radm.info

Protein domains are the structural, functional and evolutionary units of proteins. Over the last years, I have been exploring how protein evolution can be measured as a series of domain-wise events. This process, in which proteins evolve by domain-wise re-arrangements, is referred to as modular evolution. Proteins consist of domain architectures and comparative analysis between different domain architectures can help determine the rules by which new proteins evolve. My research has had two primary goals: The first objective has been to develop a quantitative model of modular evolution. By conducting genomic comparisons across 20 genomes, I have been able to derive rates for key events in modular evolution. Furthermore, I have explored the formation of new domains, and studied the impact of new domains on the functional repertoire. The second objective has been the development of algorithms and computational tools to simplify domain-based analysis of proteins, and indeed, entire proteomes. Beyond modular evolution, I am currently working on an algorithm to simplify over-representation analysis of Gene Ontology terms.

ProgressBar a text-based progress bar for Java

A text-based ProgressBar for Java. There may be alternatives around, but I was unable to find a text-based progress bar which is able to run in indeterminate mode (that is, indicate activity when the progress of the activity is unknown).
Lang: JAVA | Type: API | Web: https://github.com/radmoore/ProgressBar
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XDOMsuite an API for modelling protein evolution

The xdomsuite is a collection of classes and methods for working with domain data. It consists of three main classes (Proteome, Protein, Domain). A Proteome is a collection of protein objects, and contains methods for tasks such as searching, sorting, counting, filtering, or comparing arrangements in a proteome. It furthermore contains methods for comparing two proteomes with each other (set operations). A Protein is a collection of instances of the Domain class, and represents a domain arrangement. Similar to the Proteome class, the Domain class contains various methods for comparison etc, as well as methods for attaching annotation, genome location etc.
Lang: RUBY, PYTHON | Type: API | Web: http://iebservices.uni-muenster.de/radmoore/xdomsuite
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RTree an API for creating tree datastructures

Rtree is a class for handling tree data-structures. It creates a tree from taxonomic lineages or from newick trees. Supports different breadth-first traversal methods, and supplies an iterator to move through the tree based on the current traversal order. Any object / data structure can be associated with any node in the tree, and accessed by a predefined key. I use this for ancestral state reconstruction.
Lang: RUBY | Type: API | Web: http://iebservices.uni-muenster.de/radmoore/rtree
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DoMosaics a powerful suite of tools for the analysis of protein family evolution

DoMosaics is a tool for visual analysis of protein phylogenies and similarities in the context of protein domains. DoMosaics shows you a tree with corresponding domain arrangements of the proteins at the same time. If you want to know where your domain was lost, whether a group of proteins differs in its domain arrangements, or what are the characteristic domains for a phylogenetic group, DoMosaics is for you. DoMosaics lets you also examine the domain annotations to see whether the domains have been correctly identified. You can create dotplots, run a context- dependent similarity analysis and more. Furthermore, you can conduct phylogenetic profiling, create domain network graphs, find domain insertion/deletion events and, last but not least, simply visualize and manipulate phylogenetic trees. All output can be saved as PDF or as SVG (which can be viewed in Firefox or edited using e.g. Adobe Illustrator or Inkscape) as well as in a number of common bitmap formats.
Lang: JAVA | Type: GUIApp | Web: http://www.domosaics.uni-muenster.de
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GoZapper gene ontology simplification

GOZapper is a tool for conducting over-representation analysis of Gene Ontology categories. GOZappers input is a list of entity-GO category associations. Using the GO web resources, GOZapper creates one connected directed-acyclic graph by adding all nodes necessary to cover all paths of the input nodes to the top-level ontology. Users can see the association of entity-GO associations, and collapse along terminology paths in real time (incl. real time graph and bar plot changes.) GOZapper uses the prefuse graph library for visualization. I am currently adding methods to compare sample GO distributions to a universe distribution.
Lang: JAVA | Type: GUIApp | Web: http://iebservices.uni-muenster.de/radmoore/gozapper
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TrackRecord a web application for athletes

I am a co-founder of TrackRecord, a community platform for sports enthusiasts from professional triathletes to occasional after-work runners. This is a relatively fresh project, which we just opened to the public. TR allows users to track exercises over time, compare themselves to virtual training partners, manage equipment and favourite tracks and socialize. It is written in Ruby on Rails (a MVC framework).
Lang: RUBY/RoR | Type: WebApp | Web: http://www.track-record.org
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PfamScanner a wrapper for HMMSCAN

A simple wrapper for HMMSCAN, which produces xdom output format (which can be used in conjunction with the XDOMsuite). Beyond running HMMSCAN, the wrapper can resolve overlaps using the best matching cascade (by Evalue), and can merge split hits(successive hits to the same HMM).
Lang: JAVA | Type: CmdApp | Web: http://iebservices.uni-muenster.de/radmoore/misc/PfamScanner.jar
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RadScan

RadScan is a command line utility for performing domain achitecture-based similarity searches against UniProt. It interfaces a webapplication which runs a reference implementation of the RADS/RAMPAGE based search (http://rads.uni-muenster.de). RadScan can perfom a number of post-processing steps (e.g. overlap resolution, repeat collapsing, split-hit merging).
Lang: JAVA | Type: CmdApp | Web: http://iebservices.uni-muenster.de/radmoore/rads/radscan-0.4.3.jar
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TE Wood, G Rauch, AD Moore
Polyploidy and ecological adaptation
in prep. BioEssays (Invited) (2013)
(my involvement in this was the implementation of a system for querying online publication databases and conducting citation statistics)
in prep.

A.D. Moore, A. Held, N. Terrapon, J. Weiner, E. Bornberg-Bauer
DoMosaicS: Software for domain arrangement visualization and domain-centric analysis of proteins
in revision (2013)
submitted

N. Terrapon*, J. Weiner*, S. Grath, A. D. Moore, and E. Bornberg-Bauer
Rapid similarity search of proteins using alignments of domain arrangements
submitted (2012)
submitted

A. D. Moore, S. Grath, A. Schüler, A. K. Huylmans, and E. Bornberg-Bauer
Quantification and Functional Analysis of Modular Protein Evolution in a Dense Phylogenetic Tree
in print, Biochimica et Biophysica Acta, Proteins and Proteomics (2012)
published

A. Reineke, E. Bornberg-Bauser, A. D. Moore*, and Sonja Grath*
Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution
Genome Biol Evol. 2012; 4(3): 316-329
* joint correspondance
published

A. D. Moore and E. Bornberg-Bauer
The Dynamics and Evolutionary Potential of Domain Loss and Emergence
Mol Biol Evol. 2012 February; 29(2): 787-796
published

The Nasonia Genome Working Group
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
Science, 327:5963 (2010)
published

A. D. Moore and E. Bornberg-Bauer
Protein domains as evolutionary units
in: Evolutionary Genomics and Systems Biology, Ed. G. Caetano-Anollés (2010)
John Wiley & Sons
published

L. Wissler, E. Dattolo, A. D. Moore, T. B. H. Reusch, J. L. Olsen, M. Migliaccio, E. Bornberg-Bauer, G. Procaccini
Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs
Database; doi: 10.1093/database/bap009 (2009)
published

A. D. Moore*, A. K Bjoerklund*, D. Ekman, E. Bornberg-Bauer and A. Elofsson
Arrangements in the Modular Evolution of Proteins
TiBS33:9 (2008)
* joint authorship
published

J. Weiner 3rd, A. D. Moore, E. Bornberg-Bauer
Just how versatile are domains?
BMC Evolutionary Biology, 8:285 (2008)
published

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I have taught throughout most of my studies (both undergrad and graduate). I mostly did work as TA, and co-supervised students conducting BSc and MSc level studies during my PhD.

Bioinformatics I (Practicles (TA), WS08/09, WS09/10, WS10/11)
Bioinformatics II (Practicles (TA), SS07)
Advanced Programming for Bioinformatics (FGM, SS09)
Supervision support BSc / MSc (08/09/10)

Andrew Moore