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Items: 1 to 50 of 128

1.

scOrange-a tool for hands-on training of concepts from single-cell data analytics.

Stražar M, Žagar L, Kokošar J, Tanko V, Erjavec A, Poličar PG, Starič A, Demšar J, Shaulsky G, Menon V, Lemire A, Parikh A, Zupan B.

Bioinformatics. 2019 Jul 15;35(14):i4-i12. doi: 10.1093/bioinformatics/btz348.

2.

Fast optimization of non-negative matrix tri-factorization.

Čopar A, Zupan B, Zitnik M.

PLoS One. 2019 Jun 11;14(6):e0217994. doi: 10.1371/journal.pone.0217994. eCollection 2019.

3.

From hype to reality: data science enabling personalized medicine.

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.

BMC Med. 2018 Aug 27;16(1):150. doi: 10.1186/s12916-018-1122-7.

4.

Empathic Responses to Affective Film Clips Following Brain Injury and the Association With Emotion Recognition Accuracy.

Neumann D, Zupan B.

Arch Phys Med Rehabil. 2019 Mar;100(3):458-463. doi: 10.1016/j.apmr.2018.07.431. Epub 2018 Aug 22.

PMID:
30142314
5.

Sex differences in response to emotion recognition training after traumatic brain injury.

Babbage DR, Zupan B, Neumann D, Willer B.

Brain Inj. 2018;32(12):1492-1499. doi: 10.1080/02699052.2018.1497811. Epub 2018 Jul 17.

PMID:
30015503
6.

Sex-based differences in affective and cognitive empathy following severe traumatic brain injury.

Zupan B, Neumann D, Babbage D, Willer B.

Neuropsychology. 2018 Jul;32(5):554-563. doi: 10.1037/neu0000462.

PMID:
29952609
7.

Genome Sequence of a Lethal Strain of Xylem-Invading Verticillium nonalfalfae.

Jakše J, Jelen V, Radišek S, de Jonge R, Mandelc S, Majer A, Curk T, Zupan B, Thomma BPHJ, Javornik B.

Genome Announc. 2018 Jan 11;6(2). pii: e01458-17. doi: 10.1128/genomeA.01458-17.

8.

Scalable non-negative matrix tri-factorization.

Čopar A, Žitnik M, Zupan B.

BioData Min. 2017 Dec 29;10:41. doi: 10.1186/s13040-017-0160-6. eCollection 2017.

9.

Maternal Brain TNF-α Programs Innate Fear in the Offspring.

Zupan B, Liu B, Taki F, Toth JG, Toth M.

Curr Biol. 2017 Dec 18;27(24):3859-3863.e3. doi: 10.1016/j.cub.2017.10.071. Epub 2017 Nov 30.

10.

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family.

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.

Nat Commun. 2017 Nov 16;8(1):1541. doi: 10.1038/s41467-017-01642-w.

11.

dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond.

Stajdohar M, Rosengarten RD, Kokosar J, Jeran L, Blenkus D, Shaulsky G, Zupan B.

BMC Bioinformatics. 2017 Jun 2;18(1):291. doi: 10.1186/s12859-017-1706-9.

12.

Film clips and narrative text as subjective emotion elicitation techniques.

Zupan B, Babbage DR.

J Soc Psychol. 2017;157(2):194-210. doi: 10.1080/00224545.2016.1208138. Epub 2016 Jul 6.

PMID:
27385591
13.

Jumping across biomedical contexts using compressive data fusion.

Zitnik M, Zupan B.

Bioinformatics. 2016 Jun 15;32(12):i90-i100. doi: 10.1093/bioinformatics/btw247.

14.

Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium.

Li CL, Santhanam B, Webb AN, Zupan B, Shaulsky G.

Genome Res. 2016 Sep;26(9):1268-76. doi: 10.1101/gr.205682.116. Epub 2016 Jun 15.

15.
16.

Programming social behavior by the maternal fragile X protein.

Zupan B, Sharma A, Frazier A, Klein S, Toth M.

Genes Brain Behav. 2016 Jul;15(6):578-87. doi: 10.1111/gbb.12298. Epub 2016 Jun 10.

17.

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins.

Stražar M, Žitnik M, Zupan B, Ule J, Curk T.

Bioinformatics. 2016 May 15;32(10):1527-35. doi: 10.1093/bioinformatics/btw003. Epub 2016 Jan 18.

18.
19.

Sieve-based relation extraction of gene regulatory networks from biological literature.

Žitnik S, Žitnik M, Zupan B, Bajec M.

BMC Bioinformatics. 2015;16 Suppl 16:S1. doi: 10.1186/1471-2105-16-S16-S1. Epub 2015 Oct 30.

20.

Gene Prioritization by Compressive Data Fusion and Chaining.

Žitnik M, Nam EA, Dinh C, Kuspa A, Shaulsky G, Zupan B.

PLoS Comput Biol. 2015 Oct 14;11(10):e1004552. doi: 10.1371/journal.pcbi.1004552. eCollection 2015 Oct.

21.

Data Fusion by Matrix Factorization.

Žitnik M, Zupan B.

IEEE Trans Pattern Anal Mach Intell. 2015 Jan;37(1):41-53. doi: 10.1109/TPAMI.2014.2343973.

PMID:
26353207
22.

Gene network inference by fusing data from diverse distributions.

Žitnik M, Zupan B.

Bioinformatics. 2015 Jun 15;31(12):i230-9. doi: 10.1093/bioinformatics/btv258.

23.

Exploration of a new tool for assessing emotional inferencing after traumatic brain injury.

Zupan B, Neumann D, Babbage DR, Willer B.

Brain Inj. 2015;29(7-8):877-87. doi: 10.3109/02699052.2015.1011233. Epub 2015 May 7.

24.

Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.

Rosengarten RD, Santhanam B, Fuller D, Katoh-Kurasawa M, Loomis WF, Zupan B, Shaulsky G.

BMC Genomics. 2015 Apr 13;16:294. doi: 10.1186/s12864-015-1491-7.

25.

Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome-Mitochondria Interactions through the ERMES Complex.

Mattiazzi Ušaj M, Brložnik M, Kaferle P, Žitnik M, Wolinski H, Leitner F, Kohlwein SD, Zupan B, Petrovič U.

J Mol Biol. 2015 Jun 5;427(11):2072-87. doi: 10.1016/j.jmb.2015.03.004. Epub 2015 Mar 10.

26.

Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion.

Žitnik M, Zupan B.

J Comput Biol. 2015 Jun;22(6):595-608. doi: 10.1089/cmb.2014.0158. Epub 2015 Feb 6.

27.

Heterogeneous computing architecture for fast detection of SNP-SNP interactions.

Sluga D, Curk T, Zupan B, Lotric U.

BMC Bioinformatics. 2014 Jun 25;15:216. doi: 10.1186/1471-2105-15-216.

28.

Gene network inference by probabilistic scoring of relationships from a factorized model of interactions.

Zitnik M, Zupan B.

Bioinformatics. 2014 Jun 15;30(12):i246-i254. doi: 10.1093/bioinformatics/btu287.

29.

A randomized controlled trial of emotion recognition training after traumatic brain injury.

Neumann D, Babbage DR, Zupan B, Willer B.

J Head Trauma Rehabil. 2015 May-Jun;30(3):E12-23. doi: 10.1097/HTR.0000000000000054.

PMID:
24842590
30.

Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae.

Franco-Duarte R, Mendes I, Umek L, Drumonde-Neves J, Zupan B, Schuller D.

Yeast. 2014 Jul;31(7):265-77. doi: 10.1002/yea.3016. Epub 2014 May 26.

31.

Integrative clustering by nonnegative matrix factorization can reveal coherent functional groups from gene profile data.

Brdar S, Crnojevic V, Zupan B.

IEEE J Biomed Health Inform. 2015 Mar;19(2):698-708. doi: 10.1109/JBHI.2014.2316508. Epub 2014 Apr 10.

PMID:
24733033
32.

Recognition of facial and vocal affect following traumatic brain injury.

Zupan B, Babbage D, Neumann D, Willer B.

Brain Inj. 2014;28(8):1087-95. doi: 10.3109/02699052.2014.901560. Epub 2014 Apr 4.

PMID:
24701988
33.

KCNQ1, KCNE2, and Na+-coupled solute transporters form reciprocally regulating complexes that affect neuronal excitability.

Abbott GW, Tai KK, Neverisky DL, Hansler A, Hu Z, Roepke TK, Lerner DJ, Chen Q, Liu L, Zupan B, Toth M, Haynes R, Huang X, Demirbas D, Buccafusca R, Gross SS, Kanda VA, Berry GT.

Sci Signal. 2014 Mar 4;7(315):ra22. doi: 10.1126/scisignal.2005025.

34.

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.

Rossbach O, Hung LH, Khrameeva E, Schreiner S, König J, Curk T, Zupan B, Ule J, Gelfand MS, Bindereif A.

RNA Biol. 2014;11(2):146-55. doi: 10.4161/rna.27991. Epub 2014 Feb 7.

35.

Assessment of machine learning reliability methods for quantifying the applicability domain of QSAR regression models.

Toplak M, Močnik R, Polajnar M, Bosnić Z, Carlsson L, Hasselgren C, Demšar J, Boyer S, Zupan B, Stålring J.

J Chem Inf Model. 2014 Feb 24;54(2):431-41. doi: 10.1021/ci4006595. Epub 2014 Feb 11.

PMID:
24490838
36.
37.

Maternal hematopoietic TNF, via milk chemokines, programs hippocampal development and memory.

Liu B, Zupan B, Laird E, Klein S, Gleason G, Bozinoski M, Gal Toth J, Toth M.

Nat Neurosci. 2014 Jan;17(1):97-105. doi: 10.1038/nn.3596. Epub 2013 Dec 1.

38.

Discovering disease-disease associations by fusing systems-level molecular data.

Žitnik M, Janjić V, Larminie C, Zupan B, Pržulj N.

Sci Rep. 2013 Nov 15;3:3202. doi: 10.1038/srep03202.

39.

Affect recognition in traumatic brain injury: responses to unimodal and multimodal media.

Zupan B, Neumann D.

J Head Trauma Rehabil. 2014 Jul-Aug;29(4):E1-E12. doi: 10.1097/HTR.0b013e31829dded6.

PMID:
23982789
40.

ABC transporters in Dictyostelium discoideum development.

Miranda ER, Zhuchenko O, Toplak M, Santhanam B, Zupan B, Kuspa A, Shaulsky G.

PLoS One. 2013 Aug 14;8(8):e70040. doi: 10.1371/journal.pone.0070040. eCollection 2013.

41.

The relationship between facial affect recognition and cognitive functioning after traumatic brain injury.

Yim J, Babbage DR, Zupan B, Neumann D, Willer B.

Brain Inj. 2013;27(10):1155-61. doi: 10.3109/02699052.2013.804203. Epub 2013 Jul 29.

PMID:
23895556
42.

Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles.

Mendes I, Franco-Duarte R, Umek L, Fonseca E, Drumonde-Neves J, Dequin S, Zupan B, Schuller D.

PLoS One. 2013 Jul 16;8(7):e66523. doi: 10.1371/journal.pone.0066523. Print 2013.

43.

Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions.

Nasser W, Santhanam B, Miranda ER, Parikh A, Juneja K, Rot G, Dinh C, Chen R, Zupan B, Shaulsky G, Kuspa A.

Curr Biol. 2013 May 20;23(10):862-72. doi: 10.1016/j.cub.2013.04.034. Epub 2013 May 9.

44.

Interest propagation for knowledge extraction and representation.

Mulas F, del Fabbro E, Zupan B, Bellazzi R.

Stud Health Technol Inform. 2013;186:182-6.

PMID:
23542994
45.

Transcriptional profiling of Dictyostelium with RNA sequencing.

Miranda ER, Rot G, Toplak M, Santhanam B, Curk T, Shaulsky G, Zupan B.

Methods Mol Biol. 2013;983:139-71. doi: 10.1007/978-1-62703-302-2_8.

46.

Knowledge-based bioinformatics for the study of mammalian oocytes.

Mulas F, Sacchi L, Zagar L, Garagna S, Zuccotti M, Zupan B, Bellazzi R.

Int J Dev Biol. 2012;56(10-12):859-66. doi: 10.1387/ijdb.120138fm. Review.

47.

OCT4 and the acquisition of oocyte developmental competence during folliculogenesis.

Zuccotti M, Merico V, Belli M, Mulas F, Sacchi L, Zupan B, Redi CA, Prigione A, Adjaye J, Bellazzi R, Garagna S.

Int J Dev Biol. 2012;56(10-12):853-8. doi: 10.1387/ijdb.120174mz. Review.

48.

Relationships between alexithymia, affect recognition, and empathy after traumatic brain injury.

Neumann D, Zupan B, Malec JF, Hammond F.

J Head Trauma Rehabil. 2014 Jan-Feb;29(1):E18-27. doi: 10.1097/HTR.0b013e31827fb0b5.

PMID:
23407425
49.

Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain.

Rogelj B, Easton LE, Bogu GK, Stanton LW, Rot G, Curk T, Zupan B, Sugimoto Y, Modic M, Haberman N, Tollervey J, Fujii R, Takumi T, Shaw CE, Ule J.

Sci Rep. 2012;2:603. doi: 10.1038/srep00603. Epub 2012 Aug 28.

50.

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.

Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J.

Genome Biol. 2012 Aug 3;13(8):R67. doi: 10.1186/gb-2012-13-8-r67.

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