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1

Boosting the FM-index on the GPU: effective techniques to mitigate random memory access

Chacon, Alejandro, Marco-Sola, Santiago, Espinosa, Antonio, Ribeca, Paolo, Moure, Juan Carlos

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 995 KB

english, 2015

2

Within-Host Recombination in the Foot-and-Mouth Disease Virus Genome

Ferretti, Luca, Di Nardo, Antonello, Singer, Benjamin, Lasecka-Dykes, Lidia, Logan, Grace, Wright, Caroline, Pérez-Martín, Eva, King, Donald, Tuthill, Tobias, Ribeca, Paolo

Journal:

Year:

2018

Language:

english

File:

PDF, 12.27 MB

english, 2018

3

From useful algorithms for slowly convergent series to physical predictions based on divergent perturbative expansions

E. Caliceti, M. Meyer-Hermann, P. Ribeca, A. Surzhykov, U.D. Jentschura

Journal:

Physics Reports

Year:

2007

Language:

english

File:

PDF, 991 KB

english, 2007

4

Candidate gene association analysis for milk yield, composition, urea nitrogen and somatic cell scores in Brown Swiss cows

Cecchinato, A., Ribeca, C., Chessa, S., Cipolat-Gotet, C., Maretto, F., Casellas, J., Bittante, G.

Journal:

Year:

2014

Language:

english

File:

PDF, 221 KB

english, 2014

5

Automating Lattice Perturbation Theory in the Schrödinger Functional

Journal:

Nuclear Physics B - Proceedings Supplements

Year:

2005

Language:

english

File:

PDF, 155 KB

english, 2005

6

Association of polymorphisms in calpain 1, (mu/I) large subunit, calpastatin, and cathepsin D genes with meat quality traits in double-muscled Piemontese cattle

Cinzia Ribeca, Valentina Bonfatti, Alessio Cecchinato, Andrea Albera, Fabio Maretto, Luigi Gallo, Paolo Carnier

Journal:

Animal Genetics

Year:

2012

Language:

english

File:

PDF, 103 KB

english, 2012

7

Short communication: Effects of β-lactoglobulin, stearoyl-coenzyme A desaturase 1, and sterol regulatory element binding protein gene allelic variants on milk production, composition, acidity, and coagulation properties of Brown Swiss cows

A. Cecchinato, C. Ribeca, A. Maurmayr, M. Penasa, M. De Marchi, N.P.P. Macciotta, M. Mele, P. Secchiari, G. Pagnacco, G. Bittante

Journal:

Journal of Dairy Science

Year:

2012

Language:

english

File:

PDF, 138 KB

english, 2012

8

Erratum to “Short communication: Effects of β-lactoglobulin, stearoyl-coenzyme A desaturase 1, and sterol regulatory element binding protein gene allelic variants on milk production, composition, acidity, and coagulation properties of Brown Swiss cows” (J. Dairy Sci. 95:450–454)

A. Cecchinato, C. Ribeca, A. Maurmayr, M. Penasa, M. De Marchi, N.P.P. Macciotta, M. Mele, P. Secchiari, G. Pagnacco, G. Bittante

Journal:

Journal of Dairy Science

Year:

2012

Language:

english

File:

PDF, 99 KB

english, 2012

9

Topology of pseudoknotted homopolymers

Vernizzi, Graziano, Ribeca, Paolo, Orland, Henri, Zee, A.

Journal:

Physical Review E

Year:

2006

Language:

english

File:

PDF, 417 KB

english, 2006

10

The GEM mapper: fast, accurate and versatile alignment by filtration

Marco-Sola, Santiago, Sammeth, Michael, Guigó, Roderic, Ribeca, Paolo

Journal:

Year:

2012

Language:

english

File:

PDF, 523 KB

english, 2012

11

Effect of polymorphisms in candidate genes on carcass and meat quality traits in double muscled Piemontese cattle

Ribeca, C., Bonfatti, V., Cecchinato, A., Albera, A., Gallo, L., Carnier, P.

Journal:

Year:

2014

Language:

english

File:

PDF, 331 KB

english, 2014

12

[IEEE 2014 IEEE International Symposium on Parallel and Distributed Processing with Applications (ISPA) - Milan, Italy (2014.8.26-2014.8.28)] 2014 IEEE International Symposium on Parallel and Distributed Processing with Applications - FM-Index on GPU: A Cooperative Scheme to Reduce Memory Footprint

Chacon, Alejandro, Sola, Santiago Marco, Espinosa, Antonio, Ribeca, Paolo, Moure, Juan Carlos

Year:

2014

Language:

english

File:

PDF, 864 KB

english, 2014

13

[ACM Press the 28th ACM international conference - Munich, Germany (2014.06.10-2014.06.13)] Proceedings of the 28th ACM international conference on Supercomputing - ICS '14 - Thread-cooperative, bit-parallel computation of levenshtein distance on GPU

Chacón, Alejandro, Marco-Sola, Santiago, Espinosa, Antonio, Ribeca, Paolo, Moure, Juan Carlos

Year:

2014

Language:

english

File:

PDF, 915 KB

english, 2014

14

[IEEE 2014 IEEE 10th International Conference on e-Science (e-Science) - Sao Paulo, Brazil (2014.10.20-2014.10.24)] 2014 IEEE 10th International Conference on e-Science - Observational Data Patterns for Time Series Data Quality Assessment

Pastorello, Gilberto, Agarwal, Deb, Papale, Dario, Samak, Taghrid, Trotta, Carlo, Ribeca, Alessio, Poindexter, Cristina, Faybishenko, Boris, Gunter, Dan, Hollowgrass, Rachel, Canfora, Eleonora

Year:

2014

Language:

english

File:

PDF, 2.97 MB

english, 2014

15

Modelling and simulating generic RNA-Seq experiments with the flux simulator

Griebel, T., Zacher, B., Ribeca, P., Raineri, E., Lacroix, V., Guigo, R., Sammeth, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 8.22 MB

english, 2012

16

Computational challenges of sequence classification in microbiomic data

Ribeca, P., Valiente, G.

Journal:

Briefings in Bioinformatics

Year:

2011

Language:

english

File:

PDF, 255 KB

english, 2011

17

A more precise characterization of chaperonin substrates

Raineri, E., Ribeca, P., Serrano, L., Maier, T.

Journal:

Year:

2010

Language:

english

File:

PDF, 1.04 MB

english, 2010

18

Faster exact Markovian probability functions for motif occurrences: a DFA-only approach

Ribeca, P., Raineri, E.

Journal:

Year:

2008

Language:

english

File:

PDF, 310 KB

english, 2008

19

Towards a fully automated computation of RG functions for the three-dimensional O(N) vector model: parametrizing amplitudes

R. Guida, P. Ribeca

Year:

2006

Language:

english

File:

PDF, 2.28 MB

english, 2006

20

Genetic variation and effects of candidate-gene polymorphisms on coagulation properties, curd firmness modeling and acidity in milk from Brown Swiss cows

Cecchinato, A., Chessa, S., Ribeca, C., Cipolat-Gotet, C., Bobbo, T., Casellas, J., Bittante, G.

Journal:

Year:

2015

Language:

english

File:

PDF, 237 KB

english, 2015

21

CARGO: effective format-free compressed storage of genomic information

Roguski, Łukasz, Ribeca, Paolo

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 2.36 MB

english, 2016

22

Genome sequence of the olive tree,Olea europaea

Cruz, Fernando, Julca, Irene, Gómez-Garrido, Jèssica, Loska, Damian, Marcet-Houben, Marina, Cano, Emilio, Galán, Beatriz, Frias, Leonor, Ribeca, Paolo, Derdak, Sophia, Gut, Marta, Sánchez-Fernández, M

Journal:

Year:

2016

Language:

english

File:

PDF, 1.03 MB

english, 2016

23

Genetic correlations between measures of beef quality traits and their predictions by near-infrared spectroscopy in the Piemontese cattle breed

Cecchinato, Alessio, De Marchi, Massimo, Boukha, Aziza, Ribeca, Cinzia, Carnier, Paolo

Journal:

Italian Journal of Animal Science

Year:

2009

Language:

english

File:

PDF, 452 KB

english, 2009

24

Investigation on variability of candidate genes for meat quality traits in Piemontese cattle

Ribeca, Cinzia, Bittante, Giovanni, Albera, Andrea, Bonfatti, Valentina, Maretto, Fabio, Gallo, Luigi

Journal:

Italian Journal of Animal Science

Year:

2009

Language:

english

File:

PDF, 317 KB

english, 2009

25

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Djebali, Sarah, Lagarde, Julien, Kapranov, Philipp, Lacroix, Vincent, Borel, Christelle, Mudge, Jonathan M., Howald, Cédric, Foissac, Sylvain, Ucla, Catherine, Chrast, Jacqueline, Ribeca, Paolo, Marti

Journal:

Year:

2012

Language:

english

File:

PDF, 1.70 MB

english, 2012

26

Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco ( Junco hyemalis )

Abolins-Abols, Mikus, Kornobis, Etienne, Ribeca, Paolo, Wakamatsu, Kazumasa, Peterson, Mark P., Ketterson, Ellen D., Milá, Borja

Journal:

Molecular Ecology

Year:

2018

Language:

english

File:

PDF, 1.44 MB

english, 2018

27

The Site Frequency/Dosage Spectrum of Autopolyploid Populations

Ferretti, Luca, Ribeca, Paolo, Ramos-Onsins, Sebastian E.

Journal:

Frontiers in Genetics

Year:

2018

Language:

english

File:

PDF, 1.65 MB

english, 2018

28

Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015

Fereidouni, Sasan, Freimanis, Graham L., Orynbayev, Mukhit, Ribeca, Paolo, Flannery, John, King, Donald P., Zuther, Steffen, Beer, Martin, Höper, Dirk, Kydyrmanov, Aidyn, Karamendin, Kobey, Kock, Rich

Journal:

Emerging Infectious Diseases

Year:

2019

Language:

english

File:

PDF, 1.09 MB

english, 2019

29

SiNPle: Fast and Sensitive Variant Calling for Deep Sequencing Data

Ferretti, Luca, Tennakoon, Chandana, Silesian, Adrian, Ribeca, Graham Freimanis andPaolo

Journal:

Year:

2019

Language:

english

File:

PDF, 550 KB

english, 2019

30

Novel determinants describe chaperonin substrate proteins

Raineri, Emanuele, Ribeca, Paolo, Serrano, Luis, Maier, Tobias

Journal:

Nature Precedings

Year:

2009

Language:

english

File:

PDF, 872 KB

english, 2009

31

Evolvability of Chaperonin Substrate Proteins

Raineri, Emanuele, Ribeca, Paolo, Serrano, Luis, Maier, Tobias

Journal:

Nature Precedings

Year:

2009

Language:

english

File:

PDF, 872 KB

english, 2009

32

Bovine Derived in vitro Cultures Generate Heterogeneous Populations of Antigen Presenting Cells

Guzman, Efrain, Pujol, Myriam, Ribeca, Paolo, Montoya, Maria

Journal:

Frontiers in Immunology

Year:

2019

Language:

english

File:

PDF, 3.94 MB

english, 2019

33

Novel determinants describe chaperonin substrate proteins

Raineri, Emanuele, Ribeca, Paolo, Serrano, Luis, Maier, Tobias

Journal:

Nature Precedings

Year:

2009

File:

PDF, 872 KB

2009

34

Evolvability of Chaperonin Substrate Proteins

Raineri, Emanuele, Ribeca, Paolo, Serrano, Luis, Maier, Tobias

Journal:

Nature Precedings

Year:

2009

File:

PDF, 872 KB

2009

35

Bovine Derived in vitro Cultures Generate Heterogeneous Populations of Antigen Presenting Cells

Guzman, Efrain, Pujol, Myriam, Ribeca, Paolo, Montoya, Maria

Journal:

Frontiers in Immunology

Year:

2019

File:

PDF, 3.94 MB

2019

36

Pervasive within-host recombination and epistasis as major determinants of the molecular evolution of the foot-and-mouth disease virus capsid

Ferretti, Luca, Pérez-Martín, Eva, Zhang, Fuquan, Maree, François, de Klerk-Lorist, Lin-Mari, van Schalkwykc, Louis, Juleff, Nicholas D., Charleston, Bryan, Ribeca, Paolo, Cameron, Craig E.

Journal:

Year:

2020

File:

PDF, 8.55 MB

2020

37

Pervasive Differential Splicing in Marekâs Disease Virus can Discriminate CVI-988 Vaccine Strain from RB-1B Very Virulent Strain in Chicken Embryonic Fibroblasts

Sadigh, Yashar, Tahiri-Alaoui, Abdessamad, Spatz, Stephen, Nair, Venugopal, Ribeca, Paolo

Journal:

Year:

2020

Language:

english

File:

PDF, 1.78 MB

english, 2020

38

Full genome sequencing of archived wild type and vaccine rinderpest virus isolates prior to their destruction

King, Simon, Rajko-Nenow, Paulina, Ropiak, Honorata M., Ribeca, Paolo, Batten, Carrie, Baron, Michael D.

Journal:

Scientific Reports

Year:

2020

File:

PDF, 3.56 MB

2020

39

A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations

King, David J., Freimanis, Graham, Lasecka-Dykes, Lidia, Asfor, Amin, Ribeca, Paolo, Waters, Ryan, King, Donald P., Laing, Emma

Journal:

Year:

2020

File:

PDF, 2.49 MB

2020