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Items: 15

1.

Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array.

Bonizzoni P, Della Vedova G, Pirola Y, Previtali M, Rizzi R.

J Comput Biol. 2019 May 29. doi: 10.1089/cmb.2018.0230. [Epub ahead of print]

PMID:
31140836
2.

FSG: Fast String Graph Construction for De Novo Assembly.

Bonizzoni P, Vedova GD, Pirola Y, Previtali M, Rizzi R.

J Comput Biol. 2017 Oct;24(10):953-968. doi: 10.1089/cmb.2017.0089. Epub 2017 Jul 17.

PMID:
28715269
3.

Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations.

Biscarini F, Schwarzenbacher H, Pausch H, Nicolazzi EL, Pirola Y, Biffani S.

BMC Genomics. 2016 Nov 3;17(1):857.

4.

Transcriptional profiling of immortalized and K-ras-transformed mouse fibroblasts upon PKA stimulation by forskolin in low glucose availability.

Chiaradonna F, Pirola Y, Ricciardiello F, Palorini R.

Genom Data. 2016 Jul 7;9:100-4. doi: 10.1016/j.gdata.2016.07.004. eCollection 2016 Sep.

5.

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes.

Bonizzoni P, Dondi R, Klau GW, Pirola Y, Pisanti N, Zaccaria S.

J Comput Biol. 2016 Sep;23(9):718-36. doi: 10.1089/cmb.2015.0220. Epub 2016 Jun 9.

PMID:
27280382
6.

Protein Kinase A Activation Promotes Cancer Cell Resistance to Glucose Starvation and Anoikis.

Palorini R, Votta G, Pirola Y, De Vitto H, De Palma S, Airoldi C, Vasso M, Ricciardiello F, Lombardi PP, Cirulli C, Rizzi R, Nicotra F, Hiller K, Gelfi C, Alberghina L, Chiaradonna F.

PLoS Genet. 2016 Mar 15;12(3):e1005931. doi: 10.1371/journal.pgen.1005931. eCollection 2016 Mar.

7.

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

Bonizzoni P, Vedova GD, Pirola Y, Previtali M, Rizzi R.

J Comput Biol. 2016 Mar;23(3):137-49. doi: 10.1089/cmb.2015.0172.

PMID:
26953874
8.

HapCol: accurate and memory-efficient haplotype assembly from long reads.

Pirola Y, Zaccaria S, Dondi R, Klau GW, Pisanti N, Bonizzoni P.

Bioinformatics. 2016 Jun 1;32(11):1610-7. doi: 10.1093/bioinformatics/btv495. Epub 2015 Aug 26.

PMID:
26315913
9.

Transcriptome assembly and alternative splicing analysis.

Bonizzoni P, Della Vedova G, Pesole G, Picardi E, Pirola Y, Rizzi R.

Methods Mol Biol. 2015;1269:173-88. doi: 10.1007/978-1-4939-2291-8_11.

PMID:
25577379
10.

Modeling alternative splicing variants from RNA-Seq data with isoform graphs.

Beretta S, Bonizzoni P, Vedova GD, Pirola Y, Rizzi R.

J Comput Biol. 2014 Jan;21(1):16-40. doi: 10.1089/cmb.2013.0112. Epub 2013 Nov 7.

11.

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

Pirola Y, Della Vedova G, Biffani S, Stella A, Bonizzoni P.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1582-94.

PMID:
22848137
12.

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

Pirola Y, Rizzi R, Picardi E, Pesole G, Della Vedova G, Bonizzoni P.

BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S2. doi: 10.1186/1471-2105-13-S5-S2.

13.

An efficient algorithm for haplotype inference on pedigrees with recombinations and mutations.

Pirola Y, Bonizzoni P, Jiang T.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jan-Feb;9(1):12-25. doi: 10.1109/TCBB.2011.51. Epub 2011 Mar 3.

PMID:
21383417
14.

Pure parsimony xor haplotyping.

Bonizzoni P, Della Vedova G, Dondi R, Pirola Y, Rizzi R.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):598-610. doi: 10.1109/TCBB.2010.52.

PMID:
20498511
15.

Detecting alternative gene structures from spliced ESTs: a computational approach.

Bonizzoni P, Mauri G, Pesole G, Picardi E, Pirola Y, Rizzi R.

J Comput Biol. 2009 Jan;16(1):43-66. doi: 10.1089/cmb.2008.0028.

PMID:
19119993

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