Institute of Science and Technology Austria (IST Austria)

A consistent phylogenetic backbone for the fungi
I. Ebersberger, R. De Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, A. Von Haeseler, Molecular Biology and Evolution 29 (2012) 1319–1334.

Weak multipliers for generalized van der Corput sequences
F. Pausinger, Journal de Theorie Des Nombres Des Bordeaux 24 (2012) 729–749.

Generalized sequential tree-reweighted message passing
V. Kolmogorov, T. Schoenemann, ArXiv (2012).

Towards minimizing k-submodular functions
A. Huber, V. Kolmogorov, in:, Springer, 2012, pp. 451–462.

Geometry of maximum likelihood estimation in Gaussian graphical models
C. Uhler, Annals of Statistics 40 (2012) 238–261.

A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo
A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, P.M. Jonas, Biophysical Journal 103 (2012) 1429–1439.

The dynamics of male-male competition in Cardiocondyla obscurior ants
S. Cremer, M. Suefuji, A. Schrempf, J. Heinze, BMC Ecology 12 (2012).

Hierarchical ordering of reticular networks
Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012).

Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome
M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).

Explicit mesh surfaces for particle based fluids
J. Yu, C.J. Wojtan, G. Turk, C. Yap, in:, Computer Graphics Forum, Blackwell Publishing, 2012, pp. 815–824.

Patterns of evolutionary conservation of essential genes correlate with their compensability
T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).

Amino acid fermentation at the origin of the genetic code
H. Vladar, Biology Direct 7 (2012).

Optimizing information flow in small genetic networks. III. A self-interacting gene
G. Tkacik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 85 (2012).

A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil
G. Rieckh, W. Kreuzer, H. Waubke, P. Balazs, Engineering Analysis with Boundary Elements 36 (2012) 960–967.

Hardness preserving constructions of pseudorandom functions
A. Jain, K.Z. Pietrzak, A. Tentes, in:, Springer, 2012, pp. 369–382.

Lossy functions do not amplify well
K.Z. Pietrzak, A. Rosen, G. Segev, in:, Springer, 2012, pp. 458–475.

Cryptography from learning parity with noise
K.Z. Pietrzak, in:, Springer, 2012, pp. 99–114.

Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components
C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41.

Zwischen Technologie und Information
P. Danowski, Büchereiperspektiven 1/2012 (2012) 11.

Approximate determinization of quantitative automata
U. Boker, T.A. Henzinger, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 362–373.

Interface Simulation Distances
P. Cerny, M. Chmelik, T.A. Henzinger, A. Radhakrishna, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, 2012, pp. 29–42.

Independent implementability of viewpoints
T.A. Henzinger, D. Nickovic, in:, Conference Proceedings Monterey Workshop 2012, Springer, 2012, pp. 380–395.

Equivalence of games with probabilistic uncertainty and partial observation games
K. Chatterjee, M. Chmelik, R. Majumdar, in:, Springer, 2012, pp. 385–399.

A survey of partial-observation stochastic parity games
K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 268–284.

Efficient controller synthesis for consumption games with multiple resource types
B. Brázdil, K. Chatterjee, A. Kučera, P. Novotny, in:, Springer, 2012, pp. 23–38.

Games and Markov decision processes with mean payoff parity and energy parity objectives
K. Chatterjee, L. Doyen, in:, Springer, 2012, pp. 37–46.

A Myhill Nerode theorem for automata with advice
A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012, Open Publishing Association, 2012, pp. 238–246.

Elementary solutions of the Bernstein problem on two intervals
F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012) 63–78.

Persistent homology computation with a twist
C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200.

The role of chemotactic gradients in dendritic cell migration
K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, IST Austria, 2011.

What can we learn from single molecule trajectories?
V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide Science 12 (2011) 714–724.

Propagation models for computing biochemical reaction networks
T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.

Static scheduling in clouds
T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011, pp. 1–6.

Biology as reactivity
J. Fisher, D. Harel, T.A. Henzinger, Communications of the ACM 54 (2011) 72–82.

Learning multi-view neighborhood preserving projections
N. Quadrianto, C. Lampert, in:, Omnipress, 2011, pp. 425–432.

What’s decidable about weighted automata
S. Almagor, U. Boker, O. Kupferman, in:, T. Bultan, P.-A. Hsiung (Eds.), Springer, 2011, pp. 482–491.

The complexity of request-response games
K. Chatterjee, T.A. Henzinger, F. Horn, in:, A.-H. Dediu, S. Inenaga, C. Martín-Vide (Eds.), Springer, 2011, pp. 227–237.

Invited Lectures ‐ Symposia Area
C.-P.J. Heisenberg, FEBS Journal 278 (2011) 24–24.

Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion
L.V. Ugelvig, P. Nielsen, J. Boomsma, D. Nash, BMC Evolutionary Biology 11 (2011).

The relation between reproductive value and genetic contribution
N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.

Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas
F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological Journal of the Linnean Society 104 (2011) 407–418.

Resolution of gene regulatory conflicts caused by combinations of antibiotics
M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.

The multiple faces of RIM
A. Pernia-Andrade, P.M. Jonas, Neuron 69 (2011) 185–187.

Cells on the move in Philadelphia
M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 724.

Computing elevation maxima by searching the Gauss sphere
B. Wang, H. Edelsbrunner, D. Morozov, Journal of Experimental Algorithmics 16 (2011) 1–13.

Approximation of event probabilities in noisy cellular processes
F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, Theoretical Computer Science 412 (2011) 2128–2141.

Setting the clock for recirculating lymphocytes
A. Eichner, M.K. Sixt, Science Signaling 4 (2011).

Erratum: Species' range: Adaptation in space and time (American Naturalist 174 (E186 E204))
J. Polechova, N.H. Barton, G. Marion, American Naturalist 177 (2011) 546–547.

Bounded rationality in concurrent parity games
K. Chatterjee, ArXiv (2011) 1–51.

Decidable problems for probabilistic automata on infinite words
K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on Infinite Words, IST Austria, 2011.

Energy and mean-payoff parity Markov Decision Processes
K. Chatterjee, L. Doyen, in:, Springer, 2011, pp. 206–218.

Perceptual global illumination cancellation in complex projection environments
Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268.

Efficient computation of persistent homology for cubical data
H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011, pp. 91–106.

Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens
M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).

A general method for calculating likelihoods under the coalescent process
K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.

Magnifying lens abstraction for stochastic games with discounted and long-run average objectives
K. Chatterjee, L. De Alfaro, R. Pritam, ArXiv (2011).

Maximum margin multi-label structured prediction
C. Lampert, in:, Neural Information Processing Systems, 2011.

Maximum margin multi label structured prediction
C. Lampert, Maximum Margin Multi Label Structured Prediction, Neural Information Processing Systems, 2011.

Letter from the new editors-in-chief
H. Edelsbrunner, J. Pach, G. Ziegler, Discrete & Computational Geometry 45 (2011) 1–2.

Scheduling large jobs by abstraction refinement
T.A. Henzinger, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2011, pp. 329–342.

Inclusive fitness theory and eusociality
P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre, M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie, T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M. Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn, B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi, R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen, J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J. Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R. Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze, H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers, H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer, S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock, T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo, G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H. Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J. Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez, L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji, S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J. Zeh, A. Zink, Nature 471 (2011) E1–E4.

QUASY: quantitative synthesis tool
K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, in:, Springer, 2011, pp. 267–271.

Quantifying transversality by measuring the robustness of intersections
H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 345–361.

Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.
A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological Journal of the Linnean Society 102 (2011) 527–539.

Natural images from the birthplace of the human eye
G. Tkacik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011).

Semi supervised kernel canonical correlation analysis with application to human fMRI
M. Blaschko, J. Shelton, A. Bartels, C. Lampert, A. Gretton, Pattern Recognition Letters 32 (2011) 1572–1583.

The contribution of statistical physics to evolutionary biology
H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.

Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube
P. Stockinger, C.-P.J. Heisenberg, J.-L. Maître, Development 138 (2011) 4673–4683.

In vitro analysis of chemotactic leukocyte migration in 3D environments
M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 149–165.

Timed parity games: Complexity and robustness
K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science 7 (2011).

Verification of STM on relaxed memory models
R. Guerraoui, T.A. Henzinger, V. Singh, Formal Methods in System Design 39 (2011) 297–331.

Bounded rationality in concurrent parity games
K. Chatterjee, Bounded Rationality in Concurrent Parity Games, IST Austria, 2011.

Noise underlies switching behavior of the bacterial flagellum
H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.

Two views on multiple mean payoff objectives in Markov Decision Processes
T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, in:, IEEE, 2011.

A theory of synchronous relational interfaces
S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, ACM Transactions on Programming Languages and Systems (TOPLAS) 33 (2011).

Solving recursion-free Horn clauses over LI+UIF
A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203.

Determinizing discounted-sum automata
U. Boker, T.A. Henzinger, in:, Springer, 2011, pp. 82–96.

Temporal specifications with accumulative values
U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, Temporal Specifications with Accumulative Values, IST Austria, 2011.

Alpha shapes - a survey
H. Edelsbrunner, in:, Tessellations in the Sciences, Springer, 2011.

Root refinement for real polynomials
M. Kerber, M. Sagraloff, in:, Springer, 2011, pp. 209–216.

Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web
R. Van De Weygaert, G. Vegter, H. Edelsbrunner, B. Jones, P. Pranav, C. Park, W. Hellwing, B. Eldering, N. Kruithof, P. Bos, J. Hidding, J. Feldbrugge, E. Ten Have, M. Van Engelen, M. Caroli, M. Teillaud, in:, M. Gavrilova, K. Tan, M. Mostafavi (Eds.), Transactions on Computational Science XIV, Springer, 2011, pp. 60–101.

A generic algebraic kernel for non linear geometric applications
E. Berberich, M. Hemmer, M. Kerber, in:, ACM, 2011, pp. 179–186.

Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description
F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 485–492.

Cell sorting in development
G. Krens, C.-P.J. Heisenberg, in:, M. Labouesse (Ed.), Current Topics in Developmental Biology, Elsevier, 2011, pp. 189–213.

Covering and packing with spheres by diagonal distortion in R^n
H. Edelsbrunner, M. Kerber, in:, C. Calude, G. Rozenberg, A. Salomaa (Eds.), Rainbow of Computer Science, Springer, 2011, pp. 20–35.

Interstitial locomotion of leukocytes
M.K. Sixt, Immunology Letters 138 (2011) 32–34.

In vivo analysis of uropod function during physiological T cell trafficking
S. Soriano, M. Hons, K. Schumann, V. Kumar, T. Dennier, R. Lyck, M.K. Sixt, J. Stein, Journal of Immunology 187 (2011) 2356–2364.

The role of adhesion energy in controlling cell-cell contacts
J.-L. Maître, C.-P.J. Heisenberg, Current Opinion in Cell Biology 23 (2011) 508–514.

Modern ionotropic glutamate receptor with a K+ selectivity signature sequence
H.L. Janovjak, G. Sandoz, E. Isacoff, Nature Communications 2 (2011) 1–6.

Oct4 kinetics predict cell lineage patterning in the early mammalian embryo
N. Plachta, M.T. Bollenbach, S. Pease, S. Fraser, P. Pantazis, Nature Cell Biology 13 (2011) 117–123.

Measuring the complete force field of an optical trap
M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, S. Grill, Optics Letters 36 (2011) 1260–1262.

Persistent intersection homology
P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011) 305–336.

Mapping Mendelian traits in asexual progeny using changes in marker allele frequency
S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.

CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells
D. Schraivogel, L. Weinmann, D. Beier, G. Tabatabai, A. Eichner, J. Zhu, M. Anton, M.K. Sixt, M. Weller, C. Beier, G. Meister, EMBO Journal 30 (2011) 4309–4322.

Enforcing topological constraints in random field image segmentation
C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random Field Image Segmentation, IST Austria, 2011.

An efficient decision procedure for imperative tree data structures
T. Wies, M. Muñiz, V. Kuncak, in:, Springer, 2011, pp. 476–491.

Partial-observation stochastic games: How to win when belief fails
K. Chatterjee, L. Doyen, Partial-Observation Stochastic Games: How to Win When Belief Fails, IST Austria, 2011.

Specification-centered robustness
R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–185.

Quantitative synthesis for concurrent programs
P. Cerny, K. Chatterjee, T.A. Henzinger, A. Radhakrishna, R. Singh, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 243–259.

From boolean to quantitative synthesis
P. Cerny, T.A. Henzinger, in:, ACM, 2011, pp. 149–154.