2024

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

2023

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

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

2022

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

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

2021

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

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

2020

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

2019

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

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

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

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

2018

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

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

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

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

2017

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

2016

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

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

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

2015

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

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

2014

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

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 ; 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

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

2013

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

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

2012

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

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

2011

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

Hamacher, Kay ; Katzenbeisser, Stefan (2011)
Public Security: Simulations Need to Replace Conventional Wisdom.
In: New Security Paradigms Workshop (NSPW 2011)
Buchkapitel, Bibliographie

2010

Deiseroth, B. ; Franz, M. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, Stefan ; Schröder, Heike (2010)
Secure Computations on Real-Valued Signals.
Konferenzveröffentlichung, 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
Hrsg.: Fred, A. ; Filipe, J. ; Gamboa, H. (2010)
Protein Domain Phylogenies - Information Theory and Evolutionary Dynamics.
In: Proc. of BIOINFORMATICS 2010
Buchkapitel, 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

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 (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

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

2009

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

2008

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
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

2007

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

2006

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 (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

2005

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

2002

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

2000

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

1999

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

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

1998

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