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University of Exeter: Exeter, Devon, GB

2017-01-01 to present | Senior Lecturer (Computer Science)
Employment
Source: Self-asserted source
Fabrizio Costa

Works (43)

Learning an efficient constructive sampler for graphs

Artificial Intelligence
2017 | Journal article
EID:

2-s2.0-84956858993

Contributors: Costa, F.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments

Cell Systems
2016 | Journal article
EID:

2-s2.0-84995388262

Contributors: Dao, P.; Hoinka, J.; Takahashi, M.; Zhou, J.; Ho, M.; Wang, Y.; Costa, F.; Rossi, J.J.; Backofen, R.; Burnett, J. et al.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Characterizing leader sequences of CRISPR loci

Bioinformatics
2016 | Journal article
EID:

2-s2.0-84991018148

Contributors: Alkhnbashi, O.S.; Shah, S.A.; Garrett, R.A.; Saunders, S.J.; Costa, F.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Formalin-fixed, paraffin-embedded tissues (FFPE) as a robust source for the profiling of native and protease-generated protein amino termini

Molecular and Cellular Proteomics
2016 | Journal article
EID:

2-s2.0-84973369708

Contributors: Lai, Z.W.; Weisser, J.; Nilse, L.; Costa, F.; Keller, E.; Tholen, M.; Kizhakkedathu, J.N.; Biniossek, M.; Bronsert, P.; Schilling, O.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

RNAsynth: Constraints learning for RNA inverse folding

ESANN 2016 - 24th European Symposium on Artificial Neural Networks
2016 | Conference paper
EID:

2-s2.0-84994157870

Contributors: Costa, F.; Kohvaei, P.; Kleinkauf, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

SnoReport 2.0: New features and a refined Support Vector Machine to improve snoRNA identification

BMC Bioinformatics
2016 | Journal article
EID:

2-s2.0-85006835750

Contributors: de Araujo Oliveira, J.V.; Costa, F.; Backofen, R.; Stadler, P.F.; Machado Telles Walter, M.E.; Hertel, J.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

An updated evolutionary classification of CRISPR-Cas systems

Nature Reviews Microbiology
2015 | Journal article
EID:

2-s2.0-84944449180

Contributors: Makarova, K.S.; Wolf, Y.I.; Alkhnbashi, O.S.; Costa, F.; Shah, S.A.; Saunders, S.J.; Barrangou, R.; Brouns, S.J.J.; Charpentier, E.; Haft, D.H. et al.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

KLog: A language for logical and relational learning with kernels

IJCAI International Joint Conference on Artificial Intelligence
2015 | Conference paper
EID:

2-s2.0-84949763864

Contributors: Frasconi, P.; Costa, F.; De Raedt, L.; De Grave, K.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Bioinformatics of prokaryotic RNAs

RNA Biology
2014 | Journal article
EID:

2-s2.0-84906346427

Contributors: Backofen, R.; Amman, F.; Costa, F.; Findeib, S.; Richter, A.; Stadler, P.F.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

BlockClust: Efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles

Bioinformatics
2014 | Journal article
EID:

2-s2.0-84902479397

Contributors: Videm, P.; Rose, D.; Costa, F.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

BlockClust: Efficient clustering and classification of non-coding RNAs from short read RNA-Seq profiles

Lecture Notes in Informatics (LNI), Proceedings - Series of the Gesellschaft fur Informatik (GI)
2014 | Conference paper
EID:

2-s2.0-84919344221

Contributors: Videm, P.; Rose, D.; Costa, F.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

CRISPRstrand: Predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

Bioinformatics
2014 | Journal article
EID:

2-s2.0-84907021656

Contributors: Alkhnbashi, O.S.; Costa, F.; Shah, S.A.; Garrett, R.A.; Saunders, S.J.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

GraphProt: Modeling binding preferences of RNA-binding proteins

Genome Biology
2014 | Journal article
EID:

2-s2.0-84892636681

Contributors: Maticzka, D.; Lange, S.J.; Costa, F.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

KLog: A language for logical and relational learning with kernels

Artificial Intelligence
2014 | Journal article
EID:

2-s2.0-84908457312

Contributors: Frasconi, P.; Costa, F.; De Raedt, L.; De Grave, K.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression

Journal of Clinical Investigation
2014 | Journal article
EID:

2-s2.0-84903778038

Contributors: Ferrarese, R.; Harsh IV, G.R.; Yadav, A.K.; Bug, E.; Maticzka, D.; Reichardt, W.; Dombrowski, S.M.; Miller, T.E.; Masilamani, A.P.; Dai, F. et al.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

MoDPepInt: An interactive web server for prediction of modular domain-peptide interactions

Bioinformatics
2014 | Journal article
EID:

2-s2.0-84907482622

Contributors: Kundu, K.; Mann, M.; Costa, F.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

PTRcombiner: Mining combinatorial regulation of gene expression from post-transcriptional interaction maps

BMC Genomics
2014 | Journal article
EID:

2-s2.0-84900860015

Contributors: Corrado, G.; Tebaldi, T.; Bertamini, G.; Costa, F.; Quattrone, A.; Viero, G.; Passerini, A.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Relational regularization and feature ranking

SIAM International Conference on Data Mining 2014, SDM 2014
2014 | Conference paper
EID:

2-s2.0-84933075459

Contributors: Costa, F.; Verbeke, M.; De Raedt, L.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains

Bioinformatics
2013 | Journal article
EID:

2-s2.0-84879898400

Contributors: Kundu, K.; Costa, F.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Semi-Supervised Prediction of SH2-Peptide Interactions from Imbalanced High-Throughput Data

PLoS ONE
2013 | Journal article
EID:

2-s2.0-84877849501

Contributors: Kundu, K.; Costa, F.; Huber, M.; Reth, M.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

A relational kernel-based framework for hierarchical image understanding

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2012 | Book
EID:

2-s2.0-84868098446

Contributors: Antanas, L.; Frasconi, P.; Costa, F.; Tuytelaars, T.; De Raedt, L.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Graphclust: Alignment-free structural clustering of local RNA secondary structures

Bioinformatics
2012 | Journal article
EID:

2-s2.0-84863515320

Contributors: Heyne, S.; Costa, F.; Rose, D.; Backofen, R.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Link and node prediction in metabolic networks with probabilistic logic

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2012 | Book
EID:

2-s2.0-84864124119

Contributors: Kimmig, A.; Costa, F.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Effective feature construction by maximum common subgraph sampling

Machine Learning
2011 | Journal article
EID:

2-s2.0-79958834639

Contributors: Schietga, L.; Costa, F.; Ramon, J.; De Raed, L.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Preface

Fundamenta Informaticae
2011 | Journal article
EID:

2-s2.0-84858026679

Contributors: Ramon, J.; Costa, F.; Florêncio, C.C.; Kok, J.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Random forest based feature induction

Proceedings - IEEE International Conference on Data Mining, ICDM
2011 | Conference paper
EID:

2-s2.0-84857143316

Contributors: Vens, C.; Costa, F.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Fast neighborhood subgraph pairwise distance kernel

ICML 2010 - Proceedings, 27th International Conference on Machine Learning
2010 | Conference paper
EID:

2-s2.0-77956531773

Contributors: Costa, F.; De Grave, K.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Molecular graph augmentation with rings and functional groups

Journal of Chemical Information and Modeling
2010 | Journal article
EID:

2-s2.0-77957232924

Contributors: De Grave, K.; Costa, F.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Handling missing values and censored data in PCA of pharmacological matrices

Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics, StReBio '09
2009 | Conference paper
EID:

2-s2.0-70350680785

Contributors: Ramon, J.; Costa, F.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics, StReBio '09: Preface

Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics, StReBio '09
2009 | Conference paper
EID:

2-s2.0-70350633065

Contributors: Florêncio, C.C.; Costa, F.; Ramon, J.; Kok, J.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

A semiparametric generative model for efficient structured-output supervised learning

Annals of Mathematics and Artificial Intelligence
2008 | Journal article
EID:

2-s2.0-70350020492

Contributors: Costa, F.; Passerini, A.; Lippi, M.; Frasconi, P.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Comparing sequence classification algorithms for protein subcellular localization

Studies in Computational Intelligence
2008 | Book
EID:

2-s2.0-34548132031

Contributors: Costa, F.; Menchetti, S.; Frasconi, P.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

On the convergence of protein structure and dynamics. Statistical learning studies of pseudo folding pathways

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2008 | Book
EID:

2-s2.0-47249097119

Contributors: Vullo, A.; Passerini, A.; Frasconi, P.; Costa, F.; Pollastri, G.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Towards combining structured pattern mining and graph kernels

Proceedings - IEEE International Conference on Data Mining Workshops, ICDM Workshops 2008
2008 | Conference paper
EID:

2-s2.0-62449295456

Contributors: Costa, F.; Bringmann, B.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Classification of small molecules by two- and three-dimensional decomposition kernels

Bioinformatics
2007 | Journal article
EID:

2-s2.0-34548580482

Contributors: Ceroni, A.; Costa, F.; Frasconi, P.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Ambiguity resolution analysis in incremental parsing of natural language

IEEE Transactions on Neural Networks
2005 | Journal article
EID:

2-s2.0-23044495246

Contributors: Costa, F.; Frasconi, P.; Lombardo, V.; Sturt, P.; Soda, G.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Weighted decomposition kernels

ICML 2005 - Proceedings of the 22nd International Conference on Machine Learning
2005 | Conference paper
EID:

2-s2.0-31844432423

Contributors: Menchetti, S.; Costa, F.; Frasconi, P.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Wide coverage natural language processing using kernel methods and neural networks for structured data

Pattern Recognition Letters
2005 | Journal article
EID:

2-s2.0-22944487701

Contributors: Menchetti, S.; Costa, F.; Frasconi, P.; Pontil, M.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Distributed community crawling

Thirteenth International World Wide Web Conference Proceedings, WWW2004
2004 | Conference paper
EID:

2-s2.0-19944410179

Contributors: Costa, F.; Frasconi, P.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Learning first-pass structural attachment preferences with dynamic grammars and recursive neural networks

Cognition
2003 | Journal article
EID:

2-s2.0-0038392958

Contributors: Sturt, P.; Costa, F.; Lombardo, V.; Frasconi, P.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Towards incremental parsing of natural language using recursive neural networks

Applied Intelligence
2003 | Journal article
EID:

2-s2.0-0038604094

Contributors: Costa, F.; Frasconi, P.; Lombardo, V.; Soda, G.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Wide coverage incremental parsing by learning attachment preferences

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2001 | Book
EID:

2-s2.0-84876762187

Contributors: Costa, F.; Lombardo, V.; Frasconi, P.; Soda, G.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier

Learning incremental syntactic structures with recursive neural networks

International Conference on Knowledge-Based Intelligent Electronic Systems, Proceedings, KES
2000 | Conference paper
EID:

2-s2.0-0033646161

Contributors: Costa, F.; Frasconi, P.; Lombardo, V.; Soda, G.
Source: Self-asserted source
Fabrizio Costa via Scopus - Elsevier