Bioinformatics
Institute of Computer Science
University Freiburg
de

Publications

Publication list ordered by type
Sections:
  1. Publications by Year
  2. Edited Proceedings for International Workshop
  3. PH.D. Thesis
  4. Most cited
  5. Automatic publication list
Publications by Year
2016
Phuong Dao, Jan Hoinka, Mayumi Takahashi, Jiehua Zhou, Michelle Ho, Yijie Wang, Fabrizio Costa, John Rossi, Rolf Backofen, John Burnett, and Teresa M.Przytycka,
''AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments'',
Cell Systems, 2016
Zon Weng Lai, Juliane Weisser, Lars Nilse, Fabrizio Costa, Eva Keller, Martina Tholen, Jayachandran N. Kizhakkedathu, Martin L Biniossek, Peter Bronsert, and Oliver Schilling,
''Formalin-Fixed, Paraffin-Embedded Tissues as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini'',
Molecular and Cellular Proteomics, 2016
F. Costa,
''Learning an efficient constructive sampler for graphs'',
Artificial Intelligence, 2016
Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen and Teresa Przytycka,
''AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments'',
20th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2016
Fabrizio Costa, Parastou Kohvaei, Robert Kleinkauf,
''RNAsynth: constraints learning for RNA inverse folding'',
European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN), Brugge, Belgium 2016
Fabrizio Costa, Omer S. Alkhnbashi, Sita J. Saunders, Shiraz A. Shah, Roger A. Garrett and Rolf Backofen,
''CRISPR-cas locus and array leader sequence boundaries prediction: towards an automated annotation of CRISPR-cas systems'',
(Poster) Annual international CRISPR meeting, May 23-25, TelAviv, Israel, 2016
Omer S. Alkhnbashi, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Fabrizio Costa and Rolf Backofen,,
''Characterizing leader sequences of CRISPR loci'',
15th European Conference on Computational Biology (ECCB), 2016
F. Costa,
''Analytical Systems for Life Sciences at the Time of Big Data'',
Spring meetings on Mining and Learning (SMiLe) Titisee, Germany, 2016
F. Costa,
''Analytical Systems for Life Sciences at the Time of Big Data'',
31st Theoretical Biochemistry Institute (TBI) Winterseminar in Bled, February 2016
2015
Kira S. Makarova, Yuri I. Wolf, Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Sita J. Saunders, Rodolphe Barrangou, Stan J. J. Brouns, Emmanuelle Charpentier, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, Rebecca M. Terns, Michael P. Terns, Malcolm F. White, Alexander F. Yakunin, Roger A. Garrett, John van der Oost, Rolf Backofen, and Eugene V. Koonin,
''An updated evolutionary classification of CRISPR-Cas systems'',
Nature Reviews Microbiology, 2015
P. Frasconi, F. Costa, L. De Raedt, K. De Grave,
''kLog: A Language for Logical and Relational Learning with Kernels'',
(Extended Abstract). International Joint Conference on Artificial Intelligence (IJCAI) Buenos Aires, Argentina, 2015
Omer S. Alkhnbashi, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Fabrizio Costa and Rolf Backofen,,
''Towards an automatic annotation of CRISPR-cas subtypes'',
(Poster) Annual international CRISPR meeting, New York, USA,2015
Fabrizio Costa Robert Kleinkauf Parastou Kohvaei,
''RNAsynth: a graph kernel approach to learn constraints for RNA inverse folding'',
Constructive Machine Learning Workshop, ICML 2015, 10th July 2015, Lille, France
Fabrizio Costa Robert Kleinkauf Parastou Kohvaei,
''RNAsynth: a graph kernel approach to learn constraints for RNA inverse folding'',
Machine Learning and Data Mining Workshop, AI*IA Symposium on Artificial Intelligence, Italy, 2015
F. Costa,
''The Constructive learning Problem'',
Spring meetings on Mining and Learning (SMiLe) Dinant. Belgium, 2015
2014
R. Ferrarese, G. R. Harsh, A. K. Yadav, E. Bug, D. Maticzka, W. Reichardt, S. M. Dombrowski, T. E. Miller, A. P. Masilamani, F. Dai, H. Kim, M. Hadler, D. M. Scholtens, I. L. Y. Yu, J. Beck, V. Srinivasasainagendra, F. Costa, N. Baxan, D. Pfeifer, D. V. Elverfeldt, R. Backofen, A. Weyerbrock, C. W. Duarte, X. He, M. Prinz, J. P. Chandler, H. Vogel, A. Chakravarti, J. N. Rich, M. S. Carro, M. Bredel,
''Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression'',
J Clin Invest, 124 no. 7 pp. 2861-2876, 2014
Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen,
''BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-Seq profiles'',
German Conference on Bioinformatics (GCB), 2014
Steffen Heyne, Fabrizio Costa, Dominic Rose and Rolf Backofen,
''Scalable structural clustering of local RNA secondary structures'',
Computational Methods for Structural RNAs Workshop - CMSR'14 at the ECCB, 13th European Conference on Computational Biology, 2014
Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders and Rolf Backofen,
''CRISPRstrand: Predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci'',
ECCB, 13th European Conference on Computational Biology, 2014
P. Frasconi, F. Costa, K. De Grave, L. De Raedt,
''kLog: A Language for Logical and Relational Learning with Kernels'',
Artificial Intelligence, 2014
Kousik Kundu, Martin Mann, Fabrizio Costa, and Rolf Backofen,
''MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions'',
Bioinformatics. 2014
Videm P., Rose D., Costa F., Backofen R. ,
''BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles'',
22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) (Boston, USA) 2014
Videm P., Rose D., Costa F., Backofen R. ,
''BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles'',
Bioinformatics. 2014 Jun 15;30(12):i274-82
M. Verbeke, P. Frasconi, K. De Grave, F. Costa, L. De Raedt,
''kLogNLP: Graph kernel-based relational learning of natural language'',
Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics: System Demonstrations, 2014; Baltimore, Maryland, USA, 22-27 June 2014
Gianluca Corrado, Toma Tebaldi, Giulio Bertamini, Fabrizio Costa, Alessandro Quattrone, Gabriella Viero and Andrea Passerini,
''PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps'',
BMC Genomics, 2014; 15:304;
Rolf Backofen, Fabian Amman, Fabrizio Costa, Sven Findeiss, Andreas S. Richter, and Peter F. Stadler,
''Bioinformatics of prokaryotic RNAs'',
RNA BiologyRNA Biol, 11 no. 5, 2014
Daniel Maticzka, Sita J Lange, Fabrizio Costa, Rolf Backofen,
''GraphProt: modeling binding preferences of RNA-binding proteins'',
Genome Biology 2014, 15:R17 (22 January 2014)
Fabrizio Costa, Mathias Verbeke, Luc De Raedt
''Relational Regularization and Feature Ranking'',
SIAM International Conference on Data Mining (Philadelphia, Pennsylvania, USA) 2014
F. Costa,
''The Constructive Learning Problem: Learning to sample graphs'',
29th Theoretical Biochemistry Institute (TBI) Winterseminar in Bled, February 2014
F. Costa,
''Structural Motives for RNA Binding Proteins'',
Spring meetings on Mining and Learning (SMiLe) Dinant, Belgium, 2014
2013
Kousik Kundu, Fabrizio Costa, and Rolf Backofen,
''A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains'',
Bioinformatics, 29 no. 13 pp. i335-i343, 2013
Kousik Kundu, Fabrizio Costa, and Rolf Backofen,
''A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains'',
21th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) (Berlin, Germany)2013
Kousik Kundu, Fabrizio Costa, Michael Huber, Michael Reth, and Rolf Backofen
''Semi-Supervised Prediction of SH2-Peptide Interactions from Imbalanced High-Throughput Data'',
PLoS One, 8 no. 5 pp. e62732, 2013
F. Costa, D. Sorescu,
''The Constructive Learning Problem: an efficient approach for hypergraphs'',
Workshop on Constructive Machine Learning (CML), Lake Tahoe, Nevada, USA, 10 December, NIPS 2013.
F. Costa, D. Sorescu,
''Feature Construction for Structured Data'',
Second Italian Workshop on Machine Learning and Data Mining (MLDM), 5 December, Torino, Italy, AI*IA 2013. (Accepted)
F. Costa, D. Sorescu,
''Feature Construction for Structured Data'',
Second workshop on COmbining COnstraint solving with MIning and LEarning (CoCoMiLe) , Bellevue, Washington, USA 14-15 July, AAAI 2013.
2012
Paolo Frasconi, Fabrizio Costa, Luc De Raedt, Kurt De Grave,
''kLog: A Language for Logical and Relational Learning with Kernels.''
ArXiv 2012
Steffen Heyne, Fabrizio Costa, Dominic Rose, and Rolf Backofen,
''GraphClust: alignment-free structural clustering of local RNA secondary structures'',
Bioinformatics, 28 no. 12 pp. i224-i232, 2012
Steffen Heyne, Fabrizio Costa, Dominic Rose, and Rolf Backofen,
''GraphClust: alignment-free structural clustering of local RNA secondary structures'',
20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) (Long Beach, CA, USA) 2012
F. Costa,
''An Efficient Constructive Approach for Small Sparse Graphs'',
Italian Workshop on Machine Learning and Data Mining, 12th AI*IA Symposium on Artificial Intelligence 2012
Laura-Andreea Antanas, Paolo Frasconi, Fabrizio Costa, Tinne Tuytelaars and Luc De Raedt,
''A Relational Kernel-based Framework for Hierarchical Image Understanding'',
Joint IAPR International Workshops on Structural and Syntactic Pattern Recognition (SSPR 2012) and Statistical Techniques in Pattern Recognition (SPR 2012) Miyajima-Itsukushima, Hiroshima, 7th-9th November, 2012.
F.Costa,
''Extracting Sense from Structure: an application to functional non-coding RNA polymers'',
Spring meetings on Mining and Learning (SMiLe) Bad Neuenahr 18-20/4/2012
F. Costa,
''Extracting Sense from Structure: an application to functional non-coding RNA polymers'',
27th Theoretical Biochemistry Institute (TBI) Winterseminar in Bled, February 2012
2011
L. Schietgat, F. Costa, J. Ramon, L. De Raedt,
''Effective Feature Construction by Maximum Common Subgraph Sampling'',
Machine Learning, vol:83 issue:2 pages:137-161, 2011
C. Vens, F. Costa,
''Random Forest Based Feature Induction'',
IEEE International Conference on Data Mining (ICDM) (Vancouver, Canada), 2011
K. Kundu, F. Costa, R. Sinha, M. Reth, M. Huber, R. Backofen,
''Identification of SH2-peptide interactions using support vector machine'',
19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB-ECCB), 2011 (poster)
D. Maticzka, R. Backofen, F. Costa,
''Prediction of binding preferences of RNA-binding proteins using a novel graph representation'',
19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB-ECCB), 2011 (poster)
F.Costa,
''Making sense of non-coding RNA at genomic scale (The quest for efficient graph clustering)'',
Spring Workshop on Mining and Learning (SMILEE) Prum, Germany, March 2011
F. Costa,
''Beyond Base Pair Probabilities and Single Nucleotide Accessibility'',
26th Theoretical Biochemistry Institute (TBI) Winterseminar in Bled, February 2011
2010
K. De Grave, F. Costa,
''Molecular Graph Augmentation with Rings and Functional Groups'',
Journal of Chemical Information and Modeling, 50 (9), pp 1660-1668, 2010
F. Costa, K. De Grave,
''Fast Neighborhood Subgraph Pairwise Distance Kernel'',
27th International Conference on Machine Learning (ICML), 2010
A. Kimmig, F. Costa,
''Link and Node Prediction in Metabolic Network with Probabilistic Logic'',
7th International Symposium on Networks in Bioinformatics (ISNB), 2010
K. De Grave, F. Costa,
''Augmented molecular graph kernel QSARs',
5th Joint Sheffield Conference on Chemoinformatics, 13-15 July 2010 (poster)
A, Kimmig, F. Costa,
''Link and node prediction in metabolic networks with probabilistic logic'',
Analysis of Complex Networks, European Conference on Machine Learning (ECML), Barcelona, Spain, 20 September 2010
2009
Jan Ramon, Fabrizio Costa,
''Handling missing values and censored data in PCA of pharmacological matrices'',
KDD Workshop on Statistical and Relational Learning in Bioinformatics 2009: 32-34
L. Schietgat, F. Costa, J. Ramon and L. De Raedt,
''Maximum Common Subgraph Mining: A Fast and Effective Approach towards Feature Generation'',
7th International Workshop on Mining and Learning with Graphs (MLG), July 2009
F. Costa,
''On Molecular synthesis'',
Spring Workshop on Mining and Learning (SMILEE) Grandpre', France, 2009
2008
Costa, F., Passerini, A., Lippi, M., and Frasconi, P.
''A Semiparametric Generative Model for Efficient Structured-Output Supervised Learning'',
Annals of Mathematics and Artificial Intelligence, 54(1- 3):207-222 Special issue on Probabilistic Relational Learning, 2008
A. Vullo, A. Passerini, P. Frasconi, F. Costa, G. Pollastri,
''On the Convergence of Protein Structure and Dynamics.Statistical Learning Studies of Pseudo Folding Pathways.'',
Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 6th European Conference, EvoBIO 2008, Naples, Italy, March 26-28, 2008
F. Costa, B. Bringmann,
''Towards Structural Feature Selection'',
Machine learning and intelligent optimization in bioinformatics (MALIOB) Workshop held at Learning and Intelligent OptimizatioN (Lion 3), December 2008
F. Costa, B. Bringmann,
''Towards Combining Pattern Mining and Graph Kernels'',
Mining Complex Data (MCD) held at International Conference on Data Mining series (ICDM), Dicember 2008
F. Costa, B. Bringmann,
''Combining Pattern Mining and Graph Kernels'',
Spring Workshop on Mining and Learning (SMILEE) Traben-Trarbach, Germany, 2008
2007
A. Ceroni, F. Costa, P. Frasconi
''Classification of Small Molecules by Two- and Three-Dimensional Decomposition Kernels'',
Bioinformatics, 23 (16):2038-2045, 2007
[DOI]

Exploration and Analysis of Heterogenuous Information Networks, The Bison Project, EU FP7-ICT- 2007-C FET-Open, contract no. BISON-211898
A, Kimmig, F. Costa,
''Link and node prediction in metabolic networks with probabilistic logic''
Perspectives of Neural-Symbolic Integration
Series: Studies in Computational Intelligence , Vol. 77
Hammer, Barbara; Hitzler, Pascal (Eds.) 2007
ISBN: 978-3-540-73953-1
F. Costa, S. Menchetti, P. Frasconi,
''Comparing Sequence Classification Algorithms for Protein Subcellular Localization''
2006
F. Costa, A. Passerini, P. Frasconi,
''Learning Structured Outputs via Kernel Dependency Estimation and Stochastic Grammars'',
Mining and Learning with Graphs (MLG) held at European Conference on Machine Learning (ECML), September 2006
F. Costa, S. Menchetti, A. Ceroni, A. Passerini, P. Frasconi
''Decomposition Kernels for Natural Language Processing'',
Workshop on Learning Structured Information in Natural Language Applications at the 11th Conference of the European Chapter of the Association for Computational Linguistics (EACL), April 2006
F. Costa, A. Ceroni, P. Frasconi
''Prediction of Molecules Activity using Graphical and Geometrical Kernels'',
Joint APrIL/IQ Workshop, Titisee, Germany, March 2006
2005
F. Costa, P. Frasconi, V. Lombardo, P. Sturt, and G.Soda
''Ambiguity resolution analysis in incremental parsing of natural language'',
IEEE Transactions on Neural Networks, 16 (4):959-971, July 2005
[DOI]

S. Menchetti, F. Costa, P. Frasconi and M. Pontil,
''Wide coverage natural language processing using kernel methods and neural networks for structured data'',
Pattern Recognition Letters, 26 (12):1896-1906, September 2005
[OpenURL]

S. Menchetti, F. Costa, P. Frasconi,
''Weighted Decomposition Kernels'',
22nd International Conference on Machine Learning (ICML), 2005
[DOI]

K. Cerbioni, E. Palanca, A. Starita, F. Costa, P. Frasconi,
''A Grid Focused Community Crawling Architecture for Medical Information Retrieval Services'',
2nd International Conference on Computational Intelligence in Medicine and Healthcare, BIOPATTERN Conference, 2005
S. Menchetti, F. Costa, P. Frasconi,
''Weighted Decomposition Kernels for Protein Subcellular Localization'',
Annual Meeting of the Bioinformatics Italian Society (BITS), 2005
2004
F. Costa, P. Frasconi,
''Distributed Community Crawling'',
13th World Wide Web Conference in New York City (WWW), 2004 (poster)
[DOI]

2003
F. Costa, P. Frasconi, V. Lombardo, and G. Soda,
''Towards Incremental Parsing of Natural Language using Recursive Neural Networks'',
Applied Intelligence, 19 (1-2):9-25, July - October, 2003
[DOI]

P. Sturt, F. Costa, V. Lombardo, P. Frasconi,
''Learning first-pass structural attachment preferences with dynamic grammars and recursive neural networks'',
Cognition, 88 (2):133-169, 2003
[DOI]

S. Menchetti, F. Costa, P. Frasconi and M. Pontil,
''Comparing Convolution Kernels and Recursive Neural Networks for Learning Preferences on Structured Data'',
International Workshop on Artificial Neural Networks in Pattern Recognition (IAPR), 2003
2002
F. Costa, P. Frasconi, V. Lombardo, P. Surt, G. Soda,
''Enhancing first-pass attachment prediction'',
15th European Conference on Artificial Intelligence (ECAI), 2002
F. Costa, P. Frasconi, P. Sturt, V. Lombardo,
''Exploring the effect of experience on a recursive neural network model of structural preferences'',
15th Annual Conference on Human Sentence Processing (CUNY), 2002
2001
P. Sturt, V. Lombardo , F. Costa , P. Frasconi,
''A wide-coverage model of first-pass structural preferences in human parsing'',
14th Annual Conference on Human Sentence Processing (CUNY), 2001
F. Costa, V. Lombardo, P. Frasconi and G. Soda,
''Wide coverage incremental parsing by learning attachment preferences'',
Conference of the Italian Association for Artificial Intelligence (AIIA), 2001
F. Costa, P. Sturt, V. Lombardo, and P. Frasconi,
''The effect of experience on a hybrid model of human first-pass attachment preferences'',
Annual Conference on Architectures and Mechanisms for Language Processing (AMLAP), 2001
2000
P. Sturt, V. Lombardo, F. Costa and P. Frasconi,
''An Experience-Based Model of Incremental Parsing using Dynamic Grammars and Recursive Neural Networks'',
Annual Conference on Architectures and Mechanisms for Language Processing (AMLAP), 2000
F. Costa, P. Frasconi, V. Lombardo and G. Soda,
''Learning Incremental Syntactic Structures with Recursive Neural Networks'',
Conference on Knowledge-Based Engineering Systems (KES), vol. 2, pp. 458-461, IEEE Press, 2000
F. Costa, P. Frasconi, V. Lombardo, G. Soda,
''Learning to ranking structured alternatives: an application to incremental processing of Natural Language'',
Conference of the Italian Association for Artificial Intelligence (AIIA), 2000.
F. Costa, P.Frasconi, V. Lombardo and G. Soda,
''Learning to Rank Structured Alternatives: An Application to Incremental Processing of Natural Language'',
Workshop on Attribute-Value and Relational Learning: Crossing the Boundaries (ICML), 2000
1999
F. Costa, P. Frasconi, and G. Soda,
''A Topological Transformation for Hidden Recursive Models'',
European Symposium on Artificial Neural Networks (ESANN), 1999
F. Costa, P. Frasconi and G. Soda,
''Recursive Connectionist Networks for Trees with Large Outdegree'',
Conference of the Italian Association for Artificial Intelligence (AIIA), 1999
Edited Proceedings for International Workshop:
Ramon, J., Ed., Costa Florencio, C., Ed., Costa, F., Ed., Kok, J., Ed.,
''Proceedings of the ACM SIGKDD Workshop on Statistical and Relational Learning in Bioinformatics'',
Paris, France, June 28, 2009 ACM 2009
Ramon, J., Ed., Costa Florencio, C., Ed., Costa, F., Ed., Kok, J., Ed.,
''Proceedings of the ECML/PKDD Workshop on Statistical and Relational Learning in Bioinformatics'',
Antwerp, Belgium, September 15, 2008
PhD Thesis:
F. Costa,
''A connectionist approach to first-pass attachment prediction in natural language parsing",
PhD in Computer Science, University of Florence, Italy, 2002
Most cited publications:
According to Google Scholar
According to CiteSeer
Automatic publication list:
According to Digital Bibliography and Library Project (DBLP) of University of Trier
According to CiteSeer
According to The Collection of Computer Science Bibliographies (CSB)