Artikel

Saponaro, Andrea ; Krumbach, Jan H. ; Chaves-Sanjuan, Antonio ; Sharifzadeh, Atiyeh Sadat ; Porro, Alessandro ; Castelli, Roberta ; Hamacher, Kay ; Bolognesi, Martino ; DiFrancesco, Dario ; Clarke, Oliver B. ; Thiel, Gerhard ; Moroni, Anna (2024)
Structural determinants of ivabradine block of the open pore of HCN4.
In: Proceedings of the National Academy of Sciences of the United States of America, 121 (27)
doi: 10.1073/pnas.2402259121
Artikel, Bibliographie

Kunzmann, Patrick ; Krumbach, Jan H. ; Saponaro, Andrea ; Moroni, Anna ; Thiel, Gerhard ; Hamacher, Kay (2024)
Anisotropic network analysis of open/closed HCN4 channel advocates asymmetric subunit cooperativity in cAMP modulation of gating.
In: Journal of chemical information and modeling, 64 (12)
doi: 10.1021/acs.jcim.4c00360
Artikel, Bibliographie

Güllülü, Ömer ; Mayer, Benjamin E. ; Toplek, Fran Bačić (2024)
Linking gene fusions to bone marrow failure and malignant transformation in Dyskeratosis Congenita.
In: International Journal of Molecular Sciences, 25 (3)
doi: 10.3390/ijms25031606
Artikel, Bibliographie

Lill, Annika ; Herbst, Alexandra ; Langhans, Markus ; Paech, Steffen ; Hamacher, Kay ; Biesalski, Markus ; Meckel, Tobias ; Schmitz, Katja (2024)
Investigating cellulose binding of peptides derived from carbohydrate binding module 1.
In: Biomacromolecules, 25 (9)
doi: 10.1021/acs.biomac.4c00575
Artikel, Bibliographie

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

Wack, Julia S. ; Brahm, Kevin ; Babel, Philipp ; Dalton, James A. R. ; Schmitz, Katja (2023)
Effect of macrocyclization and tetramethylrhodamine labeling on chemokine binding peptides.
In: Journal of Peptide Science, 29 (7)
doi: 10.1002/psc.3486
Artikel, Bibliographie

Scheithauer, Lina ; Karagöz, Mustafa Safa ; Mayer, Benjamin E. ; Steinert, Michael (2023)
Protein sociology of ProA, Mip and other secreted virulence factors at the Legionella pneumophila surface.
In: Frontiers in Cellular and Infection Microbiology, 13
doi: 10.3389/fcimb.2023.1140688
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

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

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

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, 50 (1)
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

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

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

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

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

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

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

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

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

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

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

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

Ober, M. ; Katzenbeisser, S. ; Hamacher, Kay (2013)
Structure and Anonymity of the Bitcoin Transaction Graph.
In: Future Internet, 5 (2)
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

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)
Dynamical regimes due to technological change in a microeconomical model of production.
In: Chaos (Woodbury, N.Y.), 22 (3)
Artikel, Bibliographie

Hamacher, Kay (2012)
Resilience to leaking - dynamic systems modeling of information security.
In: PloS one, 7 (12)
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

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

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

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

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

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

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

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

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

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)
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 (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 (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 (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 (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 ; 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

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 (2005)
On stochastic global optimization of one-dimensional functions.
In: Physica A, 354
doi: 10.1016/j.physa.2005.02.028
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

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 ; 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

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

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

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

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

Tkachenko, Oleksandr ; Weinert, Christian ; Schneider, Thomas ; Hamacher, Kay (2018)
Large-Scale Privacy-Preserving Statistical Computations for Distributed Genome-Wide Association Studies.
13. ACM Asia Conference on Information, Computer and Communications Security (ASIACCS'18). Incheon Republic of Korea (04.06.2018-04.06.2018)
doi: 10.1145/3196494.3196541
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

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 (01.04.2014-05.04.2014)
doi: 10.1007/978-3-319-05972-3_18
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)
Towards Secure Bioinformatics Services.
Konferenzveröffentlichung, Bibliographie

Deiseroth, B. ; Franz, M. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, Stefan ; Schröder, Heike (2010)
Secure Computation on Non-Integer Values.
Konferenzveröffentlichung, Bibliographie

Hamacher, Kay (2005)
Accelerated technological change and the role of time horizons.
The Future of Life. Frankfurt / Main
Konferenzveröffentlichung, Bibliographie

Dissertation

Kunzmann, Patrick (2023)
Development of a programming library for general bioinformatics.
Technische Universität Darmstadt
doi: 10.26083/tuprints-00024784
Dissertation, Erstveröffentlichung, Verlagsversion

Kussel, Tobias (2022)
Graph Structures in Privacy-Preserving Biomedical Analyses.
Technische Universität Darmstadt
doi: 10.26083/tuprints-00021828
Dissertation, Erstveröffentlichung, Verlagsversion

Bauer, Daniel (2021)
Computational Study of Voltage-gated Sodium/Potassium channels.
Technische Universität Darmstadt
doi: 10.26083/tuprints-00018611
Dissertation, Erstveröffentlichung, Verlagsversion

Boba, Patrick (2019)
Graphenrekonstruktion anhand abhängiger Zeitreihen in biologischen Netzwerken.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Groß, Christine (2019)
In Silico Studies on Proteins for Synthetic Biology.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Jager, Sven (2019)
Development of Computer-aided Concepts for the Optimization of Single-Molecules and their Integration for High-Throughput Screenings.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Keul, Frank (2018)
On Evolution, Structure and Dynamics in Potassium Channels.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Weißgraeber, Stephanie (2015)
Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels—Structure and Evolution.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Knorr, Sabine (2014)
In Silico Strategies to Modulate DNA Damage Response.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Carbon-Mangels, Miriam (2014)
Intra-host HIV-1 evolution and the co-receptor switch.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Seehafer, Carsten (2012)
Identifikation von RNA-Motiven durch Datenbankanalysen.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung