T. Curk

发表

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

J. Ule, M. Kayikci, B. Zupan, 2010, Nature Structural &Molecular Biology.

Insights into the design and interpretation of iCLIP experiments

Nejc Haberman, Christopher R. Sibley, Julian König, 2017, Genome Biology.

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

Anne-Marie Alleaume, M. Hentze, W. Huber, 2015, Nature Communications.

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

Julian König, Tomaž Curk, Jernej Ule, 2012, Genome Biology.

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Michael Briese, Nicholas M. Luscombe, Tomaž Curk, 2010, PLoS biology.

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

T. Hughes, Shaheynoor Talukder, G. Shaulsky, 2011, Developmental biology.

Conserved developmental transcriptomes in evolutionarily divergent species

Blaz Zupan, Tomaz Curk, Anup Parikh, 2010, Genome Biology.

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

G. Shaulsky, J. Strassmann, D. Queller, 2009, Current Biology.

dictyBase—a Dictyostelium bioinformatics resource update

Blaz Zupan, Tomaz Curk, Eric M. Just, 2008, Nucleic Acids Res..

Polyketide synthase genes and the natural products potential of Dictyostelium discoideum

Blaz Zupan, Tomaz Curk, Jurica Zucko, 2007, Bioinform..

Computational approaches for gene network discovery

Tomaž Curk, T. Curk, 2007 .

Developmentally Regulated DNA Methylation in Dictyostelium discoideum

G. Shaulsky, M. Katoh, B. Zupan, 2006, Eukaryotic Cell.

Recursive splicing in long vertebrate genes

Michael Briese, Nejc Haberman, Christopher R. Sibley, 2015, Nature.

A systems view of spliceosomal assembly and branchpoints with iCLIP

Christopher R. Sibley, Andrea S. Elser, J. Ule, 2019, Nature Structural & Molecular Biology.

A systems view of spliceosomal assembly and branchpoints with iCLIP

Christopher R. Sibley, Andrea S. Elser, J. Ule, 2019, Nature Structural & Molecular Biology.

A systems view of spliceosomal assembly and branchpoints with iCLIP

Christopher R. Sibley, J. Ule, N. Luscombe, 2018, bioRxiv.

Comprehensive Identification of RNA-Binding Domains in Human Cells

Jeroen Krijgsveld, Tomaz Curk, Bernd Fischer, 2016, Molecular cell.

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

Jeroen Krijgsveld, Tomaž Curk, Wolfgang Huber, 2015, Nature Communications.

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

J. Ule, M. Kayikci, T. Hortobágyi, 2011, Nature neuroscience.

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

Anne-Marie Alleaume, M. Hentze, Alfredo Castello, 2017, Nature Protocols.

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

Anne-Marie Alleaume, M. Hentze, Tomaž Curk, 2016, Cell reports.

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

Tomaz Curk, Kathi Zarnack, Holger Brandl, 2016, Genes & development.

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

Marinka Zitnik, Blaz Zupan, Jernej Ule, 2016, Bioinform..

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

J. Ule, Tomaž Curk, M. Rogers, 2015, BMC Biology.

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

Anne-Marie Alleaume, M. Hentze, T. Schwarzl, 2015, RNA.

Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.

Jernej Ule, Tomaz Curk, Auinash Kalsotra, 2014, Molecular cell.

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

B. Zupan, Tomaž Curk, B. Thomma, 2018, Genome Announcements.

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

Jernej Ule, Tomaz Curk, Ian Henry, 2012, Genome Biology.

On Quality of Different Annotation Sources for Gene Expression Analysis

Blaz Zupan, Riccardo Bellazzi, Tomaz Curk, 2009, AIME.

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

Nejc Haberman, Tomaž Curk, Jernej Ule, 2012, Scientific Reports.

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

V. Beneš, M. Hentze, Tomaž Curk, 2016, RNA.

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

C. Walsh, J. Ule, L. Tsai, 2015, Genes & development.

An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning

James H. Crichton, Matthew R. Gazzara, Jannetta S. Steyn, 2018, eLife.

Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae

Tomaž Curk, K. Natter, C. Gostinčar, 2021, BMC Genomics.

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

Blaz Zupan, Nicholas M. Luscombe, Jernej Ule, 2011, Journal of visualized experiments : JoVE.

Combinations of Susceptibility Genes Are Associated with Higher Risk for Multiple Sclerosis and Imply Disease Course Specificity

R. Gold, J. Epplen, A. Haghikia, 2015, PloS one.

Orange: data mining toolbox in python

Martin Mozina, Marinka Zitnik, Blaz Zupan, 2013, J. Mach. Learn. Res..

The RNA-binding protein HuR (Elavl1) is essential for the B cell antibody response

Tomaž Curk, Jernej Ule, Kathi Zarnack, 2015, Nature Immunology.

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

Kathi, Manuel D. Díaz-Muñoz, J. Ule, 2016 .

Yeast as a cell factory: current state and perspectives

Tomaž Curk, K. Natter, U. Petrovič, 2015, Microbial Cell Factories.

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

Julian König, Tomaž Curk, Jernej Ule, 2014, RNA biology.

Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo

Tomaž Curk, J. Desvignes, S. Chambeyron, 2015, Cell reports.

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

J. Ule, M. Malim, Tomaž Curk, 2015, PLoS pathogens.

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

Manuel D. Díaz-Muñoz, J. Ule, Tomaž Curk, 2017, Nature Communications.

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

L. Yenush, U. Petrovič, J. Ščančar, 2015, Metallomics : integrated biometal science.

Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae

Tomaž Curk, Uroš Petrovič, Jean-Paul Meijnen, 2016, Biotechnology for Biofuels.

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

Anil Wipat, Tomaz Curk, Katherine James, 2014, Nature Communications.

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

Jacy L. Wagnon, C. Mahaffey, J. Ule, 2012, PLoS genetics.

Characterising the RNA targets and position-dependent splicing regulation by TDP-43; implications for neurodegenerative diseases

J. Ule, M. Kayikci, T. Hortobágyi, 2011, Nature Neuroscience.

miR669a and miR669q prevent skeletal muscle differentiation in postnatal cardiac progenitors

B. Zupan, Tomaž Curk, S. Janssens, 2011, The Journal of cell biology.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

Anup Parikh, Blaz Zupan, Tomaz Curk, 2009, BMC Bioinformatics.

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

Tomaž Curk, B. Koritnik, J. Zidar, 2018, Scientific Reports.

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain.

Tomaž Curk, Jernej Ule, Blaž Zupan, 2011, Genome research.

Sparse data embedding and prediction by tropical matrix factorization

H. Kazan, Tomaž Curk, Polona Oblak, 2021, BMC Bioinform..

Data embedding and prediction by sparse tropical matrix factorization pdf

Polona Oblak, Amra Omanovi'c, Hilal Kazan, 2020, ArXiv.

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

I. Gutiérrez-Aguirre, J. Kreuze, M. Ravnikar, 2015, Journal of Virology.

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

J. Ule, M. Hallegger, Tomaž Curk, 2017, Cell reports.

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

Manuel D. Díaz-Muñoz, J. Ule, N. L. Le Novère, 2017, Nature Communications.

Metabolomic profiling of CHO fed‐batch growth phases at 10, 100, and 1,000 L

Tomaž Curk, L. Lah, M. Narat, 2019, Biotechnology and bioengineering.

Orange: From Experimental Machine Learning to Interactive Data Mining

Blaz Zupan, Tomaz Curk, Janez Demsar, 2004, PKDD.

Publisher Correction: A systems view of spliceosomal assembly and branchpoints with iCLIP

Christopher R. Sibley, Andrea S. Elser, J. Ule, 2021, Nature Structural & Molecular Biology.

Microarray data mining with visual programming

Ivan Bratko, Blaz Zupan, Tomaz Curk, 2005, Bioinform..

Generating inter-dependent data streams for recommender systems

Tomaz Curk, Zoran Bosnic, Martin Jakomin, 2018, Simul. Model. Pract. Theory.

Simultaneous incremental matrix factorization for streaming recommender systems

Tomaz Curk, Martin Jakomin, Zoran Bosnic, 2020, Expert Syst. Appl..

Transcriptional profiling of Dictyostelium with RNA sequencing.

G. Shaulsky, B. Zupan, Tomaž Curk, 2013, Methods in molecular biology.

SNPsyn: detection and exploration of SNP–SNP interactions

Blaz Zupan, Tomaz Curk, Gregor Rot, 2011, Nucleic Acids Res..

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

Mark F. Rogers, J. Ule, Tomaž Curk, 2015, BMC Biology.

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

S. Grellscheid, B. Wirth, Tomaž Curk, 2011, PLoS genetics.

Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae

C. Gostinčar, T. Eisenberg, U. Petrovič, 2021, BMC genomics.

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

Tomaž Curk, H. Gautrey, D. Elliott, 2015, BioMed research international.

On utility of gene set signatures in gene expression-based cancer class prediction

Blaz Zupan, Tomaz Curk, Janez Demsar, 2009, MLSB.

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

Tomaž Curk, B. Koritnik, J. Zidar, 2018, Scientific Reports.

Approximate multiple kernel learning with least-angle regression

Tomaz Curk, Martin Strazar, Tomaž Curk, 2019, Neurocomputing.

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

J. Ule, Tomaž Curk, K. Neugebauer, 2012, Genome Biology.

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

J. Ule, Tomaž Curk, K. Neugebauer, 2012, Genome Biology.

SIMBA Method—Simultaneous Detection of Antimicrobial and Anti-biofilm Activity of New Compounds Using Salmonella Infantis

A. Klančnik, J. Sabotič, N. Janež, 2023, Bio-protocol.

Open data and quantitative techniques for anthropology of road traffic

Tomaž Curk, Tomaz Hocevar, Aj Zagar, 2021, EPJ Data Science.

VizRank: finding informative data projections in functional genomics by machine learning

Ivan Bratko, Blaz Zupan, Tomaz Curk, 2005, Bioinform..

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

T. Hughes, Shaheynoor Talukder, G. Shaulsky, 2011, Developmental biology.

Learning the kernel matrix via predictive low-rank approximations

Tomaž Curk, Martin Stražar, T. Curk, 2016, ArXiv.

Transcriptome-wide profiling of mammalian spliceosome and branchpoints with iCLIP

Christopher R. Sibley, N. Luscombe, J. König, 2018 .