--- _id: '1660' abstract: - lang: eng text: We study the pattern frequency vector for runs in probabilistic Vector Addition Systems with States (pVASS). Intuitively, each configuration of a given pVASS is assigned one of finitely many patterns, and every run can thus be seen as an infinite sequence of these patterns. The pattern frequency vector assigns to each run the limit of pattern frequencies computed for longer and longer prefixes of the run. If the limit does not exist, then the vector is undefined. We show that for one-counter pVASS, the pattern frequency vector is defined and takes one of finitely many values for almost all runs. Further, these values and their associated probabilities can be approximated up to an arbitrarily small relative error in polynomial time. For stable two-counter pVASS, we show the same result, but we do not provide any upper complexity bound. As a byproduct of our study, we discover counterexamples falsifying some classical results about stochastic Petri nets published in the 80s. alternative_title: - LICS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Stefan full_name: Kiefer, Stefan last_name: Kiefer - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Brázdil T, Kiefer S, Kučera A, Novotný P. Long-run average behaviour of probabilistic vector addition systems. In: IEEE; 2015:44-55. doi:10.1109/LICS.2015.15' apa: 'Brázdil, T., Kiefer, S., Kučera, A., & Novotný, P. (2015). Long-run average behaviour of probabilistic vector addition systems (pp. 44–55). Presented at the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.15' chicago: Brázdil, Tomáš, Stefan Kiefer, Antonín Kučera, and Petr Novotný. “Long-Run Average Behaviour of Probabilistic Vector Addition Systems,” 44–55. IEEE, 2015. https://doi.org/10.1109/LICS.2015.15. ieee: 'T. Brázdil, S. Kiefer, A. Kučera, and P. Novotný, “Long-run average behaviour of probabilistic vector addition systems,” presented at the LICS: Logic in Computer Science, Kyoto, Japan, 2015, pp. 44–55.' ista: 'Brázdil T, Kiefer S, Kučera A, Novotný P. 2015. Long-run average behaviour of probabilistic vector addition systems. LICS: Logic in Computer Science, LICS, , 44–55.' mla: Brázdil, Tomáš, et al. Long-Run Average Behaviour of Probabilistic Vector Addition Systems. IEEE, 2015, pp. 44–55, doi:10.1109/LICS.2015.15. short: T. Brázdil, S. Kiefer, A. Kučera, P. Novotný, in:, IEEE, 2015, pp. 44–55. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:19Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:52:20Z day: '01' department: - _id: KrCh doi: 10.1109/LICS.2015.15 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1505.02655 month: '07' oa: 1 oa_version: Preprint page: 44 - 55 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: IEEE publist_id: '5490' quality_controlled: '1' scopus_import: 1 status: public title: Long-run average behaviour of probabilistic vector addition systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1665' abstract: - lang: eng text: Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome. article_processing_charge: No article_type: original author: - first_name: Dan full_name: Landau, Dan last_name: Landau - first_name: Eugen full_name: Tausch, Eugen last_name: Tausch - first_name: Amaro full_name: Taylor Weiner, Amaro last_name: Taylor Weiner - first_name: Chip full_name: Stewart, Chip last_name: Stewart - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Jasmin full_name: Bahlo, Jasmin last_name: Bahlo - first_name: Sandra full_name: Kluth, Sandra last_name: Kluth - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Michael full_name: Lawrence, Michael last_name: Lawrence - first_name: Sebastian full_name: Böttcher, Sebastian last_name: Böttcher - first_name: Scott full_name: Carter, Scott last_name: Carter - first_name: Kristian full_name: Cibulskis, Kristian last_name: Cibulskis - first_name: Daniel full_name: Mertens, Daniel last_name: Mertens - first_name: Carrie full_name: Sougnez, Carrie last_name: Sougnez - first_name: Mara full_name: Rosenberg, Mara last_name: Rosenberg - first_name: Julian full_name: Hess, Julian last_name: Hess - first_name: Jennifer full_name: Edelmann, Jennifer last_name: Edelmann - first_name: Sabrina full_name: Kless, Sabrina last_name: Kless - first_name: Michael full_name: Kneba, Michael last_name: Kneba - first_name: Matthias full_name: Ritgen, Matthias last_name: Ritgen - first_name: Anna full_name: Fink, Anna last_name: Fink - first_name: Kirsten full_name: Fischer, Kirsten last_name: Fischer - first_name: Stacey full_name: Gabriel, Stacey last_name: Gabriel - first_name: Eric full_name: Lander, Eric last_name: Lander - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Hartmut full_name: Döhner, Hartmut last_name: Döhner - first_name: Michael full_name: Hallek, Michael last_name: Hallek - first_name: Donna full_name: Neuberg, Donna last_name: Neuberg - first_name: Gad full_name: Getz, Gad last_name: Getz - first_name: Stephan full_name: Stilgenbauer, Stephan last_name: Stilgenbauer - first_name: Catherine full_name: Wu, Catherine last_name: Wu citation: ama: Landau D, Tausch E, Taylor Weiner A, et al. Mutations driving CLL and their evolution in progression and relapse. Nature. 2015;526(7574):525-530. doi:10.1038/nature15395 apa: Landau, D., Tausch, E., Taylor Weiner, A., Stewart, C., Reiter, J., Bahlo, J., … Wu, C. (2015). Mutations driving CLL and their evolution in progression and relapse. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15395 chicago: Landau, Dan, Eugen Tausch, Amaro Taylor Weiner, Chip Stewart, Johannes Reiter, Jasmin Bahlo, Sandra Kluth, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15395. ieee: D. Landau et al., “Mutations driving CLL and their evolution in progression and relapse,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 525–530, 2015. ista: Landau D, Tausch E, Taylor Weiner A, Stewart C, Reiter J, Bahlo J, Kluth S, Božić I, Lawrence M, Böttcher S, Carter S, Cibulskis K, Mertens D, Sougnez C, Rosenberg M, Hess J, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K, Gabriel S, Lander E, Nowak M, Döhner H, Hallek M, Neuberg D, Getz G, Stilgenbauer S, Wu C. 2015. Mutations driving CLL and their evolution in progression and relapse. Nature. 526(7574), 525–530. mla: Landau, Dan, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 525–30, doi:10.1038/nature15395. short: D. Landau, E. Tausch, A. Taylor Weiner, C. Stewart, J. Reiter, J. Bahlo, S. Kluth, I. Božić, M. Lawrence, S. Böttcher, S. Carter, K. Cibulskis, D. Mertens, C. Sougnez, M. Rosenberg, J. Hess, J. Edelmann, S. Kless, M. Kneba, M. Ritgen, A. Fink, K. Fischer, S. Gabriel, E. Lander, M. Nowak, H. Döhner, M. Hallek, D. Neuberg, G. Getz, S. Stilgenbauer, C. Wu, Nature 526 (2015) 525–530. date_created: 2018-12-11T11:53:21Z date_published: 2015-10-22T00:00:00Z date_updated: 2021-01-12T06:52:23Z day: '22' department: - _id: KrCh doi: 10.1038/nature15395 ec_funded: 1 external_id: pmid: - '26466571' intvolume: ' 526' issue: '7574' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815041/ month: '10' oa: 1 oa_version: Submitted Version page: 525 - 530 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5484' quality_controlled: '1' scopus_import: 1 status: public title: Mutations driving CLL and their evolution in progression and relapse type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 526 year: '2015' ... --- _id: '1663' abstract: - lang: eng text: CREB-binding protein (CBP) and p300 are transcriptional coactivators involved in numerous biological processes that affect cell growth, transformation, differentiation, and development. In this study, we provide evidence of the involvement of homeodomain-interacting protein kinase 2 (HIPK2) in the regulation of CBP activity. We show that HIPK2 interacts with and phosphorylates several regions of CBP. We demonstrate that serines 2361, 2363, 2371, 2376, and 2381 are responsible for the HIPK2-induced mobility shift of CBP C-terminal activation domain. Moreover, we show that HIPK2 strongly potentiates the transcriptional activity of CBP. However, our data suggest that HIPK2 activates CBP mainly by counteracting the repressive action of cell cycle regulatory domain 1 (CRD1), located between amino acids 977 and 1076, independently of CBP phosphorylation. Our findings thus highlight a complex regulation of CBP activity by HIPK2, which might be relevant for the control of specific sets of target genes involved in cellular proliferation, differentiation and apoptosis. author: - first_name: Krisztián full_name: Kovács, Krisztián id: 2AB5821E-F248-11E8-B48F-1D18A9856A87 last_name: Kovács - first_name: Myriam full_name: Steinmann, Myriam last_name: Steinmann - first_name: Olivier full_name: Halfon, Olivier last_name: Halfon - first_name: Pierre full_name: Magistretti, Pierre last_name: Magistretti - first_name: Jean full_name: Cardinaux, Jean last_name: Cardinaux citation: ama: Kovács K, Steinmann M, Halfon O, Magistretti P, Cardinaux J. Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. 2015;27(11):2252-2260. doi:10.1016/j.cellsig.2015.08.001 apa: Kovács, K., Steinmann, M., Halfon, O., Magistretti, P., & Cardinaux, J. (2015). Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. Elsevier. https://doi.org/10.1016/j.cellsig.2015.08.001 chicago: Kovács, Krisztián, Myriam Steinmann, Olivier Halfon, Pierre Magistretti, and Jean Cardinaux. “Complex Regulation of CREB-Binding Protein by Homeodomain-Interacting Protein Kinase 2.” Cellular Signalling. Elsevier, 2015. https://doi.org/10.1016/j.cellsig.2015.08.001. ieee: K. Kovács, M. Steinmann, O. Halfon, P. Magistretti, and J. Cardinaux, “Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2,” Cellular Signalling, vol. 27, no. 11. Elsevier, pp. 2252–2260, 2015. ista: Kovács K, Steinmann M, Halfon O, Magistretti P, Cardinaux J. 2015. Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. 27(11), 2252–2260. mla: Kovács, Krisztián, et al. “Complex Regulation of CREB-Binding Protein by Homeodomain-Interacting Protein Kinase 2.” Cellular Signalling, vol. 27, no. 11, Elsevier, 2015, pp. 2252–60, doi:10.1016/j.cellsig.2015.08.001. short: K. Kovács, M. Steinmann, O. Halfon, P. Magistretti, J. Cardinaux, Cellular Signalling 27 (2015) 2252–2260. date_created: 2018-12-11T11:53:20Z date_published: 2015-11-01T00:00:00Z date_updated: 2021-01-12T06:52:22Z day: '01' ddc: - '570' department: - _id: JoCs doi: 10.1016/j.cellsig.2015.08.001 ec_funded: 1 file: - access_level: local checksum: 4ee690b6444b7a43523237f0941457d1 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:03Z date_updated: 2020-07-14T12:45:10Z file_id: '5321' file_name: IST-2016-578-v1+1_CLS-D-15-00072R1_.pdf file_size: 1735337 relation: main_file file_date_updated: 2020-07-14T12:45:10Z has_accepted_license: '1' intvolume: ' 27' issue: '11' language: - iso: eng month: '11' oa_version: Published Version page: 2252 - 2260 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Cellular Signalling publication_status: published publisher: Elsevier publist_id: '5487' pubrep_id: '578' quality_controlled: '1' scopus_import: 1 status: public title: Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2 tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2015' ... --- _id: '1667' abstract: - lang: eng text: We consider parametric version of fixed-delay continuoustime Markov chains (or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay transitions are specified by parameters, rather than concrete values. Our goal is to synthesize values of these parameters that, for a given cost function, minimise expected total cost incurred before reaching a given set of target states. We show that under mild assumptions, optimal values of parameters can be effectively approximated using translation to a Markov decision process (MDP) whose actions correspond to discretized values of these parameters. To this end we identify and overcome several interesting phenomena arising in systems with fixed delays. acknowledgement: The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n∘ [291734]. This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the Czech Science Foundation, grant No. 15-17564S, and by the CAS/SAFEA International Partnership Program for Creative Research Teams. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: L'Uboš full_name: Korenčiak, L'Uboš last_name: Korenčiak - first_name: Jan full_name: Krčál, Jan last_name: Krčál - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny - first_name: Vojtěch full_name: Řehák, Vojtěch last_name: Řehák citation: ama: Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 2015;9259:141-159. doi:10.1007/978-3-319-22264-6_10 apa: 'Brázdil, T., Korenčiak, L., Krčál, J., Novotný, P., & Řehák, V. (2015). Optimizing performance of continuous-time stochastic systems using timeout synthesis. Presented at the QEST: Quantitative Evaluation of Systems, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-22264-6_10' chicago: Brázdil, Tomáš, L’Uboš Korenčiak, Jan Krčál, Petr Novotný, and Vojtěch Řehák. “Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22264-6_10. ieee: T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, and V. Řehák, “Optimizing performance of continuous-time stochastic systems using timeout synthesis,” vol. 9259. Springer, pp. 141–159, 2015. ista: Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. 2015. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 9259, 141–159. mla: Brázdil, Tomáš, et al. Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis. Vol. 9259, Springer, 2015, pp. 141–59, doi:10.1007/978-3-319-22264-6_10. short: T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, V. Řehák, 9259 (2015) 141–159. conference: end_date: 2015-09-03 location: Madrid, Spain name: 'QEST: Quantitative Evaluation of Systems' start_date: 2015-09-01 date_created: 2018-12-11T11:53:22Z date_published: 2015-08-22T00:00:00Z date_updated: 2021-01-12T06:52:24Z day: '22' department: - _id: KrCh doi: 10.1007/978-3-319-22264-6_10 ec_funded: 1 intvolume: ' 9259' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.4777 month: '08' oa: 1 oa_version: Preprint page: 141 - 159 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5482' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Optimizing performance of continuous-time stochastic systems using timeout synthesis type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9259 year: '2015' ... --- _id: '1664' abstract: - lang: eng text: Over a century of research into the origin of turbulence in wall-bounded shear flows has resulted in a puzzling picture in which turbulence appears in a variety of different states competing with laminar background flow. At moderate flow speeds, turbulence is confined to localized patches; it is only at higher speeds that the entire flow becomes turbulent. The origin of the different states encountered during this transition, the front dynamics of the turbulent regions and the transformation to full turbulence have yet to be explained. By combining experiments, theory and computer simulations, here we uncover a bifurcation scenario that explains the transformation to fully turbulent pipe flow and describe the front dynamics of the different states encountered in the process. Key to resolving this problem is the interpretation of the flow as a bistable system with nonlinear propagation (advection) of turbulent fronts. These findings bridge the gap between our understanding of the onset of turbulence and fully turbulent flows. acknowledgement: We acknowledge the Deutsche Forschungsgemeinschaft (Project No. FOR 1182), and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. B.S. acknowledges financial support from the Chinese State Scholarship Fund under grant number 2010629145. B.S. acknowledges support from the International Max Planck Research School for the Physics of Biological and Complex Systems and the Göttingen Graduate School for Neurosciences and Molecular Biosciences. We acknowledge computing resources from GWDG (Gesellschaft für wissenschaftliche Datenverarbeitung Göttingen) and the Jülich Supercomputing Centre (grant HGU16) where the simulations were performed. author: - first_name: Dwight full_name: Barkley, Dwight last_name: Barkley - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Mukund full_name: Vasudevan, Mukund id: 3C5A959A-F248-11E8-B48F-1D18A9856A87 last_name: Vasudevan - first_name: Grégoire M full_name: Lemoult, Grégoire M id: 4787FE80-F248-11E8-B48F-1D18A9856A87 last_name: Lemoult - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. The rise of fully turbulent flow. Nature. 2015;526(7574):550-553. doi:10.1038/nature15701 apa: Barkley, D., Song, B., Vasudevan, M., Lemoult, G. M., Avila, M., & Hof, B. (2015). The rise of fully turbulent flow. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15701 chicago: Barkley, Dwight, Baofang Song, Mukund Vasudevan, Grégoire M Lemoult, Marc Avila, and Björn Hof. “The Rise of Fully Turbulent Flow.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15701. ieee: D. Barkley, B. Song, M. Vasudevan, G. M. Lemoult, M. Avila, and B. Hof, “The rise of fully turbulent flow,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 550–553, 2015. ista: Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. 2015. The rise of fully turbulent flow. Nature. 526(7574), 550–553. mla: Barkley, Dwight, et al. “The Rise of Fully Turbulent Flow.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 550–53, doi:10.1038/nature15701. short: D. Barkley, B. Song, M. Vasudevan, G.M. Lemoult, M. Avila, B. Hof, Nature 526 (2015) 550–553. date_created: 2018-12-11T11:53:20Z date_published: 2015-10-21T00:00:00Z date_updated: 2021-01-12T06:52:22Z day: '21' department: - _id: BjHo doi: 10.1038/nature15701 ec_funded: 1 intvolume: ' 526' issue: '7574' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1510.09143 month: '10' oa: 1 oa_version: Preprint page: 550 - 553 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5485' quality_controlled: '1' scopus_import: 1 status: public title: The rise of fully turbulent flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 526 year: '2015' ...