[{"file_date_updated":"2020-07-14T12:47:54Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"641","author":[{"first_name":"Sergey","last_name":"Aganezov","full_name":"Aganezov, Sergey"},{"full_name":"Zban, Ilya","first_name":"Ilya","last_name":"Zban"},{"id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov","full_name":"Aksenov, Vitalii"},{"full_name":"Alexeev, Nikita","last_name":"Alexeev","first_name":"Nikita"},{"full_name":"Schatz, Michael C.","first_name":"Michael C.","last_name":"Schatz"}],"volume":20,"date_updated":"2023-09-06T14:51:06Z","date_created":"2019-12-29T23:00:46Z","year":"2019","publisher":"BMC","department":[{"_id":"DaAl"}],"publication_status":"published","publication_identifier":{"eissn":["14712105"]},"month":"12","doi":"10.1186/s12859-019-3208-4","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000511618800007"]},"isi":1,"quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2019_BMCBioinfo_Aganezov.pdf","access_level":"open_access","file_size":1917374,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7221","date_created":"2020-01-02T16:10:58Z","date_updated":"2020-07-14T12:47:54Z","checksum":"7a30357efdcf8f66587ed495c0927724"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7214","intvolume":" 20","ddc":["570"],"title":"Recovering rearranged cancer chromosomes from karyotype graphs","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","date_published":"2019-12-17T00:00:00Z","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","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","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.","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","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).","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."},"publication":"BMC Bioinformatics","article_type":"original"},{"file":[{"access_level":"open_access","file_name":"2019_Bioengineering_Merrin.pdf","file_size":2660780,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7243","checksum":"80f1499e2a4caccdf3aa54b137fd99a0","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:49:59Z"}],"oa_version":"Published Version","_id":"7225","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 6","ddc":["620"],"status":"public","title":"Frontiers in microfluidics, a teaching resource review","issue":"4","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2019-12-03T00:00:00Z","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","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.","short":"J. Merrin, Bioengineering 6 (2019).","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109.","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109."},"publication":"Bioengineering","article_type":"review","has_accepted_license":"1","article_processing_charge":"Yes","day":"03","scopus_import":"1","author":[{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"}],"volume":6,"date_created":"2020-01-05T23:00:45Z","date_updated":"2023-09-06T14:52:49Z","pmid":1,"year":"2019","department":[{"_id":"NanoFab"}],"publisher":"MDPI","publication_status":"published","file_date_updated":"2020-07-14T12:47:54Z","article_number":"109","doi":"10.3390/bioengineering6040109","language":[{"iso":"eng"}],"external_id":{"pmid":["31816954"],"isi":["000505590000024"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["23065354"]},"month":"12"},{"volume":11725,"date_updated":"2023-09-06T14:53:59Z","date_created":"2020-01-05T23:00:46Z","author":[{"full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Elizarov, Roman","first_name":"Roman","last_name":"Elizarov"}],"publisher":"Springer Nature","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2019","publication_identifier":{"isbn":["978-3-0302-9399-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-29400-7_23","conference":{"end_date":"2019-08-30","location":"Göttingen, Germany","start_date":"2019-08-26","name":"Euro-Par: European Conference on Parallel Processing"},"quality_controlled":"1","isi":1,"external_id":{"isi":["000851061400023"]},"abstract":[{"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. ","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","intvolume":" 11725","status":"public","title":"Scalable FIFO channels for programming via communicating sequential processes","_id":"7228","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"13","scopus_import":"1","date_published":"2019-08-13T00:00:00Z","page":"317-333","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","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.","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","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.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 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.","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."},"publication":"25th Anniversary of Euro-Par"},{"conference":{"name":"ITSC: Intelligent Transportation Systems Conference","location":"Auckland, New Zealand","start_date":"2019-10-27","end_date":"2019-10-30"},"date_published":"2019-11-28T00:00:00Z","doi":"10.1109/ITSC.2019.8917514","language":[{"iso":"eng"}],"publication":"2019 IEEE Intelligent Transportation Systems Conference","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","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.","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","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.","short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019.","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.","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."},"external_id":{"isi":["000521238102050"]},"quality_controlled":"1","isi":1,"day":"28","month":"11","article_processing_charge":"No","publication_identifier":{"isbn":["9781538670248"]},"scopus_import":"1","author":[{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116","first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F"},{"full_name":"Cook, James","last_name":"Cook","first_name":"James"},{"first_name":"Alex","last_name":"Fabrikant","full_name":"Fabrikant, Alex"},{"last_name":"Gruteser","first_name":"Marco","full_name":"Gruteser, Marco"}],"date_created":"2019-12-29T23:00:47Z","date_updated":"2023-09-06T14:50:28Z","oa_version":"None","year":"2019","_id":"7216","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","status":"public","publisher":"IEEE","department":[{"_id":"HeEd"}],"abstract":[{"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.","lang":"eng"}],"article_number":"8917514","type":"conference"},{"day":"13","article_processing_charge":"No","scopus_import":"1","date_published":"2019-08-13T00:00:00Z","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","citation":{"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.","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.","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.","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.","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","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"},"page":"123-141","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."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"7231","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","intvolume":" 11750","month":"08","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","end_date":"2019-08-29","location":"Amsterdam, The Netherlands","start_date":"2019-08-27"},"doi":"10.1007/978-3-030-29662-9_8","language":[{"iso":"eng"}],"external_id":{"isi":["000611677700008"],"arxiv":["1907.11514"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Kong, Hui","last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"last_name":"Jiang","first_name":"Yu","full_name":"Jiang, Yu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:55:15Z","volume":11750,"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}]}]