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Articles (47)
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1

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

Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 323 KB

english, 2012

2

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

König, Julian, Zarnack, Kathi, Rot, Gregor, Curk, Tomaž, Kayikci, Melis, Zupan, Blaž, Turner, Daniel J, Luscombe, Nicholas M, Ule, Jernej

Journal:

Nature Structural and Molecular Biology

Année:

2010

Langue:

english

Fichier:

PDF, 1.24 MB

english, 2010

3

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

Rogelj, Boris, Easton, Laura E., Bogu, Gireesh K., Stanton, Lawrence W., Rot, Gregor, Curk, Tomaž, Zupan, Blaž, Sugimoto, Yoichiro, Modic, Miha, Haberman, Nejc, Tollervey, James, Fujii, Ritsuko, Takum

Journal:

Scientific Reports

Année:

2012

Langue:

english

Fichier:

PDF, 611 KB

english, 2012

4

Recursive splicing in long vertebrate genes

Sibley, Christopher R., Emmett, Warren, Blazquez, Lorea, Faro, Ana, Haberman, Nejc, Briese, Michael, Trabzuni, Daniah, Ryten, Mina, Weale, Michael E., Hardy, John, Modic, Miha, Curk, Tomaž, Wilson, St

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 2.19 MB

english, 2015

5

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

Rossbach, Oliver, Hung, Lee-Hsueh, Khrameeva, Ekaterina, Schreiner, Silke, König, Julian, Curk, Tomaž, Zupan, Blaž, Ule, Jernej, Gelfand, Mikhail S, Bindereif, Albrecht

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 2.92 MB

english, 2014

6

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Wang, Zhen, Kayikci, Melis, Briese, Michael, Zarnack, Kathi, Luscombe, Nicholas M., Rot, Gregor, Zupan, Blaž, Curk, Tomaž, Ule, Jernej, Misteli, Tom

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 2.05 MB

english, 2010

7

Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP

Hauer, Christian, Curk, Tomaz, Anders, Simon, Schwarzl, Thomas, Alleaume, Anne-Marie, Sieber, Jana, Hollerer, Ina, Bhuvanagiri, Madhuri, Huber, Wolfgang, Hentze, Matthias W., Kulozik, Andreas E.

Journal:

Nature Communications

Année:

2015

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2015

8

iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function

Rivers, Caroline, Idris, Jalilah, Scott, Helen, Rogers, Mark, Lee, Youn-Bok, Gaunt, Jessica, Phylactou, Leonidas, Curk, Tomaz, Campbell, Colin, Ule, Jernej, Norman, Michael, Uney, James B.

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 2.72 MB

english, 2015

9

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Konig, Julian, Zarnack, Kathi, Rot, Gregor, Curk, Tomaz, Kayikci, Melis, Zupan, Blaz, Turner, Daniel J., Luscombe, Nicholas M., Ule, Jernej

Journal:

Journal of Visualized Experiments

Année:

2011

Langue:

english

Fichier:

PDF, 546 KB

english, 2011

10

Insights into the design and interpretation of iCLIP experiments

Haberman, Nejc, Huppertz, Ina, Attig, Jan, König, Julian, Wang, Zhen, Hauer, Christian, Hentze, Matthias W., Kulozik, Andreas E., Le Hir, Hervé, Curk, Tomaž, Sibley, Christopher R., Zarnack, Kathi, Ul

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 2.75 MB

english, 2017

11

High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43

Rot, Gregor, Wang, Zhen, Huppertz, Ina, Modic, Miha, Lenče, Tina, Hallegger, Martina, Haberman, Nejc, Curk, Tomaž, von Mering, Christian, Ule, Jernej

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 2.83 MB

english, 2017

12

Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap

Castello, Alfredo, Frese, Christian K., Fischer, Bernd, Järvelin, Aino I, Horos, Rastislav, Alleaume, Anne-Marie, Foehr, Sophia, Curk, Tomaz, Krijgsveld, Jeroen, Hentze, Matthias W

Journal:

Nature Protocols

Année:

2017

Langue:

english

Fichier:

PDF, 2.61 MB

english, 2017

13

Erratum to: Insights into the design and interpretation of iCLIP experiments

Haberman, Nejc, Huppertz, Ina, Attig, Jan, König, Julian, Wang, Zhen, Hauer, Christian, Hentze, Matthias W., Kulozik, Andreas E., Le Hir, Hervé, Curk, Tomaž, Sibley, Christopher R., Zarnack, Kathi, Ul

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 222 KB

english, 2017

14

Metabolomic profiling of CHO fed‐batch growth phases at 10, 100 and 1000 L

Vodopivec, Maja, Lah, Ljerka, Narat, Mojca, Curk, Tomaž

Journal:

Biotechnology and Bioengineering

Année:

2019

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2019

15

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43

Tollervey, James R, Curk, Tomaž, Rogelj, Boris, Briese, Michael, Cereda, Matteo, Kayikci, Melis, König, Julian, Hortobágyi, Tibor, Nishimura, Agnes L, Župunski, Vera

Journal:

Nature Neuroscience

Année:

2011

Langue:

english

Fichier:

PDF, 559 KB

english, 2011

16

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

Minna-Liisa Änkö, Michaela Müller-McNicoll, Holger Brandl, Tomaz Curk, Crtomir Gorup, Ian Henry, Jernej Ule, Karla M Neugebauer

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 1.12 MB

english, 2012

17

Polymorphic Members of the lag Gene Family Mediate Kin Discrimination in Dictyostelium

Rocio Benabentos, Shigenori Hirose, Richard Sucgang, Tomaz Curk, Mariko Katoh, Elizabeth A. Ostrowski, Joan E. Strassmann, David C. Queller, Blaz Zupan, Gad Shaulsky, Adam Kuspa

Journal:

Current Biology

Année:

2009

Langue:

english

Fichier:

PDF, 776 KB

english, 2009

18

TA-clustering: Cluster analysis of gene expression profiles through Temporal Abstractions

Lucia Sacchi, Riccardo Bellazzi, Cristiana Larizza, Paolo Magni, Tomaz Curk, Uros Petrovic, Blaz Zupan

Journal:

International Journal of Medical Informatics

Année:

2005

Langue:

english

Fichier:

PDF, 703 KB

english, 2005

19

BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium

Eryong Huang, Shaheynoor Talukder, Timothy R. Hughes, Tomaz Curk, Blaz Zupan, Gad Shaulsky, Mariko Katoh-Kurasawa

Journal:

Developmental Biology

Année:

2011

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2011

20

GenePath: a system for inference of genetic networks and proposal of genetic experiments

Blaž Zupan, Ivan Bratko, Janez Demšar, Peter Juvan, Tomaž Curk, Urban Borštnik, J.Robert Beck, John Halter, Adam Kuspa, Gad Shaulsky

Journal:

Artificial Intelligence in Medicine

Année:

2003

Langue:

english

Fichier:

PDF, 379 KB

english, 2003

21

dictyExpress: aDictyostelium discoideumgene expression database with an explorative data analysis web-based interface

Gregor Rot, Anup Parikh, Tomaz Curk, Adam Kuspa, Gad Shaulsky, Blaz Zupan

Journal:

BMC Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 1.13 MB

english, 2009

22

Does replication groups scoring reduce false positive rate in SNP interaction discovery?

Marko Toplak, Tomaz Curk, Janez Demsar, Blaz Zupan

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 655 KB

english, 2010

23

Heterogeneous computing architecture for fast detection of SNP-SNP interactions

Davor Sluga,Tomaz Curk,Blaz Zupan,Uros Lotric

Journal:

BMC Bioinformatics

Année:

2014

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2014

24

Rbfox2-Coordinated Alternative Splicing of Mef2d and Rock2 Controls Myoblast Fusion during Myogenesis

Singh, Ravi K., Xia, Zheng, Bland, Christopher S., Kalsotra, Auinash, Scavuzzo, Marissa A., Curk, Tomaz, Ule, Jernej, Li, Wei, Cooper, Thomas A.

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 3.61 MB

english, 2014

25

Inference of the Molecular Mechanism of Action from Genetic Interaction and Gene Expression Data

Mattiazzi, Mojca, Curk, Tomaž, Križaj, Igor, Zupan, Blaž, Petrovič, Uroš

Journal:

Omics A Journal of Integrative Biology

Année:

2010

Langue:

english

Fichier:

PDF, 476 KB

english, 2010

26

Deep Sequencing of Virus-Derived Small Interfering RNAs and RNA from Viral Particles Shows Highly Similar Mutational Landscapes of a Plant Virus Population

Kutnjak, Denis, Rupar, Matevž, Gutierrez-Aguirre, Ion, Curk, Tomaž, Kreuze, Jan F., Ravnikar, Maja, Simon, A. E.

Journal:

Journal of Virology

Année:

2015

Langue:

english

Fichier:

PDF, 2.46 MB

english, 2015

27

The RNA-binding protein HuR is essential for the B cell antibody response

Diaz-Muñoz, Manuel D, Bell, Sarah E, Fairfax, Kirsten, Monzon-Casanova, Elisa, Cunningham, Adam F, Gonzalez-Porta, Mar, Andrews, Simon R, Bunik, Victoria I, Zarnack, Kathi, Curk, Tomaž, Heggermont, Wa

Journal:

Nature Immunology

Année:

2015

Langue:

english

Fichier:

PDF, 3.13 MB

english, 2015

28

Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt

Murn, Jernej, Zarnack, Kathi, Yang, Yawei J., Durak, Omer, Murphy, Elisabeth A., Cheloufi, Sihem, Gonzalez, Dilenny M., Teplova, Marianna, Curk, Tomaž, Zuber, Johannes, Patel, Dinshaw J., Ule, Jernej,

Journal:

Genes & Development

Année:

2015

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2015

29

Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1

Apolonia, Luis, Schulz, Reiner, Curk, Tomaž, Rocha, Paula, Swanson, Chad M., Schaller, Torsten, Ule, Jernej, Malim, Michael H., Swanstrom, Ronald

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 871 KB

english, 2015

30

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development

Grellscheid, Sushma, Dalgliesh, Caroline, Storbeck, Markus, Best, Andrew, Liu, Yilei, Jakubik, Miriam, Mende, Ylva, Ehrmann, Ingrid, Curk, Tomaz, Rossbach, Kristina, Bourgeois, Cyril F., Stévenin, Jam

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 5.57 MB

english, 2011

31

CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function

Wagnon, Jacy L., Briese, Michael, Sun, Wenzhi, Mahaffey, Connie L., Curk, Tomaž, Rot, Gregor, Ule, Jernej, Frankel, Wayne N., Barsh, Gregory S.

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 8.31 MB

english, 2012

32

Yeast Saccharomyces cerevisiae adiponectin receptor homolog Izh2 is involved in the regulation of zinc, phospholipid and pH homeostasis

Mattiazzi Ušaj, Mojca, Prelec, Metod, Brložnik, Mojca, Primo, Cecilia, Curk, Tomaž, Ščančar, Janez, Yenush, Lynne, Petrovič, Uroš

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 2.67 MB

english, 2015

33

Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons

Best, Andrew, James, Katherine, Dalgliesh, Caroline, Hong, Elaine, Kheirolahi-Kouhestani, Mahsa, Curk, Tomaz, Xu, Yaobo, Danilenko, Marina, Hussain, Rafiq, Keavney, Bernard, Wipat, Anil, Klinck, Rosco

Journal:

Nature Communications

Année:

2014

Langue:

english

Fichier:

PDF, 2.45 MB

english, 2014

34

FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation

Popow, Johannes, Alleaume, Anne-Marie, Curk, Tomaz, Schwarzl, Thomas, Sauer, Sven, Hentze, Matthias W.

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 2.91 MB

english, 2015

35

The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs

Beckmann, Benedikt M., Horos, Rastislav, Fischer, Bernd, Castello, Alfredo, Eichelbaum, Katrin, Alleaume, Anne-Marie, Schwarzl, Thomas, Curk, Tomaž, Foehr, Sophia, Huber, Wolfgang, Krijgsveld, Jeroen,

Journal:

Nature Communications

Année:

2015

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2015

36

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

Stražar, Martin, Žitnik, Marinka, Zupan, Blaž, Ule, Jernej, Curk, Tomaž

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 655 KB

english, 2016

37

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

Müller-McNicoll, Michaela, Botti, Valentina, de Jesus Domingues, Antonio M., Brandl, Holger, Schwich, Oliver D., Steiner, Michaela C., Curk, Tomaz, Poser, Ina, Zarnack, Kathi, Neugebauer, Karla M.

Journal:

Genes & Development

Année:

2016

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2016

38

Yeast as a cell factory: current state and perspectives

Kavšček, Martin, Stražar, Martin, Curk, Tomaž, Natter, Klaus, Petrovič, Uroš

Journal:

Microbial Cell Factories

Année:

2015

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2015

39

Comprehensive Identification of RNA-Binding Domains in Human Cells

Castello, Alfredo, Fischer, Bernd, Frese, Christian K., Horos, Rastislav, Alleaume, Anne-Marie, Foehr, Sophia, Curk, Tomaz, Krijgsveld, Jeroen, Hentze, Matthias W.

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 5.94 MB

english, 2016

40

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins

Hauer, Christian, Sieber, Jana, Schwarzl, Thomas, Hollerer, Ina, Curk, Tomaz, Alleaume, Anne-Marie, Hentze, Matthias W., Kulozik, Andreas E.

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 3.17 MB

english, 2016

41

The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion

Hollerer, Ina, Curk, Tomaz, Haase, Bettina, Benes, Vladimir, Hauer, Christian, Neu-Yilik, Gabriele, Bhuvanagiri, Madhuri, Hentze, Matthias W., Kulozik, Andreas E.

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2016

42

Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells

Díaz-Muñoz, Manuel D., Kiselev, Vladimir Yu., Novère, Nicolas Le, Curk, Tomaz, Ule, Jernej, Turner, Martin

Journal:

Nature Communications

Année:

2017

Langue:

english

Fichier:

PDF, 3.00 MB

english, 2017

43

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

Jakše, Jernej, Jelen, Vid, Radišek, Sebastjan, de Jonge, Ronnie, Mandelc, Stanislav, Majer, Aljaž, Curk, Tomaž, Zupan, Blaž, Thomma, Bart P. H. J., Javornik, Branka

Journal:

Genome Announcements

Année:

2018

Langue:

english

Fichier:

PDF, 141 KB

english, 2018

44

Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls

Kovanda, Anja, Leonardis, Lea, Zidar, Janez, Koritnik, Blaž, Dolenc-Groselj, Leja, Ristic Kovacic, Stanislava, Curk, Tomaž, Rogelj, Boris

Journal:

Scientific Reports

Année:

2018

Langue:

english

Fichier:

PDF, 2.64 MB

english, 2018

45

Unravelling the RNA-Binding Properties of SAFB Proteins in Breast Cancer Cells

Hong, Elaine, Best, Andrew, Gautrey, Hannah, Chin, Jas, Razdan, Anshuli, Curk, Tomaz, Elliott, David J., Tyson-Capper, Alison J.

Journal:

BioMed Research International

Année:

2015

Langue:

english

Fichier:

PDF, 1.90 MB

english, 2015

46

Generating Inter-dependent Data Streams For Recommender Systems

Jakomin, Martin, Curk, Tomaž, Bosnić, Zoran

Journal:

Simulation Modelling Practice and Theory

Année:

2018

Langue:

english

Fichier:

PDF, 2.24 MB

english, 2018

47

Approximate multiple kernel learning with least-angle regression

Stražar, Martin, Curk, Tomaž

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 6.45 MB

english, 2019