Perfect phylogeny (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Perfect phylogeny" in English language version.

refsWebsite

Global rank English rank

19nih.gov

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12doi.org

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3harvard.edu

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2web.archive.org

1^st place

2arxiv.org

69^th place

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2ucdavis.edu

1,873^rd place

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1iastate.edu

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1rice.edu

3,843^rd place

2,772^nd place

1carolineuhler.com

low place

1berkeley.edu

580^th place

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1archive-it.org

910^th place

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1ucla.edu

782^nd place

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archive-it.org

wayback.archive-it.org

Seyalioglu H. "Haplotyping as Perfect Phylogeny" (PDF). Archived from the original (PDF) on 30 September 2011. Retrieved 30 October 2012.

arxiv.org

Ray S, Jia B, Safavi S, van Opijnen T, Isberg R, Rosch J, Bento J (2019-08-22). "Exact inference under the perfect phylogeny model". arXiv:1908.08623 [q-bio.QM].
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F (April 2014). Beerenwinkel N (ed.). "Phylogenetic quantification of intra-tumour heterogeneity". PLOS Computational Biology. 10 (4): e1003535. arXiv:1306.1685. Bibcode:2014PLSCB..10E3535S. doi:10.1371/journal.pcbi.1003535. PMC 3990475. PMID 24743184.

berkeley.edu

eecs.berkeley.edu

Eskin E, Halperin E, Karp RM (April 2003). "Efficient reconstruction of haplotype structure via perfect phylogeny" (PDF). Journal of Bioinformatics and Computational Biology. 1 (1). University of California, Berkeley: 1–20. doi:10.1142/S0219720003000174. PMID 15290779. Retrieved 30 October 2012.

carolineuhler.com

Uhler C. "Finding a Perfect Phylogeny" (PDF). Archived from the original (PDF) on 4 March 2016. Retrieved 29 September 2012.

doi.org

Nikaido M, Rooney AP, Okada N (August 1999). "Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales". Proceedings of the National Academy of Sciences of the United States of America. 96 (18): 10261–6. Bibcode:1999PNAS...9610261N. doi:10.1073/pnas.96.18.10261. PMC 17876. PMID 10468596.
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ (June 2015). "Reconstruction of clonal trees and tumor composition from multi-sample sequencing data". Bioinformatics. 31 (12): i62-70. doi:10.1093/bioinformatics/btv261. PMC 4542783. PMID 26072510.
Satas G, Raphael BJ (July 2017). "Tumor phylogeny inference using tree-constrained importance sampling". Bioinformatics. 33 (14): i152–i160. doi:10.1093/bioinformatics/btx270. PMC 5870673. PMID 28882002.
Malikic S, McPherson AW, Donmez N, Sahinalp CS (May 2015). "Clonality inference in multiple tumor samples using phylogeny". Bioinformatics. 31 (9): 1349–56. doi:10.1093/bioinformatics/btv003. PMID 25568283.
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q (February 2015). "PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors". Genome Biology. 16 (1): 35. doi:10.1186/s13059-015-0602-8. PMC 4359439. PMID 25786235.
Eskin E, Halperin E, Karp RM (April 2003). "Efficient reconstruction of haplotype structure via perfect phylogeny" (PDF). Journal of Bioinformatics and Computational Biology. 1 (1). University of California, Berkeley: 1–20. doi:10.1142/S0219720003000174. PMID 15290779. Retrieved 30 October 2012.
Bafna V, Gusfield D, Lancia G, Yooseph S (2003). "Haplotyping as perfect phylogeny: a direct approach". Journal of Computational Biology. 10 (3–4): 323–40. doi:10.1089/10665270360688048. PMID 12935331.
Bonizzoni P, Carrieri AP, Della Vedova G, Trucco G (October 2014). "Explaining evolution via constrained persistent perfect phylogeny". BMC Genomics. 15 Suppl 6 (S6): S10. doi:10.1186/1471-2164-15-S6-S10. PMC 4240218. PMID 25572381.
Hajirasouliha I, Raphael BJ (2014), Brown D, Morgenstern B (eds.), "Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures", Algorithms in Bioinformatics, Lecture Notes in Computer Science, vol. 8701, Springer Berlin Heidelberg, pp. 354–367, doi:10.1007/978-3-662-44753-6_27, ISBN 9783662447529
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F (April 2014). Beerenwinkel N (ed.). "Phylogenetic quantification of intra-tumour heterogeneity". PLOS Computational Biology. 10 (4): e1003535. arXiv:1306.1685. Bibcode:2014PLSCB..10E3535S. doi:10.1371/journal.pcbi.1003535. PMC 3990475. PMID 24743184.
Letouzé E, Allory Y, Bollet MA, Radvanyi F, Guyon F (2010). "Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis". Genome Biology. 11 (7): R76. doi:10.1186/gb-2010-11-7-r76. PMC 2926787. PMID 20649963.
Gertz EM, Chowdhury SA, Lee WJ, Wangsa D, Heselmeyer-Haddad K, Ried T, et al. (2016-06-30). "FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe". PLOS ONE. 11 (6): e0158569. Bibcode:2016PLoSO..1158569G. doi:10.1371/journal.pone.0158569. PMC 4928784. PMID 27362268.

harvard.edu

ui.adsabs.harvard.edu

Nikaido M, Rooney AP, Okada N (August 1999). "Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales". Proceedings of the National Academy of Sciences of the United States of America. 96 (18): 10261–6. Bibcode:1999PNAS...9610261N. doi:10.1073/pnas.96.18.10261. PMC 17876. PMID 10468596.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F (April 2014). Beerenwinkel N (ed.). "Phylogenetic quantification of intra-tumour heterogeneity". PLOS Computational Biology. 10 (4): e1003535. arXiv:1306.1685. Bibcode:2014PLSCB..10E3535S. doi:10.1371/journal.pcbi.1003535. PMC 3990475. PMID 24743184.
Gertz EM, Chowdhury SA, Lee WJ, Wangsa D, Heselmeyer-Haddad K, Ried T, et al. (2016-06-30). "FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe". PLOS ONE. 11 (6): e0158569. Bibcode:2016PLoSO..1158569G. doi:10.1371/journal.pone.0158569. PMC 4928784. PMID 27362268.

iastate.edu

cs.iastate.edu

Fernandez-Baca D. "The Perfect Phylogeny Problem" (PDF). Kluwer Academic Publishers. Retrieved 30 September 2012.

nih.gov

pubmed.ncbi.nlm.nih.gov

Nikaido M, Rooney AP, Okada N (August 1999). "Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales". Proceedings of the National Academy of Sciences of the United States of America. 96 (18): 10261–6. Bibcode:1999PNAS...9610261N. doi:10.1073/pnas.96.18.10261. PMC 17876. PMID 10468596.
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ (June 2015). "Reconstruction of clonal trees and tumor composition from multi-sample sequencing data". Bioinformatics. 31 (12): i62-70. doi:10.1093/bioinformatics/btv261. PMC 4542783. PMID 26072510.
Satas G, Raphael BJ (July 2017). "Tumor phylogeny inference using tree-constrained importance sampling". Bioinformatics. 33 (14): i152–i160. doi:10.1093/bioinformatics/btx270. PMC 5870673. PMID 28882002.
Malikic S, McPherson AW, Donmez N, Sahinalp CS (May 2015). "Clonality inference in multiple tumor samples using phylogeny". Bioinformatics. 31 (9): 1349–56. doi:10.1093/bioinformatics/btv003. PMID 25568283.
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q (February 2015). "PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors". Genome Biology. 16 (1): 35. doi:10.1186/s13059-015-0602-8. PMC 4359439. PMID 25786235.
Eskin E, Halperin E, Karp RM (April 2003). "Efficient reconstruction of haplotype structure via perfect phylogeny" (PDF). Journal of Bioinformatics and Computational Biology. 1 (1). University of California, Berkeley: 1–20. doi:10.1142/S0219720003000174. PMID 15290779. Retrieved 30 October 2012.
Bafna V, Gusfield D, Lancia G, Yooseph S (2003). "Haplotyping as perfect phylogeny: a direct approach". Journal of Computational Biology. 10 (3–4): 323–40. doi:10.1089/10665270360688048. PMID 12935331.
Bonizzoni P, Carrieri AP, Della Vedova G, Trucco G (October 2014). "Explaining evolution via constrained persistent perfect phylogeny". BMC Genomics. 15 Suppl 6 (S6): S10. doi:10.1186/1471-2164-15-S6-S10. PMC 4240218. PMID 25572381.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F (April 2014). Beerenwinkel N (ed.). "Phylogenetic quantification of intra-tumour heterogeneity". PLOS Computational Biology. 10 (4): e1003535. arXiv:1306.1685. Bibcode:2014PLSCB..10E3535S. doi:10.1371/journal.pcbi.1003535. PMC 3990475. PMID 24743184.
Letouzé E, Allory Y, Bollet MA, Radvanyi F, Guyon F (2010). "Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis". Genome Biology. 11 (7): R76. doi:10.1186/gb-2010-11-7-r76. PMC 2926787. PMID 20649963.
Gertz EM, Chowdhury SA, Lee WJ, Wangsa D, Heselmeyer-Haddad K, Ried T, et al. (2016-06-30). "FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe". PLOS ONE. 11 (6): e0158569. Bibcode:2016PLoSO..1158569G. doi:10.1371/journal.pone.0158569. PMC 4928784. PMID 27362268.

ncbi.nlm.nih.gov

Nikaido M, Rooney AP, Okada N (August 1999). "Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales". Proceedings of the National Academy of Sciences of the United States of America. 96 (18): 10261–6. Bibcode:1999PNAS...9610261N. doi:10.1073/pnas.96.18.10261. PMC 17876. PMID 10468596.
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ (June 2015). "Reconstruction of clonal trees and tumor composition from multi-sample sequencing data". Bioinformatics. 31 (12): i62-70. doi:10.1093/bioinformatics/btv261. PMC 4542783. PMID 26072510.
Satas G, Raphael BJ (July 2017). "Tumor phylogeny inference using tree-constrained importance sampling". Bioinformatics. 33 (14): i152–i160. doi:10.1093/bioinformatics/btx270. PMC 5870673. PMID 28882002.
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q (February 2015). "PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors". Genome Biology. 16 (1): 35. doi:10.1186/s13059-015-0602-8. PMC 4359439. PMID 25786235.
Bonizzoni P, Carrieri AP, Della Vedova G, Trucco G (October 2014). "Explaining evolution via constrained persistent perfect phylogeny". BMC Genomics. 15 Suppl 6 (S6): S10. doi:10.1186/1471-2164-15-S6-S10. PMC 4240218. PMID 25572381.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F (April 2014). Beerenwinkel N (ed.). "Phylogenetic quantification of intra-tumour heterogeneity". PLOS Computational Biology. 10 (4): e1003535. arXiv:1306.1685. Bibcode:2014PLSCB..10E3535S. doi:10.1371/journal.pcbi.1003535. PMC 3990475. PMID 24743184.
Letouzé E, Allory Y, Bollet MA, Radvanyi F, Guyon F (2010). "Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis". Genome Biology. 11 (7): R76. doi:10.1186/gb-2010-11-7-r76. PMC 2926787. PMID 20649963.
Gertz EM, Chowdhury SA, Lee WJ, Wangsa D, Heselmeyer-Haddad K, Ried T, et al. (2016-06-30). "FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe". PLOS ONE. 11 (6): e0158569. Bibcode:2016PLoSO..1158569G. doi:10.1371/journal.pone.0158569. PMC 4928784. PMID 27362268.

rice.edu

cs.rice.edu

Nakhleh L, Ringe D, Warnow T. "Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages" (PDF). Retrieved 1 October 2012.

ucdavis.edu

csiflabs.cs.ucdavis.edu

Gusfield D. "An Overview of Computational Methods for Haplotype Inference" (PDF). University of California, Davis. Retrieved 18 November 2012.
Ding Z, Filkov V, Gusfield D. "A Linear Time Algorithm for the Perfect Phylogeny Haplotyping Problem". University of California, Davis. Retrieved 18 November 2012.

ucla.edu

math.ucla.edu

Seyalioglu H. "Haplotyping as Perfect Phylogeny" (PDF). Archived from the original (PDF) on 30 September 2011. Retrieved 30 October 2012.

web.archive.org

Uhler C. "Finding a Perfect Phylogeny" (PDF). Archived from the original (PDF) on 4 March 2016. Retrieved 29 September 2012.
Pe'er I, Pupko T, Shamir R, Sharan R. "Incomplete Directed Perfect Phylogeny". Tel-Aviv University. Archived from the original on 20 October 2013. Retrieved 30 October 2012.{{cite web}}: CS1 maint: bot: original URL status unknown (link)