Synthesis of Deterministic Top-down Tree Transducers from Automatic Tree Relations

We consider the synthesis of deterministic tree transducers from automaton definable specifications, given as binary relations, over finite trees. We consider the case of specifications that are deterministic top-down tree automatic, meaning the specification is recognizable by a deterministic top-down tree automaton that reads the two given trees synchronously in parallel. In this setting we study tree transducers that are allowed to have either bounded delay or arbitrary delay. Delay is caused whenever the transducer reads a symbol from the input tree but does not produce output. We provide decision procedures for both bounded and arbitrary delay that yield deterministic top-down tree transducers which realize the specification for valid input trees. Similar to the case of relations over words, we use two-player games to obtain our results.Comment: In Proceedings GandALF 2014, arXiv:1408.556

Resynchronized Uniformization and Definability Problems for Rational Relations

Regular synchronization languages can be used to define rational relations of finite words, and to characterize subclasses of rational relations, like automatic or recognizable relations. We provide a systematic study of the decidability of uniformization and definability problems for subclasses of rational relations defined in terms of such synchronization languages. We rephrase known results in this setting and complete the picture by adding several new decidability and undecidability results

SCOPPI: a structural classification of protein–protein interfaces

SCOPPI, the structural classification of protein–protein interfaces, is a comprehensive database that classifies and annotates domain interactions derived from all known protein structures. SCOPPI applies SCOP domain definitions and a distance criterion to determine inter-domain interfaces. Using a novel method based on multiple sequence and structural alignments of SCOP families, SCOPPI presents a comprehensive geometrical classification of domain interfaces. Various interface characteristics such as number, type and position of interacting amino acids, conservation, interface size, and permanent or transient nature of the interaction are further provided. Proteins in SCOPPI are annotated with Gene Ontology terms, and the ontology can be used to quickly browse SCOPPI. Screenshots are available for every interface and its participating domains. Here, we describe contents and features of the web-based user interface as well as the underlying methods used to generate SCOPPI's data. In addition, we present a number of examples where SCOPPI becomes a useful tool to analyze viral mimicry of human interface binding sites, gene fusion events, conservation of interface residues and diversity of interface localizations. SCOPPI is available at

The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry

A systematic classification of protein–protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. Here, we present a classification of domain interfaces according to their geometry. Our new algorithm uses a hybrid approach of both sequential and structural features. The accuracy is evaluated on a hand-curated dataset of 416 interfaces. Our hybrid procedure achieves 83% precision and 95% recall, which improves the earlier sequence-based method by 5% on both terms. We classify virtually all domain interfaces of known structure, which results in nearly 6,000 distinct types of interfaces. In 40% of the cases, the interacting domain families associate in multiple orientations, suggesting that all the possible binding orientations need to be explored for modelling multidomain proteins and protein complexes. In general, hub proteins are shown to use distinct surface regions (multiple faces) for interactions with different partners. Our classification provides a convenient framework to query genuine gene fusion, which conserves binding orientation in both fused and separate forms. The result suggests that the binding orientations are not conserved in at least one-third of the gene fusion cases detected by a conventional sequence similarity search. We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners. The taxonomic distribution of interface types suggests that ancient interfaces common to the three major kingdoms of life are enriched by symmetric homodimers. The classification results are online at http://www.scoppi.org

Исследование изотопного эффекта процесса кристаллизации из водного раствора в магнитном поле

Выпускная квалификационная работа проводилась с целью экспериментального исследования изменения изотопного эффекта процесса кристаллизации из водного раствора во внешнем постоянном магнитном поле. Для проведения исследований использовали насыщенный раствор NaCl. Раствор заливали в колбы Бунзена, из которых откачивался воздух с помощью вакуумного насоса. На одну из колб действовали постоянным магнитным полем. Кристаллы отбирали, высушивали и проводили рентгенодифракционный анализ.Final qualifying work was carried out with the aim experimental researches of change of isotopic effect of the process of crystallization from the aqueous solution in an external constant magnetic field. A saturated solution of NaCl was prepared for the studies. The solution was poured his flask Bunsen, of which the suction air using a vacuum pump. One of the flasks operated permanent magnet. The crystals were selected, dried and gave to x-ray diffraction analysis

MeMotif: a database of linear motifs in α-helical transmembrane proteins

Membrane proteins are important for many processes in the cell and used as main drug targets. The increasing number of high-resolution structures available makes for the first time a characterization of local structural and functional motifs in α-helical transmembrane proteins possible. MeMotif (http://projects.biotec.tu-dresden.de/memotif) is a database and wiki which collects more than 2000 known and novel computationally predicted linear motifs in α-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional features and editable. Motifs contained in MeMotif can be used in different biological applications, from the identification of biochemically important functional residues which are candidates for mutagenesis experiments to the improvement of tools for transmembrane protein modeling

Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing.

To better understand and characterize chromosomal structural variation during breast cancer progression, we enumerated chromosomal rearrangements for 11 patients by performing low-coverage whole-genome sequencing of 11 primary breast tumors and their 13 matched distant metastases. The tumor genomes harbored a median of 85 (range 18-404) rearrangements per tumor, with a median of 82 (26-310) in primaries compared to 87 (18-404) in distant metastases. Concordance between paired tumors from the same patient was high with a median of 89% of rearrangements shared (range 61-100%), whereas little overlap was found when comparing all possible pairings of tumors from different patients (median 3%). The tumors exhibited diverse genomic patterns of rearrangements: some carried events distributed throughout the genome while others had events mostly within densely clustered chromothripsis-like foci at a few chromosomal locations. Irrespectively, the patterns were highly conserved between the primary tumor and metastases from the same patient. Rearrangements occurred more frequently in genic areas than expected by chance and among the genes affected there was significant enrichment for cancer-associated genes including disruption of TP53, RB1, PTEN, and ESR1, likely contributing to tumor development. Our findings are most consistent with chromosomal rearrangements being early events in breast cancer progression that remain stable during the development from primary tumor to distant metastasis