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Items: 7

1.

Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions.

Li X, Luo OJ, Wang P, Zheng M, Wang D, Piecuch E, Zhu JJ, Tian SZ, Tang Z, Li G, Ruan Y.

Nat Protoc. 2017 May;12(5):899-915. doi: 10.1038/nprot.2017.012. Epub 2017 Mar 30.

2.

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization.

Szałaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D.

Genome Res. 2016 Dec;26(12):1697-1709. Epub 2016 Oct 27.

3.

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.

Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M, Sachs LM, Ruan X, Wei CL, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y.

Cell. 2015 Dec 17;163(7):1611-27. doi: 10.1016/j.cell.2015.11.024. Epub 2015 Dec 10.

4.

The draft genome of sweet orange (Citrus sinensis).

Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y.

Nat Genet. 2013 Jan;45(1):59-66. doi: 10.1038/ng.2472. Epub 2012 Nov 25.

PMID:
23179022
5.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

6.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

7.

Intra- and inter-individual genetic differences in gene expression.

Cowley MJ, Cotsapas CJ, Williams RB, Chan EK, Pulvers JN, Liu MY, Luo OJ, Nott DJ, Little PF.

Mamm Genome. 2009 May;20(5):281-95. doi: 10.1007/s00335-009-9181-x. Epub 2009 May 8.

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