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1

[Lecture Notes in Computer Science] Beyond the Horizon of Computability Volume 12098 (16th Conference on Computability in Europe, CiE 2020, Fisciano, Italy, June 29âJuly 3, 2020, Proceedings) ||

Anselmo, Marcella, Della Vedova, Gianluca, Manea, Florin, Pauly, Arno

Year:

2020

File:

PDF, 8.49 MB

2020

2

An Algorithm for the Modular Decomposition of Hypergraphs

Paola Bonizzoni, Gianluca Della Vedova

Journal:

Journal of Algorithms

Year:

1999

Language:

english

File:

PDF, 147 KB

english, 1999

3

Variants of constrained longest common subsequence

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola

Journal:

Information Processing Letters

Year:

2010

Language:

english

File:

PDF, 143 KB

english, 2010

4

Experimenting an approximation algorithm for the LCS

Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri

Journal:

Discrete Applied Mathematics

Year:

2001

Language:

english

File:

PDF, 126 KB

english, 2001

5

The complexity of multiple sequence alignment with SP-score that is a metric

Paola Bonizzoni, Gianluca Della Vedova

Journal:

Theoretical Computer Science

Year:

2001

Language:

english

File:

PDF, 235 KB

english, 2001

6

Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

Paul M Ruegger, Gianluca Della Vedova, Tao Jiang, James Borneman

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 275 KB

english, 2011

7

Foreword

Paola Bonizzoni, Gianluca Della Vedova, Tao Jiang

Journal:

Journal of Computer Science and Technology

Year:

2004

Language:

english

File:

PDF, 85 KB

english, 2004

8

The Haplotyping problem: An overview of computational models and solutions

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Jing Li

Journal:

Journal of Computer Science and Technology

Year:

2003

Language:

english

File:

PDF, 1.40 MB

english, 2003

9

Fingerprint Clustering with Bounded Number of

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri

Journal:

Year:

2010

Language:

english

File:

PDF, 513 KB

english, 2010

10

Anonymizing binary and small tables is

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi

Journal:

Journal of Combinatorial Optimization

Year:

2011

Language:

english

File:

PDF, 721 KB

english, 2011

11

Beyond evolutionary trees

Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola, Lusheng Wang

Journal:

Natural Computing

Year:

2010

Language:

english

File:

PDF, 339 KB

english, 2010

12

On the Approximation of Correlation Clustering and Consensus Clustering

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang

Journal:

Journal of Computer and System Sciences

Year:

2008

Language:

english

File:

PDF, 359 KB

english, 2008

13

Reconciling a gene tree to a species tree under the duplication cost model

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi

Journal:

Theoretical Computer Science

Year:

2005

Language:

english

File:

PDF, 225 KB

english, 2005

14

A randomized PTAS for the minimum Consensus Clustering with a fixed number of clusters

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi

Journal:

Theoretical Computer Science

Year:

2012

Language:

english

File:

PDF, 274 KB

english, 2012

15

PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text

Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 453 KB

english, 2012

16

Parameterized complexity ofk-anonymity: hardness and tractability

Bonizzoni, Paola, Della Vedova, Gianluca, Dondi, Riccardo, Pirola, Yuri

Journal:

Journal of Combinatorial Optimization

Year:

2013

Language:

english

File:

PDF, 792 KB

english, 2013

17

Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs

Beretta, Stefano, Bonizzoni, Paola, Vedova, Gianluca Della, Pirola, Yuri, Rizzi, Raffaella

Journal:

Journal of Computational Biology

Year:

2014

Language:

english

File:

PDF, 929 KB

english, 2014

18

[IEEE 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Orlando, FL, USA (2011.02.3-2011.02.5)] 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text

Bonizzoni, Paola, Della Vedova, Gianluca, Pirola, Yuri, Rizzi, Raffaella

Year:

2011

Language:

english

File:

PDF, 140 KB

english, 2011

19

Pure Parsimony Xor Haplotyping

Bonizzoni, P, Della Vedova, Gianluca, Dondi, R, Pirola, Y, Rizzi, R

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.42 MB

english, 2010

20

Multiple Sequence Alignment as a Facility-Location Problem

Just, Winfried, Vedova, Gianluca Della

Journal:

INFORMS Journal on Computing

Year:

2004

Language:

english

File:

PDF, 263 KB

english, 2004

21

[IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Philadelphia, PA, USA (2012.10.4-2012.10.7)] 2012 IEEE International Conference on Bioinformatics and Biomedicine - Reconstructing isoform graphs from RNA-Seq data

Beretta, Stefano, Bonizzoni, Paola, Rizzi, Raffaella, Della Vedova, Gianluca

Year:

2012

Language:

english

File:

PDF, 741 KB

english, 2012

22

A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information

Pirola, Yuri, Della Vedova, Gianluca, Biffani, Stefano, Stella, Alessandra, Bonizzoni, Paola

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.74 MB

english, 2012

23

User-only design to assess drug effectiveness in clinical practice: application to bisphosphonates and secondary prevention of fractures

Corrao, Giovanni, Ghirardi, Arianna, Segafredo, Giulia, Zambon, Antonella, Della Vedova, Gianluca, Lapi, Francesco, Cipriani, Francesco, Caputi, Achille, Vaccheri, Alberto, Gregori, Dario, Gesuita, Ro

Journal:

Pharmacoepidemiology and Drug Safety

Year:

2014

Language:

english

File:

PDF, 386 KB

english, 2014

24

[IEEE 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Las Vegas, NV, USA (2012.02.23-2012.02.25)] 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) - A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information

Pirola, Yuri, Della Vedova, Gianluca, Biffani, Stefano, Stella, Alessandra, Bonizzoni, Paola

Year:

2012

Language:

english

File:

PDF, 256 KB

english, 2012

25

APPROXIMATING THE MAXIMUM ISOMORPHIC AGREEMENT SUBTREE IS HARD

Bonizzoni, Paola, Vedova, Gianluca Della, Mauri, Giancarlo

Journal:

International Journal of Foundations of Computer Science

Year:

2000

Language:

english

File:

PDF, 1.63 MB

english, 2000

26

[ACM Press the International Conference - Wshington DC, USA (2013.09.22-2013.09.25)] Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13 - Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes

Pirola, Yuri, Vedova, Gianluca Della, Bonizzoni, Paola, Stella, Alessandra, Biscarini, Filippo

Year:

2007

Language:

english

File:

PDF, 415 KB

english, 2007

27

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly

Bonizzoni, Paola, Vedova, Gianluca Della, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaella

Journal:

Journal of Computational Biology

Year:

2016

Language:

english

File:

PDF, 286 KB

english, 2016

28

Explaining evolution via constrained persistent perfect phylogeny

Bonizzoni, Paola, Carrieri, Anna Paola, Della Vedova, Gianluca, Trucco, Gabriella

Journal:

Year:

2014

Language:

english

File:

PDF, 618 KB

english, 2014

29

Experimental analysis of a new algorithm for partial haplotype completion

Bonizzoni, Paola, Vedova, Gianluca Della, Dondi, Riccardo, Mariani, Lorenzo

Journal:

International Journal of Bioinformatics Research and Applications

Year:

2005

Language:

english

File:

PDF, 410 KB

english, 2005

30

An External-Memory Algorithm for String Graph Construction

Bonizzoni, Paola, Della Vedova, Gianluca, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaella

Journal:

Year:

2017

Language:

english

File:

PDF, 851 KB

english, 2017

31

FSG: Fast String Graph Construction for De Novo Assembly

Bonizzoni, Paola, Della Vedova, Gianluca, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaella

Journal:

Journal of Computational Biology

Year:

2017

Language:

english

File:

PDF, 435 KB

english, 2017

32

Species-Driven Persistent Phylogeny

Bonizzoni, Paola, Carrieri, Anna Paola, Della Vedova, Gianluca, Rizzi, Raffaella, Trucco, Gabriella, Păun, Gheorghe, Rozenberg, Grzegorz, Salomaa, Arto

Journal:

Fundamenta Informaticae

Year:

2017

Language:

english

File:

PDF, 167 KB

english, 2017

33

[ACM Press the 8th ACM International Conference - Boston, Massachusetts, USA (2017.08.20-2017.08.23)] Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics - ACM-BCB '17 - Beyond Perfect Phylogeny

Bonizzoni, Paola, Ciccolella, Simone, Della Vedova, Gianluca, Soto, Mauricio

Year:

2017

Language:

english

File:

PDF, 1.19 MB

english, 2017

34

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads

Beretta, Stefano, Patterson, Murray D., Zaccaria, Simone, Della Vedova, Gianluca, Bonizzoni, Paola

Journal:

BMC Bioinformatics

Year:

2018

Language:

english

File:

PDF, 990 KB

english, 2018

35

[IEEE 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Las Vegas, NV, USA (2018.10.18-2018.10.20)] 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data

Ciccolella, Simone, Gomez, Mauricio Soto, Patterson, Murray, Vedova, Gianluca Della, Hajirasouliha, Iman, Bonizzoni, Paola

Year:

2018

Language:

english

File:

PDF, 103 KB

english, 2018

36

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events

Denti, Luca, Rizzi, Raffaella, Beretta, Stefano, Vedova, Gianluca Della, Previtali, Marco, Bonizzoni, Paola

Journal:

BMC Bioinformatics

Year:

2018

File:

PDF, 1.58 MB

2018

37

Multithread Multistring Burrows–Wheeler Transform and Longest Common Prefix Array

Bonizzoni, Paola, Della Vedova, Gianluca, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaella

Journal:

Journal of Computational Biology

Year:

2019

Language:

english

File:

PDF, 1.57 MB

english, 2019

38

Does relaxing the infinite sites assumption give better tumor phylogenies? An ILP-based comparative approach

Bonizzoni, Paola, Ciccolella, Simone, Della Vedova, Gianluca, Soto Gomez, Mauricio

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2018

Language:

english

File:

PDF, 2.57 MB

english, 2018

39

[ACM Press the 10th ACM International Conference - Niagara Falls, NY, USA (2019.09.07-2019.09.10)] Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '19 - Effective Clustering for Single Cell Sequencing Cancer Data

Ciccolella, Simone, Patterson, Murray D., Bonizzoni, Paola, Della Vedova, Gianluca

Year:

2019

File:

PDF, 1.99 MB

2019

40

Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era

Rizzi, Raffaella, Beretta, Stefano, Patterson, Murray, Pirola, Yuri, Previtali, Marco, Della Vedova, Gianluca, Bonizzoni, Paola

Journal:

Quantitative Biology

Year:

2019

File:

PDF, 341 KB

2019

41

Inferring Cancer Progression from Single-Cell Sequencing while Allowing Mutation Losses

Ciccolella, Simone, Ricketts, Camir, Soto Gomez, Mauricio, Patterson, Murray, Silverbush, Dana, Bonizzoni, Paola, Hajirasouliha, Iman, Della Vedova, Gianluca, Martelli, Pier Luigi

Journal:

Year:

2020

File:

PDF, 1.01 MB

2020

42

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels

Ciccolella, Simone, Bernardini, Giulia, Denti, Luca, Bonizzoni, Paola, Previtali, Marco, Della Vedova, Gianluca, Elofsson, Arne

Journal:

Year:

2020

File:

PDF, 5.97 MB

2020

43

Shark: fishing relevant reads in an RNA-Seq sample

Denti, Luca, Pirola, Yuri, Previtali, Marco, Ceccato, Tamara, Della Vedova, Gianluca, Rizzi, Raffaella, Bonizzoni, Paola, Ponty, Yann

Journal:

Year:

2020

File:

PDF, 452 KB

2020

44

gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data

Ciccolella, Simone, Soto Gomez, Mauricio, Patterson, Murray D., Della Vedova, Gianluca, Hajirasouliha, Iman, Bonizzoni, Paola

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.96 MB

2020

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