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Items: 27

1.

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.

2.

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.

3.

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors.

Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston RH.

Genetics. 2018 Mar;208(3):937-949. doi: 10.1534/genetics.117.300657. Epub 2017 Dec 28.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks.

Wu S, Joseph A, Hammonds AS, Celniker SE, Yu B, Frise E.

Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):4290-5. doi: 10.1073/pnas.1521171113. Epub 2016 Apr 6.

10.

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.

11.

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.

12.

Toll mediated infection response is altered by gravity and spaceflight in Drosophila.

Taylor K, Kleinhesselink K, George MD, Morgan R, Smallwood T, Hammonds AS, Fuller PM, Saelao P, Alley J, Gibbs AG, Hoshizaki DK, von Kalm L, Fuller CA, Beckingham KM, Kimbrell DA.

PLoS One. 2014 Jan 24;9(1):e86485. doi: 10.1371/journal.pone.0086485. eCollection 2014.

13.

Spatial expression of transcription factors in Drosophila embryonic organ development.

Hammonds AS, Bristow CA, Fisher WW, Weiszmann R, Wu S, Hartenstein V, Kellis M, Yu B, Frise E, Celniker SE.

Genome Biol. 2013 Dec 20;14(12):R140. doi: 10.1186/gb-2013-14-12-r140.

14.

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.

15.

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA.

Genome Biol. 2011;12(5):R43. doi: 10.1186/gb-2011-12-5-r43. Epub 2011 May 11.

16.

Development of expression-ready constructs for generation of proteomic libraries.

Yu C, Wan KH, Hammonds AS, Stapleton M, Carlson JW, Celniker SE.

Methods Mol Biol. 2011;723:257-72. doi: 10.1007/978-1-61779-043-0_17.

PMID:
21370071
17.

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.

18.

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials.

Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S.

PLoS Biol. 2010 Aug 17;8(8). pii: e1000456. doi: 10.1371/journal.pbio.1000456. Erratum in: PLoS Biol. 2013 Oct;11(10). doi: 10.1371/annotation/e38f4ae8-0776-42e6-b912-50800f54436e.

19.

Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape.

Frise E, Hammonds AS, Celniker SE.

Mol Syst Biol. 2010;6:345. doi: 10.1038/msb.2009.102. Epub 2010 Jan 19.

20.

Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos.

Weiszmann R, Hammonds AS, Celniker SE.

Nat Protoc. 2009;4(5):605-18. doi: 10.1038/nprot.2009.55.

21.

Tools for neuroanatomy and neurogenetics in Drosophila.

Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, Celniker SE, Rubin GM.

Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9715-20. doi: 10.1073/pnas.0803697105. Epub 2008 Jul 9.

22.

Leflunomide and warfarin interaction: case report and review of the literature.

Chonlahan J, Halloran MA, Hammonds A.

Pharmacotherapy. 2006 Jun;26(6):868-71. Review.

PMID:
16716139
23.
24.

The Drosophila Stubble-stubbloid gene encodes an apparent transmembrane serine protease required for epithelial morphogenesis.

Appel LF, Prout M, Abu-Shumays R, Hammonds A, Garbe JC, Fristrom D, Fristrom J.

Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):4937-41.

25.

Characterization of IMP-E3, a gene active during imaginal disc morphogenesis in Drosophila melanogaster.

Moore JT, Fristrom D, Hammonds AS, Fristrom JW.

Dev Genet. 1990;11(4):299-309.

PMID:
2128624
26.

Isolation of genes active during hormone-induced morphogenesis in Drosophila imaginal discs.

Natzle JE, Hammonds AS, Fristrom JW.

J Biol Chem. 1986 Apr 25;261(12):5575-83.

27.

beta-Endorphin and deletion peptides. A correlation of opiate receptor affinity with helix potential.

Hammonds RG Jr, Hammonds AS, Ling N, Puett D.

J Biol Chem. 1982 Mar 25;257(6):2990-5. No abstract available.

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