-
1
-
-
43849099955
-
Microbiology in the post-genomic era
-
Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, et al. Microbiology in the post-genomic era. Nat Rev Microbiol. 2008; 6:419-30.
-
(2008)
Nat Rev Microbiol.
, vol.6
, pp. 419-430
-
-
Medini, D.1
Serruto, D.2
Parkhill, J.3
Relman, D.A.4
Donati, C.5
Moxon, R.6
-
2
-
-
52649132425
-
Genome-wide identification of in vivo protein-dna binding sites from chip-seq data
-
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-dna binding sites from chip-seq data. Nucleic Acids Res. 2008; 36:5221-31.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
3
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215:403-10.
-
(1990)
J Mol Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
4
-
-
62449130191
-
Alignment-free genome comparison with feature frequency profiles (ffp) and optimal resolutions
-
Sims GE, Jun S-R, Wu GA, Kim S-H. Alignment-free genome comparison with feature frequency profiles (ffp) and optimal resolutions. Proc Nat Acad Sci. 2009; 106:2677-82.
-
(2009)
Proc Nat Acad Sci.
, vol.106
, pp. 2677-2682
-
-
Sims, G.E.1
Jun, S.-R.2
Wu, G.A.3
Kim, S.-H.4
-
6
-
-
84870417740
-
Alignment-free phylogeny of whole genomes using underlying subwords
-
Comin M, Verzotto D. Alignment-free phylogeny of whole genomes using underlying subwords. Algorithms Mol Biol. 2012; 7(1):34.
-
(2012)
Algorithms Mol Biol.
, vol.7
, Issue.1
, pp. 34
-
-
Comin, M.1
Verzotto, D.2
-
7
-
-
84873598282
-
Alignment-free sequence comparison based on next-generation sequencing reads
-
Song K, Ren J, Zhai Z, Liu X, Deng M, Sun F. Alignment-free sequence comparison based on next-generation sequencing reads. J Comput Biol. 2013; 20(2):64-79.
-
(2013)
J Comput Biol.
, vol.20
, Issue.2
, pp. 64-79
-
-
Song, K.1
Ren, J.2
Zhai, Z.3
Liu, X.4
Deng, M.5
Sun, F.6
-
8
-
-
84921766593
-
Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns
-
Comin M, Schimd M. Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns. BMC Bioinformatics. 2014; 15(Suppl 9):1.
-
(2014)
BMC Bioinformatics.
, vol.15
, pp. 1
-
-
Comin, M.1
Schimd, M.2
-
9
-
-
0037342499
-
Alignment-free sequence comparison-a review
-
Vinga S, Almeida J. Alignment-free sequence comparison-a review. Bioinformatics. 2003; 19(4):513-23.
-
(2003)
Bioinformatics.
, vol.19
, Issue.4
, pp. 513-523
-
-
Vinga, S.1
Almeida, J.2
-
10
-
-
54149091987
-
Comparison study on k-word statistical measures for protein: From sequence to'sequence space'
-
Dai Q, Wang T. Comparison study on k-word statistical measures for protein: From sequence to'sequence space'. BMC Bioinformatics. 2008; 9(1):394.
-
(2008)
BMC Bioinformatics.
, vol.9
, Issue.1
, pp. 394
-
-
Dai, Q.1
Wang, T.2
-
11
-
-
34047110724
-
Whole genome molecular phylogeny of large dsdna viruses using composition vector method
-
Gao L, Qi J. Whole genome molecular phylogeny of large dsdna viruses using composition vector method. BMC Evol Biol. 2007; 7(1):41.
-
(2007)
BMC Evol Biol.
, vol.7
, Issue.1
, pp. 41
-
-
Gao, L.1
Qi, J.2
-
12
-
-
3242890106
-
Cvtree: a phylogenetic tree reconstruction tool based on whole genomes
-
Qi J, Luo H, Hao B. Cvtree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res. 2004; 32(suppl 2):45-7.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 45-47
-
-
Qi, J.1
Luo, H.2
Hao, B.3
-
13
-
-
84857867828
-
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts
-
Göke J, Schulz MH, Lasserre J, Vingron M. Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics. 2012; 28(5):656-63.
-
(2012)
Bioinformatics.
, vol.28
, Issue.5
, pp. 656-663
-
-
Göke, J.1
Schulz, M.H.2
Lasserre, J.3
Vingron, M.4
-
14
-
-
34547844142
-
A statistical method for alignment-free comparison of regulatory sequences
-
Kantorovitz MR, Robinson GE, Sinha S. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics. 2007; 23(13):249-55.
-
(2007)
Bioinformatics.
, vol.23
, Issue.13
, pp. 249-255
-
-
Kantorovitz, M.R.1
Robinson, G.E.2
Sinha, S.3
-
15
-
-
84940363594
-
Beyond fixed-resolution alignment-free measures for mammalian enhancers sequence comparison
-
Comin M, Verzotto D. Beyond fixed-resolution alignment-free measures for mammalian enhancers sequence comparison. IEEE/ACM Trans Comput Biol Bioinformatics. 2014; 11(4):628-37.
-
(2014)
IEEE/ACM Trans Comput Biol Bioinformatics.
, vol.11
, Issue.4
, pp. 628-637
-
-
Comin, M.1
Verzotto, D.2
-
16
-
-
84880712402
-
Fast computation of entropic profiles for the detection of conservation in genomes
-
Ngom A, Formenti E, Hao J-K, Zhao X-M, van Laarhoven T, editors, Berlin Heidelberg: Springer
-
Comin M, Antonello M. Fast computation of entropic profiles for the detection of conservation in genomes In: Ngom A, Formenti E, Hao J-K, Zhao X-M, van Laarhoven T, editors. Pattern recognition in Bioinformatics. vol. 7986,Berlin Heidelberg: Springer: 2013. p. 277-88.
-
(2013)
Pattern recognition in Bioinformatics
, vol.7986
-
-
Comin, M.1
Antonello, M.2
-
17
-
-
84903151147
-
Fast entropic profiler: An information theoretic approach for the discovery of patterns in genomes
-
Comin M, Antonello M. Fast entropic profiler: An information theoretic approach for the discovery of patterns in genomes. Comput Biol Bioinform IEEE/ACM Trans. 2014; 11(3):500-9.
-
(2014)
Comput Biol Bioinform IEEE/ACM Trans.
, vol.11
, Issue.3
, pp. 500-509
-
-
Comin, M.1
Antonello, M.2
-
18
-
-
75149191979
-
Classification of protein sequences by means of irredundant patterns
-
Comin M, Verzotto D. Classification of protein sequences by means of irredundant patterns. BMC bioinformatics. 2010; 11(Suppl 1):16.
-
(2010)
BMC bioinformatics.
, vol.11
, pp. 16
-
-
Comin, M.1
Verzotto, D.2
-
19
-
-
82755173954
-
The irredundant class method for remote homology detection of protein sequences
-
Comin M, Verzotto D. The irredundant class method for remote homology detection of protein sequences. J Comput Biol. 2011; 18(12):1819-29.
-
(2011)
J Comput Biol.
, vol.18
, Issue.12
, pp. 1819-1829
-
-
Comin, M.1
Verzotto, D.2
-
20
-
-
67650074197
-
Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
-
Qu W, Hashimoto S-i, Morishita S. Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res. 2009; 19(7):1309-15.
-
(2009)
Genome Res.
, vol.19
, Issue.7
, pp. 1309-1315
-
-
Qu, W.1
Hashimoto, S.2
Morishita, S.3
-
21
-
-
80052722558
-
Seed: efficient clustering of next-generation sequences
-
Bao E, Jiang T, Kaloshian I, Girke T. Seed: efficient clustering of next-generation sequences. Bioinformatics. 2011; 27(18):2502-9.
-
(2011)
Bioinformatics.
, vol.27
, Issue.18
, pp. 2502-2509
-
-
Bao, E.1
Jiang, T.2
Kaloshian, I.3
Girke, T.4
-
22
-
-
84883514471
-
Centroid based clustering of high throughput sequencing reads based on n-mer counts
-
Solovyov A, Lipkin W. Centroid based clustering of high throughput sequencing reads based on n-mer counts. BMC Bioinformatics. 2013; 14(1):268.
-
(2013)
BMC Bioinformatics.
, vol.14
, Issue.1
, pp. 268
-
-
Solovyov, A.1
Lipkin, W.2
-
23
-
-
55549097836
-
Mapping short dna sequencing reads and calling variants using mapping quality scores
-
Li H, Ruan J, Durbin R. Mapping short dna sequencing reads and calling variants using mapping quality scores. Genome Res. 2008; 18(11):1851-8.
-
(2008)
Genome Res.
, vol.18
, Issue.11
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
24
-
-
79957932376
-
Dindel: accurate indel calls from short-read data
-
Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R. Dindel: accurate indel calls from short-read data. Genome Res. 2011; 21(6):961-73.
-
(2011)
Genome Res.
, vol.21
, Issue.6
, pp. 961-973
-
-
Albers, C.A.1
Lunter, G.2
MacArthur, D.G.3
McVean, G.4
Ouwehand, W.H.5
Durbin, R.6
-
25
-
-
84864518203
-
Pacific biosciences sequencing technology for genotyping and variation discovery in human data
-
Carneiro MO, Russ C, Ross MG, Gabriel SB, Nusbaum C, DePristo MA. Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics. 2012; 13(1):375.
-
(2012)
BMC Genomics.
, vol.13
, Issue.1
, pp. 375
-
-
Carneiro, M.O.1
Russ, C.2
Ross, M.G.3
Gabriel, S.B.4
Nusbaum, C.5
DePristo, M.A.6
-
26
-
-
0022743812
-
A measure of the similarity of sets of sequences not requiring sequence alignment
-
Blaisdell BE. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc Natl Acad Sci. 1986; 83(14):5155-9.
-
(1986)
Proc Natl Acad Sci.
, vol.83
, Issue.14
, pp. 5155-5159
-
-
Blaisdell, B.E.1
-
27
-
-
0037195172
-
Distributional regimes for the number of k-word matches between two random sequences
-
Lippert RA, Huang H, Waterman MS. Distributional regimes for the number of k-word matches between two random sequences. Proc Natl Acad Sci. 2002; 99(22):13980-9.
-
(2002)
Proc Natl Acad Sci.
, vol.99
, Issue.22
, pp. 13980-13989
-
-
Lippert, R.A.1
Huang, H.2
Waterman, M.S.3
-
28
-
-
75149164526
-
Alignment-free sequence comparison (i): statistics and power
-
Reinert G, Chew D, Sun F, Waterman MS. Alignment-free sequence comparison (i): statistics and power. J Comput Biol. 2009; 16(12):1615-34.
-
(2009)
J Comput Biol.
, vol.16
, Issue.12
, pp. 1615-1634
-
-
Reinert, G.1
Chew, D.2
Sun, F.3
Waterman, M.S.4
-
29
-
-
78349292948
-
Alignment-free sequence comparison (ii): theoretical power of comparison statistics
-
Wan L, Reinert G, Sun F, Waterman MS. Alignment-free sequence comparison (ii): theoretical power of comparison statistics. J Comput Biol. 2010; 17(11):1467-90.
-
(2010)
J Comput Biol.
, vol.17
, Issue.11
, pp. 1467-1490
-
-
Wan, L.1
Reinert, G.2
Sun, F.3
Waterman, M.S.4
-
30
-
-
0031978181
-
Base-calling of automated sequencer traces using phred. ii. error probabilities
-
Ewing B, Green P. Base-calling of automated sequencer traces using phred. ii. error probabilities. Genome Res. 1998; 8(3):186-94.
-
(1998)
Genome Res.
, vol.8
, Issue.3
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
31
-
-
84924241382
-
-
NCBI dataset of human mRNA genes
-
NCBI dataset of human mRNA genes. ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/.
-
-
-
-
32
-
-
84924279216
-
-
Mason
-
Mason. http://seqan.de/projects/mason.html
-
-
-
-
34
-
-
78650916667
-
Assemblies: the good, the bad, the ugly
-
Birney E. Assemblies: the good, the bad, the ugly. Nat Methods. 2011; 8(1):59-60.
-
(2011)
Nat Methods.
, vol.8
, Issue.1
, pp. 59-60
-
-
Birney, E.1
-
35
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de bruijn graphs
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Res. 2008; 18(5):821-9.
-
(2008)
Genome Res.
, vol.18
, Issue.5
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
36
-
-
84958548439
-
Qcluster: Extending alignment-free measures with quality values for reads clustering
-
Comin M, Leoni A, Schimd M. Qcluster: Extending alignment-free measures with quality values for reads clustering. Algorithms Bioinform Lect Notes Comput Sci. 2014; 8701:1-13.
-
(2014)
Algorithms Bioinform Lect Notes Comput Sci.
, vol.8701
, pp. 1-13
-
-
Comin, M.1
Leoni, A.2
Schimd, M.3
|