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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.


Effects of Astaxanthin on the Proliferation and Migration of Breast Cancer Cells In Vitro.

McCall B, McPartland CK, Moore R, Frank-Kamenetskii A, Booth BW.

Antioxidants (Basel). 2018 Oct 4;7(10). pii: E135. doi: 10.3390/antiox7100135.


An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.

Parra M, Booth BW, Weiszmann R, Yee B, Yeo GW, Brown JB, Celniker SE, Conboy JG.

RNA. 2018 Sep;24(9):1255-1265. doi: 10.1261/rna.066951.118. Epub 2018 Jun 29.


OpenHiCAMM: High-Content Screening Software for Complex Microscope Imaging Workflows.

Booth BW, McParland C, Beattie K, Fisher WW, Hammonds AS, Celniker SE, Frise E.

iScience. 2018 Apr 27;2:136-140. doi: 10.1016/j.isci.2018.03.017.


Complete Genome Sequence of Acetobacter pomorum Oregon-R-modENCODE Strain BDGP5, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.

Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE.

Genome Announc. 2017 Nov 30;5(48). pii: e01333-17. doi: 10.1128/genomeA.01333-17.


Amphiregulin regulates proliferation and migration of HER2-positive breast cancer cells.

Schmucker H, Blanding WM, Mook JM, Wade JF, Park JP, Kwist K, Shah H, Booth BW.

Cell Oncol (Dordr). 2018 Apr;41(2):159-168. doi: 10.1007/s13402-017-0363-3. Epub 2017 Nov 27.


Complete Genome Sequence of Acetobacter tropicalis Oregon-R-modENCODE Strain BDGP1, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.

Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE.

Genome Announc. 2017 Nov 16;5(46). pii: e01020-17. doi: 10.1128/genomeA.01020-17.


Complete Genome Sequence of Lactobacillus plantarum Oregon-R-modENCODE Strain BDGP2 Isolated from Drosophila melanogaster Gut.

Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE.

Genome Announc. 2017 Oct 12;5(41). pii: e01155-17. doi: 10.1128/genomeA.01155-17.


Complete Genome Sequence of Bacillus kochii Oregon-R-modENCODE Strain BDGP4, Isolated from Drosophila melanogaster Gut.

Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE.

Genome Announc. 2017 Oct 5;5(40). pii: e01074-17. doi: 10.1128/genomeA.01074-17.


Complete Genome Sequence of Enterococcus durans Oregon-R-modENCODE Strain BDGP3, a Lactic Acid Bacterium Found in the Drosophila melanogaster Gut.

Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE.

Genome Announc. 2017 Oct 5;5(40). pii: e01041-17. doi: 10.1128/genomeA.01041-17.


HER2+ breast cancer cells undergo apoptosis upon exposure to tannic acid released from remodeled cross-linked collagen type I.

Jordan LG, Booth BW.

J Biomed Mater Res A. 2018 Jan;106(1):26-32. doi: 10.1002/jbm.a.36205. Epub 2017 Sep 23.


Cancer cell redirection biomarker discovery using a mutual information approach.

Roche K, Feltus FA, Park JP, Coissieux MM, Chang C, Chan VBS, Bentires-Alj M, Booth BW.

PLoS One. 2017 Jun 8;12(6):e0179265. doi: 10.1371/journal.pone.0179265. eCollection 2017.


RNA Expression Profiling Reveals Differentially Regulated Growth Factor and Receptor Expression in Redirected Cancer Cells.

Schmucker HS, Park JP, Coissieux MM, Bentires-Alj M, Feltus FA, Booth BW.

Stem Cells Dev. 2017 May 1;26(9):646-655. doi: 10.1089/scd.2016.0340. Epub 2017 Feb 23.


Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.

Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Booth BW, Celniker SE, Graveley BR, Brenner SE.

Genome Res. 2015 Nov;25(11):1771-80. doi: 10.1101/gr.192518.115. Epub 2015 Aug 20.


Validation of an in vitro model of erbB2(+) cancer cell redirection.

Park JP, Blanding WM, Feltracco JA, Booth BW.

In Vitro Cell Dev Biol Anim. 2015 Sep;51(8):776-86. doi: 10.1007/s11626-015-9889-8. Epub 2015 Apr 22.


A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila.

Nagarkar-Jaiswal S, Lee PT, Campbell ME, Chen K, Anguiano-Zarate S, Gutierrez MC, Busby T, Lin WW, He Y, Schulze KL, Booth BW, Evans-Holm M, Venken KJ, Levis RW, Spradling AC, Hoskins RA, Bellen HJ.

Elife. 2015 Mar 31;4. doi: 10.7554/eLife.05338.


Remodeling of tannic acid crosslinked collagen type I induces apoptosis in ER+ breast cancer cells.

Ngobili TA, Shah H, Park JP, Kwist KW, Inskeep B, Burg KJ, Booth BW.

Anticancer Res. 2015 Mar;35(3):1285-90.


The Release 6 reference sequence of the Drosophila melanogaster genome.

Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE.

Genome Res. 2015 Mar;25(3):445-58. doi: 10.1101/gr.185579.114. Epub 2015 Jan 14.


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.


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.


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.


Tannic Acid preferentially targets estrogen receptor-positive breast cancer.

Booth BW, Inskeep BD, Shah H, Park JP, Hay EJ, Burg KJ.

Int J Breast Cancer. 2013;2013:369609. doi: 10.1155/2013/369609. Epub 2013 Nov 27.


Evaluation of normal and metastatic mammary cells grown in different biomaterial matrices: establishing potential tissue test systems.

Booth BW, Park JP, Burg KJ.

J Biomater Sci Polym Ed. 2013;24(6):758-68. doi: 10.1080/09205063.2012.708189. Epub 2012 Aug 6.


Differential gene expression in nuclear label-retaining cells in the developing mouse mammary gland.

Park JP, Raafat A, Feltracco JA, Blanding WM, Booth BW.

Stem Cells Dev. 2013 Apr 15;22(8):1297-306. doi: 10.1089/scd.2012.0496. Epub 2013 Jan 18.


Multipotent PI-MECs are the true targets of MMTV-neu tumorigenesis.

Wagner KU, Booth BW, Boulanger CA, Smith GH.

Oncogene. 2013 Mar 7;32(10):1338. doi: 10.1038/onc.2012.452. Epub 2012 Oct 8. No abstract available.


Cell settling effects on a thermal inkjet bioprinter.

Pepper ME, Seshadri V, Burg T, Booth BW, Burg KJ, Groff RE.

Conf Proc IEEE Eng Med Biol Soc. 2011;2011:3609-12. doi: 10.1109/IEMBS.2011.6090605.


Assessment of a Chitosan/Hyaluronan Injectable Composite for Fat Reconstruction.

Booth BW, Yang CC, Burg KJ.

J Biomater Sci Polym Ed. 2012;23(18):2303-20. doi: 10.1163/156856211X615274. Epub 2012 May 11.


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.


Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.


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.


Post-bioprinting processing methods to improve cell viability and pattern fidelity in heterogeneous tissue test systems.

Pepper ME, Cass CA, Mattimore JP, Burg T, Booth BW, Burg KJ, Groff RE.

Conf Proc IEEE Eng Med Biol Soc. 2010;2010:259-62. doi: 10.1109/IEMBS.2010.5627467.


The normal mammary microenvironment suppresses the tumorigenic phenotype of mouse mammary tumor virus-neu-transformed mammary tumor cells.

Booth BW, Boulanger CA, Anderson LH, Smith GH.

Oncogene. 2011 Feb 10;30(6):679-89. doi: 10.1038/onc.2010.439. Epub 2010 Oct 4.


The normal microenvironment directs mammary gland development.

McCave EJ, Cass CA, Burg KJ, Booth BW.

J Mammary Gland Biol Neoplasia. 2010 Sep;15(3):291-9. doi: 10.1007/s10911-010-9190-0. Epub 2010 Sep 8. Review.


Reprogramming human cancer cells in the mouse mammary gland.

Bussard KM, Boulanger CA, Booth BW, Bruno RD, Smith GH.

Cancer Res. 2010 Aug 1;70(15):6336-43. doi: 10.1158/0008-5472.CAN-10-0591. Epub 2010 Jul 20.


ErbB/EGF signaling and EMT in mammary development and breast cancer.

Hardy KM, Booth BW, Hendrix MJ, Salomon DS, Strizzi L.

J Mammary Gland Biol Neoplasia. 2010 Jun;15(2):191-9. doi: 10.1007/s10911-010-9172-2. Epub 2010 Apr 6. Review.


Amphiregulin mediates self-renewal in an immortal mammary epithelial cell line with stem cell characteristics.

Booth BW, Boulanger CA, Anderson LH, Jimenez-Rojo L, Brisken C, Smith GH.

Exp Cell Res. 2010 Feb 1;316(3):422-32. doi: 10.1016/j.yexcr.2009.11.006. Epub 2009 Nov 12.


Stem cells and the mammary microenvironment.

Booth BW, Boulanger CA, Smith GH.

Breast Dis. 2008;29:57-67.


Selective segregation of DNA strands persists in long-label-retaining mammary cells during pregnancy.

Booth BW, Boulanger CA, Smith GH.

Breast Cancer Res. 2008;10(5):R90. doi: 10.1186/bcr2188. Epub 2008 Oct 24.


The mammary microenvironment alters the differentiation repertoire of neural stem cells.

Booth BW, Mack DL, Androutsellis-Theotokis A, McKay RD, Boulanger CA, Smith GH.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14891-6. doi: 10.1073/pnas.0803214105. Epub 2008 Sep 22.


Netrin-1 can affect morphogenesis and differentiation of the mouse mammary gland.

Strizzi L, Mancino M, Bianco C, Raafat A, Gonzales M, Booth BW, Watanabe K, Nagaoka T, Mack DL, Howard B, Callahan R, Smith GH, Salomon DS.

J Cell Physiol. 2008 Sep;216(3):824-34. doi: 10.1002/jcp.21462.


Roles of transforming growth factor-alpha in mammary development and disease.

Booth BW, Smith GH.

Growth Factors. 2007 Aug;25(4):227-35. Review.


Alveolar progenitor cells develop in mouse mammary glands independent of pregnancy and lactation.

Booth BW, Boulanger CA, Smith GH.

J Cell Physiol. 2007 Sep;212(3):729-36.


Interaction with the mammary microenvironment redirects spermatogenic cell fate in vivo.

Boulanger CA, Mack DL, Booth BW, Smith GH.

Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3871-6. Epub 2007 Feb 28.


TGFbeta1 and TGFalpha contrarily affect alveolar survival and tumorigenesis in mouse mammary epithelium.

Booth BW, Jhappan C, Merlino G, Smith GH.

Int J Cancer. 2007 Feb 1;120(3):493-9.


Proliferation of the airway epithelium in asthma: are inflammatory cells required?

Booth BW, Newcomb DC, McKane SA, Crews AL, Adler KB, Bonner JC, Martin LD.

Chest. 2003 Mar;123(3 Suppl):384S-5S. Review. No abstract available.


Interleukin-13 induces proliferation of human airway epithelial cells in vitro via a mechanism mediated by transforming growth factor-alpha.

Booth BW, Adler KB, Bonner JC, Tournier F, Martin LD.

Am J Respir Cell Mol Biol. 2001 Dec;25(6):739-43.


Hypertrophic pulmonary osteoarthropathy and breast cancer.

Booth BW, Van Nostrand D, Graeber GM.

South Med J. 1987 Mar;80(3):383-6.


Phase II trial of acivicin in advanced breast carcinoma: a Cancer and Leukemia Group B Study.

Booth BW, Korzun AH, Weiss RB, Ellison RR, Budman D, Khojasteh A, Wood W.

Cancer Treat Rep. 1986 Oct;70(10):1247-8. No abstract available.


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