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Items: 9

1.

Learning the sequence determinants of alternative splicing from millions of random sequences.

Rosenberg AB, Patwardhan RP, Shendure J, Seelig G.

Cell. 2015 Oct 22;163(3):698-711. doi: 10.1016/j.cell.2015.09.054. Epub 2015 Oct 22.

2.

Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation.

Birnbaum RY, Patwardhan RP, Kim MJ, Findlay GM, Martin B, Zhao J, Bell RJ, Smith RP, Ku AA, Shendure J, Ahituv N.

PLoS Genet. 2014 Oct 23;10(10):e1004592. doi: 10.1371/journal.pgen.1004592. eCollection 2014 Oct.

3.

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.

Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J.

Nat Biotechnol. 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.2727. Epub 2013 Nov 3.

4.

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.

Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N.

Nat Genet. 2013 Sep;45(9):1021-1028. doi: 10.1038/ng.2713. Epub 2013 Jul 28.

5.

Massively parallel functional dissection of mammalian enhancers in vivo.

Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, Ahituv N, Pennacchio LA, Shendure J.

Nat Biotechnol. 2012 Feb 26;30(3):265-70. doi: 10.1038/nbt.2136.

6.

The ecoresponsive genome of Daphnia pulex.

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL.

Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.

7.

Haplotype-resolved genome sequencing of a Gujarati Indian individual.

Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J.

Nat Biotechnol. 2011 Jan;29(1):59-63. doi: 10.1038/nbt.1740. Epub 2010 Dec 19. Erratum in: Nat Biotechnol. 2011 May;29(5):459.

8.

Parallel, tag-directed assembly of locally derived short sequence reads.

Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J.

Nat Methods. 2010 Feb;7(2):119-22. doi: 10.1038/nmeth.1416. Epub 2010 Jan 17.

9.

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.

Patwardhan RP, Lee C, Litvin O, Young DL, Pe'er D, Shendure J.

Nat Biotechnol. 2009 Dec;27(12):1173-5. doi: 10.1038/nbt.1589.

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