Publications by authors named "Susan E Celniker"

95Publications

Chromosomal Sequence of Lactobacillus brevis Oregon-R-modENCODE Strain BDGP6, a Lactic Acid Bacterium Isolated from the Gut of Drosophila melanogaster.

Microbiol Resour Announc 2020 Oct 29;9(44). Epub 2020 Oct 29.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/MRA.00931-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7595947PMC
October 2020

Complete Genome Sequence of the Citrobacter freundii Type Strain.

Microbiol Resour Announc 2020 May 7;9(19). Epub 2020 May 7.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/MRA.00240-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206489PMC
May 2020

Complete Genome Sequence of sp. Strain 33MFTa1.1, Isolated from Roots.

Microbiol Resour Announc 2019 Sep 12;8(37). Epub 2019 Sep 12.

BioSciences Area, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/MRA.00432-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742783PMC
September 2019

Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance.

Cell Host Microbe 2019 04 19;25(4):537-552.e8. Epub 2019 Mar 19.

Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Holistic Integrative Enterology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2019.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6749836PMC
April 2019

No difference in 4-nitroquinoline induced tumorigenesis between germ-free and colonized mice.

Mol Carcinog 2019 05 22;58(5):627-632. Epub 2019 Jan 22.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.

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http://dx.doi.org/10.1002/mc.22972DOI Listing
May 2019

Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy.

Proc Natl Acad Sci U S A 2019 01 31;116(3):900-908. Epub 2018 Dec 31.

Molecular Ecosystems Biology Department, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;

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http://dx.doi.org/10.1073/pnas.1808833115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338827PMC
January 2019

Improved mosquito genome points to population-control strategies.

Authors:
Susan E Celniker

Nature 2018 11;563(7732):482-483

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http://dx.doi.org/10.1038/d41586-018-07266-4DOI Listing
November 2018

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

RNA 2018 09 29;24(9):1255-1265. Epub 2018 Jun 29.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1261/rna.066951.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097662PMC
September 2018

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

iScience 2018 04;2:136-140

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S25890042183002
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http://dx.doi.org/10.1016/j.isci.2018.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993205PMC
April 2018

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

Genome Announc 2017 Nov 30;5(48). Epub 2017 Nov 30.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/genomeA.01333-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5722065PMC
November 2017

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

Genome Announc 2017 Nov 16;5(46). Epub 2017 Nov 16.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/genomeA.01020-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690321PMC
November 2017

Complete Genome Sequence of Oregon-R-modENCODE Strain BDGP2 Isolated from Gut.

Genome Announc 2017 Oct 12;5(41). Epub 2017 Oct 12.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/genomeA.01155-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5637513PMC
October 2017

Complete Genome Sequence of Oregon-R-modENCODE Strain BDGP4, Isolated from Gut.

Genome Announc 2017 Oct 5;5(40). Epub 2017 Oct 5.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/genomeA.01074-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629058PMC
October 2017

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

Genome Announc 2017 Oct 5;5(40). Epub 2017 Oct 5.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/genomeA.01041-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629054PMC
October 2017

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

Proc Natl Acad Sci U S A 2016 Apr 6;113(16):4290-5. Epub 2016 Apr 6.

Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;

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http://dx.doi.org/10.1073/pnas.1521171113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843452PMC
April 2016

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

Genome Res 2015 Nov 20;25(11):1692-702. Epub 2015 Aug 20.

Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;

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http://dx.doi.org/10.1101/gr.182675.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617965PMC
November 2015

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

Genome Res 2015 Nov 20;25(11):1771-80. Epub 2015 Aug 20.

Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.192518.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617972PMC
November 2015

Lessons from modENCODE.

Annu Rev Genomics Hum Genet 2015 26;16:31-53. Epub 2015 Jun 26.

Department of Statistics, University of California, Berkeley, California 94720; email:

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http://dx.doi.org/10.1146/annurev-genom-090413-025448DOI Listing
May 2016

Genome-wide identification of zero nucleotide recursive splicing in Drosophila.

Nature 2015 May 13;521(7552):376-9. Epub 2015 May 13.

Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.

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http://dx.doi.org/10.1038/nature14475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529404PMC
May 2015

Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation.

Cell Rep 2014 Dec 26;9(5):1966-1980. Epub 2014 Nov 26.

Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.10.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279448PMC
December 2014

Transcription factor networks in Drosophila melanogaster.

Cell Rep 2014 Sep 18;8(6):2031-2043. Epub 2014 Sep 18.

Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Biogen Idec, Inc., Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.08.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403667PMC
September 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Navigating and mining modENCODE data.

Methods 2014 Jun 15;68(1):38-47. Epub 2014 Mar 15.

Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, CA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857704PMC
June 2014

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

Nat Biotechnol 2014 Apr 16;32(4):341-6. Epub 2014 Mar 16.

1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2] Department of Statistics, University of California at Berkeley, Berkeley, California, USA. [3].

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http://search.proquest.com/openview/5a27f43084800d7458173e64
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http://www.nature.com/doifinder/10.1038/nbt.2850
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http://dx.doi.org/10.1038/nbt.2850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4037530PMC
April 2014

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy.

PLoS Genet 2013 1;9(8):e1003571. Epub 2013 Aug 1.

Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731213PMC
March 2014

An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks.

Cell 2013 Jul;154(1):228-39

Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.cell.2013.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3756661PMC
July 2013

Automated protein-DNA interaction screening of Drosophila regulatory elements.

Nat Methods 2011 Oct 30;8(12):1065-70. Epub 2011 Oct 30.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1038/nmeth.1763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929264PMC
October 2011

Characterization of MtnE, the fifth metallothionein member in Drosophila.

J Biol Inorg Chem 2011 Oct 26;16(7):1047-56. Epub 2011 Aug 26.

Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.

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http://link.springer.com/10.1007/s00775-011-0825-4
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http://dx.doi.org/10.1007/s00775-011-0825-4DOI Listing
October 2011

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

Genome Biol 2011 11;12(5):R43. Epub 2011 May 11.

Department of Genome Sciences, University of Washington, Foege S310A, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/gb-2011-12-5-r43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219966PMC
February 2012

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

Methods Mol Biol 2011 ;723:257-72

Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.1007/978-1-61779-043-0_17DOI Listing
June 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://compbio.mit.edu/publications/46_modENCODE_Science_10.
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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
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http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

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

PLoS Biol 2010 Aug 17;8(8). Epub 2010 Aug 17.

Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923081PMC
August 2010

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

Mol Syst Biol 2010 19;6:345. Epub 2010 Jan 19.

Department of Genome Dynamics, Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1038/msb.2009.102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824522PMC
February 2010

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

Nat Protoc 2009 ;4(5):605-18

Berkeley Drosophila Genome Project, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/nprot.2009.55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780369PMC
June 2009

Regulation of early endosomal entry by the Drosophila tumor suppressors Rabenosyn and Vps45.

Mol Biol Cell 2008 Oct 6;19(10):4167-76. Epub 2008 Aug 6.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1091/mbc.e08-07-0716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2555928PMC
October 2008

Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes.

Nat Genet 2008 Apr 2;40(4):476-83. Epub 2008 Mar 2.

Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ng.101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2330261PMC
April 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase.

Genome Res 2007 Dec 7;17(12):1909-18. Epub 2007 Nov 7.

Centro de Biología Molecular Severo Ochoa, Cantoblanco, 28049 Madrid, Spain.

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http://dx.doi.org/10.1101/gr.6365107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099598PMC
December 2007

Drosophila by the dozen.

Genome Biol 2007 ;8(7):309

Berkeley Drosophila Genome Project, Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2007-8-7-309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323228PMC
February 2008

High-throughput plasmid cDNA library screening.

Nat Protoc 2006 ;1(2):624-32

Department of Genome Sciences, Earnest Orlando Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/nprot.2006.90DOI Listing
September 2007

Chromatin looping mediates boundary element promoter interactions.

Bioessays 2007 Jan;29(1):7-10

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1002/bies.20520DOI Listing
January 2007

Improved repeat identification and masking in Dipterans.

Gene 2007 Mar 12;389(1):1-9. Epub 2006 Oct 12.

Department of Biology, San Francisco State University, San Francisco, CA, United States.

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http://dx.doi.org/10.1016/j.gene.2006.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1945102PMC
March 2007

RNA editing in Drosophila melanogaster: New targets and functional consequences.

RNA 2006 Nov 3;12(11):1922-32. Epub 2006 Oct 3.

Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1261/rna.254306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624909PMC
November 2006

Genomic organization of the Drosophila telomere retrotransposable elements.

Genome Res 2006 Oct 8;16(10):1231-40. Epub 2006 Sep 8.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.5348806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1581432PMC
October 2006

Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP).

Nucleic Acids Res 2005 Dec 2;33(21):e185. Epub 2005 Dec 2.

Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gni184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1301602PMC
December 2005

Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster.

Proc Natl Acad Sci U S A 2005 Apr 4;102(15):5495-500. Epub 2005 Apr 4.

Berkeley Drosophila Genome Project and Department of Genome Sciences, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1073/pnas.0501422102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555963PMC
April 2005

A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome.

Proc Natl Acad Sci U S A 2005 Feb 24;102(5):1566-71. Epub 2005 Jan 24.

Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720-3200, USA.

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http://dx.doi.org/10.1073/pnas.0409421102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545494PMC
February 2005

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.

Bioinformatics 2005 Apr 30;21(8):1747-9. Epub 2004 Nov 30.

Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti173DOI Listing
April 2005

In memoriam: Edward B. Lewis (1918-2004).

Dev Cell 2004 Oct;7(4):487-9

Department of Biology, Washington University, St. Louis, MO 63130, USA.

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http://dx.doi.org/10.1016/j.devcel.2004.09.005DOI Listing
October 2004

Benchmarking tools for the alignment of functional noncoding DNA.

BMC Bioinformatics 2004 01 21;5. Epub 2004 Jan 21.

Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/1471-2105-5-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC344529PMC
January 2004

Posterior patterning genes and the identification of a unique body region in the brine shrimp Artemia franciscana.

Development 2003 Dec 15;130(24):5915-27. Epub 2003 Oct 15.

Institute of Molecular Biology and Biotechnology (IMBB-FORTH) Vouton, 71110 Iraklio Crete, Greece.

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http://dx.doi.org/10.1242/dev.00835DOI Listing
December 2003

The Drosophila melanogaster genome.

Annu Rev Genomics Hum Genet 2003 ;4:89-117

Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1146/annurev.genom.4.070802.110323DOI Listing
December 2003

Evolution of the homeobox complex in the Diptera.

Curr Biol 2003 Aug;13(15):R587-8

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/s0960-9822(03)00520-7DOI Listing
August 2003

Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?

Genetica 2003 Mar;117(2-3):227-37

Departamento de Genética, Universidade Federal do Rio de Janeiro, Caixa Postal 68011 CEP 21944-970, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1023/a:1022900313650DOI Listing
March 2003

Systematic determination of patterns of gene expression during Drosophila embryogenesis.

Genome Biol 2002 23;3(12):RESEARCH0088. Epub 2002 Dec 23.

Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720-3200, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151190PMC
http://dx.doi.org/10.1186/gb-2002-3-12-research0088DOI Listing
June 2003