Tomaž Curk

发表

Polyketide synthase genes and the natural products potential of Dictyostelium discoideum

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

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

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

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.

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

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

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

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

A systems view of spliceosomal assembly and branchpoints with iCLIP

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

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

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

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

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

Conserved developmental transcriptomes in evolutionarily divergent species

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

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.

Computational approaches for gene network discovery

Tomaž Curk, T. Curk, 2007 .

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.

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.

iDiscover – an intelligent assistant for integrative analysis of transcriptome data

Tomaž Curk, Jernej Ule, Blaž Zupan, 2011 .

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

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

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

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

Insights into the design and interpretation of iCLIP experiments

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

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

Christopher R. Sibley, J. Ule, M. Hentze, 2017, Genome Biology.

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

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

Inference of the molecular mechanism of action from genetic interaction and gene expression data.

B. Zupan, Tomaž Curk, U. Petrovič, 2010, Omics : a journal of integrative biology.

Yeast as a cell factory: current state and perspectives

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

Orange: data mining toolbox in python

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

Sparse data embedding and prediction by tropical matrix factorization

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

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

Blaz Zupan, Riccardo Bellazzi, Tomaz Curk, 2005, Int. J. Medical Informatics.

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

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

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

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

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

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

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

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

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

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

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.

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.

miR669a and miR669q prevent skeletal muscle differentiation in postnatal cardiac progenitors

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

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

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

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.

A systems view of spliceosomal assembly and branchpoints with iCLIP

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

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

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

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.

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.

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

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

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

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

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

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

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

Ivan Bratko, Blaz Zupan, John A. Halter, 2003, Artif. Intell. Medicine.

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

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

Recursive splicing in long vertebrate genes

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

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.

Comprehensive Identification of RNA-Binding Domains in Human Cells

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

Heterogeneous computing architecture for fast detection of SNP-SNP interactions

B. Zupan, Tomaž Curk, U. Lotrič, 2014, BMC Bioinformatics.

SNPsyn: detection and exploration of SNP–SNP interactions

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

Rule-based Clustering for Gene Promoter Structure Discovery

G. Shaulsky, B. Zupan, Tomaž Curk, 2009, Methods of Information in Medicine.

Orange: From Experimental Machine Learning to Interactive Data Mining

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

Acceleration of information-theoretic data analysis with graphics processing units

Blaz Zupan, Davor Sluga, Tomaz Curk, 2012 .

Microarray data mining with visual programming

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

Heterogeneous computing architecture for fast detection of SNP-SNP interactions

Blaz Zupan, Davor Sluga, Tomaz Curk, 2014, BMC Bioinformatics.

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

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

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

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

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

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

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.

Developmentally Regulated DNA Methylation in Dictyostelium discoideum

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

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

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

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

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

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

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

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

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

Transcriptional profiling of Dictyostelium with RNA sequencing.

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

Approximate multiple kernel learning with least-angle regression

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

Simultaneous incremental matrix factorization for streaming recommender systems

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

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.

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.

Generating inter-dependent data streams for recommender systems

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

Opus: University of Bath Online Publication Store Analysis of Clip and Iclip Methods for Nucleotide-resolution Studies of Protein-rna Interactions

J. Ule, B. Zupan, J. König, 2022 .

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

J. Ule, T. Cooper, Tomaž Curk, 2014, Molecular cell.

Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students

Tomaž Curk, P. G. Policar, Martin Špendl, 2024, Bioinformatics.

Relation chaining in binary positive-only recommender systems

Tomaž Curk, Rok Gomišček, Tomaž Curk, 2020, Expert Syst. Appl..

Learning the kernel matrix via predictive low-rank approximations

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

Open data and quantitative techniques for anthropology of road traffic

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