNA Based on Variations in Local Entropy.
In: Viruses, 6 (6)
Artikel, Bibliographie
Voss, Constantin ; Scholz, Christoph ; Knorr, Sabine ; Beck, Philipp ; Stein, Martin L. ; Zall, Andrea ; Kuckelkorn, Ulrike ; Kloetzel, Peter-Michael ; Groll, Michael ; Hamacher, Kay ; Schmidt, Boris (2014)
α-Keto Phenylamides as P1'-Extended Proteasome Inhibitors.
In: ChemMedChem, 9 (11)
Artikel, Bibliographie
Waechter, Michael ; Jaeger, Kathrin ; Thuerck, Daniel ; Weissgraeber, Stephanie ; Widmer, Sven ; Goesele, Michael ; Hamacher, Kay (2014)
Using Graphics Processing Units to Investigate Molecular Coevolution.
In: Concurrency and Computation: Practice and Experience, 26 (6)
Artikel, Bibliographie
Hess, Martin ; Bremm, Sebastian ; Weissgraeber, Stephanie ; Hamacher, Kay ; Goesele, Michael ; Wiemeyer, Josef ; Landesberger von Antburg, Tatiana (2014)
Visual exploration of parameter influence on phylogenetic trees.
In: IEEE Computer Graphics and Applications, Special Issue – BioVis, 34 (2)
Artikel, Bibliographie
Hess, Martin ; Bremm, Sebastian ; Weissgraeber, Stephanie ; Hamacher, Kay ; Goesele, Michael ; Wiemeyer, Josef ; Landesberger von Antburg, Tatiana (2014)
Visual exploration of parameter influence on phylogenetic trees.
In: IEEE computer graphics and applications, 34 (2)
Artikel, Bibliographie
Franz, M. ; Deiseroth, B. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, S. ; Schröder, H. (2013)
Secure computations on non-integer values with applications to privacy-preserving sequence analysis.
In: Information Security Technical Report, 17 (3)
Artikel, Bibliographie
Pape, Susanne ; Hoffgaard, Franziska ; Dür, Mirjam ; Hamacher, Kay (2013)
Distance dependency and minimum amino acid alphabets for decoy scoring potentials.
In: Journal of computational chemistry, 34 (1)
Artikel, Bibliographie
Ober, M. ; Katzenbeisser, S. ; Hamacher, Kay (2013)
Structure and Anonymity of the Bitcoin Transaction Graph.
In: Future Internet, 5 (2)
Artikel, Bibliographie
Lauss, Georg ; Schroeder, Christina ; Dabrock, Peter ; Eder, Johann ; Hamacher, Kay ; Kuhn, Klaus A. ; Gottweis, Herbert (2013)
Towards Biobank Privacy Regimes in Responsible Innovation Societies: ESBB Conference in Granada 2012.
In: Biopreservation and Biobanking, 11 (5)
Artikel, Bibliographie
Bose, Ranjan ; Hamacher, Kay (2012)
Alternate entropy measure for assessing volatility in financial markets.
In: Physical review. E, Statistical, nonlinear, and soft matter physics, 86 (5 Pt 2)
Artikel, Bibliographie
Hamacher, Kay (2012)
Dynamical regimes due to technological change in a microeconomical model of production.
In: Chaos (Woodbury, N.Y.), 22 (3)
Artikel, Bibliographie
Hamacher, Kay ; Greiner, Timo ; Ogata, Hiroyuki ; Etten, James L. van ; Gebhardt, Manuela ; Villarreal, Luis P. ; Cosentino, Cristian ; Moroni, Anna ; Thiel, Gerhard (2012)
Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.
In: PloS one, 7 (6)
Artikel, Bibliographie
Hamacher, Kay (2012)
Resilience to leaking - dynamic systems modeling of information security.
In: PloS one, 7 (12)
Artikel, Bibliographie
Wulfmeyer, Timo ; Polzer, Christian ; Hiepler, Gregor ; Hamacher, Kay ; Shoeman, Robert ; Dunigan, David D. ; Etten, James L. van ; Lolicato, Marco ; Moroni, Anna ; Thiel, Gerhard ; Meckel, Tobias (2012)
Structural Organization of DNA in Chlorella Viruses.
In: PLoS ONE, 7 (2)
doi: 10.1371/journal.pone.0030133
Artikel, Bibliographie
Gehrmann, Eva ; Gläßer, Christine ; Jin, Yaochu ; Sendhoff, Bernhard ; Drossel, Barbara ; Hamacher, Kay (2011)
Robustness of glycolysis in yeast to internal and external noise.
In: Physical Review E, 84
doi: 10.1103/PhysRevE.84.021913
Artikel, Bibliographie
Hamacher, Kay (2011)
Efficient quantification of the importance of contacts for the dynamical stability of proteins.
In: Journal of computational chemistry, 32 (5)
Artikel, Bibliographie
Hamacher, Kay (2011)
Free energy of contact formation in proteins: Efficient computation in the elastic network approximation.
In: Physical review. E, Statistical, nonlinear, and soft matter physics, 84 (1-2)
Artikel, Bibliographie
Bremm, Sebastian ; Landesberger von Antburg, Tatiana ; Hess, Martin ; Schreck, Tobias ; Weil, Philipp ; Hamacher, Kay (2011)
Interactive Visual Comparison of Multiple Trees.
In: IEEE Visual Analytics Science and Technology
Artikel, Bibliographie
Gebhardt, Manuela ; Hoffgaard, Franziska ; Hamacher, Kay ; Kast, S. M. ; Moroni, Anna ; Thiel, Gerhard (2011)
Membrane Anchoring and Interaction between Transmembrane Domains are Crucial for K+ Channel Function.
In: The Journal of biological chemistry, 286 (13)
Artikel, Bibliographie
Strunk, Timo ; Hamacher, Kay ; Hoffgaard, Franziska ; Engelhardt, Harald ; Zillig, Martina Daniela ; Faist, Karin ; Wenzel, Wolfgang ; Pfeifer, Felicitas (2011)
Structural Model of the Gas Vesicle Protein GvpA and Analysis of GvpA Mutants in vivo.
In: Molecular microbiology, 81 (1)
Artikel, Bibliographie
Weißgraeber, Stephanie ; Hoffgaard, Franziska ; Hamacher, Kay (2011)
Structure-based, biophysical annotation of molecular coevolution of acetylcholinesterase.
In: Proteins, 79 (11)
Artikel, Bibliographie
Bremm, Sebastian ; Schreck, Tobias ; Boba, Patrick ; Held, Stephanie ; Hamacher, Kay (2010)
Computing and Visually Analyzing Mutual Information in Molecular Co-Evolution.
In: BMC Bioinformatics, 11
doi: 10.1186/1471-2105-11-330
Artikel, Bibliographie
Hoffgaard, Franziska ; Weil, P. ; Hamacher, Kay (2010)
BioPhysConnectoR : Connecting sequence information and biophysical models.
In: BMC Bioinformatics, 11 (1)
doi: 10.1186/1471-2105-11-199
Artikel, Bibliographie
Reker, D. ; Katzenbeisser, S. ; Hamacher, Kay (2010)
Computation of mutual information from Hidden Markov Models.
In: Computational biology and chemistry, 34 (5-6)
Artikel, Bibliographie
Pape, Susanne ; Hoffgaard, Franziska ; Hamacher, Kay (2010)
Distance-dependent classification of amino acids by information theory.
In: Proteins: Structure, Function, and Bioinformatics, 78 (10)
doi: 10.1002/prot.22744
Artikel, Bibliographie
Hamacher, Kay (2010)
Efficient perturbation analysis of elastic network models – Application to acetylcholinesterase of T. californica.
In: Journal of Computational Physics, 229 (19)
doi: 10.1016/j.jcp.2010.06.015
Artikel, Bibliographie
Hamacher, Kay (2010)
Temperature dependence of fluctuations in HIV1-protease.
In: Eur. Biophys. J., 39 (7)
doi: 10.1007/s00249-009-0443-z
Artikel, Bibliographie
Weil, P. ; Hoffgaard, Franziska ; Hamacher, Kay (2009)
Estimating sufficient statistics in co-evolutionary analysis by mutual information.
In: Computational Biology and Chemistry, 33 (6)
doi: 10.1016/j.compbiolchem.2009.10.003
Artikel, Bibliographie
Hamacher, Kay (2008)
Coarse-grained molecular models for high-throughput and multi-scale functional investigations.
In: Chem. Cent. J., (2)
doi: 10.1186/1752-153X-2-S1-S14
Artikel, Bibliographie
Hamacher, Kay (2008)
Relating sequence evolution of HIV1-Protease to its underlying molecular mechanics.
In: Gene, (422)
doi: 10.1016/j.gene.2008.06.007
Artikel, Bibliographie
Hamacher, Kay (2007)
Adaptive Extremal Optimization by Detrended Fluctuation Analysis.
In: J. Comp. Phys., 227 (2)
doi: 10.1016/j.jcp.2007.09.013
Artikel, Bibliographie
Hamacher, Kay (2007)
Energy landscape paving as a perfect optimization approach under detrended fluctuation analysis.
In: Physica A, 378 (2)
doi: 10.1016/j.physa.2006.11.071
Artikel, Bibliographie
Hamacher, Kay (2007)
Information Theoretical Measures to Analyze Trajectories in Rational Molecular Design.
In: J. Comp. Chem., 28 (16)
doi: 10.1002/jcc.20759
Artikel, Bibliographie
Hamacher, Kay (2006)
Adaptation in stochastic tunneling global optimization of complex potential energy landscapes.
In: Europhys. Lett., 74 (6)
doi: 10.1209/epl/i2006-10058-0
Artikel, Bibliographie
Hamacher, Kay ; McCammon, J. A. (2006)
Computing the amino acid specifity of fluctuations in biomolecular systems : application to HIV1-protease.
In: J. Chem. Theo. Comp., (2)
doi: 10.1021/ct050247s
Artikel, Bibliographie
Hamacher, Kay ; Trylska, J. ; McCammon, J. A. (2006)
Dependency map of proteins in the small ribosomal subunit.
In: PLoS Comp. Biol., 2 (2)
doi: 10.1371/journal.pcbi.0020010
Artikel, Bibliographie
Hamacher, Kay ; Hübsch, A. ; McCammon, J. A. (2006)
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking.
In: J. Chem. Phys., (124)
doi: 10.1063/1.2185645
Artikel, Bibliographie
Gros, C. ; Hamacher, Kay ; Wenzel, W. (2005)
Breakdown of the Luttinger sum rule at the Mott-Hubbard transition in the one-dimensional t1-t2 Hubbard model.
In: Europhys. Lett., 69 (4)
doi: 10.1209/epl/i2004-10379-x
Artikel, Bibliographie
Hamacher, Kay (2005)
On stochastic global optimization of one-dimensional functions.
In: Physica A, 354
doi: 10.1016/j.physa.2005.02.028
Artikel, Bibliographie
Hamacher, Kay ; Stolze, J. ; Wenzel, W. (2002)
Disorder induced quantum phase transition in random-exchange spin-1/2 chains.
In: Phys. Rev. Lett., 89
doi: 10.1103/PhysRevLett.89.127202
Artikel, Bibliographie
Sirker, J. ; Klümper, A. ; Hamacher, Kay (2002)
Ground-state properties of two-dimensional dimerized Heisenberg models.
In: Phys. Rev. B, 65 (13)
doi: 10.1103/PhysRevB.65.134409
Artikel, Bibliographie
Hamacher, Kay ; Gros, C. ; Wenzel, W. (2002)
Interaction-induced collapse of a section of the Fermi sea in the zig-zag Hubbard ladder.
In: Phys. Rev. Lett., 88 (21)
doi: 10.1103/PhysRevLett.88.217203
Artikel, Bibliographie
Gros, C. ; Valenti, R. ; Alvarez, J. V. ; Hamacher, Kay ; Wenzel, W. (2000)
Test of the frustrated spin-cluster model to describe the low-temperature physics of NaV2O5.
In: Phys. Rev. B. (Rapid Comm.), 62 (22)
doi: 10.1103/PhysRevB.62.R14617
Artikel, Bibliographie
Stampfuß, P. ; Hamacher, Kay ; Wenzel, W. (2000)
A massively parallel configuration-selecting multi-reference configuration interaction implementation.
In: J. Mol. Struc. (THEOCHEM), 506
doi: 10.1016/S0166-1280(00)00405-X
Artikel, Bibliographie
Hamacher, Kay ; Wenzel, W. (1999)
The scaling behavior of stochastic minimization algorithms in a perfect funnel landscape.
In: Phys. Rev. E, 59 (1)
doi: 10.1103/PhysRevE.59.938
Artikel, Bibliographie
Wenzel, W. ; Hamacher, Kay (1999)
A stochastic tunneling approach for global minimization.
In: Phys. Rev. Lett., 82 (15)
doi: 10.1103/PhysRevLett.82.3003
Artikel, Bibliographie
Buchkapitel
Kalabis, Lukas ; Waidner, Michael
Hrsg.: Anzinger, Heribert ; Hamacher, Kay ; Katzenbeisser, Stefan (2013)
Federated Identity Management.
In: Schutz genetischer, medizinischer und sozialer Daten als multidisziplinäre Aufgabe
Buchkapitel, Bibliographie
Hamacher, Kay ; Katzenbeisser, Stefan (2011)
Public Security: Simulations Need to Replace Conventional Wisdom.
In: New Security Paradigms Workshop (NSPW 2011)
Buchkapitel, Bibliographie
Hamacher, Kay
Hrsg.: Fred, A. ; Filipe, J. ; Gamboa, H. (2010)
Protein Domain Phylogenies - Information Theory and Evolutionary Dynamics.
In: Proc. of BIOINFORMATICS 2010
Buchkapitel, Bibliographie
Boba, P. ; Weil, P. ; Hoffgaard, F. ; Hamacher, Kay
Hrsg.: Fred, A. ; Filipe, J. ; Gamboa, H. (2010)
Co-Evolution in HIV Enzymes.
In: Proc. of BIOINFORMATICS 2010
Buchkapitel, Bibliographie
Hamacher, Kay
Hrsg.: Hansmann, U. H. E. (2008)
Coarse-grained molecular models for high-throughput and multi-scale functional investigations.
In: Proceedings of CBSB08 (From computational biophysics to systems biology)
Buchkapitel, Bibliographie
Hamacher, Kay (2006)
Accelerating changes in our epoch and the role of time-horizons.
In: The future of life and the future of our civilization
doi: 10.1007/978-1-4020-4968-2_25
Buchkapitel, Bibliographie
Wenzel, W. ; Hamacher, Kay
Hrsg.: Reguera, D. ; Vilar, J. M. G. ; Rubi, J. M. (1999)
Scaling Laws for Protein Folding.
In: Statistical Mechanics of Biocomplexity
Buchkapitel, Bibliographie
Hamacher, Kay ; Wenzel, W. (1998)
Scaling behavior of minimization algorithms in a simple model of protein folding.
In: Proceedings of the HLRZ-Workshop "Monte Carlo Approach to Bioplymers and Protein Folding"
Buchkapitel, Bibliographie
Konferenzveröffentlichung
Hamacher, Kay ; Kussel, Tobias ; Schneider, Thomas ; Tkachenko, Oleksandr (2022)
PEA: Practical private epistasis analysis using MPC.
27th European Symposium on Research in Computer Security (ESORICS 2022). Copenhagen, Denmark (26.-30.09.2022)
doi: 10.1007/978-3-031-17143-7_16
Konferenzveröffentlichung, Bibliographie
Tkachenko, Oleksandr ; Weinert, Christian ; Schneider, Thomas ; Hamacher, Kay (2018)
Large-Scale Privacy-Preserving Statistical Computations for Distributed Genome-Wide Association Studies.
doi: 10.1145/3196494.3196541
Konferenzveröffentlichung, Bibliographie
Demmler, Daniel ; Hamacher, Kay ; Schneider, Thomas ; Stammler, Sebastian (2017)
Privacy-Preserving Whole-Genome Variant Queries.
Konferenzveröffentlichung, Bibliographie
Hess, Martin ; Jente, Daniel ; Wiemeyer, Josef ; Hamacher, Kay ; Goesele, Michael (2016)
Visual Analysis and Comparison of Multiple Sequence Alignments.
6th Eurographics Workshop on Visual Computing for Biology and Medicine.
Konferenzveröffentlichung, Bibliographie
Karvelas, Nikolaos ; Peter, Andreas ; Katzenbeisser, Stefan ; Tews, Erik ; Hamacher, Kay (2014)
Privacy-Preserving Whole Genome Sequence Processing through Proxy-Aided ORAM.
Scottsdale, AZ, USA
doi: 10.1145/2665943.2665962
Konferenzveröffentlichung, Bibliographie
Hess, Martin ; Wiemeyer, Josef ; Hamacher, Kay ; Goesele, Michael (2014)
Serious Games for Solving Protein Sequence Alignments-Combining Citizen Science and Gaming.
4th International Conference on Serious Games (GameDays 2014). Darmstadt, Germany (01.-05.04.2014)
doi: 10.1007/978-3-319-05972-3_18
Konferenzveröffentlichung, Bibliographie
Lenz, Olav ; Keul, Frank ; Bremm, Sebastian ; Hamacher, Kay ; Landesberger von Antburg, Tatiana (2014)
Visual Analysis of Patterns in Multiple Amino Acid Mutation Graphs.
IEEE Conference on Visual Analytics Science and Technology. Proceedings.
doi: 10.1109/VAST.2014.7042485
Konferenzveröffentlichung, Bibliographie
Waechter, Michael ; Jaeger, Kathrin ; Weissgraeber, Stephanie ; Widmer, Sven ; Goesele, Michael ; Hamacher, Kay (2012)
Information-Theoretic Analysis of Molecular (Co)Evolution Using Graphics Processing Units.
International Workshop on Emerging Computational Methods for the Life Sciences (ECMLS). Delft, Netherlands (18 June 2012)
Konferenzveröffentlichung, Bibliographie
Bremm, Sebastian ; Landesberger von Antburg, Tatiana ; Heß, Martin ; Schreck, Tobias ; Weil, Philipp ; Hamacher, Kay (2011)
Interactive Visual Comparison of Multiple Trees.
IEEE Conference on Visual Analytics Science and Technology 2011. Proceedings.
doi: 10.1109/VAST.2011.6102439
Konferenzveröffentlichung, Bibliographie
Waechter, Michael ; Hamacher, Kay ; Hoffgaard, Franziska ; Widmer, Sven ; Goesele, Michael (2011)
Is your permutation algorithm unbiased for n<>2^m?
International Conference on Parallel Processing and Applied Mathematics (PPAM). Torun, Poland (12-14 Sept. 2011)
Konferenzveröffentlichung, Bibliographie
Deiseroth, B. ; Franz, M. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, Stefan ; Schröder, Heike (2010)
Secure Computations on Real-Valued Signals.
Konferenzveröffentlichung, Bibliographie
Deiseroth, B. ; Franz, M. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, Stefan ; Schröder, Heike (2010)
Secure Computation on Non-Integer Values.
Konferenzveröffentlichung, Bibliographie
Deiseroth, B. ; Franz, M. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, Stefan ; Schröder, Heike (2010)
Towards Secure Bioinformatics Services.
Konferenzveröffentlichung, Bibliographie
Ackermann, Jens ; Baecher, Paul ; Franzel, Thorsten ; Goesele, Michael ; Hamacher, Kay (2009)
Massively-Parallel Simulation of Biochemical Systems.
Jahrestagung der Gesellschaft für Informatik e.V.. Lübeck, Germany (September 29, 2009)
Konferenzveröffentlichung, Bibliographie
Hamacher, Kay (2005)
Accelerated technological change and the role of time horizons.
The Future of Life. Frankfurt / Main
Konferenzveröffentlichung, Bibliographie