Phylogenetic Comparative Assembly

Husemann P, Stoye J (2009)
In: Proc. of WABI 2009. LNBI, 5724. 145-156.

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WABI 2009
Philadelphia, USA
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Husemann P, Stoye J. Phylogenetic Comparative Assembly. In: Proc. of WABI 2009. LNBI. Vol 5724. 2009: 145-156.
Husemann, P., & Stoye, J. (2009). Phylogenetic Comparative Assembly. Proc. of WABI 2009, 5724, 145-156.
Husemann, P., and Stoye, J. (2009). “Phylogenetic Comparative Assembly” in Proc. of WABI 2009 LNBI, vol. 5724, 145-156.
Husemann, P., & Stoye, J., 2009. Phylogenetic Comparative Assembly. In Proc. of WABI 2009. LNBI. no.5724 pp. 145-156.
P. Husemann and J. Stoye, “Phylogenetic Comparative Assembly”, Proc. of WABI 2009, LNBI, vol. 5724, 2009, pp.145-156.
Husemann, P., Stoye, J.: Phylogenetic Comparative Assembly. Proc. of WABI 2009. LNBI. 5724, p. 145-156. (2009).
Husemann, Peter, and Stoye, Jens. “Phylogenetic Comparative Assembly”. Proc. of WABI 2009. 2009.Vol. 5724. LNBI. 145-156.
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7 Citations in Europe PMC

Data provided by Europe PubMed Central.

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PMID: 26450761
MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lio P, Crescenzi P, Fani R, Fondi M., Bioinformatics 31(15), 2015
PMID: 25810435
The inference of gene trees with species trees.
Szollosi GJ, Tannier E, Daubin V, Boussau B., Syst. Biol. 64(1), 2015
PMID: 25070970
FPSAC: fast phylogenetic scaffolding of ancient contigs.
Rajaraman A, Tannier E, Chauve C., Bioinformatics 29(23), 2013
PMID: 24068034
Linearization of ancestral multichromosomal genomes.
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PMID: 23281593
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PMID: 20015948

23 References

Data provided by Europe PubMed Central.

A strategy of DNA sequencing employing computer programs.
Staden R., Nucleic Acids Res. 6(7), 1979
PMID: 461197
Shotgun DNA sequencing using cloned DNase I-generated fragments.
Anderson S., Nucleic Acids Res. 9(13), 1981
PMID: 6269069
Bioinformatics challenges of new sequencing technology.
Pop M, Salzberg SL., Trends Genet. 24(3), 2008
PMID: 18262676
DNA sequencing with chain-terminating inhibitors.
Sanger F, Nicklen S, Coulson AR., Proc. Natl. Acad. Sci. U.S.A. 74(12), 1977
PMID: 271968
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.
van Hijum SA, Zomer AL, Kuipers OP, Kok J., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980536
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
BLAT--the BLAST-like alignment tool.
Kent WJ., Genome Res. 12(4), 2002
PMID: 11932250
OSLay: optimal syntenic layout of unfinished assemblies.
Richter DC, Schuster SC, Huson DH., Bioinformatics 23(13), 2007
PMID: 17463020
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
A new pheromone trail-based genetic algorithm for comparative genome assembly.
Zhao F, Zhao F, Li T, Bryant DA., Nucleic Acids Res. 36(10), 2008
PMID: 18445633
Efficient q-gram filters for finding all epsilon-matches over a given length.
Rasmussen KR, Stoye J, Myers EW., J. Comput. Biol. 13(2), 2006
PMID: 16597241
Fast Algorithms for Geometric Traveling Salesman Problems
The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.
Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Gotker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18367281
Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids.
Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH, Arnold W, Blom J, Brinkrolf K, Brune I, Gotker S, Weisshaar B, Goesmann A, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18430482
Database resources of the National Center for Biotechnology Information.
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA., Nucleic Acids Res. 28(1), 2000
PMID: 10592169
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL., Nucleic Acids Res. 28(1), 2000
PMID: 10592170
EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Puhler A, Vorholter FJ, Zakrzewski M, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19457249
Versatile and open software for comparing large genomes.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL., Genome Biol. 5(2), 2004
PMID: 14759262
Improved tools for biological sequence comparison.
Pearson WR, Lipman DJ., Proc. Natl. Acad. Sci. U.S.A. 85(8), 1988
PMID: 3162770
An Open Graph Visualization System and Its Applications to Software Engineering


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