Thomas Gatter
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View article: <tt>SynKit</tt> : A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis
SynKit : A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis Open
Computational modeling of chemical reactions is fundamental to modern synthetic chemistry but is often hindered by a fragmented software ecosystem and the complexity of accurately representing the reaction mechanisms. To address this, we i…
View article: SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis
SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis Open
The computational modeling of chemical reactions is fundamental to modern synthetic chemistry, yet progress is often hindered by a fragmented software ecosystem and the challenge of representing complex reaction mechanisms with high fideli…
View article: Crossover operators for molecular graphs with an application to virtual drug screening
Crossover operators for molecular graphs with an application to virtual drug screening Open
Genetic algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this…
View article: Computing Double-Pushout GraphTransformation Rules and Atom-to-Atom Mapsfrom KEGG RCLASS Data
Computing Double-Pushout GraphTransformation Rules and Atom-to-Atom Mapsfrom KEGG RCLASS Data Open
Background: Atom-to-atom maps play an important role for many applications. However, they are often difficult to obtain. The KEGG reaction database does not provide atom-to-atom maps for its reactions and instead offers a description of lo…
View article: Atom Transition Networks and Isotope Labeling Patterns in Large Chemical Reaction Networks
Atom Transition Networks and Isotope Labeling Patterns in Large Chemical Reaction Networks Open
Isotope tracing experiments are an important source of information in particular for the analysis of complex metabolic networks. Their evaluation, however, is a notoriously difficult and time-consuming task. Here, we derive a simple and co…
View article: Crossover Operators for Molecular Graphs with an Application to Virtual Drug Screening
Crossover Operators for Molecular Graphs with an Application to Virtual Drug Screening Open
Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this…
View article: Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions
Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions Open
Atom-to-atom maps (AAMs) are bijections that establish the correspondence of reactant and product atoms across chemical reactions. They capture crucial features of the reaction mechanism and thus play a central role in modeling chemistry a…
View article: Kosteneffektive hybride Genomassemblierung mit LazyB
Kosteneffektive hybride Genomassemblierung mit LazyB Open
Advances in genome sequencing have led to a paradigm shift where project costs are no longer limited by sequencing costs but rather by the computational problems associated with genome assembly. There is an urgent demand for more efficient…
View article: The Genome of the “Sea Vomit” Didemnum vexillum
The Genome of the “Sea Vomit” Didemnum vexillum Open
Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes hav…
View article: Economic Genome Assembly from Low Coverage Illumina and Nanopore Data
Economic Genome Assembly from Low Coverage Illumina and Nanopore Data Open
We describe a new approach to assemble genomes from a combination of low-coverage short and long reads. LazyBastard starts from a bipartite overlap graph between long reads and restrictively filtered short-read unitigs, which are then redu…
View article: Economic Genome Assembly from Low Coverage Illumina and Nanopore Data
Economic Genome Assembly from Low Coverage Illumina and Nanopore Data Open
Ongoing developments in genome sequencing have caused a fundamental paradigm shift in the field in recent years. With ever lower sequencing costs, projects are no longer limited by available raw data, but rather by computational demands. T…
View article: Convexity Deficit of Benzenoids
Convexity Deficit of Benzenoids Open
In 2012, a family of benzenoids was introduced by Cruz, Gutman, and Rada, which they called convex benzenoids. In this paper we introduce the convexity deficit, a new topological index intended for benzenoids and, more generally, fusenes. …
View article: Ryūtō: network-flow based transcriptome reconstruction
Ryūtō: network-flow based transcriptome reconstruction Open
Its performance compares favorably with state of the art methods on both simulated and real-life datasets. Ryūtō calls 1-4% more true transcripts, while calling 5-35% less false predictions compared to the next best competitor.
View article: Integrating Pareto Optimization into Dynamic Programming
Integrating Pareto Optimization into Dynamic Programming Open
Pareto optimization combines independent objectives by computing the Pareto front of the search space, yielding a set of optima where none scores better on all objectives than any other. Recently, it was shown that Pareto optimization seam…
View article: Tools and data services registry: a community effort to document bioinformatics resources
Tools and data services registry: a community effort to document bioinformatics resources Open
This FAIRsharing record describes: bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources.