@misc{5564, abstract = {Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication.}, author = {Steinrück, Magdalena and Guet, Calin C}, publisher = {Institute of Science and Technology Austria}, title = {{Fastq files for "Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection"}}, doi = {10.15479/AT:ISTA:65}, year = {2017}, } @misc{5568, abstract = {Includes source codes, test cases, and example data used in the thesis Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)}, author = {Hahn, David}, keywords = {Boundary elements, brittle fracture, computer graphics, fracture simulation}, publisher = {Institute of Science and Technology Austria}, title = {{Source codes: Brittle fracture simulation with boundary elements for computer graphics}}, doi = {10.15479/AT:ISTA:73}, year = {2017}, } @misc{7163, abstract = {The de novo genome assemblies generated for this study, and the associated metadata.}, author = {Fraisse, Christelle}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary Files for "The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W"}}, doi = {10.15479/AT:ISTA:7163}, year = {2017}, } @misc{5570, abstract = {Matlab script to calculate the forward migration indexes (/) from TrackMate spot-statistics files.}, author = {Hauschild, Robert}, keywords = {Cell migration, tracking, forward migration index, FMI}, publisher = {Institute of Science and Technology Austria}, title = {{Forward migration indexes}}, doi = {10.15479/AT:ISTA:75}, year = {2017}, } @misc{5567, abstract = {Immunological synapse DC-Tcells}, author = {Leithner, Alexander F}, keywords = {Immunological synapse}, publisher = {Institute of Science and Technology Austria}, title = {{Immunological synapse DC-Tcells}}, doi = {10.15479/AT:ISTA:71}, year = {2017}, } @misc{5560, abstract = {This repository contains the data collected for the manuscript "Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity". The data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication. Data is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic "mother machine" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication.}, author = {Bergmiller, Tobias and Andersson, Anna M and Tomasek, Kathrin and Balleza, Enrique and Kiviet, Daniel and Hauschild, Robert and Tkacik, Gasper and Guet, Calin C}, keywords = {single cell microscopy, mother machine microfluidic device, AcrAB-TolC pump, multi-drug efflux, Escherichia coli}, publisher = {Institute of Science and Technology Austria}, title = {{Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity}}, doi = {10.15479/AT:ISTA:53}, year = {2017}, } @misc{5571, abstract = {This folder contains all the data used in each of the main figures of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures. }, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Data for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}}, doi = {10.15479/AT:ISTA:78}, year = {2017}, } @misc{5559, abstract = {Strong amplifiers of natural selection}, author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak , Martin}, keywords = {natural selection}, publisher = {Institute of Science and Technology Austria}, title = {{Strong amplifiers of natural selection}}, doi = {10.15479/AT:ISTA:51}, year = {2017}, } @misc{5572, abstract = {Code described in the Supplementary Methods of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.)}, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Code for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}}, doi = {10.15479/AT:ISTA:79 }, year = {2017}, } @misc{5565, abstract = {One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. The Video is licensed under a CC BY NC ND license. }, author = {Von Wangenheim, Daniel and Hauschild, Robert and Friml, Jirí}, publisher = {Institute of Science and Technology Austria}, title = {{Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel}}, doi = {10.15479/AT:ISTA:66}, year = {2017}, } @misc{5566, abstract = {Current minimal version of TipTracker}, author = {Hauschild, Robert}, keywords = {tool, tracking, confocal microscopy}, publisher = {Institute of Science and Technology Austria}, title = {{Live tracking of moving samples in confocal microscopy for vertically grown roots}}, doi = {10.15479/AT:ISTA:69}, year = {2017}, } @misc{5550, abstract = {We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny. For full details of the methods see: Ellis TJ and Field DL "Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)}, author = {Ellis, Thomas and Field, David}, publisher = {Institute of Science and Technology Austria}, title = {{Flower colour data and phylogeny (NEXUS) files}}, doi = {10.15479/AT:ISTA:34}, year = {2016}, } @misc{5555, abstract = {This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.}, author = {Hauschild, Robert}, keywords = {cell migration, wide field microscopy, FIJI}, publisher = {Institute of Science and Technology Austria}, title = {{Fiji script to determine average speed and direction of migration of cells}}, doi = {10.15479/AT:ISTA:44}, year = {2016}, } @misc{5557, abstract = {Small synthetic discrete tomography problems. Sizes are 32x32, 64z64 and 256x256. Projection angles are 2, 4, and 6. Number of labels are 3 and 5.}, author = {Swoboda, Paul}, keywords = {discrete tomography}, publisher = {Institute of Science and Technology Austria}, title = {{Synthetic discrete tomography problems}}, doi = {10.15479/AT:ISTA:46}, year = {2016}, } @misc{5553, abstract = {Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016). Tissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset. Other data were retreived from an online database of this population at www.antspec.org.}, author = {Field, David and Ellis, Thomas}, keywords = {paternity assignment, pedigree, matting patterns, assortative mating, Antirrhinum majus, frequency-dependent selection, plant-pollinator interaction}, publisher = {Institute of Science and Technology Austria}, title = {{Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012}}, doi = {10.15479/AT:ISTA:37}, year = {2016}, } @misc{5551, abstract = {Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016. We placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6. After 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.}, author = {Ellis, Thomas}, publisher = {Institute of Science and Technology Austria}, title = {{Data on pollinator observations and offpsring phenotypes}}, doi = {10.15479/AT:ISTA:35}, year = {2016}, } @misc{5552, abstract = {Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016). Snapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012. Also included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.}, author = {Ellis, Thomas}, publisher = {Institute of Science and Technology Austria}, title = {{Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.}}, doi = {10.15479/AT:ISTA:36}, year = {2016}, } @misc{5554, abstract = {The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding. Magdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.}, author = {Tugrul, Murat}, keywords = {RNAP binding, de novo promoter evolution, lac promoter}, publisher = {Institute of Science and Technology Austria}, title = {{Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase}}, doi = {10.15479/AT:ISTA:43}, year = {2016}, } @misc{5558, abstract = {PhD thesis LaTeX source code}, author = {Bojsen-Hansen, Morten}, publisher = {Institute of Science and Technology Austria}, title = {{Tracking, Correcting and Absorbing Water Surface Waves}}, doi = {10.15479/AT:ISTA:48}, year = {2016}, } @misc{5556, abstract = {MATLAB code and processed datasets available for reproducing the results in: Lukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast. *equal contributions}, author = {Lukacisin, Martin and Landon, Matthieu and Jajoo, Rishi}, keywords = {transcription, pausing, backtracking, polymerase, RNA, NET-seq, nucleosome, basepairing}, publisher = {Institute of Science and Technology Austria}, title = {{MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'}}, doi = {10.15479/AT:ISTA:45}, year = {2016}, } @misc{5549, abstract = {This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. We extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees. The archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library. To execute the program, please have a look at the README.txt, which provides instructions and further information on the archive. The archive contains scripts that (if run often enough) reproduces the data presented in the publication.}, author = {Fellner, Andreas}, keywords = {Markov Decision Process, Decision Tree, Probabilistic Verification, Counterexample Explanation}, publisher = {Institute of Science and Technology Austria}, title = {{Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes}}, doi = {10.15479/AT:ISTA:28}, year = {2015}, }