--- _id: '7159' abstract: - lang: eng text: 'Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a tremendous amount of generated, measured and recorded time-series data. Extracting temporal segments that encode patterns with useful information out of these huge amounts of data is an extremely difficult problem. We propose shape expressions as a declarative formalism for specifying, querying and extracting sophisticated temporal patterns from possibly noisy data. Shape expressions are regular expressions with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters as atomic predicates and additional constraints on these parameters. We equip shape expressions with a novel noisy semantics that combines regular expression matching semantics with statistical regression. We characterize essential properties of the formalism and propose an efficient approximate shape expression matching procedure. We demonstrate the wide applicability of this technique on two case studies. ' alternative_title: - LNCS article_processing_charge: No author: - first_name: Dejan full_name: Ničković, Dejan last_name: Ničković - first_name: Xin full_name: Qin, Xin last_name: Qin - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Cristinel full_name: Mateis, Cristinel last_name: Mateis - first_name: Jyotirmoy full_name: Deshmukh, Jyotirmoy last_name: Deshmukh citation: ama: 'Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: 19th International Conference on Runtime Verification. Vol 11757. Springer Nature; 2019:292-309. doi:10.1007/978-3-030-32079-9_17' apa: 'Ničković, D., Qin, X., Ferrere, T., Mateis, C., & Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In 19th International Conference on Runtime Verification (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-32079-9_17' chicago: Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In 19th International Conference on Runtime Verification, 11757:292–309. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-32079-9_17. ieee: D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in 19th International Conference on Runtime Verification, Porto, Portugal, 2019, vol. 11757, pp. 292–309. ista: 'Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.' mla: Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” 19th International Conference on Runtime Verification, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:10.1007/978-3-030-32079-9_17. short: D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309. conference: end_date: 2019-10-11 location: Porto, Portugal name: 'RV: Runtime Verification' start_date: 2019-10-08 date_created: 2019-12-09T08:47:55Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-09-06T11:24:10Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-030-32079-9_17 external_id: isi: - '000570006300017' intvolume: ' 11757' isi: 1 language: - iso: eng month: '10' oa_version: None page: 292-309 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering publication: 19th International Conference on Runtime Verification publication_identifier: isbn: - '9783030320782' - '9783030320799' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Shape expressions for specifying and extracting signal features type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11757 year: '2019' ... --- _id: '7183' abstract: - lang: eng text: 'A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2).' alternative_title: - LNCS article_processing_charge: No author: - first_name: Tomás full_name: Brázdil, Tomás last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Antonín full_name: Kucera, Antonín last_name: Kucera - first_name: Petr full_name: Novotný, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotný - first_name: Dominik full_name: Velan, Dominik last_name: Velan citation: ama: 'Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: International Symposium on Automated Technology for Verification and Analysis. Vol 11781. Springer Nature; 2019:462-478. doi:10.1007/978-3-030-31784-3_27' apa: 'Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In International Symposium on Automated Technology for Verification and Analysis (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27' chicago: Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In International Symposium on Automated Technology for Verification and Analysis, 11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27. ieee: T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in International Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478. ista: 'Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478.' mla: Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” International Symposium on Automated Technology for Verification and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27. short: T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478. conference: end_date: 2019-10-31 location: Taipei, Taiwan name: 'ATVA: Automated TEchnology for Verification and Analysis' start_date: 2019-10-28 date_created: 2019-12-15T23:00:44Z date_published: 2019-10-21T00:00:00Z date_updated: 2023-09-06T12:40:58Z day: '21' department: - _id: KrCh doi: 10.1007/978-3-030-31784-3_27 external_id: arxiv: - '1907.11010' isi: - '000723515700027' intvolume: ' 11781' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.11010 month: '10' oa: 1 oa_version: Preprint page: 462-478 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: International Symposium on Automated Technology for Verification and Analysis publication_identifier: eissn: - '16113349' isbn: - '9783030317836' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Deciding fast termination for probabilistic VASS with nondeterminism type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11781 year: '2019' ... --- _id: '7182' abstract: - lang: eng text: During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome. article_number: '1437' article_processing_charge: No article_type: original author: - first_name: André full_name: Alcântara, André last_name: Alcântara - first_name: Jason full_name: Bosch, Jason last_name: Bosch - first_name: Fahimeh full_name: Nazari, Fahimeh last_name: Nazari - first_name: Gesa full_name: Hoffmann, Gesa last_name: Hoffmann - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Simon full_name: Uhse, Simon last_name: Uhse - first_name: Martin A. full_name: Darino, Martin A. last_name: Darino - first_name: Toluwase full_name: Olukayode, Toluwase last_name: Olukayode - first_name: Daniel full_name: Reumann, Daniel last_name: Reumann - first_name: Laura full_name: Baggaley, Laura last_name: Baggaley - first_name: Armin full_name: Djamei, Armin last_name: Djamei citation: ama: Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437 apa: Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437 chicago: Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers, 2019. https://doi.org/10.3389/fpls.2019.01437. ieee: A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019. ista: Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437. mla: Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers, 2019, doi:10.3389/fpls.2019.01437. short: A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019). date_created: 2019-12-15T23:00:43Z date_published: 2019-11-14T00:00:00Z date_updated: 2023-09-06T14:33:46Z day: '14' ddc: - '580' department: - _id: JiFr doi: 10.3389/fpls.2019.01437 external_id: isi: - '000499821700001' pmid: - '31803201' file: - access_level: open_access checksum: 995aa838aec2064d93550de82b40bbd1 content_type: application/pdf creator: dernst date_created: 2019-12-16T07:58:43Z date_updated: 2020-07-14T12:47:52Z file_id: '7185' file_name: 2019_FrontiersPlant_Alcantara.pdf file_size: 1532505 relation: main_file file_date_updated: 2020-07-14T12:47:52Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Plant Science publication_identifier: eissn: - 1664462X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Systematic Y2H screening reveals extensive effector-complex formation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10 year: '2019' ... --- _id: '7180' abstract: - lang: eng text: Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation. article_number: '5516' article_processing_charge: No article_type: original author: - first_name: Katarzyna full_name: Retzer, Katarzyna last_name: Retzer - first_name: Maria full_name: Akhmanova, Maria id: 3425EC26-F248-11E8-B48F-1D18A9856A87 last_name: Akhmanova orcid: 0000-0003-1522-3162 - first_name: Nataliia full_name: Konstantinova, Nataliia last_name: Konstantinova - first_name: Kateřina full_name: Malínská, Kateřina last_name: Malínská - first_name: Johannes full_name: Leitner, Johannes last_name: Leitner - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig citation: ama: Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 2019;10. doi:10.1038/s41467-019-13543-1 apa: Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13543-1 chicago: Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1. ieee: K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516. mla: Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications, vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1. short: K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019). date_created: 2019-12-15T23:00:43Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-09-06T14:08:21Z day: '01' ddc: - '570' department: - _id: DaSi doi: 10.1038/s41467-019-13543-1 external_id: isi: - '000500508100001' pmid: - '31797871' file: - access_level: open_access checksum: 77e8720a8e0f3091b98159f85be40893 content_type: application/pdf creator: dernst date_created: 2019-12-16T07:37:50Z date_updated: 2020-07-14T12:47:52Z file_id: '7184' file_name: 2019_NatureComm_Retzer.pdf file_size: 5156533 relation: main_file file_date_updated: 2020-07-14T12:47:52Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 264CBBAC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02379 name: Modeling epithelial tissue mechanics during cell invasion publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10 year: '2019' ... --- _id: '7181' abstract: - lang: eng text: Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6. article_processing_charge: No article_type: original author: - first_name: Edgar full_name: Garriga, Edgar last_name: Garriga - first_name: Paolo full_name: Di Tommaso, Paolo last_name: Di Tommaso - first_name: Cedrik full_name: Magis, Cedrik last_name: Magis - first_name: Ionas full_name: Erb, Ionas last_name: Erb - first_name: Leila full_name: Mansouri, Leila last_name: Mansouri - first_name: Athanasios full_name: Baltzis, Athanasios last_name: Baltzis - first_name: Hafid full_name: Laayouni, Hafid last_name: Laayouni - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Evan full_name: Floden, Evan last_name: Floden - first_name: Cedric full_name: Notredame, Cedric last_name: Notredame citation: ama: Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6 apa: Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6 chicago: Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6. ieee: E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019. ista: Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470. mla: Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6. short: E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470. date_created: 2019-12-15T23:00:43Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-09-06T14:32:52Z day: '01' department: - _id: FyKo doi: 10.1038/s41587-019-0333-6 ec_funded: 1 external_id: isi: - '000500748900021' pmid: - '31792410' intvolume: ' 37' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/ month: '12' oa: 1 oa_version: Submitted Version page: 1466-1470 pmid: 1 project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication: Nature Biotechnology publication_identifier: eissn: - '15461696' issn: - '10870156' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13059' relation: research_data status: public scopus_import: '1' status: public title: Large multiple sequence alignments with a root-to-leaf regressive method type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2019' ... --- _id: '7202' abstract: - lang: eng text: The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas. article_number: e51381 article_processing_charge: No article_type: original author: - first_name: Alfredo full_name: Llorca, Alfredo last_name: Llorca - first_name: Gabriele full_name: Ciceri, Gabriele last_name: Ciceri - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Fong Kuan full_name: Wong, Fong Kuan last_name: Wong - first_name: Giovanni full_name: Diana, Giovanni last_name: Diana - first_name: Eleni full_name: Serafeimidou-Pouliou, Eleni last_name: Serafeimidou-Pouliou - first_name: Marian full_name: Fernández-Otero, Marian last_name: Fernández-Otero - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Sebastian J. full_name: Arnold, Sebastian J. last_name: Arnold - first_name: Martin full_name: Meyer, Martin last_name: Meyer - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Miguel full_name: Maravall, Miguel last_name: Maravall - first_name: Oscar full_name: Marín, Oscar last_name: Marín citation: ama: Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381 apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381 chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381. ieee: A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381. mla: Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381. short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019). date_created: 2019-12-22T23:00:42Z date_published: 2019-11-18T00:00:00Z date_updated: 2023-09-06T14:38:39Z day: '18' ddc: - '570' department: - _id: SiHi doi: 10.7554/eLife.51381 ec_funded: 1 external_id: isi: - '000508156800001' pmid: - '31736464' file: - access_level: open_access checksum: b460ecc33e1a68265e7adea775021f3a content_type: application/pdf creator: dernst date_created: 2020-02-18T15:19:26Z date_updated: 2020-07-14T12:47:53Z file_id: '7503' file_name: 2019_eLife_Llorca.pdf file_size: 2960543 relation: main_file file_date_updated: 2020-07-14T12:47:53Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development - _id: 264E56E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02416 name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2019' ... --- _id: '7179' abstract: - lang: eng text: Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity. article_processing_charge: No article_type: original author: - first_name: Lisa full_name: Klotz, Lisa last_name: Klotz - first_name: Olaf full_name: Wendler, Olaf last_name: Wendler - first_name: Renato full_name: Frischknecht, Renato last_name: Frischknecht - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Holger full_name: Schulze, Holger last_name: Schulze - first_name: Ralf full_name: Enz, Ralf last_name: Enz citation: ama: Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746. doi:10.1096/fj.201901543R apa: Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., & Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. FASEB. https://doi.org/10.1096/fj.201901543R chicago: Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R. ieee: L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019. ista: Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746. mla: Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R. short: L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746. date_created: 2019-12-15T23:00:42Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-09-06T14:34:36Z day: '01' ddc: - '571' - '599' department: - _id: RySh doi: 10.1096/fj.201901543R external_id: isi: - '000507466100054' pmid: - '31585509' file: - access_level: open_access checksum: 79e3b72481dc32489911121cf3b7d8d0 content_type: application/pdf creator: shigemot date_created: 2020-12-06T17:30:09Z date_updated: 2020-12-06T17:30:09Z file_id: '8922' file_name: Klotz et al 2019 EMBO Reports.pdf file_size: 4766789 relation: main_file success: 1 file_date_updated: 2020-12-06T17:30:09Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version page: 13734-13746 pmid: 1 publication: FASEB Journal publication_identifier: eissn: - '15306860' publication_status: published publisher: FASEB quality_controlled: '1' scopus_import: '1' status: public title: Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 33 year: '2019' ... --- _id: '7201' abstract: - lang: eng text: Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed "data parallel" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks. article_number: a11 article_processing_charge: No author: - first_name: Cedric full_name: Renggli, Cedric last_name: Renggli - first_name: Saleh full_name: Ashkboos, Saleh id: 0D0A9058-257B-11EA-A937-9341C3D8BC8A last_name: Ashkboos - first_name: Mehdi full_name: Aghagolzadeh, Mehdi last_name: Aghagolzadeh - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Torsten full_name: Hoefler, Torsten last_name: Hoefler citation: ama: 'Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222' apa: 'Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222' chicago: 'Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.' ieee: 'C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, Denver, CO, Unites States, 2019.' ista: 'Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11.' mla: 'Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.' short: C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019. conference: end_date: 2019-11-19 location: Denver, CO, Unites States name: 'SC: Conference for High Performance Computing, Networking, Storage and Analysis' start_date: 2019-11-17 date_created: 2019-12-22T23:00:42Z date_published: 2019-11-17T00:00:00Z date_updated: 2023-09-06T14:37:55Z day: '17' department: - _id: DaAl doi: 10.1145/3295500.3356222 ec_funded: 1 external_id: arxiv: - '1802.08021' isi: - '000545976800011' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.08021 month: '11' oa: 1 oa_version: Preprint project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: International Conference for High Performance Computing, Networking, Storage and Analysis, SC publication_identifier: eissn: - '21674337' isbn: - '9781450362290' issn: - '21674329' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: 'SparCML: High-performance sparse communication for machine learning' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '13067' abstract: - lang: eng text: Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females. article_processing_charge: No author: - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Zuzanna full_name: Zagrodzka, Zuzanna last_name: Zagrodzka - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger full_name: Butlin, Roger last_name: Butlin citation: ama: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK' apa: 'Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK' chicago: 'Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.' ieee: 'K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.' ista: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.' mla: 'Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.' short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019). date_created: 2023-05-23T16:36:27Z date_published: 2019-12-02T00:00:00Z date_updated: 2023-09-06T14:48:57Z day: '02' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.TB2RBNZWK license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.tb2rbnzwk month: '12' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '7205' relation: used_in_publication status: public status: public title: 'Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7214' abstract: - lang: eng text: "Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer." article_number: '641' article_processing_charge: No article_type: original author: - first_name: Sergey full_name: Aganezov, Sergey last_name: Aganezov - first_name: Ilya full_name: Zban, Ilya last_name: Zban - first_name: Vitalii full_name: Aksenov, Vitalii id: 2980135A-F248-11E8-B48F-1D18A9856A87 last_name: Aksenov - first_name: Nikita full_name: Alexeev, Nikita last_name: Alexeev - first_name: Michael C. full_name: Schatz, Michael C. last_name: Schatz citation: ama: Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4 apa: Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4 chicago: Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4. ieee: S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019. ista: Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641. mla: Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4. short: S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019). date_created: 2019-12-29T23:00:46Z date_published: 2019-12-17T00:00:00Z date_updated: 2023-09-06T14:51:06Z day: '17' ddc: - '570' department: - _id: DaAl doi: 10.1186/s12859-019-3208-4 external_id: isi: - '000511618800007' file: - access_level: open_access checksum: 7a30357efdcf8f66587ed495c0927724 content_type: application/pdf creator: dernst date_created: 2020-01-02T16:10:58Z date_updated: 2020-07-14T12:47:54Z file_id: '7221' file_name: 2019_BMCBioinfo_Aganezov.pdf file_size: 1917374 relation: main_file file_date_updated: 2020-07-14T12:47:54Z has_accepted_license: '1' intvolume: ' 20' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: BMC Bioinformatics publication_identifier: eissn: - '14712105' publication_status: published publisher: BMC quality_controlled: '1' scopus_import: '1' status: public title: Recovering rearranged cancer chromosomes from karyotype graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 20 year: '2019' ... --- _id: '7225' abstract: - lang: eng text: "This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications." article_number: '109' article_processing_charge: Yes article_type: review author: - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 citation: ama: Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering. 2019;6(4). doi:10.3390/bioengineering6040109 apa: Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109 chicago: Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109. ieee: J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019. ista: Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109. mla: Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109. short: J. Merrin, Bioengineering 6 (2019). date_created: 2020-01-05T23:00:45Z date_published: 2019-12-03T00:00:00Z date_updated: 2023-09-06T14:52:49Z day: '03' ddc: - '620' department: - _id: NanoFab doi: 10.3390/bioengineering6040109 external_id: isi: - '000505590000024' pmid: - '31816954' file: - access_level: open_access checksum: 80f1499e2a4caccdf3aa54b137fd99a0 content_type: application/pdf creator: dernst date_created: 2020-01-07T14:49:59Z date_updated: 2020-07-14T12:47:54Z file_id: '7243' file_name: 2019_Bioengineering_Merrin.pdf file_size: 2660780 relation: main_file file_date_updated: 2020-07-14T12:47:54Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Bioengineering publication_identifier: eissn: - '23065354' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Frontiers in microfluidics, a teaching resource review tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6 year: '2019' ... --- _id: '7228' abstract: - lang: eng text: "Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) and actor models, which share data via explicit communication. These models have been known for almost half a century, and have recently had started to gain significant traction among modern programming languages. The common abstraction for communication between several processes is the channel. Although channels are similar to producer-consumer data structures, they have different semantics and support additional operations, such as the select expression. Despite their growing popularity, most known implementations of channels use lock-based data structures and can be rather inefficient.\r\n\r\nIn this paper, we present the first efficient lock-free algorithm for implementing a communication channel for CSP programming. We provide implementations and experimental results in the Kotlin and Go programming languages. Our new algorithm outperforms existing implementations on many workloads, while providing non-blocking progress guarantee. Our design can serve as an example of how to construct general communication data structures for CSP and actor models. " alternative_title: - LNCS article_processing_charge: No author: - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Roman full_name: Elizarov, Roman last_name: Elizarov citation: ama: 'Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming via communicating sequential processes. In: 25th Anniversary of Euro-Par. Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23' apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels for programming via communicating sequential processes. In 25th Anniversary of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-29400-7_23' chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23. ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming via communicating sequential processes,” in 25th Anniversary of Euro-Par, Göttingen, Germany, 2019, vol. 11725, pp. 317–333. ista: 'Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.' mla: Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23. short: N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333. conference: end_date: 2019-08-30 location: Göttingen, Germany name: 'Euro-Par: European Conference on Parallel Processing' start_date: 2019-08-26 date_created: 2020-01-05T23:00:46Z date_published: 2019-08-13T00:00:00Z date_updated: 2023-09-06T14:53:59Z day: '13' department: - _id: DaAl doi: 10.1007/978-3-030-29400-7_23 external_id: isi: - '000851061400023' intvolume: ' 11725' isi: 1 language: - iso: eng month: '08' oa_version: None page: 317-333 publication: 25th Anniversary of Euro-Par publication_identifier: eissn: - 1611-3349 isbn: - 978-3-0302-9399-4 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Scalable FIFO channels for programming via communicating sequential processes type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11725 year: '2019' ... --- _id: '7216' abstract: - lang: eng text: 'We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system to label a stream of noisy observations of transit vehicle trajectories with the transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently to large transit networks, our system first retrieves a small set of candidate routes from a geometrically indexed data structure, then applies a fine-grained scoring step to choose the best match. Given that real-time data remains unavailable for the majority of the world’s transit agencies, these inferences can help feed a real-time map of a transit system’s trips, infer transit trip delays in real time, or measure and correct noisy transit tracking data. This system can run on vehicle observations from a variety of sources that don’t attach route information to vehicle observations, such as public imagery streams or user-contributed transit vehicle sightings.We abstract away the specifics of the sensing system and demonstrate the effectiveness of our system on a "semisynthetic" dataset of all New York City buses, where we simulate sensed trajectories by starting with fully labeled vehicle trajectories reported via the GTFS-Realtime protocol, removing the transit route IDs, and perturbing locations with synthetic noise. Using just the geometric shapes of the trajectories, we demonstrate that our system converges on the correct route ID within a few minutes, even after a vehicle switches from serving one trip to the next.' article_number: '8917514' article_processing_charge: No author: - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 - first_name: James full_name: Cook, James last_name: Cook - first_name: Alex full_name: Fabrikant, Alex last_name: Fabrikant - first_name: Marco full_name: Gruteser, Marco last_name: Gruteser citation: ama: 'Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514' apa: 'Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514' chicago: 'Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” In 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019. https://doi.org/10.1109/ITSC.2019.8917514.' ieee: 'G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale,” in 2019 IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand, 2019.' ista: 'Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference, 8917514.' mla: 'Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514.' short: G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019. conference: end_date: 2019-10-30 location: Auckland, New Zealand name: 'ITSC: Intelligent Transportation Systems Conference' start_date: 2019-10-27 date_created: 2019-12-29T23:00:47Z date_published: 2019-11-28T00:00:00Z date_updated: 2023-09-06T14:50:28Z day: '28' department: - _id: HeEd doi: 10.1109/ITSC.2019.8917514 external_id: isi: - '000521238102050' isi: 1 language: - iso: eng month: '11' oa_version: None publication: 2019 IEEE Intelligent Transportation Systems Conference publication_identifier: isbn: - '9781538670248' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '7231' abstract: - lang: eng text: Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature. alternative_title: - LNCS article_processing_charge: No author: - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Yu full_name: Jiang, Yu last_name: Jiang - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8' apa: 'Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8' chicago: Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8. ieee: H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141. ista: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.' mla: Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8. short: H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141. conference: end_date: 2019-08-29 location: Amsterdam, The Netherlands name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' start_date: 2019-08-27 date_created: 2020-01-05T23:00:47Z date_published: 2019-08-13T00:00:00Z date_updated: 2023-09-06T14:55:15Z day: '13' department: - _id: ToHe doi: 10.1007/978-3-030-29662-9_8 external_id: arxiv: - '1907.11514' isi: - '000611677700008' intvolume: ' 11750' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.11514 month: '08' oa: 1 oa_version: Preprint page: 123-141 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 17th International Conference on Formal Modeling and Analysis of Timed Systems publication_identifier: eissn: - 1611-3349 isbn: - 978-3-0302-9661-2 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11750 year: '2019' ... --- _id: '7340' abstract: - lang: eng text: Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling. acknowledgement: We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments. article_number: e50793 article_processing_charge: No article_type: original author: - first_name: Niko Paresh full_name: Amin-Wetzel, Niko Paresh id: E95D3014-9D8C-11E9-9C80-D2F8E5697425 last_name: Amin-Wetzel - first_name: Lisa full_name: Neidhardt, Lisa last_name: Neidhardt - first_name: Yahui full_name: Yan, Yahui last_name: Yan - first_name: Matthias P. full_name: Mayer, Matthias P. last_name: Mayer - first_name: David full_name: Ron, David last_name: Ron citation: ama: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793 apa: Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793 chicago: Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793. ieee: N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793. mla: Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793. short: N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019). date_created: 2020-01-19T23:00:39Z date_published: 2019-12-24T00:00:00Z date_updated: 2023-09-06T14:58:02Z day: '24' ddc: - '570' department: - _id: MaDe doi: 10.7554/eLife.50793 external_id: isi: - '000512303700001' pmid: - '31873072' file: - access_level: open_access checksum: 29fcbcd8c1fc7f11a596ed7f14ea1c82 content_type: application/pdf creator: dernst date_created: 2020-11-19T11:37:41Z date_updated: 2020-11-19T11:37:41Z file_id: '8777' file_name: 2019_eLife_AminWetzel.pdf file_size: 4817384 relation: main_file success: 1 file_date_updated: 2020-11-19T11:37:41Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2019' ... --- _id: '7422' abstract: - lang: eng text: Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions. article_number: '054108' article_processing_charge: No article_type: original author: - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Joris full_name: Paijmans, Joris last_name: Paijmans - first_name: Laurens full_name: Bossen, Laurens last_name: Bossen - first_name: Thomas full_name: Miedema, Thomas last_name: Miedema - first_name: Martijn full_name: Wehrens, Martijn last_name: Wehrens - first_name: Nils B. full_name: Becker, Nils B. last_name: Becker - first_name: Kazunari full_name: Kaizu, Kazunari last_name: Kaizu - first_name: Koichi full_name: Takahashi, Koichi last_name: Takahashi - first_name: Marileen full_name: Dogterom, Marileen last_name: Dogterom - first_name: Pieter Rein full_name: ten Wolde, Pieter Rein last_name: ten Wolde citation: ama: Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867 apa: Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867 chicago: Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867. ieee: T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019. ista: Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108. mla: Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867. short: T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019). date_created: 2020-01-30T10:34:36Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-09-06T14:59:28Z day: '07' department: - _id: GaTk doi: 10.1063/1.5064867 external_id: arxiv: - '1708.09364' isi: - '000458109300009' intvolume: ' 150' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.09364 month: '02' oa: 1 oa_version: Preprint publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' status: public title: eGFRD in all dimensions type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 150 year: '2019' ... --- _id: '7230' abstract: - lang: eng text: Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G. alternative_title: - LNCS article_processing_charge: No author: - first_name: Alan M full_name: Arroyo Guevara, Alan M id: 3207FDC6-F248-11E8-B48F-1D18A9856A87 last_name: Arroyo Guevara orcid: 0000-0003-2401-8670 - first_name: Martin full_name: Derka, Martin last_name: Derka - first_name: Irene full_name: Parada, Irene last_name: Parada citation: ama: 'Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th International Symposium on Graph Drawing and Network Visualization. Vol 11904. Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18' apa: 'Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple drawings. In 27th International Symposium on Graph Drawing and Network Visualization (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18' chicago: Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization, 11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18. ieee: A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in 27th International Symposium on Graph Drawing and Network Visualization, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243. ista: 'Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.' mla: Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18. short: A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243. conference: end_date: 2019-09-20 location: Prague, Czech Republic name: 'GD: Graph Drawing and Network Visualization' start_date: 2019-09-17 date_created: 2020-01-05T23:00:47Z date_published: 2019-11-28T00:00:00Z date_updated: 2023-09-06T14:56:00Z day: '28' department: - _id: UlWa doi: 10.1007/978-3-030-35802-0_18 ec_funded: 1 external_id: arxiv: - '1908.08129' isi: - '000612918800018' intvolume: ' 11904' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.08129 month: '11' oa: 1 oa_version: Preprint page: 230-243 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 27th International Symposium on Graph Drawing and Network Visualization publication_identifier: eissn: - 1611-3349 isbn: - 978-3-0303-5801-3 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Extending simple drawings type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11904 year: '2019' ... --- _id: '7232' abstract: - lang: eng text: 'We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism which extends STL by capturing the discrete/ continuous time duality found in many cyber-physical systems (CPS), as well as mixed-signal electronic designs. In STL−MX, properties of components with continuous dynamics are expressed in STL, while specifications of components with discrete dynamics are written in LTL. To combine the two layers, we evaluate formulas on two traces, discrete- and continuous-time, and introduce two interface operators that map signals, properties and their satisfaction signals across the two time domains. We show that STL-mx has the expressive power of STL supplemented with an implicit T-periodic clock signal. We develop and implement an algorithm for monitoring STL-mx formulas and illustrate the approach using a mixed-signal example. ' alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic citation: ama: 'Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4' apa: 'Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal logic. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_4' chicago: Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4. ieee: T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75. ista: 'Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.' mla: Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4. short: T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75. conference: end_date: 2019-08-29 location: Amsterdam, The Netherlands name: 'FORMATS: Formal Modeling and Anaysis of Timed Systems' start_date: 2019-08-27 date_created: 2020-01-05T23:00:48Z date_published: 2019-08-13T00:00:00Z date_updated: 2023-09-06T14:57:17Z day: '13' department: - _id: ToHe doi: 10.1007/978-3-030-29662-9_4 external_id: isi: - '000611677700004' intvolume: ' 11750' isi: 1 language: - iso: eng month: '08' oa_version: None page: 59-75 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 17th International Conference on Formal Modeling and Analysis of Timed Systems publication_identifier: eissn: - 1611-3349 isbn: - 978-3-0302-9661-2 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Mixed-time signal temporal logic type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11750 year: '2019' ... --- _id: '7420' abstract: - lang: eng text: β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic. article_number: jcs233387 article_processing_charge: No article_type: original author: - first_name: Pranshu full_name: Sahgal, Pranshu last_name: Sahgal - first_name: Jonna H full_name: Alanko, Jonna H id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87 last_name: Alanko orcid: 0000-0002-7698-3061 - first_name: Jaroslav full_name: Icha, Jaroslav last_name: Icha - first_name: Ilkka full_name: Paatero, Ilkka last_name: Paatero - first_name: Hellyeh full_name: Hamidi, Hellyeh last_name: Hamidi - first_name: Antti full_name: Arjonen, Antti last_name: Arjonen - first_name: Mika full_name: Pietilä, Mika last_name: Pietilä - first_name: Anne full_name: Rokka, Anne last_name: Rokka - first_name: Johanna full_name: Ivaska, Johanna last_name: Ivaska citation: ama: Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387 apa: Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387 chicago: Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science. The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387. ieee: P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists, 2019. ista: Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387. mla: Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:10.1242/jcs.233387. short: P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019). date_created: 2020-01-30T10:31:42Z date_published: 2019-06-07T00:00:00Z date_updated: 2023-09-06T15:01:00Z day: '07' department: - _id: MiSi doi: 10.1242/jcs.233387 external_id: isi: - '000473327900017' pmid: - '31076515' intvolume: ' 132' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1242/jcs.233387 month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' status: public title: GGA2 and RAB13 promote activity-dependent β1-integrin recycling type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 132 year: '2019' ... --- _id: '7423' abstract: - lang: eng text: 'We compare finite rank perturbations of the following three ensembles of complex rectangular random matrices: First, a generalised Wishart ensemble with one random and two fixed correlation matrices introduced by Borodin and Péché, second, the product of two independent random matrices where one has correlated entries, and third, the case when the two random matrices become also coupled through a fixed matrix. The singular value statistics of all three ensembles is shown to be determinantal and we derive double contour integral representations for their respective kernels. Three different kernels are found in the limit of infinite matrix dimension at the origin of the spectrum. They depend on finite rank perturbations of the correlation and coupling matrices and are shown to be integrable. The first kernel (I) is found for two independent matrices from the second, and two weakly coupled matrices from the third ensemble. It generalises the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel (III) is obtained for the generalised Wishart ensemble and for two strongly coupled matrices. It further generalises the perturbed Bessel kernel of Desrosiers and Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices, provides an interpolation between the kernels (I) and (III), generalising previous findings of part of the authors.' article_processing_charge: No article_type: original author: - first_name: Gernot full_name: Akemann, Gernot last_name: Akemann - first_name: Tomasz full_name: Checinski, Tomasz last_name: Checinski - first_name: Dangzheng full_name: Liu, Dangzheng id: 2F947E34-F248-11E8-B48F-1D18A9856A87 last_name: Liu - first_name: Eugene full_name: Strahov, Eugene last_name: Strahov citation: ama: 'Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479. doi:10.1214/18-aihp888' apa: 'Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888' chicago: 'Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888.' ieee: 'G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles,” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.' ista: 'Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.' mla: 'Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888.' short: G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri Poincaré, Probabilités et Statistiques 55 (2019) 441–479. date_created: 2020-01-30T10:36:50Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-09-06T14:58:39Z day: '01' department: - _id: LaEr doi: 10.1214/18-aihp888 external_id: arxiv: - '1704.05224' isi: - '000456070200013' intvolume: ' 55' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.05224 month: '02' oa: 1 oa_version: Preprint page: 441-479 publication: Annales de l'Institut Henri Poincaré, Probabilités et Statistiques publication_identifier: issn: - 0246-0203 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' status: public title: 'Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 55 year: '2019' ...