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Items: 1 to 50 of 243

1.

Dynamic ASXL1 Exon Skipping and Alternative Circular Splicing in Single Human Cells.

Koh W, Gonzalez V, Natarajan S, Carter R, Brown PO, Gawad C.

PLoS One. 2016 Oct 13;11(10):e0164085. doi: 10.1371/journal.pone.0164085. eCollection 2016.

2.

Directed Chemical Evolution with an Outsized Genetic Code.

Krusemark CJ, Tilmans NP, Brown PO, Harbury PB.

PLoS One. 2016 Aug 10;11(8):e0154765. doi: 10.1371/journal.pone.0154765. eCollection 2016.

3.

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets.

Hogan GJ, Brown PO, Herschlag D.

PLoS Biol. 2015 Nov 20;13(11):e1002307. doi: 10.1371/journal.pbio.1002307. eCollection 2015.

4.

Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling.

Riordan DP, Varma S, West RB, Brown PO.

PLoS One. 2015 Jul 15;10(7):e0128975. doi: 10.1371/journal.pone.0128975. eCollection 2015.

5.

miR-142 regulates the tumorigenicity of human breast cancer stem cells through the canonical WNT signaling pathway.

Isobe T, Hisamori S, Hogan DJ, Zabala M, Hendrickson DG, Dalerba P, Cai S, Scheeren F, Kuo AH, Sikandar SS, Lam JS, Qian D, Dirbas FM, Somlo G, Lao K, Brown PO, Clarke MF, Shimono Y.

Elife. 2014 Nov 18;3. doi: 10.7554/eLife.01977.

6.

Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae.

Lovejoy AF, Riordan DP, Brown PO.

PLoS One. 2014 Oct 29;9(10):e110799. doi: 10.1371/journal.pone.0110799. eCollection 2014.

7.

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments.

Lareau LF, Hite DH, Hogan GJ, Brown PO.

Elife. 2014 May 9;3:e01257. doi: 10.7554/eLife.01257.

8.

Circular RNA is expressed across the eukaryotic tree of life.

Wang PL, Bao Y, Yee MC, Barrett SP, Hogan GJ, Olsen MN, Dinneny JR, Brown PO, Salzman J.

PLoS One. 2014 Mar 7;9(6):e90859. doi: 10.1371/journal.pone.0090859. eCollection 2014. Erratum in: PLoS One. 2014;9(4):e95116.

9.

Cell-type specific features of circular RNA expression.

Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO.

PLoS Genet. 2013;9(9):e1003777. doi: 10.1371/journal.pgen.1003777. Epub 2013 Sep 5. Erratum in: PLoS Genet. 2013 Dec;9(12). doi:10.1371/annotation/f782282b-eefa-4c8d-985c-b1484e845855.

10.

Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae.

Klass DM, Scheibe M, Butter F, Hogan GJ, Mann M, Brown PO.

Genome Res. 2013 Jun;23(6):1028-38. doi: 10.1101/gr.153031.112. Epub 2013 May 1.

11.

An interview with Patrick O Brown on the origins and future of open access.

Brown PO.

BMC Biol. 2013 Apr 15;11:33. doi: 10.1186/1741-7007-11-33. No abstract available.

12.

Improved discovery of molecular interactions in genome-scale data with adaptive model-based normalization.

Salzman J, Klass DM, Brown PO.

PLoS One. 2013;8(1):e53930. doi: 10.1371/journal.pone.0053930. Epub 2013 Jan 22.

13.

The yeast Rab GTPase Ypt1 modulates unfolded protein response dynamics by regulating the stability of HAC1 RNA.

Tsvetanova NG, Riordan DP, Brown PO.

PLoS Genet. 2012;8(7):e1002862. doi: 10.1371/journal.pgen.1002862. Epub 2012 Jul 26.

14.

Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation.

Bates JG, Salzman J, May D, Garcia PB, Hogan GJ, McIntosh M, Schlissel MS, Brown PO.

PLoS One. 2012;7(5):e37108. doi: 10.1371/journal.pone.0037108. Epub 2012 May 31.

15.

Widespread mRNA association with cytoskeletal motor proteins and identification and dynamics of myosin-associated mRNAs in S. cerevisiae.

Casolari JM, Thompson MA, Salzman J, Champion LM, Moerner WE, Brown PO.

PLoS One. 2012;7(2):e31912. doi: 10.1371/journal.pone.0031912. Epub 2012 Feb 16.

16.

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types.

Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO.

PLoS One. 2012;7(2):e30733. doi: 10.1371/journal.pone.0030733. Epub 2012 Feb 1.

17.

ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma.

Salzman J, Marinelli RJ, Wang PL, Green AE, Nielsen JS, Nelson BH, Drescher CW, Brown PO.

PLoS Biol. 2011 Sep;9(9):e1001156. doi: 10.1371/journal.pbio.1001156. Epub 2011 Sep 20.

18.

Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes.

del Alamo M, Hogan DJ, Pechmann S, Albanese V, Brown PO, Frydman J.

PLoS Biol. 2011 Jul;9(7):e1001100. doi: 10.1371/journal.pbio.1001100. Epub 2011 Jul 12.

19.

Integration.

Brown PO.

In: Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997.

20.

Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus.

Rubins KH, Hensley LE, Relman DA, Brown PO.

PLoS One. 2011 Jan 18;6(1):e15615. doi: 10.1371/journal.pone.0015615.

21.

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.

Riordan DP, Herschlag D, Brown PO.

Nucleic Acids Res. 2011 Mar;39(4):1501-9. doi: 10.1093/nar/gkq920. Epub 2010 Oct 18.

22.

Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function.

Thompson MA, Casolari JM, Badieirostami M, Brown PO, Moerner WE.

Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17864-71. doi: 10.1073/pnas.1012868107. Epub 2010 Oct 4.

23.

Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae.

Tsvetanova NG, Klass DM, Salzman J, Brown PO.

PLoS One. 2010 Sep 10;5(9). pii: e12671. doi: 10.1371/journal.pone.0012671.

24.

Climate change and the integrity of science.

Gleick PH, Adams RM, Amasino RM, Anders E, Anderson DJ, Anderson WW, Anselin LE, Arroyo MK, Asfaw B, Ayala FJ, Bax A, Bebbington AJ, Bell G, Bennett MV, Bennetzen JL, Berenbaum MR, Berlin OB, Bjorkman PJ, Blackburn E, Blamont JE, Botchan MR, Boyer JS, Boyle EA, Branton D, Briggs SP, Briggs WR, Brill WJ, Britten RJ, Broecker WS, Brown JH, Brown PO, Brunger AT, Cairns J Jr, Canfield DE, Carpenter SR, Carrington JC, Cashmore AR, Castilla JC, Cazenave A, Chapin FS 3rd, Ciechanover AJ, Clapham DE, Clark WC, Clayton RN, Coe MD, Conwell EM, Cowling EB, Cowling RM, Cox CS, Croteau RB, Crothers DM, Crutzen PJ, Daily GC, Dalrymple GB, Dangl JL, Darst SA, Davies DR, Davis MB, De Camilli PV, Dean C, DeFries RS, Deisenhofer J, Delmer DP, DeLong EF, DeRosier DJ, Diener TO, Dirzo R, Dixon JE, Donoghue MJ, Doolittle RF, Dunne T, Ehrlich PR, Eisenstadt SN, Eisner T, Emanuel KA, Englander SW, Ernst WG, Falkowski PG, Feher G, Ferejohn JA, Fersht A, Fischer EH, Fischer R, Flannery KV, Frank J, Frey PA, Fridovich I, Frieden C, Futuyma DJ, Gardner WR, Garrett CJ, Gilbert W, Goldberg RB, Goodenough WH, Goodman CS, Goodman M, Greengard P, Hake S, Hammel G, Hanson S, Harrison SC, Hart SR, Hartl DL, Haselkorn R, Hawkes K, Hayes JM, Hille B, Hökfelt T, House JS, Hout M, Hunten DM, Izquierdo IA, Jagendorf AT, Janzen DH, Jeanloz R, Jencks CS, Jury WA, Kaback HR, Kailath T, Kay P, Kay SA, Kennedy D, Kerr A, Kessler RC, Khush GS, Kieffer SW, Kirch PV, Kirk K, Kivelson MG, Klinman JP, Klug A, Knopoff L, Kornberg H, Kutzbach JE, Lagarias JC, Lambeck K, Landy A, Langmuir CH, Larkins BA, Le Pichon XT, Lenski RE, Leopold EB, Levin SA, Levitt M, Likens GE, Lippincott-Schwartz J, Lorand L, Lovejoy CO, Lynch M, Mabogunje AL, Malone TF, Manabe S, Marcus J, Massey DS, McWilliams JC, Medina E, Melosh HJ, Meltzer DJ, Michener CD, Miles EL, Mooney HA, Moore PB, Morel FM, Mosley-Thompson ES, Moss B, Munk WH, Myers N, Nair GB, Nathans J, Nester EW, Nicoll RA, Novick RP, O'Connell JF, Olsen PE, Opdyke ND, Oster GF, Ostrom E, Pace NR, Paine RT, Palmiter RD, Pedlosky J, Petsko GA, Pettengill GH, Philander SG, Piperno DR, Pollard TD, Price PB Jr, Reichard PA, Reskin BF, Ricklefs RE, Rivest RL, Roberts JD, Romney AK, Rossmann MG, Russell DW, Rutter WJ, Sabloff JA, Sagdeev RZ, Sahlins MD, Salmond A, Sanes JR, Schekman R, Schellnhuber J, Schindler DW, Schmitt J, Schneider SH, Schramm VL, Sederoff RR, Shatz CJ, Sherman F, Sidman RL, Sieh K, Simons EL, Singer BH, Singer MF, Skyrms B, Sleep NH, Smith BD, Snyder SH, Sokal RR, Spencer CS, Steitz TA, Strier KB, Südhof TC, Taylor SS, Terborgh J, Thomas DH, Thompson LG, Tjian RT, Turner MG, Uyeda S, Valentine JW, Valentine JS, Van Etten JL, van Holde KE, Vaughan M, Verba S, von Hippel PH, Wake DB, Walker A, Walker JE, Watson EB, Watson PJ, Weigel D, Wessler SR, West-Eberhard MJ, White TD, Wilson WJ, Wolfenden RV, Wood JA, Woodwell GM, Wright HE Jr, Wu C, Wunsch C, Zoback ML.

Science. 2010 May 7;328(5979):689-90. doi: 10.1126/science.328.5979.689. No abstract available. Erratum in: Science. 2010 May 14;328(5980):826.

25.

Dissecting interferon-induced transcriptional programs in human peripheral blood cells.

Waddell SJ, Popper SJ, Rubins KH, Griffiths MJ, Brown PO, Levin M, Relman DA.

PLoS One. 2010 Mar 22;5(3):e9753. doi: 10.1371/journal.pone.0009753.

26.

DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines.

Houshdaran S, Hawley S, Palmer C, Campan M, Olsen MN, Ventura AP, Knudsen BS, Drescher CW, Urban ND, Brown PO, Laird PW.

PLoS One. 2010 Feb 22;5(2):e9359. doi: 10.1371/journal.pone.0009359.

27.

Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA.

Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO.

PLoS Biol. 2009 Nov;7(11):e1000238. doi: 10.1371/journal.pbio.1000238. Epub 2009 Nov 10.

28.

The preclinical natural history of serous ovarian cancer: defining the target for early detection.

Brown PO, Palmer C.

PLoS Med. 2009 Jul;6(7):e1000114. doi: 10.1371/journal.pmed.1000114. Epub 2009 Jul 28.

29.

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.

Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO.

PLoS Biol. 2008 Oct 28;6(10):e255. doi: 10.1371/journal.pbio.0060255.

30.

Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes.

Rubins KH, Hensley LE, Bell GW, Wang C, Lefkowitz EJ, Brown PO, Relman DA.

PLoS One. 2008 Jul 9;3(7):e2628. doi: 10.1371/journal.pone.0002628.

31.

Systematic evaluation of candidate blood markers for detecting ovarian cancer.

Palmer C, Duan X, Hawley S, Scholler N, Thorpe JD, Sahota RA, Wong MQ, Wray A, Bergan LA, Drescher CW, McIntosh MW, Brown PO, Nelson BH, Urban N.

PLoS One. 2008 Jul 9;3(7):e2633. doi: 10.1371/journal.pone.0002633.

32.

Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance.

Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO.

PLoS One. 2008 May 7;3(5):e2126. doi: 10.1371/journal.pone.0002126. Erratum in: PLoS ONE. 2008;3(11).doi.org/10.1371/annotation/c8902b4c-30fc-42e7-b506-fc756a3cdd4e.

33.

Gene-expression patterns reveal underlying biological processes in Kawasaki disease.

Popper SJ, Shimizu C, Shike H, Kanegaye JT, Newburger JW, Sundel RP, Brown PO, Burns JC, Relman DA.

Genome Biol. 2007;8(12):R261.

34.

The Stanford Tissue Microarray Database.

Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA.

Nucleic Acids Res. 2008 Jan;36(Database issue):D871-7. Epub 2007 Nov 7.

35.

Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers.

Chi JT, Rodriguez EH, Wang Z, Nuyten DS, Mukherjee S, van de Rijn M, van de Vijver MJ, Hastie T, Brown PO.

PLoS Genet. 2007 Sep;3(9):1770-84.

36.
37.

Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

Buess M, Nuyten DS, Hastie T, Nielsen T, Pesich R, Brown PO.

Genome Biol. 2007;8(9):R191.

38.

The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever.

Rubins KH, Hensley LE, Wahl-Jensen V, Daddario DiCaprio KM, Young HA, Reed DS, Jahrling PB, Brown PO, Relman DA, Geisbert TW.

Genome Biol. 2007;8(8):R174.

39.
40.

Parallels between global transcriptional programs of polarizing Caco-2 intestinal epithelial cells in vitro and gene expression programs in normal colon and colon cancer.

Sääf AM, Halbleib JM, Chen X, Yuen ST, Leung SY, Nelson WJ, Brown PO.

Mol Biol Cell. 2007 Nov;18(11):4245-60. Epub 2007 Aug 15.

41.

Development of the human infant intestinal microbiota.

Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO.

PLoS Biol. 2007 Jul;5(7):e177. Epub 2007 Jun 26.

42.

Virtual Northern analysis of the human genome.

Hurowitz EH, Drori I, Stodden VC, Donoho DL, Brown PO.

PLoS One. 2007 May 23;2(5):e460.

43.

Nanocrystalline Ag from supramolecular stabilization of metals in 4-tert-butylcalix[4]arene lattices.

Brown PO, Enright GD, Ripmeester JA.

Chem Asian J. 2006 Oct 20;1(4):529-35.

PMID:
17441090
44.

Gene expression patterns in pancreatic tumors, cells and tissues.

Lowe AW, Olsen M, Hao Y, Lee SP, Taek Lee K, Chen X, van de Rijn M, Brown PO.

PLoS One. 2007 Mar 28;2(3):e323.

45.

The Stanford Microarray Database: implementation of new analysis tools and open source release of software.

Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA.

Nucleic Acids Res. 2007 Jan;35(Database issue):D766-70. Epub 2006 Dec 20.

46.

Predicting a local recurrence after breast-conserving therapy by gene expression profiling.

Nuyten DS, Kreike B, Hart AA, Chi JT, Sneddon JB, Wessels LF, Peterse HJ, Bartelink H, Brown PO, Chang HY, van de Vijver MJ.

Breast Cancer Res. 2006;8(5):R62.

47.

Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation.

Sneddon JB, Zhen HH, Montgomery K, van de Rijn M, Tward AD, West R, Gladstone H, Chang HY, Morganroth GS, Oro AE, Brown PO.

Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14842-7. Epub 2006 Sep 26.

48.

Discovery and validation of breast cancer subtypes.

Kapp AV, Jeffrey SS, Langerød A, Børresen-Dale AL, Han W, Noh DY, Bukholm IR, Nicolau M, Brown PO, Tibshirani R.

BMC Genomics. 2006 Sep 11;7:231. Erratum in: BMC Genomics. 2007 Apr 13;8(1):101.

49.
50.

2005 Curt Stern Award address. Exploring along a crooked path.

Brown PO.

Am J Hum Genet. 2006 Sep;79(3):429-33. No abstract available.

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