TitleAssistant Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
AddressOne Baylor Plaza
Houston, TX 77030
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    P01HD039691     (KUSPA, ADAM)Jun 19, 2001 - Apr 30, 2018
    Functional Genomics of Dictyostelium
    Role: Co-Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B. From hype to reality: data science enabling personalized medicine. BMC Med. 2018 08 27; 16(1):150. PMID: 30145981.
      Citations: 39     Fields:    Translation:Humans
    2. Carreras-Puigvert J, Zitnik M, Jemth AS, Carter M, Unterlass JE, Hallström B, Loseva O, Karem Z, Calderón-Montaño JM, Lindskog C, Edqvist PH, Matuszewski DJ, Ait Blal H, Berntsson RPA, Häggblad M, Martens U, Studham M, Lundgren B, Wählby C, Sonnhammer ELL, Lundberg E, Stenmark P, Zupan B, Helleday T. A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family. Nat Commun. 2017 11 16; 8(1):1541. PMID: 29142246.
      Citations: 28     Fields:    Translation:HumansCells
    3. Stajdohar M, Rosengarten RD, Kokosar J, Jeran L, Blenkus D, Shaulsky G, Zupan B. dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond. BMC Bioinformatics. 2017 Jun 02; 18(1):291. PMID: 28578698.
      Citations: 6     Fields:    Translation:AnimalsCells
    4. Zitnik M, Zupan B. Jumping across biomedical contexts using compressive data fusion. Bioinformatics. 2016 06 15; 32(12):i90-i100. PMID: 27307649.
      Citations: 2     Fields:    Translation:Humans
      Citations: 6     Fields:    Translation:Humans
    6. Rosengarten RD, Santhanam B, Fuller D, Katoh-Kurasawa M, Loomis WF, Zupan B, Shaulsky G. Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum. BMC Genomics. 2015 Apr 13; 16:294. PMID: 25887420.
      Citations: 25     Fields:    Translation:AnimalsCells
    7. Sluga D, Curk T, Zupan B, Lotric U. Heterogeneous computing architecture for fast detection of SNP-SNP interactions. BMC Bioinformatics. 2014 Jun 25; 15:216. PMID: 24964802.
      Citations: 3     Fields:    
    8. Franco-Duarte R, Mendes I, Umek L, Drumonde-Neves J, Zupan B, Schuller D. Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae. Yeast. 2014 Jul; 31(7):265-77. PMID: 24752995.
      Citations: 5     Fields:    Translation:AnimalsCells
    9. Brdar S, Crnojevic V, Zupan B. Integrative clustering by nonnegative matrix factorization can reveal coherent functional groups from gene profile data. IEEE J Biomed Health Inform. 2015 Mar; 19(2):698-708. PMID: 24733033.
      Citations:    Fields:    Translation:Animals
    10. Miranda ER, Zhuchenko O, Toplak M, Santhanam B, Zupan B, Kuspa A, Shaulsky G. ABC transporters in Dictyostelium discoideum development. PLoS One. 2013; 8(8):e70040. PMID: 23967067.
      Citations: 12     Fields:    Translation:AnimalsCells
    11. Mendes I, Franco-Duarte R, Umek L, Fonseca E, Drumonde-Neves J, Dequin S, Zupan B, Schuller D. Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles. PLoS One. 2013; 8(7):e66523. PMID: 23874393.
      Citations: 7     Fields:    Translation:Animals
    12. Nasser W, Santhanam B, Miranda ER, Parikh A, Juneja K, Rot G, Dinh C, Chen R, Zupan B, Shaulsky G, Kuspa A. Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions. Curr Biol. 2013 May 20; 23(10):862-72. PMID: 23664307.
      Citations: 24     Fields:    Translation:AnimalsCells
    13. Mulas F, del Fabbro E, Zupan B, Bellazzi R. Interest propagation for knowledge extraction and representation. Stud Health Technol Inform. 2013; 186:182-6. PMID: 23542994.
      Citations: 1     Fields:    
    14. Miranda ER, Rot G, Toplak M, Santhanam B, Curk T, Shaulsky G, Zupan B. Transcriptional profiling of Dictyostelium with RNA sequencing. Methods Mol Biol. 2013; 983:139-71. PMID: 23494306.
      Citations: 9     Fields:    Translation:AnimalsCells
    15. Zuccotti M, Merico V, Belli M, Mulas F, Sacchi L, Zupan B, Redi CA, Prigione A, Adjaye J, Bellazzi R, Garagna S. OCT4 and the acquisition of oocyte developmental competence during folliculogenesis. Int J Dev Biol. 2012; 56(10-12):853-8. PMID: 23417407.
      Citations: 4     Fields:    Translation:AnimalsCells
    16. Mulas F, Sacchi L, Zagar L, Garagna S, Zuccotti M, Zupan B, Bellazzi R. Knowledge-based bioinformatics for the study of mammalian oocytes. Int J Dev Biol. 2012; 56(10-12):859-66. PMID: 23417408.
      Citations:    Fields:    Translation:HumansAnimalsCells
    17. Huang E, Talukder S, Hughes TR, Curk T, Zupan B, Shaulsky G, Katoh-Kurasawa M. BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium. Dev Biol. 2011 Oct 01; 358(1):137-46. PMID: 21810415.
      Citations: 9     Fields:    Translation:AnimalsCells
    18. Zagar L, Mulas F, Garagna S, Zuccotti M, Bellazzi R, Zupan B. Stage prediction of embryonic stem cell differentiation from genome-wide expression data. Bioinformatics. 2011 Sep 15; 27(18):2546-53. PMID: 21765096.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    19. Crippa S, Cassano M, Messina G, Galli D, Galvez BG, Curk T, Altomare C, Ronzoni F, Toelen J, Gijsbers R, Debyser Z, Janssens S, Zupan B, Zaza A, Cossu G, Sampaolesi M. miR669a and miR669q prevent skeletal muscle differentiation in postnatal cardiac progenitors. J Cell Biol. 2011 Jun 27; 193(7):1197-212. PMID: 21708977.
      Citations: 30     Fields:    Translation:AnimalsCells
    20. Curk T, Rot G, Zupan B. SNPsyn: detection and exploration of SNP-SNP interactions. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W444-9. PMID: 21576219.
      Citations: 9     Fields:    
    21. Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp. 2011 Apr 30; (50). PMID: 21559008.
      Citations: 102     Fields:    Translation:Cells
    22. Smrke D, Biscevic M, Smrke BU, Zupan B. Biomechanical and clinical alterations of the hip joint following femoral neck fracture and implantation of bipolar hip endoprosthesis. Coll Antropol. 2010 Sep; 34(3):931-5. PMID: 20977085.
      Citations:    Fields:    Translation:Humans
    23. Mattiazzi M, Curk T, Krizaj I, Zupan B, Petrovic U. Inference of the molecular mechanism of action from genetic interaction and gene expression data. OMICS. 2010 Aug; 14(4):357-67. PMID: 20726796.
      Citations:    Fields:    
    24. König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol. 2010 Jul; 17(7):909-15. PMID: 20601959.
      Citations: 470     Fields:    Translation:HumansCells
    25. Parikh A, Huang E, Dinh C, Zupan B, Kuspa A, Subramanian D, Shaulsky G. New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. BMC Bioinformatics. 2010 Mar 31; 11:163. PMID: 20356373.
      Citations: 4     Fields:    Translation:AnimalsCells
    26. Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, Shaulsky G. Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol. 2010; 11(3):R35. PMID: 20236529.
      Citations: 91     Fields:    Translation:AnimalsCells
    27. Toplak M, Curk T, Demsar J, Zupan B. Does replication groups scoring reduce false positive rate in SNP interaction discovery? BMC Genomics. 2010 Jan 22; 11:58. PMID: 20092660.
      Citations: 1     Fields:    
    28. Nuzzo A, Mulas F, Gabetta M, Arbustini E, Zupan B, Larizza C, Bellazzi R. Text Mining approaches for automated literature knowledge extraction and representation. Stud Health Technol Inform. 2010; 160(Pt 2):954-8. PMID: 20841825.
      Citations: 5     Fields:    
    29. Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B. dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. BMC Bioinformatics. 2009 Aug 25; 10:265. PMID: 19706156.
      Citations: 34     Fields:    Translation:Animals
    30. Benabentos R, Hirose S, Sucgang R, Curk T, Katoh M, Ostrowski EA, Strassmann JE, Queller DC, Zupan B, Shaulsky G, Kuspa A. Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium. Curr Biol. 2009 Apr 14; 19(7):567-72. PMID: 19285397.
      Citations: 57     Fields:    Translation:Animals
    31. Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 2009 Feb; 3(1):9-17. PMID: 19383362.
      Citations: 11     Fields:    Translation:Humans
    32. Fey P, Gaudet P, Curk T, Zupan B, Just EM, Basu S, Merchant SN, Bushmanova YA, Shaulsky G, Kibbe WA, Chisholm RL. dictyBase--a Dictyostelium bioinformatics resource update. Nucleic Acids Res. 2009 Jan; 37(Database issue):D515-9. PMID: 18974179.
      Citations: 44     Fields:    Translation:AnimalsCells
    33. Zupan B, Demsar J. Open-source tools for data mining. Clin Lab Med. 2008 Mar; 28(1):37-54, vi. PMID: 18194717.
      Citations: 4     Fields:    Translation:Humans
    34. Mramor M, Leban G, Demsar J, Zupan B. Visualization-based cancer microarray data classification analysis. Bioinformatics. 2007 Aug 15; 23(16):2147-54. PMID: 17586552.
      Citations: 14     Fields:    Translation:Humans
    35. Bellazzi R, Zupan B. Towards knowledge-based gene expression data mining. J Biomed Inform. 2007 Dec; 40(6):787-802. PMID: 17683991.
      Citations: 13     Fields:    Translation:Cells
    36. Demsar J, Leban G, Zupan B. FreeViz--an intelligent multivariate visualization approach to explorative analysis of biomedical data. J Biomed Inform. 2007 Dec; 40(6):661-71. PMID: 17531544.
      Citations: 9     Fields:    
    37. Aoki N, Demsar J, Zupan B, Mozina M, Pretto EA, Oda J, Tanaka H, Sugimoto K, Yoshioka T, Fukui T. Predictive model for estimating risk of crush syndrome: a data mining approach. J Trauma. 2007 Apr; 62(4):940-5. PMID: 17426552.
      Citations: 3     Fields:    Translation:Humans
    38. Bellazzi R, Zupan B. Predictive data mining in clinical medicine: current issues and guidelines. Int J Med Inform. 2008 Feb; 77(2):81-97. PMID: 17188928.
      Citations: 123     Fields:    
    39. Zupan B, Holmes JH, Bellazzi R. Knowledge-based data analysis and interpretation. Artif Intell Med. 2006 Jul; 37(3):163-5. PMID: 16690309.
      Citations: 3     Fields:    Translation:Humans
    40. Katoh M, Curk T, Xu Q, Zupan B, Kuspa A, Shaulsky G. Developmentally regulated DNA methylation in Dictyostelium discoideum. Eukaryot Cell. 2006 Jan; 5(1):18-25. PMID: 16400165.
      Citations: 25     Fields:    Translation:AnimalsCells
    41. Sacchi L, Bellazzi R, Larizza C, Magni P, Curk T, Petrovic U, Zupan B. TA-clustering: cluster analysis of gene expression profiles through Temporal Abstractions. Int J Med Inform. 2005 Aug; 74(7-8):505-17. PMID: 15941669.
      Citations: 5     Fields:    Translation:Animals
    42. Juvan P, Demsar J, Shaulsky G, Zupan B. GenePath: from mutations to genetic networks and back. Nucleic Acids Res. 2005 Jul 01; 33(Web Server issue):W749-52. PMID: 15980576.
      Citations: 2     Fields:    Translation:Animals
    43. Van Driessche N, Demsar J, Booth EO, Hill P, Juvan P, Zupan B, Kuspa A, Shaulsky G. Epistasis analysis with global transcriptional phenotypes. Nat Genet. 2005 May; 37(5):471-7. PMID: 15821735.
      Citations: 46     Fields:    Translation:AnimalsCells
    44. Leban G, Bratko I, Petrovic U, Curk T, Zupan B. VizRank: finding informative data projections in functional genomics by machine learning. Bioinformatics. 2005 Feb 01; 21(3):413-4. PMID: 15358614.
      Citations: 8     Fields:    
    45. Curk T, Demsar J, Xu Q, Leban G, Petrovic U, Bratko I, Shaulsky G, Zupan B. Microarray data mining with visual programming. Bioinformatics. 2005 Feb 01; 21(3):396-8. PMID: 15308546.
      Citations: 32     Fields:    
    46. Zupan B, Bratko I, Demsar J, Juvan P, Curk T, Borstnik U, Beck JR, Halter J, Kuspa A, Shaulsky G. GenePath: a system for inference of genetic networks and proposal of genetic experiments. Artif Intell Med. 2003 Sep-Oct; 29(1-2):107-30. PMID: 12957783.
      Citations: 3     Fields:    Translation:HumansAnimals
    47. Zupan B, Demsar J, Bratko I, Juvan P, Halter JA, Kuspa A, Shaulsky G. GenePath: a system for automated construction of genetic networks from mutant data. Bioinformatics. 2003 Feb 12; 19(3):383-9. PMID: 12584124.
      Citations: 9     Fields:    Translation:Animals
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