[{"abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:11Z","doi":"10.15479/at:ista:/5757","type":"research_data","file":[{"checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758","file_name":"FileS1.zip","access_level":"open_access","creator":"cfraisse","file_size":369837892,"date_created":"2018-12-19T14:19:52Z","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","content_type":"application/zip"},{"content_type":"application/zip","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS2.zip","access_level":"open_access","relation":"main_file","file_size":84856909,"date_created":"2018-12-19T14:19:49Z","checksum":"3592e467b4d8206650860b612d6e12f3","file_id":"5759"},{"checksum":"c37ac5d5437c457338afc128c1240655","file_id":"5760","file_name":"FileS3.txt","access_level":"open_access","creator":"cfraisse","file_size":881133,"date_created":"2018-12-19T14:19:49Z","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain"},{"file_id":"5761","checksum":"943dfd14da61817441e33e3e3cb8cdb9","date_created":"2018-12-19T14:19:49Z","file_size":883742,"relation":"main_file","access_level":"open_access","file_name":"FileS4.txt","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain"},{"content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","relation":"main_file","date_created":"2018-12-19T14:19:49Z","file_size":2495437,"creator":"cfraisse","file_name":"FileS5.txt","access_level":"open_access","file_id":"5762","checksum":"1c669b6c4690ec1bbca3e2da9f566d17"},{"file_id":"5763","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","date_created":"2018-12-19T14:19:50Z","file_size":15913457,"relation":"main_file","access_level":"open_access","file_name":"FileS6.txt","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain"},{"content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","access_level":"open_access","file_name":"FileS7.txt","relation":"main_file","file_size":2584120,"date_created":"2018-12-19T14:19:50Z","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_id":"5764"},{"access_level":"open_access","file_name":"FileS8.txt","creator":"cfraisse","date_created":"2018-12-19T14:19:50Z","file_size":2446059,"relation":"main_file","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","file_id":"5765","content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z"},{"checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","file_id":"5766","access_level":"open_access","file_name":"FileS9.txt","creator":"cfraisse","date_created":"2018-12-19T14:19:50Z","file_size":100737,"relation":"main_file","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075"}],"oa":1,"ec_funded":1,"_id":"5757","related_material":{"record":[{"status":"public","id":"6089","relation":"research_paper"}]},"oa_version":"Published Version","contributor":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"ddc":["576"],"citation":{"short":"C. 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Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108.","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","mla":"Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. 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It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:47:03Z","content_type":"application/octet-stream","file_id":"5622","checksum":"e620eff260646f57b479a69492c8b765","relation":"main_file","file_size":1336936,"date_created":"2018-12-12T13:03:04Z","creator":"system","access_level":"open_access","file_name":"IST-2017-61-v1+1_bint_fishmovie32_100.mat"},{"date_updated":"2020-07-14T12:47:03Z","content_type":"application/zip","checksum":"de83f9b81ea0aae3cddfc3ed982e0759","file_id":"5623","creator":"system","access_level":"open_access","file_name":"IST-2017-61-v1+2_bint_fishmovie32_100.zip","relation":"main_file","file_size":1897543,"date_created":"2018-12-12T13:03:05Z"}],"type":"research_data","oa":1,"author":[{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Amodei, Dario","last_name":"Amodei","first_name":"Dario"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"2257","status":"public","relation":"research_paper"}]},"_id":"5562","ddc":["570"],"oa_version":"Published Version","datarep_id":"61","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61","mla":"Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:61.","short":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).","ista":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:61.","chicago":"Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.","apa":"Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). 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Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017."},"article_processing_charge":"No","date_created":"2018-12-12T12:31:33Z","title":"Multi-electrode array recording from salamander retinal ganglion cells"},{"day":"13","status":"public","department":[{"_id":"VlKo"}],"keyword":["graph matching","feature matching","QAP","MAP-inference"],"year":"2017","date_updated":"2024-02-21T13:46:31Z","date_published":"2017-02-13T00:00:00Z","month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"first_name":"Dagmar","full_name":"Kainmueller, Dagmar","last_name":"Kainmueller"},{"full_name":"Jug, Florian","last_name":"Jug","first_name":"Florian"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"},{"full_name":"Meyers, Gene","last_name":"Meyers","first_name":"Gene"}],"type":"research_data","file":[{"relation":"main_file","date_created":"2018-12-12T13:02:54Z","file_size":327042819,"creator":"system","file_name":"IST-2017-57-v1+1_wormMatchingProblems.zip","access_level":"open_access","file_id":"5614","checksum":"3dc3e1306a66028a34181ebef2923139","content_type":"application/zip","date_updated":"2020-07-14T12:47:03Z"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Graph matching problems as described in \"Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans.\" by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in \"Feature Correspondence via Graph Matching: Models and Global Optimization.\" by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:03Z","doi":"10.15479/AT:ISTA:57","title":"Graph matching problems for annotating C. Elegans","date_created":"2018-12-12T12:31:32Z","article_processing_charge":"No","citation":{"apa":"Kainmueller, D., Jug, F., Rother, C., & Meyers, G. (2017). Graph matching problems for annotating C. Elegans. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:57","ieee":"D. Kainmueller, F. Jug, C. Rother, and G. Meyers, “Graph matching problems for annotating C. Elegans.” Institute of Science and Technology Austria, 2017.","ista":"Kainmueller D, Jug F, Rother C, Meyers G. 2017. Graph matching problems for annotating C. Elegans, Institute of Science and Technology Austria, 10.15479/AT:ISTA:57.","chicago":"Kainmueller, Dagmar, Florian Jug, Carsten Rother, and Gene Meyers. “Graph Matching Problems for Annotating C. Elegans.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:57.","mla":"Kainmueller, Dagmar, et al. Graph Matching Problems for Annotating C. Elegans. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:57.","short":"D. Kainmueller, F. Jug, C. Rother, G. Meyers, (2017).","ama":"Kainmueller D, Jug F, Rother C, Meyers G. Graph matching problems for annotating C. Elegans. 2017. doi:10.15479/AT:ISTA:57"},"acknowledgement":"We thank Vladimir Kolmogorov and Stephan Saalfeld forinspiring discussions.","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa_version":"Published Version","datarep_id":"57","ddc":["000"],"_id":"5561"},{"_id":"5563","datarep_id":"64","oa_version":"Published Version","ddc":["571"],"tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"article_processing_charge":"No","citation":{"ama":"Lukacisin M. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2017. doi:10.15479/AT:ISTA:64","mla":"Lukacisin, Martin. MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:64.","short":"M. Lukacisin, (2017).","ista":"Lukacisin M. 2017. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:64.","chicago":"Lukacisin, Martin. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:64.","apa":"Lukacisin, M. (2017). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:64","ieee":"M. Lukacisin, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017."},"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","date_created":"2018-12-12T12:31:33Z","doi":"10.15479/AT:ISTA:64","file_date_updated":"2020-07-14T12:47:03Z","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"file":[{"file_size":296722548,"date_created":"2018-12-12T13:02:37Z","relation":"main_file","file_name":"IST-2016-45-v1+1_PaperCode.zip","access_level":"open_access","creator":"system","file_id":"5602","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","content_type":"application/zip","date_updated":"2020-07-14T12:47:03Z"}],"type":"research_data","author":[{"first_name":"Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin","full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"03","date_published":"2017-03-20T00:00:00Z","date_updated":"2024-02-21T13:46:47Z","year":"2017","license":"https://creativecommons.org/licenses/by-sa/4.0/","status":"public","department":[{"_id":"ToBo"}],"day":"20"}]