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Items: 1 to 20 of 22

1.

Benchmarking of alignment-free sequence comparison methods.

Zielezinski A, Girgis HZ, Bernard G, Leimeister CA, Tang K, Dencker T, Lau AK, Röhling S, Choi JJ, Waterman MS, Comin M, Kim SH, Vinga S, Almeida JS, Chan CX, James BT, Sun F, Morgenstern B, Karlowski WM.

Genome Biol. 2019 Jul 25;20(1):144. doi: 10.1186/s13059-019-1755-7.

2.

Efficient computation of spaced seed hashing with block indexing.

Girotto S, Comin M, Pizzi C.

BMC Bioinformatics. 2018 Nov 30;19(Suppl 15):441. doi: 10.1186/s12859-018-2415-8.

3.

FSH: fast spaced seed hashing exploiting adjacent hashes.

Girotto S, Comin M, Pizzi C.

Algorithms Mol Biol. 2018 Mar 22;13:8. doi: 10.1186/s13015-018-0125-4. eCollection 2018.

4.

Higher recall in metagenomic sequence classification exploiting overlapping reads.

Girotto S, Comin M, Pizzi C.

BMC Genomics. 2017 Dec 6;18(Suppl 10):917. doi: 10.1186/s12864-017-4273-6.

5.

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures.

Girotto S, Pizzi C, Comin M.

Bioinformatics. 2016 Sep 1;32(17):i567-i575. doi: 10.1093/bioinformatics/btw466.

PMID:
27587676
6.

Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values.

Comin M, Schimd M.

BMC Med Genomics. 2016 Aug 12;9 Suppl 1:36. doi: 10.1186/s12920-016-0193-6.

7.

On the comparison of regulatory sequences with multiple resolution Entropic Profiles.

Comin M, Antonello M.

BMC Bioinformatics. 2016 Mar 18;17:130. doi: 10.1186/s12859-016-0980-2.

8.

Clustering of reads with alignment-free measures and quality values.

Comin M, Leoni A, Schimd M.

Algorithms Mol Biol. 2015 Jan 28;10:4. doi: 10.1186/s13015-014-0029-x. eCollection 2015.

9.

Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.

Comin M, Schimd M.

BMC Bioinformatics. 2014;15 Suppl 9:S1. doi: 10.1186/1471-2105-15-S9-S1. Epub 2014 Sep 10.

10.

Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison.

Comin M, Verzotto D.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jul-Aug;11(4):628-37. doi: 10.1109/TCBB.2014.2306830.

PMID:
26356333
11.

Fast Entropic Profiler: An Information Theoretic Approach for the Discovery of Patterns in Genomes.

Comin M, Antonello M.

IEEE/ACM Trans Comput Biol Bioinform. 2014 May-Jun;11(3):500-9. doi: 10.1109/TCBB.2013.2297924.

PMID:
26356018
12.

Parallel continuous flow: a parallel suffix tree construction tool for whole genomes.

Comin M, Farreras M.

J Comput Biol. 2014 Apr;21(4):330-44. doi: 10.1089/cmb.2012.0256. Epub 2014 Mar 5.

13.

Ultrametric networks: a new tool for phylogenetic analysis.

Apostolico A, Comin M, Dress A, Parida L.

Algorithms Mol Biol. 2013 Mar 5;8(1):7. doi: 10.1186/1748-7188-8-7.

14.

Alignment-free phylogeny of whole genomes using underlying subwords.

Comin M, Verzotto D.

Algorithms Mol Biol. 2012 Dec 6;7(1):34. doi: 10.1186/1748-7188-7-34.

15.

The irredundant class method for remote homology detection of protein sequences.

Comin M, Verzotto D.

J Comput Biol. 2011 Dec;18(12):1819-29. doi: 10.1089/cmb.2010.0171. Epub 2011 May 6.

PMID:
21548811
16.

VARUN: discovering extensible motifs under saturation constraints.

Apostolico A, Comin M, Parida L.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):752-26. doi: 10.1109/TCBB.2008.123.

PMID:
21030741
17.

Classification of protein sequences by means of irredundant patterns.

Comin M, Verzotto D.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S16. doi: 10.1186/1471-2105-11-S1-S16.

18.

Binding balls: fast detection of binding sites using a property of spherical Fourier transform.

Comin M, Guerra C, Dellaert F.

J Comput Biol. 2009 Nov;16(11):1577-91. doi: 10.1089/cmb.2009.0045.

PMID:
19958084
19.

Mining overrepresented 3D patterns of secondary structures in proteins.

Comin M, Guerra C, Zanotti G.

J Bioinform Comput Biol. 2008 Dec;6(6):1067-87.

PMID:
19090018
20.

Mining, compressing and classifying with extensible motifs.

Apostolico A, Comin M, Parida L.

Algorithms Mol Biol. 2006 Mar 23;1(1):4.

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