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Items: 1 to 50 of 56

1.

Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.

Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM.

Inf Fusion. 2019 Oct;50:71-91. doi: 10.1016/j.inffus.2018.09.012. Epub 2018 Sep 21.

PMID:
30467459
2.

Cross-type Biomedical Named Entity Recognition with Deep Multi-Task Learning.

Wang X, Zhang Y, Ren X, Zhang Y, Zitnik M, Shang J, Langlotz C, Han J.

Bioinformatics. 2018 Oct 11. doi: 10.1093/bioinformatics/bty869. [Epub ahead of print]

PMID:
30307536
3.

Network enhancement as a general method to denoise weighted biological networks.

Wang B, Pourshafeie A, Zitnik M, Zhu J, Bustamante CD, Batzoglou S, Leskovec J.

Nat Commun. 2018 Aug 6;9(1):3108. doi: 10.1038/s41467-018-05469-x.

4.

Prioritizing network communities.

Zitnik M, Sosič R, Leskovec J.

Nat Commun. 2018 Jun 29;9(1):2544. doi: 10.1038/s41467-018-04948-5.

5.

Modeling polypharmacy side effects with graph convolutional networks.

Zitnik M, Agrawal M, Leskovec J.

Bioinformatics. 2018 Jul 1;34(13):i457-i466. doi: 10.1093/bioinformatics/bty294.

6.

Role of ultrafast dissociation in the fragmentation of chlorinated methanes.

Kokkonen E, Jänkälä K, Patanen M, Cao W, Hrast M, Bučar K, Žitnik M, Huttula M.

J Chem Phys. 2018 May 7;148(17):174301. doi: 10.1063/1.5026720.

PMID:
29739226
7.

Potential Energy Surface Reconstruction and Lifetime Determination of Molecular Double-Core-Hole States in the Hard X-Ray Regime.

Marchenko T, Goldsztejn G, Jänkälä K, Travnikova O, Journel L, Guillemin R, Sisourat N, Céolin D, Žitnik M, Kavčič M, Bučar K, Mihelič A, de Miranda BC, Ismail I, Lago AF, Gel'mukhanov F, Püttner R, Piancastelli MN, Simon M.

Phys Rev Lett. 2017 Sep 29;119(13):133001. doi: 10.1103/PhysRevLett.119.133001. Epub 2017 Sep 27.

PMID:
29341715
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.

Large-scale analysis of disease pathways in the human interactome.

Agrawal M, Zitnik M, Leskovec J.

Pac Symp Biocomput. 2018;23:111-122.

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.

Predicting multicellular function through multi-layer tissue networks.

Zitnik M, Leskovec J.

Bioinformatics. 2017 Jul 15;33(14):i190-i198. doi: 10.1093/bioinformatics/btx252.

12.

Thermal pretreatment and bioaugmentation improve methane yield of microalgal mix produced in thermophilic anaerobic digestate.

Lavrič L, Cerar A, Fanedl L, Lazar B, Žitnik M, Logar RM.

Anaerobe. 2017 Aug;46:162-169. doi: 10.1016/j.anaerobe.2017.02.001. Epub 2017 Feb 8.

PMID:
28189831
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.

Electronic Structure of Third-Row Elements in Different Local Symmetries Studied by Valence-to-Core X-ray Emission Spectroscopy.

Petric M, Bohinc R, Bučar K, Nowak SH, Žitnik M, Kavčič M.

Inorg Chem. 2016 Jun 6;55(11):5328-36. doi: 10.1021/acs.inorgchem.6b00237. Epub 2016 May 13. No abstract available.

PMID:
27176734
15.

Structural and dynamical properties of chlorinated hydrocarbons studied with resonant inelastic x-ray scattering.

Bohinc R, Žitnik M, Bučar K, Kavčič M, Carniato S, Journel L, Guillemin R, Marchenko T, Kawerk E, Simon M, Cao W.

J Chem Phys. 2016 Apr 7;144(13):134309. doi: 10.1063/1.4945402.

PMID:
27059572
16.

Sulphur Kβ emission spectra reveal protonation states of aqueous sulfuric acid.

Niskanen J, Sahle CJ, Ruotsalainen KO, Müller H, Kavčič M, Žitnik M, Bučar K, Petric M, Hakala M, Huotari S.

Sci Rep. 2016 Feb 18;6:21012. doi: 10.1038/srep21012.

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.

Use of hydrodynamic cavitation in (waste)water treatment.

Dular M, Griessler-Bulc T, Gutierrez-Aguirre I, Heath E, Kosjek T, Krivograd Klemenčič A, Oder M, Petkovšek M, Rački N, Ravnikar M, Šarc A, Širok B, Zupanc M, Žitnik M, Kompare B.

Ultrason Sonochem. 2016 Mar;29:577-88. doi: 10.1016/j.ultsonch.2015.10.010. Epub 2015 Oct 19. Review.

PMID:
26515938
21.

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.

22.

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
23.

Exercise-induced effects on a gym atmosphere.

Žitnik M, Bučar K, Hiti B, Barba Ž, Rupnik Z, Založnik A, Žitnik E, Rodrìguez L, Mihevc I, Žibert J.

Indoor Air. 2016 Jun;26(3):468-77. doi: 10.1111/ina.12226. Epub 2015 Jul 1.

PMID:
26095910
24.

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.

25.

Chemical State Analysis of Phosphorus Performed by X-ray Emission Spectroscopy.

Petric M, Bohinc R, Bučar K, Žitnik M, Szlachetko J, Kavčič M.

Anal Chem. 2015 Jun 2;87(11):5632-9. doi: 10.1021/acs.analchem.5b00782. Epub 2015 May 14.

PMID:
25927339
26.

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.

27.

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.

28.

Single photon simultaneous K-shell ionization and K-shell excitation. II. Specificities of hollow nitrogen molecular ions.

Carniato S, Selles P, Andric L, Palaudoux J, Penent F, Žitnik M, Bučar K, Nakano M, Hikosaka Y, Ito K, Lablanquie P.

J Chem Phys. 2015 Jan 7;142(1):014308. doi: 10.1063/1.4904274.

PMID:
25573562
29.

Single photon simultaneous K-shell ionization and K-shell excitation. I. Theoretical model applied to the interpretation of experimental results on H2O.

Carniato S, Selles P, Andric L, Palaudoux J, Penent F, Žitnik M, Bučar K, Nakano M, Hikosaka Y, Ito K, Lablanquie P.

J Chem Phys. 2015 Jan 7;142(1):014307. doi: 10.1063/1.4904273.

PMID:
25573561
30.

High resolution multiphoton spectroscopy by a tunable free-electron-laser light.

Žitnik M, Mihelič A, Bučar K, Kavčič M, Rubensson JE, Svanquist M, Söderström J, Feifel R, Såthe C, Ovcharenko Y, Lyamayev V, Mazza T, Meyer M, Simon M, Journel L, Lüning J, Plekan O, Coreno M, Devetta M, Di Fraia M, Finetti P, Richter R, Grazioli C, Prince KC, Callegari C.

Phys Rev Lett. 2014 Nov 7;113(19):193201. Epub 2014 Nov 7.

PMID:
25415905
31.

Resonant inelastic x-ray scattering on iso-C₂H₂Cl₂ around the chlorine K-edge: structural and dynamical aspects.

Kawerk E, Carniato S, Journel L, Marchenko T, Piancastelli MN, Žitnik M, Bučar K, Bohnic R, Kavčič M, Céolin D, Khoury A, Simon M.

J Chem Phys. 2014 Oct 14;141(14):144301. doi: 10.1063/1.4897251.

PMID:
25318716
32.

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.

33.

Dissociation dynamics of simple chlorine containing molecules upon resonant Cl K-σ* excitation.

Bohinc R, Žitnik M, Bučar K, Kavčič M.

J Chem Phys. 2014 Apr 28;140(16):164304. doi: 10.1063/1.4871878.

PMID:
24784267
34.
35.

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.

36.

Dissociation of chloromethanes upon resonant σ* excitation studied by x-ray scattering.

Bohinc R, Žitnik M, Bučar K, Kavčič M, Journel L, Guillemin R, Marchenko T, Simon M, Cao W.

J Chem Phys. 2013 Oct 7;139(13):134302. doi: 10.1063/1.4822326.

PMID:
24116563
37.

Single photon K(-2) and K(-1)K(-1) double core ionization in C(2)H(2n) (n=1-3), CO, and N(2) as a potential new tool for chemical analysis.

Nakano M, Penent F, Tashiro M, Grozdanov TP, Žitnik M, Carniato S, Selles P, Andric L, Lablanquie P, Palaudoux J, Shigemasa E, Iwayama H, Hikosaka Y, Soejima K, Suzuki IH, Kouchi N, Ito K.

Phys Rev Lett. 2013 Apr 19;110(16):163001. Epub 2013 Apr 18.

PMID:
23679597
38.

A local chemical environment effect in site-specific Auger spectra of ethyl trifluoroacetate.

Iwayama H, Sisourat N, Lablanquie P, Penent F, Palaudoux J, Andric L, Eland JH, Bučar K, Žitnik M, Velkov Y, Hikosaka Y, Nakano M, Shigemasa E.

J Chem Phys. 2013 Jan 14;138(2):024306. doi: 10.1063/1.4773294.

PMID:
23320682
39.

Temperature dependence of the electrical resistivity and electronic structure of amorphous Fe100-xZrx films and multilayers.

Kapaklis V, Pálsson GK, Vegelius J, Haverhals MM, Korelis PT, Butorin SM, Modin A, Kavčič M, Zitnik M, Bučar K, Kvashnina KO, Hjörvarsson B.

J Phys Condens Matter. 2012 Dec 12;24(49):495402. doi: 10.1088/0953-8984/24/49/495402. Epub 2012 Nov 16.

PMID:
23160094
40.

Design and performance of a versatile curved-crystal spectrometer for high-resolution spectroscopy in the tender x-ray range.

Kavčič M, Budnar M, Mühleisen A, Gasser F, Žitnik M, Bučar K, Bohinc R.

Rev Sci Instrum. 2012 Mar;83(3):033113. doi: 10.1063/1.3697862. Erratum in: Rev Sci Instrum. 2012 Jun;83(6):069901.

PMID:
22462912
41.

Evidence of single-photon two-site core double ionization of C2H2 molecules.

Lablanquie P, Grozdanov TP, Zitnik M, Carniato S, Selles P, Andric L, Palaudoux J, Penent F, Iwayama H, Shigemasa E, Hikosaka Y, Soejima K, Nakano M, Suzuki IH, Ito K.

Phys Rev Lett. 2011 Nov 4;107(19):193004. Epub 2011 Nov 4.

PMID:
22181603
42.

Resonant inelastic x-ray scattering at the limit of subfemtosecond natural lifetime.

Marchenko T, Journel L, Marin T, Guillemin R, Carniato S, Žitnik M, Kavčič M, Bučar K, Mihelič A, Hoszowska J, Cao W, Simon M.

J Chem Phys. 2011 Apr 14;134(14):144308. doi: 10.1063/1.3575514.

PMID:
21495756
43.

Properties of hollow molecules probed by single-photon double ionization.

Lablanquie P, Penent F, Palaudoux J, Andric L, Selles P, Carniato S, Bučar K, Zitnik M, Huttula M, Eland JH, Shigemasa E, Soejima K, Hikosaka Y, Suzuki IH, Nakano M, Ito K.

Phys Rev Lett. 2011 Feb 11;106(6):063003. Epub 2011 Feb 11.

PMID:
21405466
44.

Electronic state interferences in resonant x-ray emission after K-shell excitation in HCl.

Kavcic M, Zitnik M, Bucar K, Mihelic A, Carniato S, Journel L, Guillemin R, Simon M.

Phys Rev Lett. 2010 Sep 10;105(11):113004. Epub 2010 Sep 10.

PMID:
20867570
45.

Sulfur-metal orbital hybridization in sulfur-bearing compounds studied by X-ray emission spectroscopy.

Mori RA, Paris E, Giuli G, Eeckhout SG, Kavcic M, Zitnik M, Bucar K, Pettersson LG, Glatzel P.

Inorg Chem. 2010 Jul 19;49(14):6468-73. doi: 10.1021/ic100304z.

PMID:
20553025
46.

Excitation of 1S and 3S metastable helium atoms to doubly excited states.

Alagia M, Coreno M, Farrokhpour H, Franceschi P, Mihelic A, Moise A, Omidyan R, Prince KC, Richter R, Söderström J, Stranges S, Tabrizchi M, Zitnik M.

Phys Rev Lett. 2009 Apr 17;102(15):153001. Epub 2009 Apr 14.

PMID:
19518627
47.

Separation of two-electron photoexcited atomic processes near the inner-shell threshold.

Kavcic M, Zitnik M, Bucar K, Mihelic A, Stuhec M, Szlachetko J, Cao W, Alonso Mori R, Glatzel P.

Phys Rev Lett. 2009 Apr 10;102(14):143001. Epub 2009 Apr 6.

PMID:
19392433
48.
49.

Detection of the 1pe series of doubly excited helium states below N=2 via the stark effect.

Prince KC, Coreno M, Richter R, de Simone M, Feyer V, Kivimäki A, Mihelic A, Zitnik M.

Phys Rev Lett. 2006 Mar 10;96(9):093001. Epub 2006 Mar 6.

PMID:
16606259
50.

The gas-phase photoemission beamline at Elettra.

Prince KC, Blyth RR, Delaunay R, Zitnik M, Krempasky J, Slezak J, Camilloni R, Avaldi L, Coreno M, Stefani G, Furlani C, De Simone M, Stranges S.

J Synchrotron Radiat. 1998 May 1;5(Pt 3):565-8. Epub 1998 May 1.

PMID:
15263580

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