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Items: 11

1.

BBMerge - Accurate paired shotgun read merging via overlap.

Bushnell B, Rood J, Singer E.

PLoS One. 2017 Oct 26;12(10):e0185056. doi: 10.1371/journal.pone.0185056. eCollection 2017.

2.

In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits.

Scarano D, Rao R, Corrado G.

PLoS One. 2017 Feb 10;12(2):e0171504. doi: 10.1371/journal.pone.0171504. eCollection 2017.

3.

Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans.

Rogers RL.

Mol Biol Evol. 2015 Dec;32(12):3064-78. doi: 10.1093/molbev/msv204. Epub 2015 Sep 23.

4.

Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags.

Gong Q, Tao Y, Yang JR, Cai J, Yuan Y, Ruan J, Yang J, Liu H, Li W, Lu X, Zhuang SM, Wang SM, Wu CI.

BMC Genomics. 2013 Jan 24;14:51. doi: 10.1186/1471-2164-14-51.

5.

Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.

Hampton OA, Koriabine M, Miller CA, Coarfa C, Li J, Den Hollander P, Schoenherr C, Carbone L, Nefedov M, Ten Hallers BF, Lee AV, De Jong PJ, Milosavljevic A.

Cancer Genet. 2011 Aug;204(8):447-57. doi: 10.1016/j.cancergen.2011.07.009. Erratum in: Cancer Genet. 2011 Dec;204(12):694. Coarfa, Cristian [added];Schoenherr, Caroline [added].

6.

Identification of genomic indels and structural variations using split reads.

Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M.

BMC Genomics. 2011 Jul 25;12:375. doi: 10.1186/1471-2164-12-375.

7.

Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia.

Kim YC, Jung YC, Chen J, Alhasan AH, Kaewsaard P, Zhang Y, Ma S, Rosen S, Wang SM.

BMC Res Notes. 2010 Dec 20;3:341. doi: 10.1186/1756-0500-3-341.

8.

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses.

Fullwood MJ, Wei CL, Liu ET, Ruan Y.

Genome Res. 2009 Apr;19(4):521-32. doi: 10.1101/gr.074906.107. Review.

9.

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.

Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB.

Genome Biol. 2009 Feb 23;10(2):R23. doi: 10.1186/gb-2009-10-2-r23.

10.

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae.

Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL.

Genome Res. 2009 Feb;19(2):294-305. doi: 10.1101/gr.083311.108. Epub 2008 Nov 17.

11.

Poly A- transcripts expressed in HeLa cells.

Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM.

PLoS One. 2008 Jul 30;3(7):e2803. doi: 10.1371/journal.pone.0002803.

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