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Items: 16

1.

Fast and Automatic Reconstruction of Semantically Rich 3D Indoor Maps from Low-quality RGB-D Sequences.

Tang S, Zhang Y, Li Y, Yuan Z, Wang Y, Zhang X, Li X, Zhang Y, Guo R, Wang W.

Sensors (Basel). 2019 Jan 27;19(3). pii: E533. doi: 10.3390/s19030533.

2.

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects.

Regier AA, Farjoun Y, Larson DE, Krasheninina O, Kang HM, Howrigan DP, Chen BJ, Kher M, Banks E, Ames DC, English AC, Li H, Xing J, Zhang Y, Matise T, Abecasis GR, Salerno W, Zody MC, Neale BM, Hall IM.

Nat Commun. 2018 Oct 2;9(1):4038. doi: 10.1038/s41467-018-06159-4.

3.

De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis.

Wang S, Mandell JD, Kumar Y, Sun N, Morris MT, Arbelaez J, Nasello C, Dong S, Duhn C, Zhao X, Yang Z, Padmanabhuni SS, Yu D, King RA, Dietrich A, Khalifa N, Dahl N, Huang AY, Neale BM, Coppola G, Mathews CA, Scharf JM; Tourette International Collaborative Genetics Study (TIC Genetics); Tourette Syndrome Genetics Southern and Eastern Europe Initiative (TSGENESEE); Tourette Association of America International Consortium for Genetics (TAAICG), Fernandez TV, Buxbaum JD, De Rubeis S, Grice DE, Xing J, Heiman GA, Tischfield JA, Paschou P, Willsey AJ, State MW.

Cell Rep. 2018 Sep 25;24(13):3441-3454.e12. doi: 10.1016/j.celrep.2018.08.082. Erratum in: Cell Rep. 2018 Dec 18;25(12):3544.

4.

PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool.

Zhou A, Zhang Y, Sun Y, Xing J.

Bioinformatics. 2018 May 1;34(9):1603-1605. doi: 10.1093/bioinformatics/btx759.

PMID:
29186378
5.

Using whole-exome sequencing to investigate the genetic bases of lysosomal storage diseases of unknown etiology.

Wang N, Zhang Y, Gedvilaite E, Loh JW, Lin T, Liu X, Liu CG, Kumar D, Donnelly R, Raymond K, Schuchman EH, Sleat DE, Lobel P, Xing J.

Hum Mutat. 2017 Nov;38(11):1491-1499. doi: 10.1002/humu.23291. Epub 2017 Jul 25.

PMID:
28703315
6.

De Novo Coding Variants Are Strongly Associated with Tourette Disorder.

Willsey AJ, Fernandez TV, Yu D, King RA, Dietrich A, Xing J, Sanders SJ, Mandell JD, Huang AY, Richer P, Smith L, Dong S, Samocha KE; Tourette International Collaborative Genetics (TIC Genetics); Tourette Syndrome Association International Consortium for Genetics (TSAICG), Neale BM, Coppola G, Mathews CA, Tischfield JA, Scharf JM, State MW, Heiman GA.

Neuron. 2017 May 3;94(3):486-499.e9. doi: 10.1016/j.neuron.2017.04.024.

7.

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation.

Yang Z, Zhang Y, Wafula EK, Honaas LA, Ralph PE, Jones S, Clarke CR, Liu S, Su C, Zhang H, Altman NS, Schuster SC, Timko MP, Yoder JI, Westwood JH, dePamphilis CW.

Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):E7010-E7019. doi: 10.1073/pnas.1608765113. Epub 2016 Oct 24.

8.

Analysis of large-scale whole exome sequencing data to determine the prevalence of genetically-distinct forms of neuronal ceroid lipofuscinosis.

Sleat DE, Gedvilaite E, Zhang Y, Lobel P, Xing J.

Gene. 2016 Nov 30;593(2):284-91. doi: 10.1016/j.gene.2016.08.031. Epub 2016 Aug 20.

9.

A FASTQ compressor based on integer-mapped k-mer indexing for biologist.

Zhang Y, Patel K, Endrawis T, Bowers A, Sun Y.

Gene. 2016 Mar 15;579(1):75-81. doi: 10.1016/j.gene.2015.12.053. Epub 2015 Dec 30.

PMID:
26743127
10.

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH, dePamphilis CW.

PLoS One. 2016 Jan 5;11(1):e0146062. doi: 10.1371/journal.pone.0146062. eCollection 2016.

11.

A method for de novo nucleic acid diagnostic target discovery.

Zhang Y, Sun Y.

Bioinformatics. 2014 Nov 15;30(22):3174-80. doi: 10.1093/bioinformatics/btu515. Epub 2014 Aug 7.

PMID:
25104813
12.

A hybrid spatio-temporal data indexing method for trajectory databases.

Ke S, Gong J, Li S, Zhu Q, Liu X, Zhang Y.

Sensors (Basel). 2014 Jul 21;14(7):12990-3005. doi: 10.3390/s140712990.

13.

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species.

Zhang Y, Fernandez-Aparicio M, Wafula EK, Das M, Jiao Y, Wickett NJ, Honaas LA, Ralph PE, Wojciechowski MF, Timko MP, Yoder JI, Westwood JH, Depamphilis CW.

BMC Evol Biol. 2013 Feb 20;13:48. doi: 10.1186/1471-2148-13-48.

14.

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).

McKain MR, Wickett N, Zhang Y, Ayyampalayam S, McCombie WR, Chase MW, Pires JC, dePamphilis CW, Leebens-Mack J.

Am J Bot. 2012 Feb;99(2):397-406. doi: 10.3732/ajb.1100537. Epub 2012 Feb 1.

15.

A genome triplication associated with early diversification of the core eudicots.

Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter EJ, Deyholos MK, Kutchan TM, Chanderbali AS, Soltis PS, Stevenson DW, McCombie R, Pires JC, Wong GK, Soltis DE, Depamphilis CW.

Genome Biol. 2012 Jan 26;13(1):R3. doi: 10.1186/gb-2012-13-1-r3.

16.

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).

Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MT, Dalén L, Arsuaga JL, Ericson PG, Huson DH, Helgen KM, Murphy WJ, Götherström A, Schuster SC.

Genome Res. 2009 Feb;19(2):213-20. doi: 10.1101/gr.082628.108. Epub 2009 Jan 12.

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