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Items: 31

1.

Metalearners for estimating heterogeneous treatment effects using machine learning.

Künzel SR, Sekhon JS, Bickel PJ, Yu B.

Proc Natl Acad Sci U S A. 2019 Feb 15. pii: 201804597. doi: 10.1073/pnas.1804597116. [Epub ahead of print]

2.

Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy.

Arbel H, Basu S, Fisher WW, Hammonds AS, Wan KH, Park S, Weiszmann R, Booth BW, Keranen SV, Henriquez C, Shams Solari O, Bickel PJ, Biggin MD, Celniker SE, Brown JB.

Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):900-908. doi: 10.1073/pnas.1808833115. Epub 2018 Dec 31.

3.

Projection pursuit in high dimensions.

Bickel PJ, Kur G, Nadler B.

Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):9151-9156. doi: 10.1073/pnas.1801177115. Epub 2018 Aug 27.

4.

Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila.

Stoiber MH, Olson S, May GE, Duff MO, Manent J, Obar R, Guruharsha KG, Bickel PJ, Artavanis-Tsakonas S, Brown JB, Graveley BR, Celniker SE.

Genome Res. 2015 Nov;25(11):1692-702. doi: 10.1101/gr.182675.114. Epub 2015 Aug 20.

5.

Comparative analysis of regulatory information and circuits across distant species.

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668.

6.

Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

7.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S.

Genome Res. 2014 Jul;24(7):1209-23. doi: 10.1101/gr.159384.113.

8.

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.

Li JJ, Huang H, Bickel PJ, Brenner SE.

Genome Res. 2014 Jul;24(7):1086-101. doi: 10.1101/gr.170100.113.

9.

System wide analyses have underestimated protein abundances and the importance of transcription in mammals.

Li JJ, Bickel PJ, Biggin MD.

PeerJ. 2014 Feb 27;2:e270. doi: 10.7717/peerj.270. eCollection 2014.

10.

Diversity and dynamics of the Drosophila transcriptome.

Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE.

Nature. 2014 Aug 28;512(7515):393-9.

11.

Navigating and mining modENCODE data.

Boley N, Wan KH, Bickel PJ, Celniker SE.

Methods. 2014 Jun 15;68(1):38-47. doi: 10.1016/j.ymeth.2014.03.007. Epub 2014 Mar 15. Review.

12.

Genome-guided transcript assembly by integrative analysis of RNA sequence data.

Boley N, Stoiber MH, Booth BW, Wan KH, Hoskins RA, Bickel PJ, Celniker SE, Brown JB.

Nat Biotechnol. 2014 Apr;32(4):341-6. doi: 10.1038/nbt.2850. Epub 2014 Mar 16.

13.

On robust regression with high-dimensional predictors.

El Karoui N, Bean D, Bickel PJ, Lim C, Yu B.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14557-62. doi: 10.1073/pnas.1307842110. Epub 2013 Aug 16.

14.

Optimal M-estimation in high-dimensional regression.

Bean D, Bickel PJ, El Karoui N, Yu B.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14563-8. doi: 10.1073/pnas.1307845110. Epub 2013 Aug 16.

15.

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila.

Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21330-5. doi: 10.1073/pnas.1209589110. Epub 2012 Dec 10.

16.

Systematic evaluation of factors influencing ChIP-seq fidelity.

Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS.

Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985. Epub 2012 Apr 22.

17.

[Splice sites are overrepresented in Pasilla binding motif clusters in D. melanogaster genes].

Polishchuk MS, Brown JB, Favorov AV, Bickel PJ, Tumanian VG.

Biofizika. 2011 Nov-Dec;56(6):1065-70. Russian.

PMID:
22279750
18.

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.

Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19867-72. doi: 10.1073/pnas.1113972108. Epub 2011 Dec 1.

19.

The developmental transcriptome of Drosophila melanogaster.

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE.

Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22.

20.

Genome-wide analysis of promoter architecture in Drosophila melanogaster.

Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE.

Genome Res. 2011 Feb;21(2):182-92. doi: 10.1101/gr.112466.110. Epub 2010 Dec 22.

21.

A nonparametric view of network models and Newman-Girvan and other modularities.

Bickel PJ, Chen A.

Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21068-73. doi: 10.1073/pnas.0907096106. Epub 2009 Nov 23.

22.

An overview of recent developments in genomics and associated statistical methods.

Bickel PJ, Brown JB, Huang H, Li Q.

Philos Trans A Math Phys Eng Sci. 2009 Nov 13;367(1906):4313-37. doi: 10.1098/rsta.2009.0164. Review.

PMID:
19805447
23.

Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study.

Kechris KJ, Lin JC, Bickel PJ, Glazer AN.

Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9584-9. Epub 2006 Jun 12.

24.

Estimating motifs under order restrictions.

van Zwet EW, Kechris KJ, Bickel PJ, Eisen MB.

Stat Appl Genet Mol Biol. 2005;4:Article1. Epub 2005 Jan 10.

PMID:
16646826
25.

Detecting DNA regulatory motifs by incorporating positional trends in information content.

Kechris KJ, van Zwet E, Bickel PJ, Eisen MB.

Genome Biol. 2004;5(7):R50. Epub 2004 Jun 24.

26.

Finding important sites in protein sequences.

Bickel PJ, Kechris KJ, Spector PC, Wedemayer GJ, Glazer AN.

Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14764-71. Epub 2002 Nov 4.

27.

Discussion of "The evaluation of forensic DNA evidence".

Bickel PJ.

Proc Natl Acad Sci U S A. 1997 May 27;94(11):5497. No abstract available.

28.

What is a linear process?

Bickel PJ, Bühlmann P.

Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12128-31.

29.

Covariability of V3 loop amino acids.

Bickel PJ, Cosman PC, Olshen RA, Spector PC, Rodrigo AG, Mullins JI.

AIDS Res Hum Retroviruses. 1996 Oct 10;12(15):1401-11.

PMID:
8893048
30.

Estimating linear functionals of a PET image.

Bickel PJ, Ritov Y.

IEEE Trans Med Imaging. 1995;14(1):81-7.

PMID:
18215812
31.

Sex bias in graduate admissions: data from berkeley.

Bickel PJ, Hammel EA, O'connell JW.

Science. 1975 Feb 7;187(4175):398-404.

PMID:
17835295

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