Dependency Map of Proteins in the Small Ribosomal Subunit. - Kay Hamacher; Joanna Trylska; James Andrew McCammon (PLoS Comput. Biol., 2006)

Information theoretical measures to analyze trajectories in rational molecular design. - Kay Hamacher (J. Comput. Chem., 2007)

Adaptive extremal optimization by detrended fluctuation analysis. - Kay Hamacher (J. Comput. Phys., 2007)

Massively-Parallel Simulation of Biochemical Systems. - Jens Ackermann; Paul Baecher; Thorsten Franzel; Michael Goesele; Kay Hamacher (GI Jahrestagung, 2009)

Vorwort zum Workshop "Massively parallel computational biology on GPUs". - Kay Hamacher; Michael Goesele (GI Jahrestagung, 2009)

Estimating sufficient statistics in co-evolutionary analysis by mutual information. - Philipp Weil; Franziska Hoffgaard; Kay Hamacher (Comput. Biol. Chem., 2009)

Co-evolution in HIV Enzymes. - Patrick Boba; Philipp Weil; Franziska Hoffgaard; Kay Hamacher (BIOINFORMATICS, 2010)

Intra- and Inter-Molecular Coevolution: The Case of HIV1 Protease and Reverse Transcriptase. - Patrick Boba; Philipp Weil; Franziska Hoffgaard; Kay Hamacher (BIOSTEC (Selected Papers), 2010)

Protein Domain Phylogenies - Information Theory and Evolutionary Dynamics. - Kay Hamacher (BIOINFORMATICS, 2010)

Computing and visually analyzing mutual information in molecular co-evolution. - Sebastian Bremm; Tobias Schreck; Patrick Boba; Stephanie Held; Kay Hamacher (BMC Bioinform., 2010)

BioPhysConnectoR: Connecting Sequence Information and Biophysical Models. - Franziska Hoffgaard; Philipp Weil; Kay Hamacher (BMC Bioinform., 2010)

Computation of mutual information from Hidden Markov Models. - Daniel Reker; Stefan Katzenbeisser 001; Kay Hamacher (Comput. Biol. Chem., 2010)

Secure Computations on Non-Integer Values. - Martin Franz; Björn Deiseroth; Kay Hamacher; Somesh Jha; Stefan Katzenbeisser 001; Heike Schröder (IACR Cryptol. ePrint Arch., 2010)

Efficient perturbation analysis of elastic network models - Application to acetylcholinesterase of T. californica. - Kay Hamacher (J. Comput. Phys., 2010)

Towards Secure Bioinformatics Services (Short Paper). - Martin Franz; Björn Deiseroth; Kay Hamacher; Somesh Jha; Stefan Katzenbeisser 001; Heike Schröder (Financial Cryptography, 2011)

Interactive visual comparison of multiple trees. - Sebastian Bremm; Tatiana von Landesberger; Martin Hess; Tobias Schreck; Philipp Weil; Kay Hamacher (IEEE VAST, 2011)

Public security: simulations need to replace conventional wisdom. - Kay Hamacher; Stefan Katzenbeisser 001 (NSPW, 2011)

Is Your Permutation Algorithm Unbiased for n ≠ 2 m ? - Michael Waechter; Kay Hamacher; Franziska Hoffgaard; Sven Widmer; Michael Goesele (PPAM (1), 2011)

Efficient quantification of the importance of contacts for the dynamical stability of proteins. - Kay Hamacher (J. Comput. Chem., 2011)

A New Hybrid Metaheuristic - Combining Stochastic Tunneling and Energy Landscape Paving. - Kay Hamacher (Hybrid Metaheuristics, 2013)

Genomic Privacy (Dagstuhl Seminar 13412). - Kay Hamacher; Jean-Pierre Hubaux; Gene Tsudik (Dagstuhl Reports, 2013)

Structure and Anonymity of the Bitcoin Transaction Graph. - Micha Ober; Stefan Katzenbeisser 001; Kay Hamacher (Future Internet, 2013)

Secure computations on non-integer values with applications to privacy-preserving sequence analysis. - Martin Franz; Björn Deiseroth; Kay Hamacher; Somesh Jha; Stefan Katzenbeisser 001; Heike Schröder (Inf. Secur. Tech. Rep., 2013)

Distance dependency and minimum amino acid alphabets for decoy scoring potentials. - Susanne Pape; Franziska Hoffgaard; Mirjam Dür; Kay Hamacher (J. Comput. Chem., 2013)

Serious Games for Solving Protein Sequence Alignments - Combining Citizen Science and Gaming. - Martin Hess; Josef Wiemeyer; Kay Hamacher; Michael Goesele (GameDays, 2014)

Stochastic tunneling transformation during selection in genetic algorithm. - Benjamin E. Mayer; Kay Hamacher (GECCO, 2014)

R as an Integration Tool in High Performance Computing - Lessons Learned. - Patrick Boba; Stefan Gries 002; Kay Hamacher (GI-Jahrestagung, 2014)

Online Performance Measures for Metaheuristic Optimization. - Kay Hamacher (Hybrid Metaheuristics, 2014)

Visual analysis of patterns in multiple amino acid mutation graphs. - Olav Lenz; Frank Keul; Sebastian Bremm; Kay Hamacher; Tatiana von Landesberger (IEEE VAST, 2014)

Privacy-Preserving Whole Genome Sequence Processing through Proxy-Aided ORAM. - Nikolaos P. Karvelas; Andreas Peter 001; Stefan Katzenbeisser 001; Erik Tews; Kay Hamacher (WPES, 2014)

Visual Exploration of Parameter Influence on Phylogenetic Trees. - Martin Hess; Sebastian Bremm; Stephanie Weissgraeber; Kay Hamacher; Michael Goesele; Josef Wiemeyer; Tatiana von Landesberger (IEEE Computer Graphics and Applications, 2014)

Using graphics processing units to investigate molecular coevolution. - Michael Waechter; Kathrin Jaeger; Daniel Thuerck; Stephanie Weissgraeber; Sven Widmer; Michael Goesele; Kay Hamacher (Concurr. Comput. Pract. Exp., 2014)

StreaM - A Stream-Based Algorithm for Counting Motifs in Dynamic Graphs. - Benjamin Schiller; Sven Jager; Kay Hamacher; Thorsten Strufe (AlCoB, 2015)

DOCKTITE - A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in the Molecular Operating Environment. - Christoph Scholz 003; Sabine Knorr; Kay Hamacher; Boris Schmidt (J. Chem. Inf. Model., 2015)

Using Lisp Macro-Facilities for Transferable Statistical Tests. - Kay Hamacher (ELS, 2016)

Evolving Smoothing Kernels for Global Optimization. - Paul Manns; Kay Hamacher (EvoApplications (2), 2016)

Correcting Finite Sampling Issues in Entropy l-diversity. - Sebastian Stammler; Stefan Katzenbeisser 001; Kay Hamacher (PSD, 2016)

Visual Analysis and Comparison of Multiple Sequence Alignments. - Martin Hess; Daniel Jente; Josef Wiemeyer; Kay Hamacher; Michael Goesele (VCBM/MedViz, 2016)

StreAM- T_g : Algorithms for Analyzing Coarse Grained RNA Dynamics Based on Markov Models of Connectivity-Graphs. - Sven Jager; Benjamin Schiller; Thorsten Strufe; Kay Hamacher (WABI, 2016)

Addressing inaccuracies in BLOSUM computation improves homology search performance. - Martin Hess; Frank Keul; Michael Goesele; Kay Hamacher (BMC Bioinform., 2016)

Privacy-Preserving Whole-Genome Variant Queries. - Daniel Demmler; Kay Hamacher; Thomas Schneider 003; Sebastian Stammler (CANS, 2017)

TransferEntropyPT: An R Package to Assess Transfer Entropies via Permutation Tests. - Patrick Boba; Kay Hamacher (CMSB, 2017)

StreAM-Tg: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs. - Sven Jager; Benjamin Schiller; Philipp Babel; Malte Blumenroth; Thorsten Strufe; Kay Hamacher (Algorithms Mol. Biol., 2017)

PFASUM: a substitution matrix from Pfam structural alignments. - Frank Keul; Martin Hess; Michael Goesele; Kay Hamacher (BMC Bioinform., 2017)

Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis. - Christine Groß 001; Kay Hamacher; Katja Schmitz; Sven Jager (J. Chem. Inf. Model., 2017)

Large-Scale Privacy-Preserving Statistical Computations for Distributed Genome-Wide Association Studies. - Oleksandr Tkachenko; Christian Weinert; Thomas Schneider 003; Kay Hamacher (AsiaCCS, 2018)

Biotite: a unifying open source computational biology framework in Python. - Patrick Kunzmann; Kay Hamacher (BMC Bioinform., 2018)

hoDCA: higher order direct-coupling analysis. - Michael Schmidt 013; Kay Hamacher (BMC Bioinform., 2018)

StreaMD: Advanced analysis of molecular dynamics using R. - Maximilian J. Dombrowsky; Sven Jager; Benjamin Schiller; Benjamin E. Mayer; Sebastian Stammler; Kay Hamacher (J. Comput. Chem., 2018)

Hybridization of Stochastic Tunneling with (Quasi)-Infinite Time-Horizon Tabu Search. - Kay Hamacher (HM, 2019)

Long-term integrity protection of genomic data. - Johannes Buchmann 001; Matthias Geihs; Kay Hamacher; Stefan Katzenbeisser 001; Sebastian Stammler (EURASIP J. Inf. Secur., 2019)

Substitution matrix based color schemes for sequence alignment visualization. - Patrick Kunzmann; Benjamin E. Mayer; Kay Hamacher (BMC Bioinform., 2020)

Genomische Daten und der Datenschutz. - Kay Hamacher; Stefan Katzenbeisser 001; Tobias Kussel; Sebastian Stammler (Datenschutz und Datensicherheit, 2020)

SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures. - Michael Schmidt 013; Kay Hamacher; Felix Reinhardt; Thea S. Lotz; Florian Groher; Beatrix Suess; Sven Jager (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Genetic algorithm niching by (Quasi-)infinite memory. - Adrian Worring; Benjamin E. Mayer; Kay Hamacher (GECCO, 2021)

Secure Multi-Party Computation Based Distributed Feasibility Queries - A HiGHmed Use Case. - Reto Wettstein; Tobias Kussel; Hauke Hund; Christian Fegeler; Martin Dugas; Kay Hamacher (GMDS, 2022)

Adding hydrogen atoms to molecular models via fragment superimposition. - Patrick Kunzmann; Jacob Marcel Anter; Kay Hamacher (Algorithms Mol. Biol., 2022)

Mainzelliste SecureEpiLinker (MainSEL): privacy-preserving record linkage using secure multi-party computation. - Sebastian Stammler; Tobias Kussel; Phillipp Schoppmann; Florian Stampe; Galina Tremper; Stefan Katzenbeisser 001; Kay Hamacher; Martin Lablans (Bioinform., 2022)

EasySMPC: a simple but powerful no-code tool for practical secure multiparty computation. - Felix Nikolaus Wirth; Tobias Kussel; Armin Müller; Kay Hamacher; Fabian Prasser (BMC Bioinform., 2022)

Fallzahlen, Re-Identifikation und der technische Datenschutz. - Kay Hamacher; Tobias Kussel; Tatiana von Landesberger; Tom Baumgartl; Markus Höhn; Simone Scheithauer; Michael Marschollek; Antje Wulff (Datenschutz und Datensicherheit, 2022)

Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure. - Frank Keul; Kay Hamacher (Entropy, 2022)

PEA: Practical private epistasis analysis using MPC. - Kay Hamacher; Tobias Kussel; Thomas Schneider 003; Oleksandr Tkachenko (IACR Cryptol. ePrint Arch., 2022)

SPIKE: secure and private investigation of the kidney exchange problem. - Timm Birka; Kay Hamacher; Tobias Kussel; Helen Möllering; Thomas Schneider 003 (BMC Medical Informatics Decis. Mak., 2022)

Biotite: new tools for a versatile Python bioinformatics library. - Patrick Kunzmann; Tom David Müller; Maximilian Greil; Jan Hendrik Krumbach; Jacob Marcel Anter; Daniel Bauer; Faisal Islam; Kay Hamacher (BMC Bioinform., 2023)

Anisotropic Network Analysis of Open/Closed HCN4 Channel Advocates Asymmetric Subunit Cooperativity in cAMP Modulation of Gating. - Patrick Kunzmann; Jan Hendrik Krumbach; Andrea Saponaro; Anna Moroni; Gerhard Thiel; Kay Hamacher (J. Chem. Inf. Model., 2024)