Publikacije

WP1. Metode rudarjenja heterogenih informacijskih omrežij (M1-M24):

  1. KRALJ, Jan, VALMARSKA, Anita, GRČAR, Miha, ROBNIK ŠIKONJA, Marko, LAVRAČ, Nada. Analysis of text-enriched heterogeneous information networks. V: JAPKOWICZ, Nathalie (ur.), STEFANOWSKI, Jerzy (ur.). Big data analysis : new algorithms for a new society, (Studies in big data, ISSN 2197-6503, volume 16). Cham: Springer, 2016, str. 115-139. [link][pdf][COBISS.SI-ID 29316135]
  2. KRALJ, Jan, ROBNIK ŠIKONJA, Marko, LAVRAČ, Nada. Heterogeneous network decomposition and weighting with text mining heuristics. V: CECI, Michelangelo (ur.). New frontiers in mining complex patterns : 4th International Workshop, NFMCP 2015 held in conjunction with ECML-PKDD 2015 Porto, Portugal, September 7, 2015 : revised selected papers, (Lecture notes in computer science, ISSN 0302-9743, Lecture notes in artificial intelligene, 9607). [S. l.]: Springer, 2016, vol. 9607, str. 194-208. [link][pdf][COBISS.SI-ID 29560359]
  3. KRALJ, Jan, VAVPETIČ, Anže, DUMONTIER, Michel, LAVRAČ, Nada. Network ranking assisted semantic data mining. Lecture notes in computer science, ISSN 0302-9743. [Print ed.], str. 752-764. [link][pdf][COBISS.SI-ID 29482535]
  4. KRALJ, Jan, ROBNIK ŠIKONJA, Marko, LAVRAČ, Nada. HINMINE : heterogeneous information network mining with information retrieval heuristics. Journal of intelligent information systems, ISSN 0925-9902, 2018, vol. 50, no. 1, str. 29-61, doi: 10.1007/s10844-017-0444-9. [COBISS.SI-ID 30214439]
  5. ŠKRLJ, Blaž, KRALJ, Jan, LAVRAČ, Nada. CBSSD : community-based semantic subgroup discovery. Journal of intelligent information systems, ISSN 0925-9902, [in press] 2019, 40 str., doi: 10.1007/s10844-019-00545-0. [COBISS.SI-ID 32057639]
  6. PODPEČAN, V., RAMŠAK, Ž., LAVRAČ, N., GRUDEN, K., MILJKOVIĆ, D. BioMine update at M24. Delovno poročilo IJS-DP[COBISS.SI-ID 31186471]
  7. PODPEČAN, V., MILJKOVIĆ, D., LAVRAČ, N. Upgrading the Biomine heterogeneous network. Delovno poročilo IJS-DP [COBISS.SI-ID 30094119]

WP2. Razvoj in primerjalne meritve za programsko okolje (M6-M36):

  1. KRANJC, Janez, ORAČ, Roman, PODPEČAN, Vid, LAVRAČ, Nada, ROBNIK ŠIKONJA, Marko. ClowdFlows : online workflows for distributed big data mining. FGCS, ISSN 0167-739X. [Print ed.], 2017, vol. 68, str. 38-58, doi: 10.1016/j.future.2016.07.018. [link][pdf][COBISS.SI-ID 29851943]
  2. PEROVŠEK, Matic, KRANJC, Janez, ERJAVEC, Tomaž, CESTNIK, Bojan, LAVRAČ, Nada. TextFlows : a visual programming platform for text mining and natural language processing. Science of computer programming, ISSN 0167-6423, 2016, vol. 121, str. 128-152, doi: 10.1016/j.scico.2016.01.001. [link][pdf][COBISS.SI-ID 29549095]
  3. ŠKRLJ, Blaž, KRALJ, Jan, LAVRAČ, Nada. Targeted end-to-end knowledge graph decomposition. V: RIGUZZI, Fabrizio (ur.), BELLODI, Elena (ur.), ZESE, Riccardo (ur.). Inductive logic programming : 28th International Conference, ILP 2018 Ferrara, Italy, September 2-4, 2018 : proceedings, (Lecture notes in computer science, ISSN 0302-9743, LNCS 11105). Cham: Springer. 2018, str. 157-171. [COBISS.SI-ID 31643431]
  4. KRALJ, J., LAVRAČ, N. Implementing workflows, developed in WP1, in the ClowdFlows development environment. Delovno poročilo IJS-DP [COBISS.SI-ID 32154151].
  5. POLLAK, S. Bisociative knowledge discovery for cross-domain literature mining: invited talk, Seminar Series of Centre For Medical Informatics, United Kingdom, University of Edinburgh, 10th December 2018, GB. [COBISS.SI-ID 31960615]
  6. MILJKOVIĆ, D., VAVPETIČ, A., LAVRAČ, N., PODPEČAN, V., KRANJC, J., CESTNIK, B. Upgrading the ClowdFlows browser-based workflow management platform. Delovno poročilo IJS-DP [COBISS.SI-ID 30084647]
  7. KRALJ, Jan, ŠKRLJ, Blaž. Final implementation of ClowdFlows or TextFlows, including the final HINMINE workflow, demonstratedon nontrivial knowledge discovery benchmarkproblems. 2.3., (Analysis of heterogeneous information networks for knowledge discovery inlifesciences, number J7-7303). Ljubljana: Institut Jožes Stefan, 2018. 32 str., ilustr. [COBISS.SI-ID 32176679]

WP3. Aplikacija tehnologij (M6-M36):

  1. MILJKOVIĆ, Dragana, LAVRAČ, Nada, BOHANEC, Marko, MILEVA-BOSHKOSKA, Biljana. Detection of dependencies between literature domains through relation extraction and copulas. V: International Conference on Control, Decision and Information Technologies, CoDIt 2016, April 6-8, 2016, St. Paul’s Bay, Malta. Danvers: IEEE = Institute of Electrical and Electronics Engineers, 2016, str. 302-307. [link][pdf][COBISS.SI-ID 29894439]
  2. RAMŠAK, Živa, STARE, Tjaša, LUKAN, Tjaša, MILJKOVIĆ, Dragana, LAVRAČ, Nada, GRUDEN, Kristina. Modellling of potato immune signalling response. V: 16th Triennial Meeting of the Virology Section of the European Association of Potato Research & 8th Annual Meeting of PVYwide Organization, May 31st -June 3rd 2016 Ljubljana, Slovenia. [S. l.: s. n., 2016], str. 24. [pdf][COBISS.SI-ID 3900239]
  3. CESTNIK, Bojan, FABBRETTI, Elsa, GUBIANI, Donatella, LAVRAČ, Nada, URBANČIČ, Tanja. Exploring outlier documents to investigate potential links between gut microbiota and Alzheimer’s disease. V: ORTUÑO, Francisco (ur.), ROJAS RUIZ, Ignacio (ur.). Proceedings, extended abstracs, IWBBIO 2016, International Work-Conference on Bioinformatics and Biomedical Engineering, April 20-22, 2016, Granada, Spain. [S. l.: s. n.], 2016, str. 475-486. [pdf][COBISS.SI-ID 29481511]
  4. GUBIANI, Donatella, FABBRETTI, Elsa, CESTNIK, Bojan, LAVRAČ, Nada, URBANČIČ, Tanja. Outlier based literature exploration for cross-domain linking of Alzheimer’s disease and gut microbiota. Expert systems with applications, ISSN 0957-4174. [Print ed.], 2017, vol. 85, str. 386-396, ilustr., doi: 10.1016/j.eswa.2017.05.026. [link][pdf][COBISS.SI-ID 4787451]
  5. CESTNIK, Bojan, FABBRETTI, Elsa, GUBIANI, Donatella, URBANČIČ, Tanja, LAVRAČ, Nada. Reducing the search space in literature-based discovery by exploring outlier documents : a case study in finding links between gut microbiome and Alzheimer’s disease. Genomics and computational biology, ISSN 2365-7154, 2017, vol. 3, no. 3, str. e58-1-e58-10, doi: 10.18547/gcb.2017.vol3.iss3.e58. [link][pdf][COBISS.SI-ID 30497575]
  6. DOBNIK, David, LAZAR, Ana, STARE, Tjaša, GRUDEN, Kristina, VLEESHOUWERS, Vivianne G. A. A., ŽEL, Jana. Solanum venturii, a suitable model system for virus-induced gene silencing studies in potato reveals StMKK6 as an important player in plant immunity. Plant methods, ISSN 1746-4811, 2016, vol. 12, no. 29, str. 1-12 [link][pdf][COBISS.SI-ID 3877967]
  7. WANG, Lei, NÄGELE, Thomas, DOERFLER, Hannes, FRAGNER, Lena, CHATURVEDI, Palak, NUKARINEN, Ella, BELLAIRE, Anke, HUBER, Werner, WEISZMANN, Jakob, ENGELMEIER, Doris, RAMŠAK, Živa, GRUDEN, Kristina, WECKWERTH, Wolfram. System level analysis of cacao seed ripening reveals a sequential interplay of primary and secondary metabolism leading to polyphenol accumulation and preparation of stress resistance. The Plant journal, ISSN 0960-7412, 2016, vol. 87, iss. 3, str. 318-332. [link][pdf][COBISS.SI-ID 3869775]
  8. BAEBLER, Špela, RAMŠAK, Živa, STARE, Tjaša, COLL RIUS, Anna, TZFADIA, Oren, GRUDEN, Kristina. Genes & pathways (gene expression, proteomics, metabolomics) : cellular processes and regulatory networks novel hormonal cross-talks in potato discovered by network analysis. V: International Plant & Animal Genome XXV, January 14-18, 2017 – San Diego, CA, USA. [S. l.: s. n.], 2016-2017. [pdf][COBISS.SI-ID 4243279]
  9. BAEBLER, Špela, RAMŠAK, Živa, STARE, Tjaša, COLL RIUS, Anna, TZFADIA, Oren, GRUDEN, Kristina. Network analysis unravels crosstalk between ethylene and salicylic acid signalling pathways in virus-infected potato. V: SolGenomics : from advances to applications : conference program, 13th Annual Solanaceae Conference, September 12 – 16, 2016, Davis, California, USA. [S. l.: s. n., 2016], str. 41. [link][pdf][COBISS.SI-ID 4043087]
  10. COLL RIUS, Anna, RAMŠAK, Živa, BAEBLER, Špela, STARE, Tjaša, TZFADIA, Oren, GRUDEN, Kristina. Novel crosstalk between ethylene and salicylic acid signalling pathways in virus infected potato unravelled by network analysis. V: GERIČ STARE, Barbara (ur.), KROJ, Thomas (ur.), ŠIRCA, Saša (ur.). Program & abstracts book : 4th Annual Conference of the COST Action, 1st – 3rd March 2017, Bled, Slovenia : COST FA 1208 : [pathogen-informed strategies for sustainable broad-spectrum crop resistance]. Ljubljana: Agricultural Institute of Slovenia, 2017, str. 33. [COBISS.SI-ID 4258383]
  11. RAMŠAK, Živa, BAEBLER, Špela, STARE, Tjaša, COLL RIUS, Anna, TZFADIA, Oren, GRUDEN, Kristina. Novel hormonal cross-talks in potato discovered by network analysis. V: BIERE, Arjen (ur.), et al. Book of abstracts, (Cost action FA1405, CAMo (Crop-Arthropod Microbe) interactions). Ljubljana: National Institute of Biology: Faculty of Computer and Informations Science, 2017, str. 21. [COBISS.SI-ID 4256335]
  12. MILJKOVIĆ, Dragana, LAVRAČ, Nada, BOHANEC, Marko, MILEVA BOSHKOSKA, Biljana. Discovering dependencies between domains of redox potential and plant defence through triplet extraction and copulas. International journal of intelligent engineering informatics, ISSN 1758-8723, 2018, vol. 6, no. 1/2, str. 61-77. http://www.inderscience.com/info/ingeneral/forthcoming.php?jcode=ijiei, doi: 10.1504/IJIEI.2018.10012065. [COBISS.SI-ID 2048463379]
  13. ŠKRLJ, Blaž, KRALJ, Jan, VAVPETIČ, Anže, LAVRAČ, Nada. Community-based semantic subgroup discove. V: APPICE, Annalisa (ur.). New frontiers in mining complex patterns : 6th International Workshop, NFMCP 2017, in conjunction with ECML-PKDD 2017, Skopje, Macedonia, September 18-22, 2017 : revised selected papers, (Lecture notes in computer science, ISSN 0302-9743, Lecture notes in artificial intelligence, LNCS 10785). Cham: Springer. 2018, lNCS 10785, str. 182-196. [COBISS.SI-ID 31643687]
  14. GAMBERGER, Dragan, STARE, Tjaša, MILJKOVIĆ, Dragana, GRUDEN, Kristina, LAVRAČ, Nada. Discovery of relevant response in infected potato plants from time series of gene expression data. Machine learning and knowledge extraction, 2019, vol. 1, no. 1, str. 401-413, doi: 10.3390/make1010023. [COBISS.SI-ID 32031015]
  15. RAMŠAK, Živa, COLL RIUS, Anna, STARE, Tjaša, TZFADIA, Oren, BAEBLER, Špela, VAN DE PEER, Yves, GRUDEN, Kristina. Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato. Plant physiology, ISSN 0032-0889, 2018, vol. , no. , 30 str., [in press], doi: 10.1104/pp.18.00450. [COBISS.SI-ID 4778575]
  16. POMPE NOVAK, M., PODPEČAN, V., MILJKOVIĆ, D., POLLAK, S., CESTNIK, B., LAVRAČ, N. Refined vocabulary for cross-context knowledge discovery in plant immune signalling. Delovno poročilo IJS-DP [COBISS.SI-ID 32171815]