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Items: 1 to 50 of 136

1.

Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, Yue J, Nelson DR, Huang L, Li Z, Xu H, Zhou D, Wang Y, Hu W, Lin J, Deng Y, Pandey N, Mancini M, Zerpa D, Nguyen JK, Wang L, Yu L, Xin Y, Ge L, Arro J, Han JO, Chakrabarty S, Pushko M, Zhang W, Ma Y, Ma P, Lv M, Chen F, Zheng G, Xu J, Yang Z, Deng F, Chen X, Liao Z, Zhang X, Lin Z, Lin H, Yan H, Kuang Z, Zhong W, Liang P, Wang G, Yuan Y, Shi J, Hou J, Lin J, Jin J, Cao P, Shen Q, Jiang Q, Zhou P, Ma Y, Zhang X, Xu R, Liu J, Zhou Y, Jia H, Ma Q, Qi R, Zhang Z, Fang J, Fang H, Song J, Wang M, Dong G, Wang G, Chen Z, Ma T, Liu H, Dhungana SR, Huss SE, Yang X, Sharma A, Trujillo JH, Martinez MC, Hudson M, Riascos JJ, Schuler M, Chen LQ, Braun DM, Li L, Yu Q, Wang J, Wang K, Schatz MC, Heckerman D, Van Sluys MA, Souza GM, Moore PH, Sankoff D, VanBuren R, Paterson AH, Nagai C, Ming R.

Nat Genet. 2018 Dec;50(12):1754. doi: 10.1038/s41588-018-0293-7.

PMID:
30425353
2.

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, Yue J, Nelson DR, Huang L, Li Z, Xu H, Zhou D, Wang Y, Hu W, Lin J, Deng Y, Pandey N, Mancini M, Zerpa D, Nguyen JK, Wang L, Yu L, Xin Y, Ge L, Arro J, Han JO, Chakrabarty S, Pushko M, Zhang W, Ma Y, Ma P, Lv M, Chen F, Zheng G, Xu J, Yang Z, Deng F, Chen X, Liao Z, Zhang X, Lin Z, Lin H, Yan H, Kuang Z, Zhong W, Liang P, Wang G, Yuan Y, Shi J, Hou J, Lin J, Jin J, Cao P, Shen Q, Jiang Q, Zhou P, Ma Y, Zhang X, Xu R, Liu J, Zhou Y, Jia H, Ma Q, Qi R, Zhang Z, Fang J, Fang H, Song J, Wang M, Dong G, Wang G, Chen Z, Ma T, Liu H, Dhungana SR, Huss SE, Yang X, Sharma A, Trujillo JH, Martinez MC, Hudson M, Riascos JJ, Schuler M, Chen LQ, Braun DM, Li L, Yu Q, Wang J, Wang K, Schatz MC, Heckerman D, Van Sluys MA, Souza GM, Moore PH, Sankoff D, VanBuren R, Paterson AH, Nagai C, Ming R.

Nat Genet. 2018 Nov;50(11):1565-1573. doi: 10.1038/s41588-018-0237-2. Epub 2018 Oct 8. Erratum in: Nat Genet. 2018 Dec;50(12):1754.

PMID:
30297971
3.

Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics.

Sankoff D, Zheng C, Zhang Y, Meidanis J, Lyons E, Tang H.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul 31. doi: 10.1109/TCBB.2018.2849377. [Epub ahead of print]

PMID:
30072336
4.

Accurate prediction of orthologs in the presence of divergence after duplication.

Lafond M, Meghdari Miardan M, Sankoff D.

Bioinformatics. 2018 Jul 1;34(13):i366-i375. doi: 10.1093/bioinformatics/bty242.

5.

Resolution effects in reconstructing ancestral genomes.

Zheng C, Jeong Y, Turcotte MG, Sankoff D.

BMC Genomics. 2018 May 9;19(Suppl 2):100. doi: 10.1186/s12864-018-4462-y.

6.

Pinning down ploidy in paleopolyploid plants.

Zhang Y, Zheng C, Sankoff D.

BMC Genomics. 2018 May 8;19(Suppl 5):287. doi: 10.1186/s12864-018-4624-y.

7.

Whole Genome Duplication in Plants: Implications for Evolutionary Analysis.

Sankoff D, Zheng C.

Methods Mol Biol. 2018;1704:291-315. doi: 10.1007/978-1-4939-7463-4_10.

PMID:
29277870
8.

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory.

Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang TH, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Pálfalvi G, Pollard ST, Rozas J, Sánchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M.

Nat Ecol Evol. 2017 Feb 6;1(3):59. doi: 10.1038/s41559-016-0059.

PMID:
28812732
9.

Evolutionary Model for the Statistical Divergence of Paralogous and Orthologous Gene Pairs Generated by Whole Genome Duplication and Speciation.

Yue Zhang, Chunfang Zheng, Sankoff D.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1579-1584. doi: 10.1109/TCBB.2017.2712695. Epub 2017 Jul 14.

PMID:
28715335
10.

Statistical analysis of fractionation resistance by functional category and expression.

Chen ECH, Morin A, Chauchat JH, Sankoff D.

BMC Genomics. 2017 May 24;18(Suppl 4):366. doi: 10.1186/s12864-017-3736-0.

11.

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome.

Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH, Cervantes-Pérez SA, Zheng C, Sankoff D, Tang H, Purbojati RW, Putra A, Drautz-Moses DI, Schuster SC, Herrera-Estrella L, Albert VA.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):E4435-E4441. doi: 10.1073/pnas.1702072114. Epub 2017 May 15. Erratum in: Proc Natl Acad Sci U S A. 2017 Jun 19;:.

12.

A continuous analog of run length distributions reflecting accumulated fractionation events.

Yu Z, Sankoff D.

BMC Bioinformatics. 2016 Nov 11;17(Suppl 14):412. doi: 10.1186/s12859-016-1265-5.

13.

Economic importance, taxonomic representation and scientific priority as drivers of genome sequencing projects.

Vallée GC, Muñoz DS, Sankoff D.

BMC Genomics. 2016 Nov 11;17(Suppl 10):782. doi: 10.1186/s12864-016-3100-9.

14.

Compromise or optimize? The breakpoint anti-median.

Larlee CA, Brandts A, Sankoff D.

BMC Bioinformatics. 2016 Dec 15;17(Suppl 18):473. doi: 10.1186/s12859-016-1340-y.

15.

The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae.

Sabir JS, Jansen RK, Arasappan D, Calderon V, Noutahi E, Zheng C, Park S, Sabir MJ, Baeshen MN, Hajrah NH, Khiyami MA, Baeshen NA, Obaid AY, Al-Malki AL, Sankoff D, El-Mabrouk N, Ruhlman TA.

Sci Rep. 2016 Sep 22;6:33782. doi: 10.1038/srep33782.

16.

Locating rearrangement events in a phylogeny based on highly fragmented assemblies.

Zheng C, Sankoff D.

BMC Genomics. 2016 Jan 11;17 Suppl 1:1. doi: 10.1186/s12864-015-2294-6.

17.

Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling.

Sankoff D, Zheng C, Wang B, Abad Najar C.

BMC Bioinformatics. 2015;16 Suppl 17:S9. doi: 10.1186/1471-2105-16-S17-S9. Epub 2015 Dec 7.

18.

The pineapple genome and the evolution of CAM photosynthesis.

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JA, Cushman JC, Paull RE, Yu Q.

Nat Genet. 2015 Dec;47(12):1435-42. doi: 10.1038/ng.3435. Epub 2015 Nov 2.

19.

Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events.

Zheng C, Santos Muñoz D, Albert VA, Sankoff D.

BMC Genomics. 2015;16 Suppl 10:S8. doi: 10.1186/1471-2164-16-S10-S8. Epub 2015 Oct 2.

20.

Gene expression and fractionation resistance.

Chen EC, Sankoff D.

BMC Genomics. 2014;15 Suppl 6:S19. doi: 10.1186/1471-2164-15-S6-S19. Epub 2014 Oct 17.

21.

Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants.

Zheng C, Kononenko A, Leebens-Mack J, Lyons E, Sankoff D.

BMC Genomics. 2014;15 Suppl 6:S8. doi: 10.1186/1471-2164-15-S6-S8. Epub 2014 Oct 17.

22.

Near-medians that avoid the corners; a combinatorial probability approach.

Larlee C, Zheng C, Sankoff D.

BMC Genomics. 2014;15 Suppl 6:S1. doi: 10.1186/1471-2164-15-S6-S1. Epub 2014 Oct 17.

23.

Sets of medians in the non-geodesic pseudometric space of unsigned genomes with breakpoints.

Jamshidpey A, Jamshidpey A, Sankoff D.

BMC Genomics. 2014;15 Suppl 6:S3. doi: 10.1186/1471-2164-15-S6-S3. Epub 2014 Oct 17.

24.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P.

Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.

25.

The dynamics of functional classes of plant genes in rediploidized ancient polyploids.

Chen EC, Buen Abad Najar C, Zheng C, Brandts A, Lyons E, Tang H, Carretero-Paulet L, Albert VA, Sankoff D.

BMC Bioinformatics. 2013;14 Suppl 15:S19. doi: 10.1186/1471-2105-14-S15-S19. Epub 2013 Oct 15.

26.

Ancient eudicot hexaploidy meets ancestral eurosid gene order.

Zheng C, Chen E, Albert VA, Lyons E, Sankoff D.

BMC Genomics. 2013;14 Suppl 7:S3. doi: 10.1186/1471-2164-14-S7-S3. Epub 2013 Nov 5.

27.

Practical aliquoting of flowering plant genomes.

Zheng C, Sankoff D.

BMC Bioinformatics. 2013;14 Suppl 15:S8. doi: 10.1186/1471-2105-14-S15-S8. Epub 2013 Oct 15.

28.

Phase change for the accuracy of the median value in estimating divergence time.

Jamshidpey A, Sankoff D.

BMC Bioinformatics. 2013;14 Suppl 15:S7. doi: 10.1186/1471-2105-14-S15-S7. Epub 2013 Oct 15.

29.

Practical halving; the Nelumbo nucifera evidence on early eudicot evolution.

Zheng C, Sankoff D.

Comput Biol Chem. 2014 Jun;50:75-81. doi: 10.1016/j.compbiolchem.2014.01.010. Epub 2014 Jan 26.

PMID:
24525373
30.

A consolidation algorithm for genomes fractionated after higher order polyploidization.

Jahn K, Zheng C, Kováč J, Sankoff D.

BMC Bioinformatics. 2012;13 Suppl 19:S8. doi: 10.1186/1471-2105-13-S19-S8. Epub 2012 Dec 19.

31.

Medians seek the corners, and other conjectures.

Haghighi M, Sankoff D.

BMC Bioinformatics. 2012;13 Suppl 19:S5. doi: 10.1186/1471-2105-13-S19-S5. Epub 2012 Dec 19.

32.

Fractionation, rearrangement and subgenome dominance.

Sankoff D, Zheng C.

Bioinformatics. 2012 Sep 15;28(18):i402-i408. doi: 10.1093/bioinformatics/bts392.

33.

Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals.

Yang Z, Sankoff D.

BMC Bioinformatics. 2012 Jun 11;13 Suppl 9:S8. doi: 10.1186/1471-2105-13-S9-S8.

34.

Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes.

Zheng C, Sankoff D.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S9. doi: 10.1186/1471-2105-13-S10-S9.

35.

Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution.

Muñoz A, Sankoff D.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S6. doi: 10.1186/1471-2105-13-S3-S6.

36.

Scaffold filling under the breakpoint and related distances.

Jiang H, Zheng C, Sankoff D, Zhu B.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1220-9. doi: 10.1109/TCBB.2012.57.

PMID:
22529329
37.

Analysis of gene order evolution beyond single-copy genes.

El-Mabrouk N, Sankoff D.

Methods Mol Biol. 2012;855:397-429. doi: 10.1007/978-1-61779-582-4_15. Review.

PMID:
22407718
38.

A model for biased fractionation after whole genome duplication.

Sankoff D, Zheng C, Wang B.

BMC Genomics. 2012;13 Suppl 1:S8. doi: 10.1186/1471-2164-13-S1-S8. Epub 2012 Jan 17.

39.

The Kernel of Maximum Agreement Subtrees.

Swenson KM, Chen E, Pattengale ND, Sankoff D.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1023-31. doi: 10.1109/TCBB.2012.11.

PMID:
22231622
40.

Fractionation statistics.

Wang B, Zheng C, Sankoff D.

BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S5. doi: 10.1186/1471-2105-12-S9-S5.

41.

Listing all parsimonious reversal sequences: new algorithms and perspectives.

Badr G, Swenson KM, Sankoff D.

J Comput Biol. 2011 Sep;18(9):1201-10. doi: 10.1089/cmb.2011.0133.

PMID:
21899425
42.

Genome aliquoting revisited.

Warren R, Sankoff D.

J Comput Biol. 2011 Sep;18(9):1065-75. doi: 10.1089/cmb.2011.0087.

PMID:
21899416
43.

Listing all sorting reversals in quadratic time.

Swenson KM, Badr G, Sankoff D.

Algorithms Mol Biol. 2011 Apr 19;6:11. doi: 10.1186/1748-7188-6-11.

44.

On the PATHGROUPS approach to rapid small phylogeny.

Zheng C, Sankoff D.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S4. doi: 10.1186/1471-2105-12-S1-S4.

45.

A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances.

Adam Z, Sankoff D.

J Comput Biol. 2010 Sep;17(9):1299-314. doi: 10.1089/cmb.2010.0121.

PMID:
20874410
46.

Natural parameter values for generalized gene adjacency.

Yang Z, Sankoff D.

J Comput Biol. 2010 Sep;17(9):1113-28. doi: 10.1089/cmb.2010.0099.

PMID:
20874399
47.

Rearrangement phylogeny of genomes in contig form.

Muñoz A, Sankoff D.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):579-87. doi: 10.1109/TCBB.2010.66.

PMID:
20714028
48.

Scaffold filling, contig fusion and comparative gene order inference.

Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D.

BMC Bioinformatics. 2010 Jun 4;11:304. doi: 10.1186/1471-2105-11-304.

49.

The collapse of gene complement following whole genome duplication.

Sankoff D, Zheng C, Zhu Q.

BMC Genomics. 2010 May 19;11:313. doi: 10.1186/1471-2164-11-313.

50.

Towards improved reconstruction of ancestral gene order in angiosperm phylogeny.

Sankoff D, Zheng C, Wall PK, dePamphilis C, Leebens-Mack J, Albert VA.

J Comput Biol. 2009 Oct;16(10):1353-67. doi: 10.1089/cmb.2009.0103.

PMID:
19803735

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