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), p. 531. ISSN 1471-2105,
DOI: 10.1186/s12859-022-05044-8,
[Article]

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), p. 458. ISSN 1479-5876,
DOI: 10.1186/s12967-022-03671-6,
[Article]

Hamacher, Kay ; Kussel, Tobias ; Schneider, Thomas ; Tkachenko, Oleksandr (2022):
PEA: Practical private epistasis analysis using MPC.
In: Lecture Notes in Computer Science, 13556, In: Computer Security - ESORICS 2022, pp. 320-339,
Springer, 27th European Symposium on Research in Computer Security (ESORICS 2022), Copenhagen, Denmark, 26.-30.09.2022, ISBN 978-3-031-17142-0,
DOI: 10.1007/978-3-031-17143-7_16,
[Conference or Workshop Item]

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), p. 253. ISSN 1472-6947,
DOI: 10.1186/s12911-022-01994-4,
[Article]

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, pp. 41-49. ISSN 1879-8365,
DOI: 10.3233/shti220802,
[Article]

Keul, Frank ; Hamacher, Kay (2022):
Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure.
In: Entropy (Basel, Switzerland), 24 (4), p. 505. ISSN 1099-4300,
DOI: 10.3390/e24040505,
[Article]

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), p. 7. ISSN 1748-7188,
DOI: 10.1186/s13015-022-00215-x,
[Article]

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), pp. 143-148. Springer, ISSN 1862-2607,
DOI: 10.1007/s11623-022-1579-6,
[Article]

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), pp. 1657-1668. ISSN 1367-4811,
DOI: 10.1093/bioinformatics/btaa764,
[Article]

Kunzmann, Patrick ; Anter, Jacob Marcel ; Hamacher, Kay (2022):
Adding hydrogen atoms to molecular models via fragment superimposition. (Publisher's Version)
In: Algorithms for Molecular Biology, 17, BioMed Central, ISSN 1748-7188,
DOI: 10.26083/tuprints-00021427,
[Article]

Kunzmann, Patrick ; Hamacher, Kay (2022):
Biotite: a unifying open source computational biology framework in Python. (Publisher's Version)
In: BMC Bioinformatics, 19, Springer Nature, ISSN 1471-2105,
DOI: 10.26083/tuprints-00012854,
[Article]

Keul, Frank ; Hamacher, Kay (2022):
Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure. (Publisher's Version)
In: Entropy, 24 (4), MDPI, e-ISSN 1099-4300,
DOI: 10.26083/tuprints-00021285,
[Article]

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. (Publisher's Version)
In: eLife, 2019, eLife Sciences Publications, ISSN 2050-084X,
DOI: 10.26083/tuprints-00013344,
[Article]

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), ISSN 2633-8823,
DOI: 10.1093/function/zqac019,
[Article]

Schmidt, Michael ; Hamacher, Kay (2022):
hoDCA: higher order direct-coupling analysis. (Publisher's Version)
In: BMC Bioinformatics, 19, Springer Nature, e-ISSN 1471-2105,
DOI: 10.26083/tuprints-00012863,
[Article]

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), pp. 2929-2943. ISSN 1097-4164,
DOI: 10.1016/j.molcel.2021.05.033,
[Article]

Schmidt, Michael ; Hamacher, Kay (2021):
Identification of biophysical interaction patterns in direct coupling analysis.
In: Physical review. E, 103 (4), pp. 042418. ISSN 2470-0053,
DOI: 10.1103/PhysRevE.103.042418,
[Article]

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, ISSN 1432-1017,
DOI: 10.1007/s00249-020-01480-7,
[Article]

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), pp. 2304-2317. ISSN 1538-7445,
DOI: 10.1158/0008-5472.CAN-20-2931,
[Article]

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), pp. 2189-2195. ISSN 1545-5963,
DOI: 10.1109/TCBB.2019.2926711,
[Article]

Kunzmann, Patrick ; Mayer, Benjamin E. ; Hamacher, Kay (2020):
Substitution matrix based color schemes for sequence alignment visualization.
In: BMC bioinformatics, 21 (1), p. 209. ISSN 1471-2105,
DOI: 10.1186/s12859-020-3526-6,
[Article]

Kunzmann, Patrick ; Mayer, Benjamin E. ; Hamacher, Kay (2020):
Substitution matrix based color schemes for sequence alignment visualization.
In: BMC Bioinformatics, 21 (1), ISSN 1471-2105,
DOI: 10.25534/tuprints-00013521,
[Article]

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, pp. e49672. ISSN 2050-084X,
DOI: 10.7554/eLife.49672,
[Article]

Buchmann, Johannes ; Geihs, Matthias ; Hamacher, Kay ; Katzenbeisser, Stefan ; Stammler, Sebastian (2019):
Long-term integrity protection of genomic data.
In: EURASIP Journal on Information Security, p. 16. SpringerOpen, DOI: 10.1186/s13635-019-0099-x,
[Article]

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), pp. 4883-4895. ISSN 1362-4962,
DOI: 10.1093/nar/gkz216,
[Article]

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), pp. 34-44. ISSN 2161-5063,
DOI: 10.1021/acssynbio.8b00207,
[Article]

Buchmann, Johannes ; Geihs, Matthias ; Hamacher, Kay ; Katzenbeisser, Stefan ; Stammler, Sebastian (2019):
Long-term integrity protection of genomic data.
In: EURASIP Journal on Information Security, 2019 (1), Springer Open, ISSN 2510-523X,
DOI: 10.25534/tuprints-00011399,
[Article]

Schmidt, Michael ; Hamacher, Kay (2018):
hoDCA: higher order direct-coupling analysis.
In: BMC bioinformatics, 19 (1), p. 546. ISSN 1471-2105,
[Article]

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), pp. 3160-3178. Oxford University Press, ISSN 1460-2156,
[Article]

Kunzmann, Patrick ; Hamacher, Kay (2018):
Biotite: a unifying open source computational biology framework in Python.
In: BMC bioinformatics, 19 (1), p. 346. ISSN 1471-2105,
[Article]

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), pp. 12908-12918. ISSN 1083-351X,
DOI: 10.1074/jbc.RA118.002139,
[Article]

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), pp. 1666-1674. ISSN 1096-987X,
[Article]

Tkachenko, Oleksandr ; Weinert, Christian ; Schneider, Thomas ; Hamacher, Kay (2018):
Large-Scale Privacy-Preserving Statistical Computations for Distributed Genome-Wide Association Studies.
In: 13. ACM Asia Conference on Information, Computer and Communications Security (ASIACCS'18), pp. 221-235,
ACM, DOI: 10.1145/3196494.3196541,
[Conference or Workshop Item]

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), pp. 2121-2132. ISSN 1362-4962,
[Article]

Schmidt, M. ; Hamacher, Kay (2017):
Three-body interactions improve contact prediction within direct-coupling analysis.
In: Physical Review E, 96 (5), pp. 10.1103/PhysRevE. ISSN 1063-651X,
[Article]

Demmler, Daniel ; Hamacher, Kay ; Schneider, Thomas ; Stammler, Sebastian (2017):
Privacy-Preserving Whole-Genome Variant Queries.
In: 16. International Conference on Cryptology And Network Security (CANS'17),
Springer, [Conference or Workshop Item]

Keul, Frank ; Hess, Martin ; Goesele, Michael ; Hamacher, Kay (2017):
PFASUM: a substitution matrix from Pfam structural alignments.
In: BMC Bioinformatics, 18 (1), Biomed Central, ISSN 1471-2105,
[Article]

Weißgraeber, Stephanie ; Saponaro, Andrea ; Thiel, Gerhard ; Hamacher, Kay (2017):
A reduced mechanical model for cAMP-modulated gating in HCN channels.
In: Scientific reports, 7, p. 40168. ISSN 2045-2322,
[Article]

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), pp. 243-255. ISSN 1549-960X,
[Article]

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, 12 (1), Biomed Central, ISSN 1748-7188,
DOI: 10.1186/s13015-017-0105-0,
[Article]

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, p. 15. ISSN 1748-7188,
[Article]

Hess, Martin ; Keul, Frank ; Goesele, Michael ; Hamacher, Kay (2016):
Addressing inaccuracies in BLOSUM computation improves homology search performance.
In: BMC Bioinformatics, 17 (1), p. 189. BioMed Central, ISSN 1471-2105,
[Article]

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), pp. 1800-1804. ISSN 1554-8937,
[Article]

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), p. 325. ISSN 1999-4915,
[Article]

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), pp. e0146104. ISSN 1932-6203,
[Article]

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, [Conference or Workshop Item]

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), pp. 398-406. ISSN 1549-960X,
[Article]

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), pp. 3197-3204. ISSN 0006-3002,
[Article]

Karvelas, Nikolaos ; Peter, Andreas ; Katzenbeisser, Stefan ; Tews, Erik ; Hamacher, Kay (2014):
Privacy-Preserving Whole Genome Sequence Processing through Proxy-Aided ORAM.
In: ACM, In: Proceedings of the 13th annual {ACM} Workshop on Privacy in the Electronic Society, {WPES} 2014, Scottsdale, AZ, USA, November 2, 2014, pp. 25-35,
Scottsdale, AZ, USA, DOI: 10.1145/2665943.2665962,
[Conference or Workshop Item]

Bose, Ranjan ; Thiel, Gerhard ; Hamacher, Kay (2014):
Clustering of Giant Virus-DNA Based on Variations in Local Entropy.
In: Viruses, 6 (6), pp. 2259-67. ISSN 1999-4915,
[Article]

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), pp. 2557-2564. ISSN 1860-7187,
[Article]

Hess, Martin ; Wiemeyer, Josef ; Hamacher, Kay ; Goesele, Michael (2014):
Serious Games for Solving Protein Sequence Alignments-Combining Citizen Science and Gaming.
In: Lecture Notes in Computer Science, 8395, In: Games for Training, Education, Health and Sports, pp. 175-185,
Springer, 4th International Conference on Serious Games (GameDays 2014), Darmstadt, Germany, 01.-05.04.2014, ISBN 978-3-319-05971-6,
DOI: 10.1007/978-3-319-05972-3_18,
[Conference or Workshop Item]

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), pp. 1278-1296. [Article]

Lenz, Olav ; Keul, Frank ; Bremm, Sebastian ; Hamacher, Kay ; Landesberger von Antburg, Tatiana (2014):
Visual Analysis of Patterns in Multiple Amino Acid Mutation Graphs.
pp. 93-102, IEEE Computer Society, Los Alamitos, Calif., IEEE Conference on Visual Analytics Science and Technology. Proceedings, DOI: 10.1109/VAST.2014.7042485,
[Conference or Workshop Item]

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), pp. 48-56. IEEE, [Article]

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), pp. 48-56. ISSN 1558-1756,
[Article]

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), pp. 117-128. [Article]

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), pp. 10-20. ISSN 1096-987X,
[Article]

Kalabis, Lukas ; Waidner, Michael
Anzinger, Heribert ; Hamacher, Kay ; Katzenbeisser, Stefan (eds.) (2013):
Federated Identity Management.
In: Schutz genetischer, medizinischer und sozialer Daten als multidisziplinäre Aufgabe, pp. 189-218, Berlin, Springer, ISBN 978-3-642-34741-2,
[Book Section]

Ober, M. ; Katzenbeisser, S. ; Hamacher, Kay (2013):
Structure and Anonymity of the Bitcoin Transaction Graph.
In: Future Internet, 5 (2), pp. 237-250. [Article]

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), pp. 319-323. ISSN 1947-5535,
[Article]

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), pp. 056112. ISSN 1550-2376,
[Article]

Hamacher, Kay (2012):
Dynamical regimes due to technological change in a microeconomical model of production.
In: Chaos (Woodbury, N.Y.), 22 (3), pp. 033149. ISSN 1089-7682,
[Article]

Waechter, Michael ; Jaeger, Kathrin ; Weissgraeber, Stephanie ; Widmer, Sven ; Goesele, Michael ; Hamacher, Kay (2012):
Information-Theoretic Analysis of Molecular (Co)Evolution Using Graphics Processing Units.
In: Proceedings of the 3rd International Workshop on Emerging Computational Methods for the Life Sciences, pp. 49-58,
ACM, International Workshop on Emerging Computational Methods for the Life Sciences (ECMLS), Delft, Netherlands, 18 June 2012, [Conference or Workshop Item]

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), pp. e38826. ISSN 1932-6203,
[Article]

Hamacher, Kay (2012):
Resilience to leaking - dynamic systems modeling of information security.
In: PloS one, 7 (12), pp. e49804. ISSN 1932-6203,
[Article]

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), pp. e30133. [Article]

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, pp. 021913, 1-11. ISSN 1539-3755,
[Article]

Hamacher, Kay (2011):
Efficient quantification of the importance of contacts for the dynamical stability of proteins.
In: Journal of computational chemistry, 32 (5), pp. 810-815. ISSN 1096-987X,
[Article]

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), pp. 016703. ISSN 1550-2376,
[Article]

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, [Article]

Bremm, Sebastian ; Landesberger von Antburg, Tatiana ; Heß, Martin ; Schreck, Tobias ; Weil, Philipp ; Hamacher, Kay (2011):
Interactive Visual Comparison of Multiple Trees.
pp. 31-40, IEEE Press, New York, IEEE Conference on Visual Analytics Science and Technology 2011. Proceedings, DOI: 10.1109/VAST.2011.6102439,
[Conference or Workshop Item]

Waechter, Michael ; Hamacher, Kay ; Hoffgaard, Franziska ; Widmer, Sven ; Goesele, Michael (2011):
Is your permutation algorithm unbiased for n<>2^m?
In: Proceedings of the 9th International Conference on Parallel Processing and Applied Mathematics (PPAM), pp. 297-306,
Springer, International Conference on Parallel Processing and Applied Mathematics (PPAM), Torun, Poland, 12-14 Sept. 2011, [Conference or Workshop Item]

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), pp. 11299-306. ISSN 1083-351X,
[Article]

Hamacher, Kay ; Katzenbeisser, Stefan (2011):
Public Security: Simulations Need to Replace Conventional Wisdom.
In: New Security Paradigms Workshop (NSPW 2011), pp. 115-124, ACM Press, [Book Section]

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), pp. 56-68. ISSN 1365-2958,
[Article]

Weißgraeber, Stephanie ; Hoffgaard, Franziska ; Hamacher, Kay (2011):
Structure-based, biophysical annotation of molecular coevolution of acetylcholinesterase.
In: Proteins, 79 (11), pp. 3144-3154. ISSN 1097-0134,
[Article]

Deiseroth, B. ; Franz, M. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, Stefan ; Schröder, Heike (2010):
Secure Computations on Real-Valued Signals.
In: IEEE Workshop on Information Forensics and Security (WIFS'10),
IEEE Press, [Conference or Workshop Item]

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, p. 330. DOI: 10.1186/1471-2105-11-330,
[Article]

Hamacher, Kay
Fred, A. ; Filipe, J. ; Gamboa, H. (eds.) (2010):
Protein Domain Phylogenies - Information Theory and Evolutionary Dynamics.
In: Proc. of BIOINFORMATICS 2010, pp. 114-122, ISBN 978-989-674-019-1,
[Book Section]

Hoffgaard, Franziska ; Weil, P. ; Hamacher, Kay (2010):
BioPhysConnectoR : Connecting sequence information and biophysical models.
In: BMC Bioinformatics, 11 (1), p. 199. [Article]

Boba, P. ; Weil, P. ; Hoffgaard, F. ; Hamacher, Kay
Fred, A. ; Filipe, J. ; Gamboa, H. (eds.) (2010):
Co-Evolution in HIV Enzymes.
In: Proc. of BIOINFORMATICS 2010, pp. 39-47, ISBN 978-989-674-019-1,
[Book Section]

Reker, D. ; Katzenbeisser, S. ; Hamacher, Kay (2010):
Computation of mutual information from Hidden Markov Models.
In: Computational biology and chemistry, 34 (5-6), pp. 328-333. ISSN 1476-928X,
[Article]

Pape, Susanne ; Hoffgaard, Franziska ; Hamacher, Kay (2010):
Distance-dependent classification of amino acids by information theory.
In: Proteins: Structure, Function, and Bioinformatics, 78 (10), pp. 2322-2328. [Article]

Hamacher, Kay (2010):
Efficient perturbation analysis of elastic network models – Application to acetylcholinesterase of T. californica.
In: Journal of Computational Physics, 229 (19), pp. 7309-7316. [Article]

Deiseroth, B. ; Franz, M. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, Stefan ; Schröder, Heike (2010):
Secure Computation on Non-Integer Values.
In: 2010 IEEE International Workshop on Information Forensics and Security (WIFS-2010), pp. 1-6,
IEEE Press, ISBN 978-1-4244-9078-3,
[Conference or Workshop Item]

Hamacher, Kay (2010):
Temperature dependence of fluctuations in HIV1-protease.
In: Eur. Biophys. J., 39 (7), pp. 1051-1056. ISSN 1432-1017,
[Article]

Deiseroth, B. ; Franz, M. ; Hamacher, Kay ; Jha, Somesh ; Katzenbeisser, Stefan ; Schröder, Heike (2010):
Towards Secure Bioinformatics Services.
In: Financial Cryptography and Data Security (FC2011),
[Conference or Workshop Item]

Weil, P. ; Hoffgaard, Franziska ; Hamacher, Kay (2009):
Estimating sufficient statistics in co-evolutionary analysis by mutual information.
In: Computational Biology and Chemistry, 33 (6), pp. 440-444. ISSN 1476-928X,
[Article]

Ackermann, Jens ; Baecher, Paul ; Franzel, Thorsten ; Goesele, Michael ; Hamacher, Kay (2009):
Massively-Parallel Simulation of Biochemical Systems.
In: Proceedings of Massively Parallel Computational Biology on GPUs, pp. 739-750,
Jahrestagung der Gesellschaft für Informatik e.V., Lübeck, Germany, September 29, 2009, [Conference or Workshop Item]

Hamacher, Kay (2008):
Coarse-grained molecular models for high-throughput and multi-scale functional investigations.
In: Chem. Cent. J., (2), p. 14. [Article]

Hamacher, Kay
Hansmann, U. H. E. (ed.) (2008):
Coarse-grained molecular models for high-throughput and multi-scale functional investigations.
In: NIC Series, In: Proceedings of CBSB08 (From computational biophysics to systems biology), pp. 97-100, ISBN 978-3-9810843-6-8,
[Book Section]

Hamacher, Kay (2008):
Relating sequence evolution of HIV1-Protease to its underlying molecular mechanics.
In: Gene, (422), pp. 30-36. [Article]

Hamacher, Kay (2007):
Adaptive Extremal Optimization by Detrended Fluctuation Analysis.
In: J. Comp. Phys., 227 (2), pp. 1500-1509. ISSN 00219991,
[Article]

Hamacher, Kay (2007):
Energy landscape paving as a perfect optimization approach under detrended fluctuation analysis.
In: Physica A, 378 (2), pp. 307-314. ISSN 03784371,
[Article]

Hamacher, Kay (2007):
Information Theoretical Measures to Analyze Trajectories in Rational Molecular Design.
In: J. Comp. Chem., 28 (16), pp. 2576-2580. [Article]

Hamacher, Kay (2006):
Accelerating changes in our epoch and the role of time-horizons.
3, In: The future of life and the future of our civilization, pp. 205-215, Springer, [Book Section]

Hamacher, Kay (2006):
Adaptation in stochastic tunneling global optimization of complex potential energy landscapes.
In: Europhys. Lett., 74 (6), p. 944. ISSN 0295-5075,
[Article]

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), p. 873. [Article]

Hamacher, Kay ; Trylska, J. ; McCammon, J. A. (2006):
Dependency map of proteins in the small ribosomal subunit.
In: PLoS Comp. Biol., 2 (2), pp. e10. [Article]

Hamacher, Kay ; Hübsch, A. ; McCammon, J. A. (2006):
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking.
In: J. Chem. Phys., (124), p. 164907. [Article]

Hamacher, Kay (2005):
Accelerated technological change and the role of time horizons.
The Future of Life, Frankfurt / Main, [Conference or Workshop Item]

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), p. 616. ISSN 0295-5075,
[Article]

Hamacher, Kay (2005):
On stochastic global optimization of one-dimensional functions.
In: Physica A, 354, p. 547. ISSN 03784371,
[Article]

Hamacher, Kay ; Stolze, J. ; Wenzel, W. (2002):
Disorder induced quantum phase transition in random-exchange spin-1/2 chains.
In: Phys. Rev. Lett., 89, p. 127202. [Article]

Sirker, J. ; Klümper, A. ; Hamacher, Kay (2002):
Ground-state properties of two-dimensional dimerized Heisenberg models.
In: Phys. Rev. B, 65 (13), p. 134409. ISSN 0163-1829,
[Article]

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), p. 217203. [Article]

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), pp. R14617-R14620. [Article]

Stampfuß, P. ; Hamacher, Kay ; Wenzel, W. (2000):
A massively parallel configuration-selecting multi-reference configuration interaction implementation.
In: J. Mol. Struc. (THEOCHEM), 506, pp. 99-106. [Article]

Wenzel, W. ; Hamacher, Kay
Reguera, D. ; Vilar, J. M. G. ; Rubi, J. M. (eds.) (1999):
Scaling Laws for Protein Folding.
In: Springer Lecture Notes in Physics, In: Statistical Mechanics of Biocomplexity, pp. 62-71, New York, Springer, [Book Section]

Hamacher, Kay ; Wenzel, W. (1999):
The scaling behavior of stochastic minimization algorithms in a perfect funnel landscape.
In: Phys. Rev. E, 59 (1), pp. 938-941. [Article]

Wenzel, W. ; Hamacher, Kay (1999):
A stochastic tunneling approach for global minimization.
In: Phys. Rev. Lett., 82 (15), pp. 3003-3007. [Article]

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", Singapore, World Scientific, [Book Section]