[{"date_updated":"2021-01-12T08:03:37Z","type":"journal_article","oa_version":"None","day":"09","year":"2015","citation":{"ieee":"R. Biswas and P. Bhowmick, “On different topological classes of spherical geodesic paths and circles inZ3,” <i>Theoretical Computer Science</i>, vol. 605, no. 11. Elsevier, pp. 146–163, 2015.","ama":"Biswas R, Bhowmick P. On different topological classes of spherical geodesic paths and circles inZ3. <i>Theoretical Computer Science</i>. 2015;605(11):146-163. doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.09.003\">10.1016/j.tcs.2015.09.003</a>","short":"R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” <i>Theoretical Computer Science</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tcs.2015.09.003\">https://doi.org/10.1016/j.tcs.2015.09.003</a>.","ista":"Biswas R, Bhowmick P. 2015. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 146–163.","mla":"Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” <i>Theoretical Computer Science</i>, vol. 605, no. 11, Elsevier, 2015, pp. 146–63, doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.09.003\">10.1016/j.tcs.2015.09.003</a>.","apa":"Biswas, R., &#38; Bhowmick, P. (2015). On different topological classes of spherical geodesic paths and circles inZ3. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2015.09.003\">https://doi.org/10.1016/j.tcs.2015.09.003</a>"},"author":[{"last_name":"Biswas","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publication_status":"published","title":"On different topological classes of spherical geodesic paths and circles inZ3","publication":"Theoretical Computer Science","language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2015.09.003","_id":"5807","publisher":"Elsevier","date_published":"2015-11-09T00:00:00Z","page":"146-163","issue":"11","volume":605,"date_created":"2019-01-08T20:44:52Z","month":"11","status":"public","intvolume":"       605","publication_identifier":{"issn":["0304-3975"]}},{"publisher":"Springer Nature","page":"787-797","volume":31,"issue":"6-8","date_published":"2015-05-08T00:00:00Z","status":"public","month":"05","date_created":"2019-01-08T20:45:05Z","publication_identifier":{"issn":["0178-2789","1432-2315"]},"intvolume":"        31","year":"2015","day":"08","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:03:37Z","extern":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","last_name":"Biswas","first_name":"Ranita"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"citation":{"ama":"Biswas R, Bhowmick P. Layer the sphere. <i>The Visual Computer</i>. 2015;31(6-8):787-797. doi:<a href=\"https://doi.org/10.1007/s00371-015-1101-3\">10.1007/s00371-015-1101-3</a>","ieee":"R. Biswas and P. Bhowmick, “Layer the sphere,” <i>The Visual Computer</i>, vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015.","chicago":"Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” <i>The Visual Computer</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1007/s00371-015-1101-3\">https://doi.org/10.1007/s00371-015-1101-3</a>.","short":"R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797.","ista":"Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8), 787–797.","apa":"Biswas, R., &#38; Bhowmick, P. (2015). Layer the sphere. <i>The Visual Computer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00371-015-1101-3\">https://doi.org/10.1007/s00371-015-1101-3</a>","mla":"Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” <i>The Visual Computer</i>, vol. 31, no. 6–8, Springer Nature, 2015, pp. 787–97, doi:<a href=\"https://doi.org/10.1007/s00371-015-1101-3\">10.1007/s00371-015-1101-3</a>."},"publication_status":"published","_id":"5808","language":[{"iso":"eng"}],"doi":"10.1007/s00371-015-1101-3","publication":"The Visual Computer","title":"Layer the sphere"},{"title":"Structural basis of transcription initiation by RNA polymerase II","publication":"Nature Reviews Molecular Cell Biology","doi":"10.1038/nrm3952","language":[{"iso":"eng"}],"_id":"594","publication_status":"published","abstract":[{"text":"Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter.","lang":"eng"}],"citation":{"chicago":"Sainsbury, Sarah, Carrie Bernecky, and Patrick Cramer. “Structural Basis of Transcription Initiation by RNA Polymerase II.” <i>Nature Reviews Molecular Cell Biology</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nrm3952\">https://doi.org/10.1038/nrm3952</a>.","short":"S. Sainsbury, C. Bernecky, P. Cramer, Nature Reviews Molecular Cell Biology 16 (2015) 129–143.","ista":"Sainsbury S, Bernecky C, Cramer P. 2015. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3), 129–143.","ama":"Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation by RNA polymerase II. <i>Nature Reviews Molecular Cell Biology</i>. 2015;16(3):129-143. doi:<a href=\"https://doi.org/10.1038/nrm3952\">10.1038/nrm3952</a>","ieee":"S. Sainsbury, C. Bernecky, and P. Cramer, “Structural basis of transcription initiation by RNA polymerase II,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 16, no. 3. Nature Publishing Group, pp. 129–143, 2015.","apa":"Sainsbury, S., Bernecky, C., &#38; Cramer, P. (2015). Structural basis of transcription initiation by RNA polymerase II. <i>Nature Reviews Molecular Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrm3952\">https://doi.org/10.1038/nrm3952</a>","mla":"Sainsbury, Sarah, et al. “Structural Basis of Transcription Initiation by RNA Polymerase II.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 16, no. 3, Nature Publishing Group, 2015, pp. 129–43, doi:<a href=\"https://doi.org/10.1038/nrm3952\">10.1038/nrm3952</a>."},"author":[{"last_name":"Sainsbury","first_name":"Sarah","full_name":"Sainsbury, Sarah"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A"},{"first_name":"Patrick","last_name":"Cramer","full_name":"Cramer, Patrick"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","extern":"1","date_updated":"2021-01-12T08:05:16Z","type":"journal_article","oa_version":"None","day":"26","year":"2015","intvolume":"        16","publist_id":"7206","date_created":"2018-12-11T11:47:23Z","month":"03","status":"public","date_published":"2015-03-26T00:00:00Z","issue":"3","volume":16,"page":"129 - 143","publisher":"Nature Publishing Group"},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1423808112","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2021-01-12T08:06:12Z","oa_version":"Published Version","day":"07","publication_identifier":{"issn":["0027-8424","1091-6490"]},"date_published":"2015-07-07T00:00:00Z","file":[{"file_size":2822681,"creator":"kschuh","content_type":"application/pdf","relation":"main_file","date_created":"2019-03-19T14:21:07Z","file_name":"2015_PNAS_Fenk.pdf","checksum":"3d2da5af8d72467e382a565abc2e003d","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","file_id":"6119"}],"external_id":{"pmid":["26100886"]},"page":"E3525-E3534","title":"Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity","publication":"Proceedings of the National Academy of Sciences","pmid":1,"ddc":["570"],"oa":1,"_id":"6118","publication_status":"published","abstract":[{"text":"Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information about their environment, such as the potential presence of prey or predators. The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli. Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can detect CO2 independently of these sensory pathways. Many of the C. elegans sensory neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’ major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore may couple detection of CO2 to that of other cues at the earliest stages of sensory processing. We show that C. elegans persistently suppresses oviposition at high CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying, are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system partly through the AWC olfactory neurons: High CO2 tonically activates AWC by a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that CO2 is a more complex sensory cue for C. elegans than previously thought, both in terms of behavior and neural circuitry.","lang":"eng"}],"citation":{"short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112 (2015) E3525–E3534.","chicago":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1423808112\">https://doi.org/10.1073/pnas.1423808112</a>.","ista":"Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534.","ama":"Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. <i>Proceedings of the National Academy of Sciences</i>. 2015;112(27):E3525-E3534. doi:<a href=\"https://doi.org/10.1073/pnas.1423808112\">10.1073/pnas.1423808112</a>","ieee":"L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity,” <i>Proceedings of the National Academy of Sciences</i>, vol. 112, no. 27. National Academy of Sciences, pp. E3525–E3534, 2015.","apa":"Fenk, L. A., &#38; de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1423808112\">https://doi.org/10.1073/pnas.1423808112</a>","mla":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” <i>Proceedings of the National Academy of Sciences</i>, vol. 112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:<a href=\"https://doi.org/10.1073/pnas.1423808112\">10.1073/pnas.1423808112</a>."},"quality_controlled":"1","extern":"1","author":[{"first_name":"Lorenz A.","last_name":"Fenk","full_name":"Fenk, Lorenz A."},{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono"}],"year":"2015","intvolume":"       112","date_created":"2019-03-19T14:15:50Z","month":"07","status":"public","volume":112,"issue":"27","file_date_updated":"2020-07-14T12:47:20Z","publisher":"National Academy of Sciences"},{"external_id":{"pmid":["25760081"]},"file":[{"creator":"kschuh","content_type":"application/pdf","file_size":6723528,"date_created":"2019-03-19T14:29:43Z","relation":"main_file","access_level":"open_access","checksum":"cf641b7a363aecd0a101755d23dee7e0","file_name":"2015_elife_Laurent.pdf","file_id":"6121","date_updated":"2020-07-14T12:47:20Z"}],"date_published":"2015-03-11T00:00:00Z","publication_identifier":{"issn":["2050-084X"]},"day":"11","oa_version":"Published Version","date_updated":"2021-01-12T08:06:13Z","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","doi":"10.7554/elife.04241","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:20Z","volume":4,"status":"public","article_number":"e04241","month":"03","date_created":"2019-03-19T14:23:51Z","intvolume":"         4","year":"2015","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"extern":"1","author":[{"full_name":"Laurent, Patrick","last_name":"Laurent","first_name":"Patrick"},{"first_name":"Zoltan","last_name":"Soltesz","full_name":"Soltesz, Zoltan"},{"last_name":"Nelson","first_name":"Geoffrey M","full_name":"Nelson, Geoffrey M"},{"full_name":"Chen, Changchun","last_name":"Chen","first_name":"Changchun"},{"first_name":"Fausto","last_name":"Arellano-Carbajal","full_name":"Arellano-Carbajal, Fausto"},{"last_name":"Levy","first_name":"Emmanuel","full_name":"Levy, Emmanuel"},{"last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"}],"quality_controlled":"1","citation":{"apa":"Laurent, P., Soltesz, Z., Nelson, G. M., Chen, C., Arellano-Carbajal, F., Levy, E., &#38; de Bono, M. (2015). Decoding a neural circuit controlling global animal state in C. elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.04241\">https://doi.org/10.7554/elife.04241</a>","mla":"Laurent, Patrick, et al. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” <i>ELife</i>, vol. 4, e04241, eLife Sciences Publications, 2015, doi:<a href=\"https://doi.org/10.7554/elife.04241\">10.7554/elife.04241</a>.","ama":"Laurent P, Soltesz Z, Nelson GM, et al. Decoding a neural circuit controlling global animal state in C. elegans. <i>eLife</i>. 2015;4. doi:<a href=\"https://doi.org/10.7554/elife.04241\">10.7554/elife.04241</a>","ieee":"P. Laurent <i>et al.</i>, “Decoding a neural circuit controlling global animal state in C. elegans,” <i>eLife</i>, vol. 4. eLife Sciences Publications, 2015.","short":"P. Laurent, Z. Soltesz, G.M. Nelson, C. Chen, F. Arellano-Carbajal, E. Levy, M. de Bono, ELife 4 (2015).","chicago":"Laurent, Patrick, Zoltan Soltesz, Geoffrey M Nelson, Changchun Chen, Fausto Arellano-Carbajal, Emmanuel Levy, and Mario de Bono. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” <i>ELife</i>. eLife Sciences Publications, 2015. <a href=\"https://doi.org/10.7554/elife.04241\">https://doi.org/10.7554/elife.04241</a>.","ista":"Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono M. 2015. Decoding a neural circuit controlling global animal state in C. elegans. eLife. 4, e04241."},"abstract":[{"lang":"eng","text":"Brains organize behavior and physiology to optimize the response to threats or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms C. elegans' global state, inducing sustained locomotory arousal and altering expression of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing neurons drive arousal at 21% O2 by tonically activating the RMG interneurons. Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL, or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal. However, disrupting cation currents in these neurons curtails RMG neurosecretion and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters reveal neural circuit state, as neurosecretion stimulates neuropeptide expression. Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration rather than behavior, while the activity of downstream interneurons such as AVB and AIY reflect both O2 levels and the behavior being executed."}],"publication_status":"published","_id":"6120","oa":1,"ddc":["570"],"pmid":1,"title":"Decoding a neural circuit controlling global animal state in C. elegans","publication":"eLife"},{"intvolume":"       127","publication_identifier":{"issn":["0006-4971","1528-0020"]},"month":"11","date_created":"2019-05-31T09:38:50Z","status":"public","external_id":{"pmid":["26552697"]},"date_published":"2015-11-02T00:00:00Z","page":"529-537","volume":127,"issue":"5","publisher":"American Society of Hematology","pmid":1,"title":"Structural basis for collagen recognition by the immune receptor OSCAR","publication":"Blood","_id":"6507","doi":"10.1182/blood-2015-08-667055","language":[{"iso":"eng"}],"abstract":[{"text":"The osteoclast-associated receptor (OSCAR) is a collagen-binding immune receptor with important roles in dendritic cell maturation and activation of inflammatory monocytes as well as in osteoclastogenesis. The crystal structure of the OSCAR ectodomain is presented, both free and in complex with a consensus triple-helical peptide (THP). The structures revealed a collagen-binding site in each immunoglobulin-like domain (D1 and D2). The THP binds near a predicted collagen-binding groove in D1, but a more extensive interaction with D2 is facilitated by the unusually wide D1-D2 interdomain angle in OSCAR. Direct binding assays, combined with site-directed mutagenesis, confirm that the primary collagen-binding site in OSCAR resides in D2, in marked contrast to the related collagen receptors, glycoprotein VI (GPVI) and leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1). Monomeric OSCAR D1D2 binds to the consensus THP with a KD of 28 µM measured in solution, but shows a higher affinity (KD 1.5 μM) when binding to a solid-phase THP, most likely due to an avidity effect. These data suggest a 2-stage model for the interaction of OSCAR with a collagen fibril, with transient, low-affinity interactions initiated by the membrane-distal D1, followed by firm adhesion to the primary binding site in D2.","lang":"eng"}],"publication_status":"published","citation":{"ieee":"L. Zhou <i>et al.</i>, “Structural basis for collagen recognition by the immune receptor OSCAR,” <i>Blood</i>, vol. 127, no. 5. American Society of Hematology, pp. 529–537, 2015.","ama":"Zhou L, Hinerman JM, Blaszczyk M, et al. Structural basis for collagen recognition by the immune receptor OSCAR. <i>Blood</i>. 2015;127(5):529-537. doi:<a href=\"https://doi.org/10.1182/blood-2015-08-667055\">10.1182/blood-2015-08-667055</a>","ista":"Zhou L, Hinerman JM, Blaszczyk M, Miller JLC, Conrady DG, Barrow AD, Chirgadze DY, Bihan D, Farndale RW, Herr AB. 2015. Structural basis for collagen recognition by the immune receptor OSCAR. Blood. 127(5), 529–537.","chicago":"Zhou, Long, J. M. Hinerman, M. Blaszczyk, J. L. C. Miller, D. G. Conrady, A. D. Barrow, D. Y. Chirgadze, D. Bihan, R. W. Farndale, and A. B. Herr. “Structural Basis for Collagen Recognition by the Immune Receptor OSCAR.” <i>Blood</i>. American Society of Hematology, 2015. <a href=\"https://doi.org/10.1182/blood-2015-08-667055\">https://doi.org/10.1182/blood-2015-08-667055</a>.","short":"L. Zhou, J.M. Hinerman, M. Blaszczyk, J.L.C. Miller, D.G. Conrady, A.D. Barrow, D.Y. Chirgadze, D. Bihan, R.W. Farndale, A.B. Herr, Blood 127 (2015) 529–537.","mla":"Zhou, Long, et al. “Structural Basis for Collagen Recognition by the Immune Receptor OSCAR.” <i>Blood</i>, vol. 127, no. 5, American Society of Hematology, 2015, pp. 529–37, doi:<a href=\"https://doi.org/10.1182/blood-2015-08-667055\">10.1182/blood-2015-08-667055</a>.","apa":"Zhou, L., Hinerman, J. M., Blaszczyk, M., Miller, J. L. C., Conrady, D. G., Barrow, A. D., … Herr, A. B. (2015). Structural basis for collagen recognition by the immune receptor OSCAR. <i>Blood</i>. American Society of Hematology. <a href=\"https://doi.org/10.1182/blood-2015-08-667055\">https://doi.org/10.1182/blood-2015-08-667055</a>"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","author":[{"full_name":"Zhou, Long","orcid":"0000-0002-1864-8951","id":"3E751364-F248-11E8-B48F-1D18A9856A87","first_name":"Long","last_name":"Zhou"},{"first_name":"J. M.","last_name":"Hinerman","full_name":"Hinerman, J. M."},{"last_name":"Blaszczyk","first_name":"M.","full_name":"Blaszczyk, M."},{"full_name":"Miller, J. L. C.","first_name":"J. L. C.","last_name":"Miller"},{"first_name":"D. G.","last_name":"Conrady","full_name":"Conrady, D. G."},{"full_name":"Barrow, A. D.","last_name":"Barrow","first_name":"A. D."},{"full_name":"Chirgadze, D. Y.","last_name":"Chirgadze","first_name":"D. Y."},{"full_name":"Bihan, D.","first_name":"D.","last_name":"Bihan"},{"full_name":"Farndale, R. W.","last_name":"Farndale","first_name":"R. W."},{"first_name":"A. B.","last_name":"Herr","full_name":"Herr, A. B."}],"oa_version":"None","date_updated":"2021-01-12T08:07:47Z","type":"journal_article","year":"2015","day":"02"},{"_id":"6736","language":[{"iso":"eng"}],"oa":1,"doi":"10.1109/tit.2015.2453315","title":"Scaling exponent of list decoders with applications to polar codes","publication":"IEEE Transactions on Information Theory","abstract":[{"text":"Motivated by the significant performance gains which polar codes experience under successive cancellation list decoding, their scaling exponent is studied as a function of the list size. In particular, the error probability is fixed, and the tradeoff between the block length and back-off from capacity is analyzed. A lower bound is provided on the error probability under MAP decoding with list size L for any binary-input memoryless output-symmetric channel and for any class of linear codes such that their minimum distance is unbounded as the block length grows large. Then, it is shown that under MAP decoding, although the introduction of a list can significantly improve the involved constants, the scaling exponent itself, i.e., the speed at which capacity is approached, stays unaffected for any finite list size. In particular, this result applies to polar codes, since their minimum distance tends to infinity as the block length increases. A similar result is proved for genie-aided successive cancellation decoding when transmission takes place over the binary erasure channel, namely, the scaling exponent remains constant for any fixed number of helps from the genie. Note that since genie-aided successive cancellation decoding might be strictly worse than successive cancellation list decoding, the problem of establishing the scaling exponent of the latter remains open.","lang":"eng"}],"publication_status":"published","extern":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"full_name":"Urbanke, Rudiger","first_name":"Rudiger","last_name":"Urbanke"}],"citation":{"mla":"Mondelli, Marco, et al. “Scaling Exponent of List Decoders with Applications to Polar Codes.” <i>IEEE Transactions on Information Theory</i>, vol. 61, no. 9, IEEE, 2015, pp. 4838–51, doi:<a href=\"https://doi.org/10.1109/tit.2015.2453315\">10.1109/tit.2015.2453315</a>.","apa":"Mondelli, M., Hassani, H., &#38; Urbanke, R. (2015). Scaling exponent of list decoders with applications to polar codes. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/tit.2015.2453315\">https://doi.org/10.1109/tit.2015.2453315</a>","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “Scaling exponent of list decoders with applications to polar codes,” <i>IEEE Transactions on Information Theory</i>, vol. 61, no. 9. IEEE, pp. 4838–4851, 2015.","ama":"Mondelli M, Hassani H, Urbanke R. Scaling exponent of list decoders with applications to polar codes. <i>IEEE Transactions on Information Theory</i>. 2015;61(9):4838-4851. doi:<a href=\"https://doi.org/10.1109/tit.2015.2453315\">10.1109/tit.2015.2453315</a>","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “Scaling Exponent of List Decoders with Applications to Polar Codes.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/tit.2015.2453315\">https://doi.org/10.1109/tit.2015.2453315</a>.","short":"M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory 61 (2015) 4838–4851.","ista":"Mondelli M, Hassani H, Urbanke R. 2015. Scaling exponent of list decoders with applications to polar codes. IEEE Transactions on Information Theory. 61(9), 4838–4851."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.5220"}],"year":"2015","day":"01","oa_version":"Preprint","type":"journal_article","date_updated":"2021-01-12T08:08:45Z","intvolume":"        61","status":"public","arxiv":1,"month":"09","date_created":"2019-07-31T06:50:34Z","volume":61,"issue":"9","page":"4838-4851","external_id":{"arxiv":["1304.5220"]},"date_published":"2015-09-01T00:00:00Z","publisher":"IEEE"},{"publication_status":"published","abstract":[{"text":"This paper presents polar coding schemes for the two-user discrete memoryless broadcast channel (DM-BC) which achieve Marton's region with both common and private messages. This is the best achievable rate region known to date, and it is tight for all classes of two-user DM-BCs whose capacity regions are known. To accomplish this task, we first construct polar codes for both the superposition as well as binning strategy. By combining these two schemes, we obtain Marton's region with private messages only. Finally, we show how to handle the case of common information. The proposed coding schemes possess the usual advantages of polar codes, i.e., they have low encoding and decoding complexity and a superpolynomial decay rate of the error probability. We follow the lead of Goela, Abbe, and Gastpar, who recently introduced polar codes emulating the superposition and binning schemes. To align the polar indices, for both schemes, their solution involves some degradedness constraints that are assumed to hold between the auxiliary random variables and channel outputs. To remove these constraints, we consider the transmission of k blocks and employ a chaining construction that guarantees the proper alignment of the polarized indices. The techniques described in this paper are quite general, and they can be adopted to many other multiterminal scenarios whenever there polar indices need to be aligned.","lang":"eng"}],"doi":"10.1109/tit.2014.2368555","oa":1,"language":[{"iso":"eng"}],"_id":"6737","title":"Achieving Marton’s region for broadcast channels using polar codes","publication":"IEEE Transactions on Information Theory","day":"01","year":"2015","type":"journal_article","date_updated":"2021-01-12T08:08:46Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"full_name":"Sason, Igal","last_name":"Sason","first_name":"Igal"},{"full_name":"Urbanke, Rudiger","last_name":"Urbanke","first_name":"Rudiger"}],"extern":"1","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.6060"}],"citation":{"ista":"Mondelli M, Hassani H, Sason I, Urbanke R. 2015. Achieving Marton’s region for broadcast channels using polar codes. IEEE Transactions on Information Theory. 61(2), 783–800.","short":"M. Mondelli, H. Hassani, I. Sason, R. Urbanke, IEEE Transactions on Information Theory 61 (2015) 783–800.","chicago":"Mondelli, Marco, Hamed Hassani, Igal Sason, and Rudiger Urbanke. “Achieving Marton’s Region for Broadcast Channels Using Polar Codes.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/tit.2014.2368555\">https://doi.org/10.1109/tit.2014.2368555</a>.","ieee":"M. Mondelli, H. Hassani, I. Sason, and R. Urbanke, “Achieving Marton’s region for broadcast channels using polar codes,” <i>IEEE Transactions on Information Theory</i>, vol. 61, no. 2. IEEE, pp. 783–800, 2015.","ama":"Mondelli M, Hassani H, Sason I, Urbanke R. Achieving Marton’s region for broadcast channels using polar codes. <i>IEEE Transactions on Information Theory</i>. 2015;61(2):783-800. doi:<a href=\"https://doi.org/10.1109/tit.2014.2368555\">10.1109/tit.2014.2368555</a>","mla":"Mondelli, Marco, et al. “Achieving Marton’s Region for Broadcast Channels Using Polar Codes.” <i>IEEE Transactions on Information Theory</i>, vol. 61, no. 2, IEEE, 2015, pp. 783–800, doi:<a href=\"https://doi.org/10.1109/tit.2014.2368555\">10.1109/tit.2014.2368555</a>.","apa":"Mondelli, M., Hassani, H., Sason, I., &#38; Urbanke, R. (2015). Achieving Marton’s region for broadcast channels using polar codes. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/tit.2014.2368555\">https://doi.org/10.1109/tit.2014.2368555</a>"},"status":"public","date_created":"2019-07-31T07:03:38Z","month":"02","arxiv":1,"intvolume":"        61","publisher":"IEEE","page":"783-800","volume":61,"issue":"2","date_published":"2015-02-01T00:00:00Z","external_id":{"arxiv":["1401.6060"]}},{"year":"2015","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy"},{"full_name":"Zhang, Can","last_name":"Zhang","first_name":"Can"},{"full_name":"Naibert, Tyler","last_name":"Naibert","first_name":"Tyler"},{"full_name":"Eckstein, James","first_name":"James","last_name":"Eckstein"},{"full_name":"Budakian, Raffi","first_name":"Raffi","last_name":"Budakian"}],"quality_controlled":"1","extern":"1","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR15/Event/238442","open_access":"1"}],"citation":{"chicago":"Polshyn, Hryhoriy, Can Zhang, Tyler Naibert, James Eckstein, and Raffi Budakian. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” In <i>APS March Meeting 2015</i>, Vol. 60. American Physical Society, 2015.","short":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, R. Budakian, in:, APS March Meeting 2015, American Physical Society, 2015.","ista":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. 2015. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. APS March Meeting 2015. APS: American Physical Society, Bulletin of the American Physical Society, vol. 60, G16.00009.","ama":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In: <i>APS March Meeting 2015</i>. Vol 60. American Physical Society; 2015.","ieee":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, and R. Budakian, “Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy,” in <i>APS March Meeting 2015</i>, San Antonio, TX, United States, 2015, vol. 60, no. 1.","mla":"Polshyn, Hryhoriy, et al. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” <i>APS March Meeting 2015</i>, vol. 60, no. 1, G16.00009, American Physical Society, 2015.","apa":"Polshyn, H., Zhang, C., Naibert, T., Eckstein, J., &#38; Budakian, R. (2015). Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In <i>APS March Meeting 2015</i> (Vol. 60). San Antonio, TX, United States: American Physical Society."},"abstract":[{"lang":"eng","text":"The study of fluxoid states and fluxoid dynamics in mesoscopic iron-based superconducting rings is valuable for characterizing the basic properties of the superconductor, and may also provide important insight into the superconducting paring symmetry. We report the fabrications of micron-sized rings and disks from thin films of Fe(Se, Te) grown by molecular beam epitaxy. In order to study fluxoid states in rings we developed a custom-tailored version of magnetic force microscopy (MFM). This technique has a number of qualitative advantages for working with mesoscopic superconducting samples in comparison to the conventional MFM and other imaging techniques. We observed metastable fluxoid states in rings of different sizes. Thermally activated fluxoid dynamics of these states was studied and modeled. In addition, we found different regimes of interaction between Fe(Se, Te) ring and MFM tip which are explained. Possibilities of the existence of exotic vortex states and proposals for experiments to test the symmetry of the superconducting order parameter in iron based superconductors are analyzed."}],"publication_status":"published","_id":"10748","oa":1,"publication":"APS March Meeting 2015","title":"Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy","publisher":"American Physical Society","issue":"1","volume":60,"status":"public","article_number":"G16.00009","conference":{"start_date":"2015-03-02","location":"San Antonio, TX, United States","end_date":"2015-03-06","name":"APS: American Physical Society"},"month":"03","date_created":"2022-02-08T10:17:09Z","intvolume":"        60","day":"01","oa_version":"Published Version","type":"conference","date_updated":"2022-02-08T10:42:53Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"date_published":"2015-03-01T00:00:00Z","publication_identifier":{"issn":["0003-0503"]},"alternative_title":["Bulletin of the American Physical Society"]},{"year":"2015","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Parise","first_name":"Francesca","full_name":"Parise, Francesca"},{"full_name":"Lygeros, John","last_name":"Lygeros","first_name":"John"},{"last_name":"Ruess","first_name":"Jakob","orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","citation":{"ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. 2015;3. doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>","ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” <i>Frontiers in Environmental Science</i>, vol. 3. Frontiers, 2015.","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>. Frontiers, 2015. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","apa":"Parise, F., Lygeros, J., &#38; Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>, vol. 3, 42, Frontiers, 2015, doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation."}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ddc":["000","570"],"oa":1,"_id":"10794","title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","publication":"Frontiers in Environmental Science","article_type":"original","publisher":"Frontiers","file_date_updated":"2022-02-25T11:55:26Z","volume":3,"status":"public","article_number":"42","date_created":"2022-02-25T11:42:25Z","month":"06","intvolume":"         3","day":"10","type":"journal_article","date_updated":"2022-02-25T11:59:23Z","oa_version":"Published Version","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","doi":"10.3389/fenvs.2015.00042","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"ec_funded":1,"date_published":"2015-06-10T00:00:00Z","file":[{"relation":"main_file","date_created":"2022-02-25T11:55:26Z","creator":"dernst","content_type":"application/pdf","file_size":1371201,"success":1,"file_id":"10795","date_updated":"2022-02-25T11:55:26Z","file_name":"2015_FrontiersEnvironmScience_Parise.pdf","checksum":"26c222487564e1be02a11d688d6f769d","access_level":"open_access"}],"keyword":["General Environmental Science"],"publication_identifier":{"issn":["2296-665X"]},"scopus_import":"1"},{"volume":2015,"issue":"1","publisher":"SIAM","intvolume":"      2015","status":"public","conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2015-01-06","location":"San Diego, CA, United States","start_date":"2015-01-04"},"month":"01","date_created":"2022-02-25T12:18:43Z","quality_controlled":"1","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"}],"citation":{"apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>.","ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2015. SIAM; 2015:1018-1029. doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2015:1018–29. SIAM, 2015. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>.","ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029."},"year":"2015","_id":"10796","publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games","abstract":[{"lang":"eng","text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy)."}],"publication_status":"published","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"page":"1018-1029","external_id":{"arxiv":["1409.6690"]},"date_published":"2015-01-01T00:00:00Z","scopus_import":"1","publication_identifier":{"isbn":["978-161197374-7"]},"arxiv":1,"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Preprint","type":"conference","date_updated":"2022-02-25T12:33:32Z","department":[{"_id":"KrCh"}],"doi":"10.1137/1.9781611973730.69","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award."},{"date_updated":"2021-12-14T07:58:15Z","type":"journal_article","oa_version":"Published Version","day":"15","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","doi":"10.1101/gad.269902.115","has_accepted_license":"1","department":[{"_id":"DaZi"}],"date_published":"2015-12-15T00:00:00Z","file":[{"success":1,"file_id":"9533","date_updated":"2021-06-08T09:55:10Z","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","checksum":"086a88cfca4677646da26ed960cb02e9","access_level":"open_access","relation":"main_file","date_created":"2021-06-08T09:55:10Z","content_type":"application/pdf","creator":"asandaue","file_size":1116846}],"external_id":{"pmid":["26680300"]},"page":"2517–2531","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"scopus_import":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"year":"2015","citation":{"ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2015. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>.","apa":"Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>"},"extern":"1","author":[{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"title":"Evolution and function of genomic imprinting in plants","publication":"Genes and Development","pmid":1,"oa":1,"ddc":["570"],"_id":"9532","file_date_updated":"2021-06-08T09:55:10Z","publisher":"Cold Spring Harbor Laboratory Press","article_type":"review","issue":"24","volume":29,"date_created":"2021-06-08T09:56:24Z","month":"12","status":"public","intvolume":"        29"},{"arxiv":1,"publication_identifier":{"issn":["1571-0653"]},"scopus_import":"1","date_published":"2015-11-01T00:00:00Z","external_id":{"arxiv":["1501.04816"]},"page":"181-187","doi":"10.1016/j.endm.2015.06.027","language":[{"iso":"eng"}],"type":"journal_article","date_updated":"2023-02-23T14:01:28Z","oa_version":"Preprint","day":"01","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-06-21T06:40:34Z","month":"11","status":"public","intvolume":"        49","publisher":"Elsevier","article_type":"original","volume":49,"publication_status":"published","abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"publication":"Electronic Notes in Discrete Mathematics","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","oa":1,"_id":"9575","year":"2015","citation":{"mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49, Elsevier, 2015, pp. 181–87, doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>.","apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49. Elsevier, pp. 181–187, 2015.","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. 2015;49:181-187. doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.04816"}],"author":[{"full_name":"Krivelevich, Michael","first_name":"Michael","last_name":"Krivelevich"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"quality_controlled":"1","extern":"1"},{"date_created":"2021-07-15T14:09:32Z","month":"04","status":"public","intvolume":"        67","publication_identifier":{"issn":["0749-6419"]},"scopus_import":"1","publisher":"Elsevier","article_type":"original","date_published":"2015-04-01T00:00:00Z","page":"1-25","volume":67,"publication_status":"published","abstract":[{"text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation.","lang":"eng"}],"publication":"International Journal of Plasticity","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","language":[{"iso":"eng"}],"doi":"10.1016/j.ijplas.2014.09.009","_id":"9673","date_updated":"2023-02-23T14:04:28Z","type":"journal_article","oa_version":"None","day":"01","year":"2015","citation":{"mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” <i>International Journal of Plasticity</i>, vol. 67, Elsevier, 2015, pp. 1–25, doi:<a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">10.1016/j.ijplas.2014.09.009</a>.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., &#38; Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. <i>International Journal of Plasticity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">https://doi.org/10.1016/j.ijplas.2014.09.009</a>","ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25.","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” <i>International Journal of Plasticity</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">https://doi.org/10.1016/j.ijplas.2014.09.009</a>.","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” <i>International Journal of Plasticity</i>, vol. 67. Elsevier, pp. 1–25, 2015.","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. <i>International Journal of Plasticity</i>. 2015;67:1-25. doi:<a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">10.1016/j.ijplas.2014.09.009</a>"},"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"H.S.","last_name":"Leung","full_name":"Leung, H.S."},{"first_name":"P.S.S.","last_name":"Leung","full_name":"Leung, P.S.S."},{"last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Ngan, A.H.W.","first_name":"A.H.W.","last_name":"Ngan"}],"extern":"1"},{"article_processing_charge":"No","author":[{"last_name":"Leung","first_name":"P S S","full_name":"Leung, P S S"},{"last_name":"Leung","first_name":"H S","full_name":"Leung, H S"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng"},{"last_name":"Ngan","first_name":"A H W","full_name":"Ngan, A H W"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","quality_controlled":"1","extern":"1","citation":{"ista":"Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001.","short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015).","chicago":"Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” <i>Modelling and Simulation in Materials Science and Engineering</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">https://doi.org/10.1088/0965-0393/23/3/035001</a>.","ieee":"P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” <i>Modelling and Simulation in Materials Science and Engineering</i>, vol. 23, no. 3. IOP Publishing, 2015.","ama":"Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. <i>Modelling and Simulation in Materials Science and Engineering</i>. 2015;23(3). doi:<a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">10.1088/0965-0393/23/3/035001</a>","mla":"Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” <i>Modelling and Simulation in Materials Science and Engineering</i>, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">10.1088/0965-0393/23/3/035001</a>.","apa":"Leung, P. S. S., Leung, H. S., Cheng, B., &#38; Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. <i>Modelling and Simulation in Materials Science and Engineering</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">https://doi.org/10.1088/0965-0393/23/3/035001</a>"},"year":"2015","day":"01","oa_version":"None","type":"journal_article","date_updated":"2023-02-23T14:04:54Z","_id":"9684","language":[{"iso":"eng"}],"doi":"10.1088/0965-0393/23/3/035001","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","publication":"Modelling and Simulation in Materials Science and Engineering","abstract":[{"text":"The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept.","lang":"eng"}],"publication_status":"published","volume":23,"issue":"3","date_published":"2015-04-01T00:00:00Z","publisher":"IOP Publishing","article_type":"original","scopus_import":"1","publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"intvolume":"        23","status":"public","article_number":"035001","month":"04","date_created":"2021-07-19T09:11:12Z"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","type":"journal_article","date_updated":"2021-08-09T12:38:49Z","oa_version":"Preprint","day":"01","doi":"10.1103/physrevb.92.180102","language":[{"iso":"eng"}],"date_published":"2015-11-01T00:00:00Z","external_id":{"arxiv":["1511.08668"]},"publication_identifier":{"issn":["1098-0121"],"eissn":["1550-235X"]},"scopus_import":"1","arxiv":1,"citation":{"ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 92, no. 18. American Physical Society, 2015.","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2015;92(18). doi:<a href=\"https://doi.org/10.1103/physrevb.92.180102\">10.1103/physrevb.92.180102</a>","ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/physrevb.92.180102\">https://doi.org/10.1103/physrevb.92.180102</a>.","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/physrevb.92.180102\">10.1103/physrevb.92.180102</a>.","apa":"Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.92.180102\">https://doi.org/10.1103/physrevb.92.180102</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1511.08668","open_access":"1"}],"quality_controlled":"1","extern":"1","author":[{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"full_name":"Tribello, Gareth A.","last_name":"Tribello","first_name":"Gareth A."},{"last_name":"Ceriotti","first_name":"Michele","full_name":"Ceriotti, Michele"}],"year":"2015","title":"Solid-liquid interfacial free energy out of equilibrium","publication":"Physical Review B - Condensed Matter and Materials Physics","oa":1,"_id":"9688","publication_status":"published","abstract":[{"text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.","lang":"eng"}],"issue":"18","volume":92,"publisher":"American Physical Society","article_type":"original","intvolume":"        92","date_created":"2021-07-19T10:07:22Z","month":"11","article_number":"180102","status":"public"},{"publisher":"Public Library of Science","date_published":"2015-11-18T00:00:00Z","month":"11","date_created":"2021-07-23T11:53:50Z","status":"public","oa_version":"Published Version","type":"research_data_reference","date_updated":"2023-02-23T10:07:02Z","year":"2015","day":"18","citation":{"chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">https://doi.org/10.1371/journal.pbio.1002299.s001</a>.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>","ieee":"G. Chevereau <i>et al.</i>, “Excel file containing the raw data for all figures.” Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., &#38; Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">https://doi.org/10.1371/journal.pbio.1002299.s001</a>","mla":"Chevereau, Guillaume, et al. <i>Excel File Containing the Raw Data for All Figures</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume","first_name":"Guillaume","last_name":"Chevereau"},{"full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","first_name":"Marta"},{"last_name":"Batur","first_name":"Tugce","full_name":"Batur, Tugce"},{"full_name":"Guvenek, Aysegul","first_name":"Aysegul","last_name":"Guvenek"},{"first_name":"Dilay Hazal","last_name":"Ayhan","full_name":"Ayhan, Dilay Hazal"},{"first_name":"Erdal","last_name":"Toprak","full_name":"Toprak, Erdal"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias"}],"title":"Excel file containing the raw data for all figures","_id":"9711","department":[{"_id":"ToBo"}],"doi":"10.1371/journal.pbio.1002299.s001","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1619"}]}},{"date_updated":"2025-05-28T11:57:04Z","type":"research_data_reference","oa_version":"Published Version","day":"06","year":"2015","citation":{"apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Other fitness models for comparison &#38; for interacting TFBSs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>","mla":"Tugrul, Murat, et al. <i>Other Fitness Models for Comparison &#38; for Interacting TFBSs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison &#38; for interacting TFBSs.” Public Library of Science, 2015.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison &#38; for interacting TFBSs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison &#38; for interacting TFBSs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison &#38; for Interacting TFBSs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul","first_name":"Murat"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"title":"Other fitness models for comparison & for interacting TFBSs","doi":"10.1371/journal.pgen.1005639.s001","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1666"}]},"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"9712","publisher":"Public Library of Science","date_published":"2015-11-06T00:00:00Z","date_created":"2021-07-23T12:00:37Z","month":"11","status":"public"},{"citation":{"apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., &#38; Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures - submission to PLOS journals. Public Library of Science . <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">https://doi.org/10.1371/journal.pcbi.1004541.s001</a>","mla":"Gómez Sicilia, Àngel, et al. <i>An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals</i>. Public Library of Science , 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>.","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures - submission to PLOS journals. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures - submission to PLOS journals.” Public Library of Science , 2015.","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures - submission to PLOS journals, Public Library of Science , <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals.” Public Library of Science , 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">https://doi.org/10.1371/journal.pcbi.1004541.s001</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"},{"last_name":"Carrión Vázquez","first_name":"Mariano","full_name":"Carrión Vázquez, Mariano"}],"article_processing_charge":"No","oa_version":"Published Version","date_updated":"2023-02-23T10:04:35Z","type":"research_data_reference","year":"2015","day":"23","title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals","_id":"9714","department":[{"_id":"CaHe"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1566"}]},"doi":"10.1371/journal.pcbi.1004541.s001","date_published":"2015-10-23T00:00:00Z","publisher":"Public Library of Science ","month":"10","date_created":"2021-07-23T12:05:28Z","status":"public"},{"title":"Mathematical inference of the results","_id":"9715","department":[{"_id":"NiBa"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1809"}]},"doi":"10.1371/journal.pone.0126907.s001","oa_version":"Published Version","type":"research_data_reference","date_updated":"2023-02-23T10:15:25Z","year":"2015","day":"18","citation":{"chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. <i>Mathematical Inference of the Results</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Mathematical inference of the results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"article_processing_charge":"No","month":"05","date_created":"2021-07-23T12:11:30Z","status":"public","publisher":"Public Library of Science","date_published":"2015-05-18T00:00:00Z"}]