The evolution of standards and data management practices in systems biology - Stanford, Natalie J; Wolstencroft, Katherine; Golebiewski, Martin; Kania, Renate; Juty, Nick; Tomlinson, Christopher; Owen, Stuart; Butcher, Sarah; Hermjakob, Henning; Le Novère, Nicolas; Müller, Wolfgang; Snoep, Jacky; et al. (Molecular Systems Biology, 2015)

SABIO-RK--database for biochemical reaction kinetics. - Wittig, U.; Kania, R.; Golebiewski, M.; Rey, M.; Shi, L.; Jong, L.; Algaa, E.; Weidemann, A.; Sauer-Danzwith, H.; Mir, S.; Krebs, O.; Bittkowski, M.; et al. (Nucleic Acids Res, 2012)
SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually extracted from the literature and data directly submitted from lab experiments. The database content includes kinetic parameters in relation to biochemical reactions and their biological sources with no restriction on any particular set of organisms. Additionally, kinetic rate laws and corresponding equations as well as experimental conditions are represented. All the data are manually curated and annotated by biological experts, supported by automated consistency checks. SABIO-RK can be accessed via web-based user interfaces or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language), e.g. for import in modelling tools.
Keywords: *Biochemical Phenomena; *Databases, Factual; Enzymes/metabolism; Internet; Kinetics; User-Computer Interface

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research - Wolstencroft, Katherine; Krebs, Olga; Snoep, Jacky L.; Stanford, Natalie J.; Bacall, Finn; Golebiewski, Martin; Kuzyakiv, Rostyk; Nguyen, Quyen; Owen, Stuart; Soiland-Reyes, Stian; Straszewski, Jakub; van Niekerk, David D.; et al. (Nucleic Acids Res, 2017)

Data extraction for the reaction kinetics database SABIO-RK - Wittig, Ulrike; Kania, Renate; Bittkowski, Meik; Wetsch, Elina; Shi, Lei; Jong, Lenneke; Golebiewski, Martin; Rey, Maja; Weidemann, Andreas; Rojas, Isabel; Müller, Wolfgang (Perspectives in Science, 2014)
SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has been established as a resource for biochemical reactions and their kinetic properties with a focus on supporting the computational modeling to create models of biochemical reaction networks. SABIO-RK data are mainly extracted from literature but also directly submitted from lab experiments. In most cases the information in the literature is distributed across the whole publication, insufficiently structured and often described without standard terminology. Therefore the manual extraction of knowledge from the literature requires biological experts to understand the paper and interpret the data. The database offers the literature data in a structured format including annotations to controlled vocabularies, ontologies and external databases which supports modellers, as well as experimentalists, in the very time consuming process of collecting information from different publications.

Challenges for an enzymatic reaction kinetics database. - Wittig, U.; Rey, M.; Kania, R.; Bittkowski, M.; Shi, L.; Golebiewski, M.; Weidemann, A.; Muller, W.; Rojas, I. (FEBS J, 2014)
The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create models of biochemical reaction networks and to obtain a better understanding of the processes in living cells. To extract the knowledge from the literature, biocurators are required to understand a paper and interpret the data. For modellers, as well as experimentalists, this process is very time consuming because the information is distributed across the publication and, in most cases, is insufficiently structured and often described without standard terminology. In recent years, biological databases for different data types have been developed. The advantages of these databases lie in their unified structure, searchability and the potential for augmented analysis by software, which supports the modelling process. We have developed the SABIO-RK database for biochemical reaction kinetics. In the present review, we describe the challenges for database developers and curators, beginning with an analysis of relevant publications up to the export of database information in a standardized format. The aim of the present review is to draw the experimentalist's attention to the problem (from a data integration point of view) of incompletely and imprecisely written publications. We describe how to lower the barrier to curators and improve this situation. At the same time, we are aware that curating experimental data takes time. There is a community concerned with making the task of publishing data with the proper structure and annotation to ontologies much easier. In this respect, we highlight some useful initiatives and tools.
Keywords: Database Management Systems; *Databases, Protein; Enzyme Assays/methods/standards; Enzymes/*chemistry; Kinetics; Molecular Sequence Annotation; Reference Standards; Terminology as Topic

SEEK: a systems biology data and model management platform. - Wolstencroft, K.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N. J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J. L.; Mueller, W.; et al. (BMC Syst Biol, 2015)
BACKGROUND: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. RESULTS: The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. CONCLUSION: The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.
Keywords: Carbon/metabolism; *Database Management Systems; Internet; *Models, Biological; Sulfolobus/metabolism; *Systems Biology; User-Computer Interface

Web-based visualisation of the transcriptional control network of Escherichia coli. - Sosa, N.; Kremling, A.; Ratsch, E.; Rojas, I. (In Silico Biol, 2004)
Transcription is one of the basic processes of gene expression, controlled by a complex network of biochemical reactions. Despite its importance, most work on the visualisation of biochemical networks focuses on the representation of metabolic pathways. The visualisation of the complex networks controlling transcription requires the implementation of a hierarchical approach that allows the display of the structure of each regulatory region with its transcription factors and regulated operons. This paper presents a web-based application for the visualisation of transcriptional control networks. It takes as case study the organism Escherichia coli. The definition of the visual components implemented is mainly based on those proposed by Shen-Orr et al., 2002, slightly extended to visualise complex networks.
Keywords: Computational Biology; Computer Simulation; Escherichia coli/*genetics; *Gene Expression Regulation, Bacterial; Internet; *Software; *Transcription, Genetic

A-R-E: The Author-Review-Execute Environment - Müller, Wolfgang; Rojas, Isabel; Eberhart, Andreas; Haase, Peter; Schmidt, Michael (Procedia Computer Science, 2011)
The Author-Review-Execute (A-R-E) is an innovative concept to offer under a single principle and platform an environment to support the life cycle of an (executable) paper; namely the authoring of the paper, its submission, the reviewing process, the author's revisions, its publication, and finally the study (reading/interaction) of the paper as well as extensions (follow ups) of the paper. It combines Semantic Wiki technology, a resolver that solves links both between parts of documents to executable code or to data, an anonymizing component to support the authoring and reviewing tasks, and web services providing link perennity.

Enzyme kinetics informatics: from instrument to browser. - Swainston, N.; Golebiewski, M.; Messiha, H. L.; Malys, N.; Kania, R.; Kengne, S.; Krebs, O.; Mir, S.; Sauer-Danzwith, H.; Smallbone, K.; Weidemann, A.; Wittig, U.; et al. (FEBS J, 2010)
A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw experimental data from which the parameters were calculated. This is largely due to the lack of software or standards to support the capture, analysis, storage and dissemination of such experimental data. Introduced here is an integrative system to manage experimental enzyme kinetics data from instrument to browser. The approach is based on two interrelated databases: the existing SABIO-RK database, containing kinetic data and corresponding metadata, and the newly introduced experimental raw data repository, MeMo-RK. Both systems are publicly available by web browser and web service interfaces and are configurable to ensure privacy of unpublished data. Users of this system are provided with the ability to view both kinetic parameters and the experimental raw data from which they are calculated, providing increased confidence in the data. A data analysis and submission tool, the kineticswizard, has been developed to allow the experimentalist to perform data collection, analysis and submission to both data resources. The system is designed to be extensible, allowing integration with other manufacturer instruments covering a range of analytical techniques.
Keywords: Data Mining; *Databases, Protein; Electronic Data Processing; Enzymes/*metabolism; Internet; Kinetics; Recombinant Proteins/metabolism; Software; Systems Biology/*methods

Storing and annotating of kinetic data. - Rojas, I.; Golebiewski, M.; Kania, R.; Krebs, O.; Mir, S.; Weidemann, A.; Wittig, U. (In Silico Biol, 2007)
This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such annotations support the definition of cross links to other related databases and augment the semantics of the data stored in the database.
Keywords: Animals; *Databases, Protein; Enzymes/*chemistry; Humans; Kinetics; *Software; Vocabulary, Controlled

Analysis and comparison of metabolic pathway databases. - Wittig, U.; De Beuckelaer, A. (Brief Bioinform, 2001)
Enormous amounts of data result from genome sequencing projects and new experimental methods. Within this tremendous amount of genomic data 30-40 per cent of the genes being identified in an organism remain unknown in terms of their biological function. As a consequence of this lack of information the overall schema of all the biological functions occurring in a specific organism cannot be properly represented. To understand the functional properties of the genomic data more experimental data must be collected. A pathway database is an effort to handle the current knowledge of biochemical pathways and in addition can be used for interpretation of sequence data. Some of the existing pathway databases can be interpreted as detailed functional annotations of genomes because they are tightly integrated with genomic information. However, experimental data are often lacking in these databases. This paper summarises a list of pathway databases and some of their corresponding biological databases, and also focuses on information about the content and the structure of these databases, the organisation of the data and the reliability of stored information from a biological point of view. Moreover, information about the representation of the pathway data and tools to work with the data are given. Advantages and disadvantages of the analysed databases are pointed out, and an overview to biological scientists on how to use these pathway databases is given.
Keywords: Animals; Computational Biology; *Databases, Factual; Genome; Humans; Internet; *Metabolism; User-Computer Interface

Classification of chemical compounds to support complex queries in a pathway database. - Wittig, U.; Weidemann, A.; Kania, R.; Peiss, C.; Rojas, I. (Comp Funct Genomics, 2004)
Data quality in biological databases has become a topic of great discussion. To provide high quality data and to deal with the vast amount of biochemical data, annotators and curators need to be supported by software that carries out part of their work in an (semi-) automatic manner. The detection of errors and inconsistencies is a part that requires the knowledge of domain experts, thus in most cases it is done manually, making it very expensive and time-consuming. This paper presents two tools to partially support the curation of data on biochemical pathways. The tool enables the automatic classification of chemical compounds based on their respective SMILES strings. Such classification allows the querying and visualization of biochemical reactions at different levels of abstraction, according to the level of detail at which the reaction participants are described. Chemical compounds can be classified in a flexible manner based on different criteria. The support of the process of data curation is provided by facilitating the detection of compounds that are identified as different but that are actually the same. This is also used to identify similar reactions and, in turn, pathways.

Developing a protein-interactions ontology. - Ratsch, E.; Schultz, J.; Saric, J.; Lavin, P. C.; Wittig, U.; Reyle, U.; Rojas, I. (Comp Funct Genomics, 2003)

Notes on the use of ontologies in the biochemical domain. - Rojas, I.; Ratsch, E.; Saric, J.; Wittig, U. (In Silico Biol, 2004)
In this paper we aim at presenting the main flavours and uses that are given to the term ontology in the bio-domains. The paper does not intend to be a thorough review of the existing work in the area. It highlights the uses that are given to ontologies in the Scientific Databases and Visualisation Group at EML Research, in Heidelberg.
Keywords: Biochemical Phenomena; *Biochemistry; Computational Biology; *Databases, Factual; Databases, Genetic; Vocabulary, Controlled

A database system for the analysis of biochemical pathways. - Rojas, I.; Bernardi, L.; Ratsch, E.; Kania, R.; Wittig, U.; Saric, J. (In Silico Biol, 2002)
To provide support for the analysis of biochemical pathways a database system based on a model that represents the characteristics of the domain is needed. This domain has proven to be difficult to model by using conventional data modelling techniques. We are building an ontology for biochemical pathways, which acts as the basis for the generation of a database on the same domain, allowing the definition of complex queries and complex data representation. The ontology is used as a modelling and analysis tool which allows the expression of complex semantics based on a first-order logic representation language. The induction capabilities of the system can help the scientist in formulating and testing research hypotheses that are difficult to express with the standard relational database mechanisms. An ontology representing the shared formalisation of the knowledge in a scientific domain can also be used as data integration tool clarifying the mapping of concepts to the developers of different databases. In this paper we describe the general structure of our system, concentrating on the ontology-based database as the key component of the system.
Keywords: *Biochemical Phenomena; Database Management Systems; *Databases, Factual; Humans; Information Storage and Retrieval/*methods; *Information Systems; Software; User-Computer Interface

Excemplify: a flexible template based solution, parsing and managing data in spreadsheets for experimentalists. - Shi, L.; Jong, L.; Wittig, U.; Lucarelli, P.; Stepath, M.; Mueller, S.; D'Alessandro, L. A.; Klingmuller, U.; Muller, W. (J Integr Bioinform, 2013)
In systems biology, quantitative experimental data is the basis of building mathematical models. In most of the cases, they are stored in Excel files and hosted locally. To have a public database for collecting, retrieving and citing experimental raw data as well as experimental conditions is important for both experimentalists and modelers. However, the great effort needed in the data handling procedure and in the data submission procedure becomes the crucial limitation for experimentalists to contribute to a database, thereby impeding the database to deliver its benefit. Moreover, manual copy and paste operations which are commonly used in those procedures increase the chance of making mistakes. Excemplify, a web-based application, proposes a flexible and adaptable template-based solution to solve these problems. Comparing to the normal template based uploading approach, which is supported by some public databases, rather than predefining a format that is potentiall impractical, Excemplify allows users to create their own experiment-specific content templates in different experiment stages and to build corresponding knowledge bases for parsing. Utilizing the embedded knowledge of used templates, Excemplify is able to parse experimental data from the initial setup stage and generate following stages spreadsheets automatically. The proposed solution standardizes the flows of data traveling according to the standard procedures of applying the experiment, cuts down the amount of manual effort and reduces the chance of mistakes caused by manual data handling. In addition, it maintains the context of meta-data from the initial preparation manuscript and improves the data consistency. It interoperates and complements RightField and SEEK as well.
Keywords: Animals; *Database Management Systems; Knowledge Management; Mice; *Software; *Systems Biology

SYCAMORE--a systems biology computational analysis and modeling research environment - Weidemann, A.; Richter, S.; Stein, M.; Sahle, S.; Gauges, R.; Gabdoulline, R.; Surovtsova, I.; Semmelrock, N.; Besson, B.; Rojas, I.; Wade, R.; Kummer, U. (Bioinformatics, 2008)
SYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model checking and the estimation of unknown kinetic parameters based on protein structures. In addition, it offers some guidance in order to allow non-expert users to perform basic computational modelling tasks.

Big data: The future of biocuration - Howe, Doug; Costanzo, Maria; Fey, Petra; Gojobori, Takashi; Hannick, Linda; Hide, Winston; Hill, David P.; Kania, Renate; Schaeffer, Mary; St Pierre, Susan; Twigger, Simon; White, Owen; et al. (Nature, 2008)

Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation - Zakhartsev, Maksim; Medvedeva, Irina; Orlov, Yury; Akberdin, Ilya; Krebs, Olga; Schulze, Waltraud X. (BMC Plant Biol, 2016)

Determining spectroscopic redshifts by using k nearest neighbor regression. I. Description of method and analysis - Kügler, S. D.; Polsterer, Kai; Hoecker, Maximilian (Astronomy and Astrophysics, 2015)

Autoencoding Time Series for Visualisation - Gianniotis, Nikos; Kügler, S. D.; Tino, P.; Polsterer, Kai; Misra, R. (2015)

Analyzing Complex and Structured Data via Unsupervised Learning Techniques - Polsterer, Kai; Gieseke, F.; Gianniotis, Nikos; Kuegler, S. D. (IAU General Assembly, 2015)

Featureless classification of light curves - Kügler, S. D.; Gianniotis, Nikos; Polsterer, Kai (Monthly Notices of the RAS, 2015)

Automatic Galaxy Classification via Machine Learning Techniques: Parallelized Rotation/Flipping INvariant Kohonen Maps (PINK) - Polsterer, Kai; Gieseke, F.; Igel, C. (2015)

Radio Galaxy Zoo: host galaxies and radio morphologies derived from visual inspection - López-Sánchez, A. R.; Maksym, W. P.; Polsterer, Kai; Borden, K.; Hollow, R. P.; Whyte, L. (Monthly Notices of the RAS, 2015)

Clustering of Complex Data-Sets Using Fractal Similarity Measures and Uncertainties - Hoecker, Maximilian; Polsterer, Kai; Kugler, Sven Dennis; Heuveline, Vincent (2015 IEEE 18th International Conference on Computational Science and Engineering, 2015)

New numerical solver for flows at various Mach numbers - Miczek, F.; Röpke, Friedrich; Edelmann, P. V. F. (Astronomy & Astrophysics, 2015)

Type Ia supernovae from exploding oxygen-neon white dwarfs - Marquardt, Kai S.; Sim, Stuart A.; Ruiter, Ashley J.; Seitenzahl, Ivo R.; Ohlmann, Sebastian T.; Kromer, Markus; Pakmor, Rüdiger; Röpke, Friedrich (Astronomy & Astrophysics, 2015)

Deflagrations in hybrid CONe white dwarfs: a route to explain the faint Type Iax supernova 2008ha - Kromer, M.; Ohlmann, S. T.; Pakmor, R.; Ruiter, A. J.; Hillebrandt, W.; Marquardt, K. S.; Röpke, Friedrich; Seitenzahl, I. R.; Sim, S. A.; Taubenberger, S. (Monthly Notices of the Royal Astronomical Society, 2015)

OGLE-2013-SN-079: A Lonely Supernova Consistent with a Helium Shell Detonation - Inserra, C.; Sim, S. A.; Wyrzykowski, L.; Smartt, S. J.; Fraser, M.; Nicholl, M.; Shen, K. J.; Jerkstrand, A.; Gal-Yam, A.; Howell, D. A.; Maguire, K.; Mazzali, P.; et al. (Astrophys. J. Lett., 2015)

Testing the Role of SNe Ia for Galactic Chemical Evolution of p-nuclei with Two-dimensional Models and with s-process Seeds at Different Metallicities - Travaglio, C.; Gallino, R.; Rauscher, T.; Röpke, Friedrich; Hillebrandt, W. (Astrophys. J., 2015)

Neutrino and gravitational wave signal of a delayed-detonation model of type Ia supernovae - Seitenzahl, Ivo R.; Herzog, Matthias; Ruiter, Ashley J.; Marquardt, Kai; Ohlmann, Sebastian T.; Röpke, Friedrich (Phys. Rev. D, 2015)

Nuclear robustness of the r process in neutron-star mergers - Mendoza-Temis, Joel de Jesús; Wu, Meng-Ru; Langanke, Karlheinz; Martínez-Pinedo, Gabriel; Bauswein, Andreas; Janka, Hans-Thomas (Phys. Rev. C, 2015)

SN2014J gamma rays from the 56Ni decay chain - Diehl, Roland; Siegert, Thomas; Hillebrandt, Wolfgang; Krause, Martin; Greiner, Jochen; Maeda, Keiichi; Röpke, Friedrich; Sim, Stuart A.; Wang, Wei; Zhang, Xiaoling (Astronomy & Astrophysics, 2015)

500 days of SN 2013dy: spectra and photometry from the ultraviolet to the infrared - Pan, Y.-C.; Foley, R. J.; Kromer, M.; Fox, O. D.; Zheng, W.; Challis, P.; Clubb, K. I.; Filippenko, A. V.; Folatelli, G.; Graham, M. L.; Hillebrandt, W.; Kirshner, R. P.; et al. (Monthly Notices of the Royal Astronomical Society, 2015)

The interaction of core-collapse supernova ejecta with a companion star - Liu, Zheng-Wei; Tauris, T. M.; Röpke, Friedrich; Moriya, T. J.; Kruckow, M.; Stancliffe, R. J.; Izzard, R. G. (Astronomy & Astrophysics, 2015)

Log‐normal distribution based ensemble model output statistics models for probabilistic wind‐speed forecasting - Baran, S.; Lerch, Sebastian (Quarterly Journal of the Royal Meteorological Society, 2015)

Of quantiles and expectiles: Consistent scoring functions, Choquet representations and forecast rankings (with discussion and reply) - Ehm, W.; Gneiting, Tilmann; Jordan, A.; Krueger, F.. (Journal of the Royal Statistical Society Series B, 2016)

Spatial postprocessing of ensemble forecasts for temperature using nonhomogeneous Gaussian regression - Feldmann, K.; Scheuerer, M.; Thorarinsdottir, T. L. (Monthly Weather Review, 2015)

Gaussian random particles with flexible Hausdorff dimension - Hansen, L. V.; Thorarinsdottir, T. L.; Ovcharov, E.; Gneiting, Tilmann; Richards, D. (Advances in Applied Probability, 2015)

Multi-model combination and seamless prediction - Hemri, Stephan (Handbook of Hydrometeorological Ensemble Forecasting, 2019)

Multivariate postprocessing techniques for probabilistic hydrological forecasting - Hemri, S.; Lisniak, D.; Klein, B. (Water Resources Research, 2015)

Existence and uniqueness of proper scoring rules - Ovcharov, E. (Journal of Machine Learning Research, 2015)

Calibration of ECMWF forecasts - Richardson, D.; Hemri, S.; Bogner, K.; Gneiting, Tilmann; Haiden, T.; Pappenberger, F.; Scheuerer, M. (ECMWF Newsletter, 2014)

Multivariate discrete copulas, with applications in probabilistic weather forecasting - Schefzik, R. (Publications de l'Institut de Statistique de l'Université de Paris, 2015)

SEEK: a systems biology data and model management platform - Wolstencroft, Katherine; Owen, Stuart; Krebs, Olga; Nguyen, Quyen; Stanford, Natalie J; Golebiewski, Martin; Weidemann, Andreas; Bittkowski, Meik; An, Lihua; Shockley, David; Snoep, Jacky L.; Müller, Wolfgang; et al. (BMC Systems Biology, 2015)
Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models.

A Multilevel Domain Decomposition approach for solving time constrained Optimal Power Flow problems - Gerstner, Philipp; Schick, Michael; Heuveline, Vincent (Preprint Series of the Engineering Mathematics and Computing Lab, 2015)

Clustering of Complex Data-Sets Using Fractal Similarity Measures and Uncertainties - Hoecker, Maximilian; Polsterer, Kai; Kugler, Sven Dennis; Heuveline, Vincent (2015)

Time Constrained Optimal Power Flow Calculations on the German Power Grid - Meyer-Hübner, Nico; Suriyah, Michael; Leibfried, Thomas; Slednev, Viktor; Bertsch, Valentin; Fichtner, Wolf; Gerstner, Philipp; Schick, Michael; Heuveline, Vincent (2015)

A Polynomial Chaos Method for Uncertainty Quantification in Blood Pump Simulation - Song, Chen; Schick, Michael; Heuveline, Vincent (2015)

Fluid-Structure Interaction Simulation of an Aortic Phantom with Uncertain Young’s Modulus Using the Polynomial Chaos Expansion - Kratzke, Jonas; Schick, Michael; Heuveline, Vincent (Applied Mechanics and Materials, 2015)

Enhancing 4D PC-MRI in an aortic phantom considering numerical simulations - Kratzke, Jonas; Schoch, Nicolai; Weis, Christian; Mueller-Eschner, Matthias; Speidel, Stefanie; Farag, Mina; Beller, Carsten; Heuveline, Vincent (2015)

Integration of a biomechanical simulation for mitral valve reconstruction into a knowledge-based surgery assistance system - Schoch, Nicolai; Engelhardt, Sandy; Zimmermann, Norbert; Speidel, Stefanie; Simone, Raffaele De; Wolf, Ivo; Heuveline, Vincent (2015)

FPGA-accelerated Richardson-Lucy Deconvolution for 3D Image Data - Bromberger, Michael; Bastian, Pascal; Bergeest, Jan-Philip; Conrad, Christian; Heuveline, Vincent; Rohr, Karl; Karl, Wolfgang (2016)

Reducing Energy Consumption of Data Transfers using Runtime Data Type Conversion - Bromberger, Michael; Karl, Wolfgang; Heuveline, Vincent (2016)

Exploiting approximate computing methods in FPGAs to accelerate stereo correspondence algorithms - Bromberger, Michael; Karl, Wolfgang; Heuveline, Vincent (2015)

The phylogenetic likelihood library - Flouri, T; Izquierdo-Carrasco, F; Darriba, D; Aberer, AJ; Nguyen, L-T; Minh, BQ; Von Häseler, A; Stamatakis, Alexandros (Systematic Biology, 2015)

Impacts of Terraces on Phylogenetic Inference - Sanderson, Michael J.; McMahon, Michelle M.; Stamatakis, Alexandros; Zwickl, Derrick J.; Steel, Mike (Systematic Biology, 2015)

Phylogenomic analyses data of the avian phylogenomics project - Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon YW; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; others, (GigaScience, 2015)

ExaML version 3: a tool for phylogenomic analyses on supercomputers - Kozlov, Alexey; Aberer, Andre J.; Stamatakis, Alexandros (Bioinformatics, 2015)

Computing the Internode Certainty and related measures from partial gene trees. - Kobert, Kassian; Salichos, Leonidas; Rokas, Antonis; Stamatakis, Alexandros (bioRxiv, 2015)

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies - Leaché, Adam D.; Banbury, Barbara L.; Felsenstein, Joseph; de Oca, Adrián nieto-Montes; Stamatakis, Alexandros (Systematic Biology, 2015)

An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees - Aberer, Andre J.; Stamatakis, Alexandros; Ronquist, Fredrik (Systematic Biology, 2015)

Using RAxML to Infer Phylogenies - Stamatakis, Alexandros (Current Protocols in Bioinformatics, 2015)

Are all global alignment algorithms and implementations correct? - Flouri, Tomáš; Kobert, Kassian; Rognes, Torbjørn; Stamatakis, Alexandros (bioRxiv, 2015)

The State of Software in Evolutionary Biology - Darriba, Diego; Flouri, Tomas; Stamatakis, Alexandros (bioRxiv, 2015)

Two Independent and Highly Efficient Open Source TKF91 Implementations - Baudis, Nikolai; Barbera, Pierre; Graf, Sebastian; Lutteropp, Sarah; Opitz, Daniel; Flouri, Tomas; Stamatakis, Alexandros (bioRxiv, 2015)
In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by Thorne, Kishino, and Felsenstein in 1991. This paper has two parts. In the educational part, we cover teaching issues regarding the setup of the course and the practical and summarize student and teacher experiences. In the scientific part, the two student teams (Team I: Nikolai, Sebastian, Daniel; Team II: Sarah, Pierre) present their solutions for implementing efficient and numerically stable implementations of the TKF91 algorithm. The two teams worked independently on implementing the same algorithm. Hence, since the implementations yield identical results -with slight numerical deviations- we are confident that the implementations are correct. We describe the optimizations applied and make them available as open-source codes in the hope that our findings and software will be useful to the community as well as for similar programming practicals at other universities.

Do Phylogenetic Tree Viewers correctly display Support Values? - Czech, Lucas; Stamatakis, Alexandros (bioRxiv, 2015)

Phylesystem: a git-based data store for community-curated phylogenetic estimates - McTavish, Emily Jane; Hinchliff, Cody E.; Allman, James F.; Brown, Joseph W.; Cranston, Karen A.; Holder, Mark T.; Rees, Jonathan A.; Smith, Stephen A. (Bioinformatics, 2015)

How do SNP ascertainment schemes and population demographics affect inferences about population history? - McTavish, Emily Jane; Hillis, David M (BMC Genomics, 2015)

Twisted trees and inconsistency of tree estimation when gaps are treated as missing data – The impact of model mis-specification in distance corrections - McTavish, Emily Jane; Steel, Mike; Holder, Mark T. (Molecular Phylogenetics and Evolution, 2015)

Longest common substrings with k mismatches - Flouri, Tomas; Giaquinta, Emanuele; Kobert, Kassian; Ukkonen, Esko (Information Processing Letters, 2015)

Global and local sequence alignment with a bounded number of gaps - Barton, Carl; Flouri, Tomáš; Iliopoulos, Costas S.; Pissis, Solon P. (Theoretical Computer Science, 2015)

Transition path sampling with quantum/classical mechanics for reaction rates. - Grater, F.; Li, W. (Methods Mol Biol, 2015)
Predicting rates of biochemical reactions through molecular simulations poses a particular challenge for two reasons. First, the process involves bond formation and/or cleavage and thus requires a quantum mechanical (QM) treatment of the reaction center, which can be combined with a more efficient molecular mechanical (MM) description for the remainder of the system, resulting in a QM/MM approach. Second, reaction time scales are typically many orders of magnitude larger than the (sub-)nanosecond scale accessible by QM/MM simulations. Transition path sampling (TPS) allows to efficiently sample the space of dynamic trajectories from the reactant to the product state without an additional biasing potential. We outline here the application of TPS and QM/MM to calculate rates for biochemical reactions, by means of a simple toy system. In a step-by-step protocol, we specifically refer to our implementation within the MD suite Gromacs, which we have made available to the research community, and include practical advice on the choice of parameters.
Keywords: *Algorithms; Computer Simulation; Kinetics; *Mechanical Phenomena; *Quantum Theory; Thermodynamics

A proton relay enhances H2O2 sensitivity of GAPDH to facilitate metabolic adaptation. - Peralta, D.; Bronowska, A. K.; Morgan, B.; Doka, E.; Van Laer, K.; Nagy, P.; Grater, F.; Dick, T. P. (Nat Chem Biol, 2015)
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is sensitive to reversible oxidative inactivation by hydrogen peroxide (H2O2). Here we show that H2O2 reactivity of the active site thiolate (C152) is catalyzed by a previously unrecognized mechanism based on a dedicated proton relay promoting leaving group departure. Disruption of the peroxidatic reaction mechanism does not affect the glycolytic activity of GAPDH. Therefore, specific and separate mechanisms mediate the reactivity of the same thiolate nucleophile toward H2O2 and glyceraldehyde 3-phosphate, respectively. The generation of mutants in which the glycolytic and peroxidatic activities of GAPDH are comprehensively uncoupled allowed for a direct assessment of the physiological relevance of GAPDH H2O2 sensitivity. Using yeast strains in which wild-type GAPDH was replaced with H2O2-insensitive mutants retaining full glycolytic activity, we demonstrate that H2O2 sensitivity of GAPDH is a key component of the cellular adaptive response to increased H2O2 levels.
Keywords: *Adaptation, Biological; Cysteine/genetics/metabolism; Enzyme Activation; Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/antagonists & inhibitors/genetics/*metabolism; Humans; Hydrogen Peroxide/*pharmacology; Mutation; Oxidation-Reduction; *Protons; Saccharomyces cerevisiae/enzymology; Saccharomyces cerevisiae Proteins/antagonists & inhibitors/genetics/*metabolism

A fast recoiling silk-like elastomer facilitates nanosecond nematocyst discharge. - Beckmann, A.; Xiao, S.; Muller, J. P.; Mercadante, D.; Nuchter, T.; Kroger, N.; Langhojer, F.; Petrich, W.; Holstein, T. W.; Benoit, M.; Grater, F.; Ozbek, S. (BMC Biol, 2015)
BACKGROUND: The discharge of the Cnidarian stinging organelle, the nematocyst, is one of the fastest processes in biology and involves volume changes of the highly pressurised (150 bar) capsule of up to 50%. Hitherto, the molecular basis for the unusual biomechanical properties of nematocysts has been elusive, as their structure was mainly defined as a stress-resistant collagenous matrix. RESULTS: Here, we characterise Cnidoin, a novel elastic protein identified as a structural component of Hydra nematocysts. Cnidoin is expressed in nematocytes of all types and immunostainings revealed incorporation into capsule walls and tubules concomitant with minicollagens. Similar to spider silk proteins, to which it is related at sequence level, Cnidoin possesses high elasticity and fast coiling propensity as predicted by molecular dynamics simulations and quantified by force spectroscopy. Recombinant Cnidoin showed a high tendency for spontaneous aggregation to bundles of fibrillar structures. CONCLUSIONS: Cnidoin represents the molecular factor involved in kinetic energy storage and release during the ultra-fast nematocyst discharge. Furthermore, it implies an early evolutionary origin of protein elastomers in basal metazoans.
Keywords: Amino Acid Sequence; Animals; Blotting, Western; Collagen/metabolism; Elasticity; Elastomers/*chemistry; Gene Expression Regulation; Hydra/physiology; Hydrophobic and Hydrophilic Interactions; Immunohistochemistry; Microscopy, Atomic Force; Molecular Dynamics Simulation; Molecular Sequence Data; Nematocyst/*physiology; Protein Aggregates; Protein Structure, Tertiary; Recombinant Proteins/metabolism/ultrastructure; Silk/*chemistry/ultrastructure; Time Factors

Allosteric regulation of focal adhesion kinase by PIP(2) and ATP. - Zhou, J.; Bronowska, A.; Le Coq, J.; Lietha, D.; Grater, F. (Biophys J, 2015)
Focal adhesion kinase (FAK) is a nonreceptor tyrosine kinase that regulates cell signaling, proliferation, migration, and development. A major mechanism of regulation of FAK activity is an intramolecular autoinhibitory interaction between two of its domains--the catalytic and FERM domains. Upon cell adhesion to the extracellular matrix, FAK is being translocated toward focal adhesion sites and activated. Interactions of FAK with phosphoinositide phosphatidylinsositol-4,5-bis-phosphate (PIP(2)) are required to activate FAK. However, the molecular mechanism of the activation remains poorly understood. Recent fluorescence resonance energy transfer experiments revealed a closure of the FERM-kinase interface upon ATP binding, which is reversed upon additional binding of PIP(2). Here, we addressed the allosteric regulation of FAK by performing all-atom molecular-dynamics simulations of a FAK fragment containing the catalytic and FERM domains, and comparing the dynamics in the absence or presence of ATP and PIP(2). As a major conformational change, we observe a closing and opening motion upon ATP and additional PIP(2) binding, respectively, in good agreement with the fluorescence resonance energy transfer experiments. To reveal how the binding of the regulatory PIP(2) to the FERM F2 lobe is transduced to the very distant F1/N-lobe interface, we employed force distribution analysis. We identified a network of mainly charged residue-residue interactions spanning from the PIP(2) binding site to the distant interface between the kinase and FERM domains, comprising candidate residues for mutagenesis to validate the predicted mechanism of FAK activation.
Keywords: Adenosine Triphosphate/*pharmacology; Allosteric Regulation/drug effects; Animals; Focal Adhesion Protein-Tyrosine Kinases/chemistry/*metabolism; Inositol Phosphates/*pharmacology; Molecular Dynamics Simulation; Principal Component Analysis; Protein Conformation; Thermodynamics

Redox potentials of protein disulfide bonds from free-energy calculations. - Li, W.; Baldus, I. B.; Grater, F. (J Phys Chem B, 2015)
Thiol/disulfide exchange in proteins is a vital process in all organisms. To ensure specificity, the involved thermodynamics and kinetics are believed to be tailored by the structure and dynamics of the protein hosting the thiol/disulfide pair. We here aim at predicting the thermodynamics of thiol/disulfide pairs in proteins. We devise a free-energy calculation scheme, which makes use of the Crooks Gaussian intersection method to estimate the redox potential of thiol/disulfide pairs in 12 proteins belonging to the thioredoxin superfamily, namely, thioredoxins, glutaredoxins, and thiol-disulfide oxidoreductases in disulfide bond formation systems. We obtained a satisfying correlation of computed with experimental redox potentials (varying by 160 mV), with a residual error of approximately 40 mV (8 kJ/mol), which drastically reduces when considering a less diverse set of only thioredoxins. Our simple and transferrable approach provides a route toward estimating redox potentials of any disulfide-containing protein given that its (reduced or oxidized) structure is known and thereby represents a step toward a rational design of redox proteins.
Keywords: Amino Acid Motifs; Disulfides/*chemistry; *Models, Molecular; Oxidation-Reduction; Thermodynamics; Thioredoxins/*chemistry

Force-sensitive autoinhibition of the von Willebrand factor is mediated by interdomain interactions. - Aponte-Santamaria, C.; Huck, V.; Posch, S.; Bronowska, A. K.; Grassle, S.; Brehm, M. A.; Obser, T.; Schneppenheim, R.; Hinterdorfer, P.; Schneider, S. W.; Baldauf, C.; Grater, F. (Biophys J, 2015)
Von Willebrand factor (VWF) plays a central role in hemostasis. Triggered by shear-stress, it adheres to platelets at sites of vascular injury. Inactivation of VWF has been associated to the shielding of its adhesion sites and proteolytic cleavage. However, the molecular nature of this shielding and its coupling to cleavage under shear-forces in flowing blood remain unknown. In this study, we describe, to our knowledge, a new force-sensory mechanism for VWF-platelet binding, which addresses these questions, based on a combination of molecular dynamics (MD) simulations, atomic force microscopy (AFM), and microfluidic experiments. Our MD simulations demonstrate that the VWF A2 domain targets a specific region at the VWF A1 domain, corresponding to the binding site of the platelet glycoprotein Ibalpha (GPIbalpha) receptor, thereby causing its blockage. This implies autoinhibition of the VWF for the binding of platelets mediated by the A1-A2 protein-protein interaction. During force-probe MD simulations, a stretching force dissociated the A1A2 complex, thereby unblocking the GPIbalpha binding site. Dissociation was found to be coupled to the unfolding of the A2 domain, with dissociation predominantly occurring before exposure of the cleavage site in A2, an observation that is supported by our AFM experiments. This suggests that the A2 domain prevents platelet binding in a force-dependent manner, ensuring that VWF initiates hemostasis before inactivation by proteolytic cleavage. Microfluidic experiments with an A2-deletion VWF mutant resulted in increased platelet binding, corroborating the key autoinhibitory role of the A2 domain within VWF multimers. Overall, autoinhibition of VWF mediated by force-dependent interdomain interactions offers the molecular basis for the shear-sensitive growth of VWF-platelet aggregates, and might be similarly involved in shear-induced VWF self-aggregation and other force-sensing functions in hemostasis.
Keywords: Amino Acid Sequence; Binding Sites; Humans; *Molecular Dynamics Simulation; Molecular Sequence Data; Platelet Glycoprotein GPIb-IX Complex/metabolism; von Willebrand Factor/*chemistry/metabolism

Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields. - Mercadante, D.; Milles, S.; Fuertes, G.; Svergun, D. I.; Lemke, E. A.; Grater, F. (J Phys Chem B, 2015)
Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.
Keywords: Escherichia coli; Fluorescence Resonance Energy Transfer; Humans; Intrinsically Disordered Proteins/*chemistry; *Models, Chemical; Molecular Dynamics Simulation; Monte Carlo Method; Nuclear Pore Complex Proteins/*chemistry/genetics; Protein Conformation; Scattering, Small Angle; Solutions; Water/chemistry; X-Ray Diffraction

Origin of Orthogonality of Strain-Promoted Click Reactions. - Wagner, J. A.; Mercadante, D.; Nikic, I.; Lemke, E. A.; Grater, F. (Chemistry, 2015)
Site-specific labeling of biomolecules is rapidly advancing due to the discovery of novel mutually orthogonal reactions. Quantum chemistry studies have also increased our understanding of their relative rates, although these have until now been based on highly simplified reactants. Here we examine a set of strain-promoted click-type cycloaddition reactions of n-propyl azide, 3-benzyl tetrazine and 3-benzyl-6-methyl tetrazine with cyclooctenes/ynes, in which we aim to address all relevant structural details of the reactants. Our calculations have included the obligatory handles used to attach the label and biomolecule as these can critically influence the stereochemistry and electron demand of the reaction. We systematically computed orbital gaps, activation and distortion energies using density functional theory and determined experimental rates for validation. Our results challenge the current paradigm of the inverse electron demand for this class of reactions. We found that the ubiquitous handles, when next to the triple bond of cyclooctynes, can switch the Diels-Alder type ligations to normal electron demand, a class we term as SPINEDAC reactions. Electron donating substituents on tetrazine can enhance normal demand but also increase distortion penalties. The presence and isomeric configuration of handles thus determine the reaction speed and regioselectivity. Our findings can be directly utilized in engineering genuine cycloaddition click chemistries for biological labeling.

Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces. - Louet, M.; Seifert, C.; Hensen, U.; Grater, F. (PLoS Comput Biol, 2015)
The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals.
Keywords: *Allosteric Site; Cyclic AMP Receptor Protein/*chemistry/*metabolism; Entropy; Escherichia coli Proteins/chemistry/metabolism; Molecular Dynamics Simulation; Nuclear Magnetic Resonance, Biomolecular; Principal Component Analysis; Protein Binding

Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors. - Milles, S.; Mercadante, D.; Aramburu, I. V.; Jensen, M. R.; Banterle, N.; Koehler, C.; Tyagi, S.; Clarke, J.; Shammas, S. L.; Blackledge, M.; Grater, F.; Lemke, E. A. (Cell, 2015)
The mechanisms by which intrinsically disordered proteins engage in rapid and highly selective binding is a subject of considerable interest and represents a central paradigm to nuclear pore complex (NPC) function, where nuclear transport receptors (NTRs) move through the NPC by binding disordered phenylalanine-glycine-rich nucleoporins (FG-Nups). Combining single-molecule fluorescence, molecular simulations, and nuclear magnetic resonance, we show that a rapidly fluctuating FG-Nup populates an ensemble of conformations that are prone to bind NTRs with near diffusion-limited on rates, as shown by stopped-flow kinetic measurements. This is achieved using multiple, minimalistic, low-affinity binding motifs that are in rapid exchange when engaging with the NTR, allowing the FG-Nup to maintain an unexpectedly high plasticity in its bound state. We propose that these exceptional physical characteristics enable a rapid and specific transport mechanism in the physiological context, a notion supported by single molecule in-cell assays on intact NPCs.
Keywords: *Active Transport, Cell Nucleus; Crystallography, X-Ray; Fluorescence Resonance Energy Transfer; Humans; Karyopherins/chemistry/metabolism; Models, Molecular; Nuclear Pore Complex Proteins/*chemistry/metabolism; Nuclear Proteins/*chemistry/metabolism; Saccharomyces cerevisiae

Mechanism of Focal Adhesion Kinase Mechanosensing. - Zhou, J.; Aponte-Santamaria, C.; Sturm, S.; Bullerjahn, J. T.; Bronowska, A.; Grater, F. (PLoS Comput Biol, 2015)
Mechanosensing at focal adhesions regulates vital cellular processes. Here, we present results from molecular dynamics (MD) and mechano-biochemical network simulations that suggest a direct role of Focal Adhesion Kinase (FAK) as a mechano-sensor. Tensile forces, propagating from the membrane through the PIP2 binding site of the FERM domain and from the cytoskeleton-anchored FAT domain, activate FAK by unlocking its central phosphorylation site (Tyr576/577) from the autoinhibitory FERM domain. Varying loading rates, pulling directions, and membrane PIP2 concentrations corroborate the specific opening of the FERM-kinase domain interface, due to its remarkably lower mechanical stability compared to the individual alpha-helical domains and the PIP2-FERM link. Analyzing downstream signaling networks provides further evidence for an intrinsic mechano-signaling role of FAK in broadcasting force signals through Ras to the nucleus. This distinguishes FAK from hitherto identified focal adhesion mechano-responsive molecules, allowing a new interpretation of cell stretching experiments.
Keywords: Computational Biology; Cytoskeletal Proteins/chemistry/metabolism; Cytoskeleton/chemistry/metabolism; Focal Adhesion Protein-Tyrosine Kinases/chemistry/*metabolism; Focal Adhesions/chemistry/*metabolism; Mechanotransduction, Cellular/*physiology; Membrane Proteins/chemistry/metabolism; *Models, Biological; Molecular Dynamics Simulation

An analysis of feature relevance in the classification of astronomical transients with machine learning methods - D'Isanto, Antonio; Cavuoti, S.; Brescia, M.; Donalek, C.; Longo, G.; Riccio, G.; Djorgovski, S. G. (Monthly Notices of the Royal Astronomical Society, 2016)

An explorative approach for inspecting Kepler data - Kügler, Sven D.; Gianniotis, Nikos; Polsterer, Kai (Monthly Notices of the Royal Astronomical Society, 2016)

Parallelized rotation and flipping INvariant Kohonen maps (PINK) on GPUs - Polsterer, Kai; Gieseke, Fabian; Igel, Christian; Doser, Bernd; Gianniotis, Nikos (2016)

WTF? Discovering the Unexpected in next-generation radio continuum surveys - Crawford, E.; Norris, R. P.; Polsterer, Kai (2016)

Dealing with Uncertain Multimodal Photometric Redshift Estimations - Polsterer, Kai (IAU Symposium, Astroinformatics, 2016)

Uncertain Photometric Redshifts with Deep Learning Methods - D'Isanto, Antonio (IAU Symposium, Astroinformatics, 2016)

Probability Density Functions for Astronomy - Polsterer, Kai; Gieseke, Fabian (2016)

Efficient and Massively Parallel Implementation of the Evolutionary Placement Algorithm - Barbera, Pierre (2016)

Selection of models of genomic evolution in HPC environments - Darriba, Diego (2016)

Mathematical Problems in Molecular Evolution and Next Generation Sequencing - Kobert, Kassian (2016)

Molecular Phylogeny and Phylogeography of the Podarcis tauricus (Sauria: Lacertidae) Species Subgroup - Psonis, Nikolaos (2016)

A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits - Czech, Lucas; Huerta-Cepas, Jaime; Stamatakis, Alexandros (Molecular Biology and Evolution, 2017)

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites - Mahé, Frédéric; de Vargas, Colomban; Bass, David; Czech, Lucas; Stamatakis, Alexandros; Lara, Enrique; Singer, David; Mayor, Jordan; Bunge, John; Sernaker, Sarah; Siemensmeyer, Tobias; Trautmann, Isabelle; et al. (bioRxiv, 2016)

The divisible load balance problem with shared cost and its application to phylogenetic inference - Scholl, Constantin; Kobert, Kassian; Flouri, Tomá; Stamatakis, Alexandros (2016)

Prediction of missing sequences and branch lengths in phylogenomic data - Darriba, Diego; Weiß, Michael; Stamatakis, Alexandros (Bioinformatics, 2016)

Does the choice of nucleotide substitution models matter topologically? - Hoff, Michael; Orf, Stefan; Riehm, Benedikt; Darriba, Diego; Stamatakis, Alexandros (BMC Bioinformatics, 2016)

A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes - Skourtanioti, Eirini; Kapli, Paschalia; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Ahmadzadeh, Faraham; Crnobrnja–Isailović, Jelka; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos (Molecular Phylogenetics and Evolution, 2016)

Separate histories in both sides of the Mediterranean: phylogeny and niche evolution of ocellated lizards - Ahmadzadeh, Faraham; Flecks, Morris; Carretero, Miguel A.; Böhme, Wolfgang; Ihlow, Flora; Kapli, Paschalia; Miraldo, Andreia; Rödder, Dennis (Journal of Biogeography, 2016)

Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae - Kornilios, Panagiotis; Thanou, Evanthia; Kapli, Paschalia; Parmakelis, Aristidis; Chatzaki, Maria (Molecular Phylogenetics and Evolution, 2016)

Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth–death clock model - Renner, Susanne S; Grimm, Guido W; Kapli, Paschalia; Denk, Thomas (Phil. Trans. R. Soc. B, 2016)

Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations - Kobert, Kassian; Stamatakis, Alexandros; Flouri, Tomáš (Systematic Biology, 2016)

VSEARCH: a versatile open source tool for metagenomics - Rognes, Torbjørn; Flouri, Tomáš; Nichols, Ben; Quince, Christopher; Mahé, Frédéric (PeerJ, 2016)

Phylogeny-aware identification and correction of taxonomically mislabeled sequences - Kozlov, Alexey; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros (Nucleic Acids Research, 2016)

Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo - Kapli, P.; Lutteropp, Sarah; Zhang, J.; Kobert, K.; Pavlidis, P.; Stamatakis, Alexandros; Flouri, T. (bioRxiv, 2016)

The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life - Zhou, Xin; Frandsen, Paul B; Holzenthal, Ralph W; Beet, Clare R; Bennett, Kristi R; Blahnik, Roger J; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V; others, (Phil. Trans. R. Soc. B, 2016)

A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation - Hoang, Diep Thi; Vinh, Le Sy; Flouri, Tomas; Stamatakis, Alexandros; von Häseler, Arndt; Minh, Bui Quang (2016)

Mixture EMOS model for calibrating ensemble forecasts of wind speed - Baran, S.; Lerch, Sebastian (Environmetrics, 2016)

Reproducibility from the perspective of meta-analysis - Ehm, W. (Reproducibility: Principles, Problems, Practices, and Prospects, 2016)

Geometric–optical illusions and Riemannian geometry - Ehm, W.; Wackermann, J. (Journal of Mathematical Psychology, 2016)

Forecasting conditional probabilities of binary outcomes under misspecification - Elliott, Graham; Ghanem, Dalia; Krüger, Fabian (Review of Economics and Statistics, 2016)

Distances, Gegenbauer expansions, curls, and dimples: On dependence measures for random fields - Fiedler, Jochen (2016)

Probabilistic forecasting based on hydrometeorological ensembles - Hemri, Stephan (2016)

Discrete postprocessing of total cloud cover ensemble forecasts - Hemri, S.; Haiden, T.; Pappenberger, F. (Monthly Weather Review, 2016)

Facets of forecast evaluation - Jordan, Alexander I. (2016)

Disagreement versus uncertainty: Evidence from distribution forecasts - Krüger, F.; Nolte, I. (Journal of Banking & Finance, 2016)

Probabilistic forecasting and comparative model assessment, with focus on extreme events - Lerch, Sebastian (2016)

A similarity-based implementation of the Schaake shuffle - Schefzik, R. (Monthly Weather Review, 2016)

Combining parametric low‐dimensional ensemble postprocessing with reordering methods - Schefzik, R. (Quarterly Journal of the Royal Meteorological Society, 2016)

Expected shortfall is jointly elicitable with value-at-risk: Implications for backtesting - Fissler, T.; Ziegel, J. F.; Gneiting, Tilmann (Risk Magazine, 2016)

Towards an open-source semantic data infrastructure for integrating clinical and scientific data in cognition-guided surgery - Fetzer, Andreas; Metzger, Jasmin; Katic, Darko; März, Keno; Wagner, Martin; Philipp, Patrick; Engelhardt, Sandy; Weller, Tobias; Zelzer, Sascha; Franz, Florian; Schoch, Nicolai; Heuveline, Vincent; et al. (Proc. SPIE, 2016)

In vitro flow assessment: from PC-MRI to computational fluid dynamics including fluid-structure interaction - Kratzke, Jonas; Rengier, Fabian; Weis, Christian; Beller, Carsten J.; Heuveline, Vincent (Proc. SPIE, 2016)

Enhancing a diffusion algorithm for 4D image segmentation using local information - Lösel, Philipp; Heuveline, Vincent (Proc. SPIE, 2016)

Comprehensive patient-specific information preprocessing for cardiac surgery simulations - Schoch, N.; Kißler, F.; Stoll, M.; Engelhardt, S.; de Simone, R.; Wolf, I.; Bendl, R.; Heuveline, Vincent (International Journal of Computer Assisted Radiology and Surgery, 2016)

Cognitive tools pipeline for assistance of mitral valve surgery - Schoch, Nicolai; Philipp, Patrick; Weller, Tobias; Engelhardt, Sandy; Volovyk, Mykola; Fetzer, Andreas; Nolden, Marco; De Simone, Raffaele; Wolf, Ivo; Maleshkova, Maria; Rettinger, Achim; Studer, Rudi; et al. (Proc. SPIE, 2016)

Towards Semantic Simulation for Patient-Specific Surgery Assistance - Schoch, N.; Speidel, S.; Sure-Vetter, Y.; Heuveline, Vincent (Proc. First International Workshop on Surgical Data Science, 2016)

Parallel multiphysics simulations using OpenPALM with application to hydro-biogeochemistry coupling - Wlotzka, M.; Heuveline, Vincent; Klatt, S.; Kraus, D.; Haas, E.; Kiese, K.; Butterbach-Bahl, K.; Kraft, P.; Breuer, L. (Proc. 6th International Conference on High-Performance Scientific Computing 2015 (LNCS Springer), 2016)

von Willebrand factor is dimerized by protein disulfide isomerase - Lippok, Svenja; Kolšek, Katra; Löf, Achim; Eggert, Dennis; Vanderlinden, Willem; Müller, Jochen P.; König, Gesa; Obser, Tobias; Röhrs, Karoline; Schneppenheim, Sonja; Budde, Ulrich; Baldauf, Carsten; et al. (Blood, 2016)

Mutual A domain interactions in the force sensing protein von Willebrand factor - Posch, Sandra; Aponte-Santamaría, Camilo; Schwarzl, Richard; Karner, Andreas; Radtke, Matthias; Gräter, Frauke; Obser, Tobias; König, Gesa; Brehm, Maria A.; Gruber, Hermann J.; Netz, Roland R.; Baldauf, Carsten; et al. (Journal of Structural Biology, 2017)

Organic Filling Mitigates Flaw-Sensitivity of Nanoscale Aragonite - Cruz-Chú, Eduardo R.; Xiao, Shijun; Patil, Sandeep P.; Gkagkas, Konstantinos; Gräter, Frauke (ACS Biomaterials Science & Engineering, 2017)

Rescuing the Over-Collapse of Intrinsically Disordered Proteins using a Force Field Derived by a New Paradigm - Mercadante, Davide; Milles, Sigrid; Fuertes, Gustavo; Svergun, Dmitri; Lemke, Edward A; Gräter, Frauke (Biophysical Journal, 2016)

Combined Experimental and computational approaches reveal distinct pH-dependence of pectin methyl esterase inhibitors - Hocq, Ludivine; Sénéchal, Fabien; Lefebvre, Valérie; Lehner, Arnaud; Domon, Jean-Marc; Mollet, Jean-Claude; Dehors, Jérémy; Pageau, Karine; Marcelo, Paulo; Guérineau, François; Kolšek, Katra; Mercadante, Davide; et al. (Plant Physiology, 2017)

The Cell Wall Arabinose-Deficient Arabidopsis thaliana Mutant murus5 Encodes a Defective Allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2 - Dugard, Christopher K.; Mertz, Rachel A.; Rayon, Catherine; Mercadante, Davide; Hart, Christopher; Benatti, Matheus R.; Olek, Anna T.; SanMiguel, Phillip J.; Cooper, Bruce R.; Reiter, Wolf-Dieter; McCann, Maureen C.; Carpita, Nicholas C. (Plant Physiology, 2016)

Plasticity of Nucleoporin Nuclear Transport Receptor Interactions-Molecular Description of a Highly Dynamic, Ultrafast Interaction Mechanism - Aramburu, Iker Valle; Mercadante, Davide; Milles, Sigrid; Ringkjøbing, Malene; Banterle, Niccolò; Koehler, Christine; Tyagi, Swati; Clarke, Jane; Shammas, Sarah L; Blackledge, Martin; others, (Biophysical Journal, 2016)

Minicollagen cysteine-rich domains encode distinct modes of polymerization to form stable nematocyst capsules. - Tursch, A.; Mercadante, D.; Tennigkeit, J.; Grater, F.; Ozbek, S. (Sci Rep, 2016)
The stinging capsules of cnidarians, nematocysts, function as harpoon-like organelles with unusual biomechanical properties. The nanosecond discharge of the nematocyst requires a dense protein network of the capsule structure withstanding an internal pressure of up to 150 bar. Main components of the capsule are short collagens, so-called minicollagens, that form extended polymers by disulfide reshuffling of their cysteine-rich domains (CRDs). Although CRDs have identical cysteine patterns, they exhibit different structures and disulfide connectivity at minicollagen N and C-termini. We show that the structurally divergent CRDs have different cross-linking potentials in vitro and in vivo. While the C-CRD can participate in several simultaneous intermolecular disulfides and functions as a cystine knot after minicollagen synthesis, the N-CRD is monovalent. Our combined experimental and computational analyses reveal the cysteines in the C-CRD fold to exhibit a higher structural propensity for disulfide bonding and a faster kinetics of polymerization. During nematocyst maturation, the highly reactive C-CRD is instrumental in efficient cross-linking of minicollagens to form pressure resistant capsules. The higher ratio of C-CRD folding types evidenced in the medusozoan lineage might have fostered the evolution of novel, predatory nematocyst types in cnidarians with a free-swimming medusa stage.
Keywords: Amino Acid Sequence; Animals; Antibody Specificity; Cnidaria/chemistry; Collagen/*chemistry; Cross-Linking Reagents/chemistry; Cysteine/*chemistry; Disulfides/chemistry; Fluorescence; Green Fluorescent Proteins/metabolism; Morphogenesis; Nematocyst/*metabolism; *Polymerization; Protein Structure, Tertiary; Structure-Activity Relationship

Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control - Kent, Lisa M; Loo, Trevor S; Melton, Laurence D; Mercadante, Davide; Williams, Martin AK; Jameson, Geoffrey B (Journal of Biological Chemistry, 2016)

Reaction–diffusion basis of retroviral infectivity - Sadiq, Kashif (Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, 2016)

Human DPP III – Keap1 Interactions: A Combined Experimental And Computational study - Gundić, Mario; Tomić, Antonija; Wade, Rebecca C.; Matovina, Mihaela; Karačić, Zrinka; Kazazić, Saša; Tomić, Sanja (Croat. Chem. Acta., 2016)

Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties - Tong, Rudi; Wade, Rebecca C.; Bruce, Neil J. (Proteins, 2016)

Global profiling of SRP interaction with nascent polypeptides - Schibich, Daniela; Gloge, Felix; Pöhner, Ina; Björkholm, Patrik; Wade, Rebecca C.; von Heijne, Gunnar; Bukau, Bernd; Kramer, Günter (Nature, 2016)

An efficient low storage and memory treatment of gridded interaction fields for simulations of macromolecular association - Ozboyaci, Musa; Martinez, Michael; Wade, Rebecca C. (Journal of Chemical Theory and Computation, 2016)

Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs - Borsari, Chiara; Luciani, Rosaria; Pozzi, Cecilia; Pöhner, Ina; Henrich, Stefan; Trande, Matteo; Cordeiro-da-Silva, Anabela; Santarem, Nuno; Baptista, Catarina; Tait, Annalisa; Di Pisa, Flavio; Dello Iacono, Lucia; et al. (J. Med. Chem., 2016)

Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets - Kokh, Daria; Czodrowski, Paul; Rippmann, Friedrich; Wade, Rebecca C. (Journal of Chemical Theory and Computation, 2016)

Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome - Öztürk, Mehmet Ali; Pachov, Georgi V.; Wade, Rebecca C.; Cojocaru, Vlad (Nucleic Acids Research, 2016)

Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex - Wild, Klemens; Bange, Gert; Motiejunas, Domantas; Kribelbauer, Judith; Hendricks, Astrid; Segnitz, Bernd; Wade, Rebecca C.; Sinning, Irmgard (Journal of Molecular Biology, 2016)

ProSAT+: visualizing sequence annotations on 3D structure - Stank, Antonia; Richter, Stefan; Wade, Rebecca C. (Protein Engineering, Design and Selection, 2016)

Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen - Subramanian, Sundar Raman; Singam, Ettayapuram Ramaprasad Azhagiya; Berinski, Michael; Subramanian, Venkatesan; Wade, Rebecca C. (J. Phys. Chem. B, 2016)

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment - Lensink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy; Huang, Shen-You; Schneidman-Duhovny, Dina; Sali, Andrej; Segura, Joan; Fernandez-Fuentes, Narcis; Viswanath, Shruthi; Elber, Ron; Grudinin, Sergei; Popov, Petr; et al. (Proteins, 2016)

Protein Binding Pocket Dynamics - Stank, Antonia; Kokh, Daria; Fuller, Jonathan C.; Wade, Rebecca C. (Acc. Chem. Res., 2016)

Three steps to Gold: Mechanism of protein adsorption to a gold surface revealed by Brownian and molecular dynamics simulations - Ozboyaci, M.; Kokh, Daria; Wade, Rebecca C. (Phys. Chem. Chem. Phys., 2016)

Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer - Yu, Xiaofeng; Kokh, Daria; Nandekar, Prajwal; Mustafa, Ghulam; Richter, Stefan; Wade, Rebecca C. (High Performance Computing in Science and Engineering ´15, 2016)

Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family - Rafiullah, Rafiullah; Aslamkhan, Muhammad; Paramasivam, Nagarajan; Thiel, Christian; Mustafa, Ghulam; Wiemann, Stefan; Schlesner, Matthias; Wade, Rebecca C.; Rappold, Gudrun A; Berkel, Simone (J. Med. Genetics, 2016)

Modeling and simulation of protein–surface interactions: achievements and challenges - Ozboyaci, Musa; Kokh, Daria; Corni, Stefano; Wade, Rebecca C. (Quarterly Reviews of Biophysics, 2016)
Understanding protein–inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein–surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein–surface interactions and discuss the successes and limitations of current approaches.

The immunomodulation potential of the synthetic derivatives of benzothiazoles: Implications in immune system disorders through in vitro and in silico studies - Khan, Khalid Mohammed; Mesaik, Mohammad A.; Abdalla, Omer M.; Rahim, Fazal; Soomro, Samreen; Halim, Sobia A.; Mustafa, Ghulam; Ambreen, Nida; Khalid, Ahmad Shukralla; Taha, Muhammad; Perveen, Shahnaz; Alam, Muhammad Tanveer; et al. (Bioorg. Chem., 2016)

Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design - Yu, Xiaofeng; Nandekar, Prajwal; Mustafa, Ghulam; Cojocaru, Vlad; Lepesheva, Galina I.; Wade, Rebecca C. (Biochimica et Biophysica Acta (BBA) - General Subjects, 2016)
AbstractBackground Cytochrome P450 sterol 14α-demethylase (CYP51) is an essential enzyme for sterol biosynthesis and a target for anti-parasitic drug design. However, the design of parasite-specific drugs that inhibit parasitic CYP51 without severe side effects remains challenging. The active site of CYP51 is situated in the interior of the protein. Here, we characterize the potential ligand egress routes and mechanisms in Trypanosoma brucei and human CYP51 enzymes. Methods We performed Random Acceleration Molecular Dynamics simulations of the egress of four different ligands from the active site of models of soluble and membrane-bound T. brucei CYP51 and of soluble human CYP51. Results In the simulations, tunnel 2 f, which leads to the membrane, was found to be the predominant ligand egress tunnel for all the ligands studied. Tunnels S, 1 and W, which lead to the cytosol, were also used in T. brucei CYP51, whereas tunnel 1 was the only other tunnel used significantly in human CYP51. The common tunnels found previously in other CYPs were barely used. The ligand egress times were shorter for human than T. brucei CYP51, suggesting lower barriers to ligand passage. Two gating residues, F105 and M460, in T. brucei CYP51 that modulate the opening of tunnels 2 f and S were identified. Conclusions Although the main egress tunnel was the same, differences in the tunnel-lining residues, ligand passage and tunnel usage were found between T. brucei and human CYP51s. General Significance The results provide a basis for the design of selective anti-parasitic agents targeting the ligand tunnels.

HITS at TAC KBP 2015: Entity discovery and linking, and event nugget detection - Heinzerling, Benjamin; Judea, Alex; Strube, Michael (2016)

Incremental global event extraction - Judea, Alex; Strube, Michael (2016)

Lexical coherence graph modeling using word embeddings - Mesgar, Mohsen; Strube, Michael (2016)

Search space pruning: A simple solution for better coreference resolvers - Moosavi, Nafise Sadat; Strube, Michael (2016)

Which coreference evaluation metric do you trust? A proposal for a link-based entity aware metric - Moosavi, Nafise Sadat; Strube, Michael (2016)

Generating coherent summaries of scientific articles using coherence patterns - Parveen, Daraksha; Mesgar, Mohsen; Strube, Michael (2016)

Feature-rich error detection in scientific writing using logistic regression - Remse, Madeline; Mesgar, Mohsen; Strube, Michael (2016)

Citizen-centric urban planning through extracting emotion information from Twitter in an interdisciplinary space-time-linguistics algorithm - Resch, Bernd; Summa, Anja; Zeile, Peter; Strube, Michael (Urban Planning, 2016)

Microblog emotion classification by computing similarity in text, time, and space - Summa, Anja; Resch, Bernd; Strube, Michael (2016)

Notions of similarity for systems biology models. - Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar (Briefings in Bioinformatics (2016) pii: bbw090., 2016)

FAIRDOM approach for semantic interoperability of systems biology data and models. - Krebs, Olga; Wolstencroft, K.; Stanford, NJ.; Morrison, N.; Golebiewski, Martin; Owen, S.; Nguyen, Quyen; Snoep, JL.; Müller, Wolfgang; Goble, C. (Proceedings International Conference on Biomedical Ontology, ICBO 2015. no. CEUR Workshop Proceedings 1515, 2016)

The Human Physiome: how standards, software, and innovative service infrastructures are providing the building blocks to make it achievable. - Nickerson, David; Atalag, Koray; de Bono, Bernard; Geiger, Jörg; Goble, Carole; Hollmann, Susanne; Lonien, Joachim; Müller, Wolfgang; Regierer, Babette; Stanford, Natalie J.; Golebiewski, Martin; Hunter, Peter (Interface Focus (2016), 2016)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016 - Schreiber, F.; Bader, GD.; Gleeson, P.; Golebiewski, Martin; Hucka, M.; Le, Novère.; Myers, CJ.; Nickerson, D.; Sommer, B.; Waltemath, D. (Journal of Integrative Bioinformatics (2016), 2016)

STON: exploring biological pathways using the SBGN standard and graph databases. - Touré, Vasundra; Mazein, Alexander; Waltemath, Dagmar; Balaur, Irina; Saqi, Mansoor; Henkel, Ron; Pellet, Johann; Auffray, Charles (BMC Bioinformatics (2016), 2016)

Generalised model-independent characterisation of strong gravitational lenses. I. Theoretical foundations - Wagner, J. (Astronomy & Astrophysics, 2017)

Photometric redshift estimation via deep learning. Generalized and pre-classification-less, image based, fully probabilistic redshifts - D'Isanto, Antonio; Polsterer, Kai (Astronomy & Astrophysics, 2018)

Massively-parallel best subset selection for ordinary least-squares regression - Gieseke, Fabian; Polsterer, Kai; Mahabal, Ashish; Igel, Christian; Heskes, Tom (2017 IEEE Symposium Series on Computational Intelligence (SSCI), 2017)

Dealing with Uncertain Multimodal Photometric Redshift Estimations. - Polsterer, Kai (Proc. IAU, 2016)

Astroinformatics; a new discipline or business as usual? - Polsterer, Kai (2017)

MC3 für phylogenetische Bäume und molekulare Datierung - Schwaiger, Nico (2017)

Error-Profile-Aware Correction of Next Generation Sequencing Read - Lutteropp, Sarah (2017)

UniEuk: Time to Speak a Common Language in Protistology! - Berney, Cédric; Ciuprina, Andreea; Bender, Sara; Brodie, Juliet; Edgcomb, Virginia; Kim, Eunsoo; Rajan, Jeena; Parfrey, Laura Wegener; Adl, Sina; Audic, Stéphane; others, (Journal of Eukaryotic Microbiology, 2017)

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences - Ratmann, Oliver; Wymant, Chris; Colijn, Caroline; Danaviah, Siva; Essex, M; Frost, Simon DW; Gall, Astrid; Gaiseitsiwe, Simani; Grabowski, Mary; Gray, Ronald; others, (AIDS Research and Human Retroviruses, 2017)

Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence - Zhou, Xiaofan; Lutteropp, Sarah; Czech, Lucas; Stamatakis, Alexandros; von Looz, Moritz; Rokas, Antonis (bioRxiv, 2017)

An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties - Flouri, Tomas; Zhang, Jiajie; Czech, Lucas; Kobert, Kassian; Stamatakis, Alexandros (2017)

Two C++ Libraries for Counting Trees on a Phylogenetic Terrace - Biczok, R.; Bozsoky, P.; Eisenmann, P.; Ernst, J.; Ribizel, T.; Scholz, F.; Trefzer, A.; Weber, F.; Hamann, M.; Stamatakis, Alexandros (bioRxiv, 2017)

A novel heuristic for data distribution in massively parallel phylogenetic inference using site repeats - Morel, Benoit; Flouri, Tomas; Stamatakis, Alexandros (2017)

Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae) - Bank, Sarah; Sann, Manuela; Mayer, Christoph; Meusemann, Karen; Donath, Alexander; Podsiadlowski, Lars; Kozlov, Alexey; Petersen, Malte; Krogmann, Lars; Meier, Rudolf; others, (Molecular Phylogenetics and Evolution, 2017)

Evolutionary history of the Hymenoptera - Peters, Ralph S; Krogmann, Lars; Mayer, Christoph; Donath, Alexander; Gunkel, Simon; Meusemann, Karen; Kozlov, Alexey; Podsiadlowski, Lars; Petersen, Malte; Lanfear, Robert; others, (Current Biology, 2017)

Cutting the Gordian Knot: Phylogenetic and ecological diversification of the Mesalina brevirostris species complex (Squamata, Lacertidae) - Šmíd, J; Moravec, J; Gvoždík, V; Štundl, J; Frynta, D; Lymberakis, P; Kapli, P; Wilms, T; Schmitz, A; Shobrak, M; Yousefkhani, SH; Rastegar-Pouyani, E; et al. (Zoologica Scripta, 2017)

The evolutionary history of two lizards (Squamata: Lacertidae) is linked to the geological development of Iran - Ahmadzadeh, Faraham; Lymberakis, Petros; Pirouz, Reyhaneh Saberi; Kapli, Paschalia (Zoologischer Anzeiger - A Journal of Comparative Zoology, 2017)

Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family - Grímsson, F; Kapli, P; Hofmann, C-C; Zetter, R; Grimm, GW (PeerJ, 2017)

Bias-corrected score decomposition for generalized quantiles - Ehm, W.; Ovcharov, E. (Biometrika, 2017)

When is the mode functional the Bayes classifier? - Gneiting, Tilmann (Stat, 2017)

Analog-based postprocessing of navigation-related hydrological ensemble forecasts - Hemri, S.; Klein, B. (Water Resources Research, 2017)

Similarity-based semilocal estimation of post-processing models - Lerch, Sebastian; Baran, S. (Journal of the Royal Statistical Society: Series C (Applied Statistics), 2017)

Forecaster’s dilemma: Extreme events and forecast evaluation - Lerch, Sebastian; Thorarinsdottir, T. L.; Ravazzolo, F.; Gneiting, Tilmann (Statistical Science, 2017)

Discussion of “Elicitability and backtesting: Perspectives for banking regulation” - Schmidt, Patrick (The Annals of Applied Statistics, 2017)

heiMAP: Virtueller Kartentisch - Baumann, Martin; Effinger, Maria; Eller, Dirk; Heuveline, Vincent; Kempf, Christian; Loos, Lukas; Maylein, Leonhard; Peltzer, Jörg; Pfeiffer, Michelle; Probst, Veit; others, (2017)

Development and implementation of a temperature monitoring system for HPC systems - Baumann, Martin; Gehbart, Fabian; Mattes, Oliver; Nikas, Sotirios; Heuveline, Vincent (2017)

Advances in Energy System Optimization: Proceedings of the first International Symposium on Energy System Optimization - Bertsch, Valentin; Fichtner, Wolf; Heuveline, Vincent; Leibfried, Thomas (Advances in Energy System Optimization, 2017)

Surgical Data Science: Enabling Next-Generation Surgery - Maier-Hein, Lena; Vedula, S. Swaroop; Speidel, Stefanie; Navab, Nassir; Kikinis, Ron; Park, Adrian; Eisenmann, Matthias; Feussner, Hubertus; Forestier, Germain; Giannarou, Stamatia; Hashizume, Makoto; Katic, Darko; et al. (arXiv, 2017)