Publications by authors named "Thomas C Kaufman"

57Publications

The end of a monolith: Deconstructing the Cnn-Polo interaction.

Fly (Austin) 2016 04 20;10(2):60-72. Epub 2016 Apr 20.

a Department of Biology , Indiana University , Bloomington , IN , USA.

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http://dx.doi.org/10.1080/19336934.2016.1178419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934712PMC
April 2016

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

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

A molecularly defined duplication set for the X chromosome of Drosophila melanogaster.

Genetics 2010 Dec 27;186(4):1111-25. Epub 2010 Sep 27.

Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1534/genetics.110.121285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998297PMC
December 2010

Insights into aging through measurements of the Drosophila proteome as a function of temperature.

Mech Ageing Dev 2010 Sep 21;131(9):584-90. Epub 2010 Aug 21.

Department of Chemistry, University of Pittsburgh, Eberly Hall 111, 200 University Drive, Pittsburgh, PA 15260, United States.

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http://dx.doi.org/10.1016/j.mad.2010.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949476PMC
September 2010

New research resources at the Bloomington Drosophila Stock Center.

Fly (Austin) 2010 Jan-Mar;4(1):88-91. Epub 2010 Jan 15.

Bloomington Drosophila Stock Center, Department of Biology, Indiana University, Bloomington, IN, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997732PMC
http://dx.doi.org/10.4161/fly.4.1.11230DOI Listing
August 2010

In situ hybridization of large milkweed bug (Oncopeltus) tissues.

Cold Spring Harb Protoc 2009 Aug;2009(8):pdb.prot5262

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1101/pdb.prot5262DOI Listing
August 2009

Dissection and fixation of large milkweed bug (Oncopeltus) embryos.

Cold Spring Harb Protoc 2009 Aug;2009(8):pdb.prot5261

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1101/pdb.prot5261DOI Listing
August 2009

Morphology and husbandry of the large milkweed bug, Oncopeltus fasciatus.

Cold Spring Harb Protoc 2009 Aug;2009(8):pdb.emo127

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1101/pdb.emo127DOI Listing
August 2009

Stable isotope labeling and label-free proteomics of Drosophila parkin null mutants.

J Proteome Res 2009 Oct;8(10):4500-10

Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1021/pr9006238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766925PMC
October 2009

Centrosomin: a complex mix of long and short isoforms is required for centrosome function during early development in Drosophila melanogaster.

Genetics 2009 Aug 15;182(4):979-97. Epub 2009 Jun 15.

Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1534/genetics.109.103887DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728885PMC
August 2009

Cytological investigation of the mechanism of parthenogenesis in Drosophila mercatorum.

Fly (Austin) 2007 Nov-Dec;1(6):317-29. Epub 2007 Nov 12.

Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.4161/fly.5408DOI Listing
December 2008

Proteome response to the panneural expression of human wild-type alpha-synuclein: a Drosophila model of Parkinson's disease.

J Proteome Res 2008 Sep 7;7(9):3911-21. Epub 2008 Aug 7.

Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1021/pr800207hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3780383PMC
September 2008

Quantitative proteomics of a presymptomatic A53T alpha-synuclein Drosophila model of Parkinson disease.

Mol Cell Proteomics 2008 Jul 18;7(7):1191-203. Epub 2008 Mar 18.

Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA.

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http://dx.doi.org/10.1074/mcp.M700467-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493378PMC
July 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

Examining the proteome of Drosophila across organism lifespan.

J Proteome Res 2007 Sep 16;6(9):3637-47. Epub 2007 Aug 16.

Departments of Chemistry and Biology, Indiana University, Bloomington, Indiana 47405, USA.

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http://pubs.acs.org/doi/abs/10.1021/pr070224h
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http://dx.doi.org/10.1021/pr070224hDOI Listing
September 2007

Lifetime proteomic profiling of an A30P alpha-synuclein Drosophila model of Parkinson's disease.

J Proteome Res 2007 Sep 7;6(9):3729-38. Epub 2007 Aug 7.

Department of Chemistry and Biology, Indiana University, Bloomington, Indiana, 47405, USA.

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http://dx.doi.org/10.1021/pr0700504DOI Listing
September 2007

Protein expression in a Drosophila model of Parkinson's disease.

J Proteome Res 2007 Jan;6(1):348-57

Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1021/pr060488oDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597372PMC
January 2007

centrosomin's beautiful sister (cbs) encodes a GRIP-domain protein that marks Golgi inheritance and functions in the centrosome cycle in Drosophila.

J Cell Sci 2006 Aug 1;119(Pt 16):3399-412. Epub 2006 Aug 1.

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1242/jcs.03088DOI Listing
August 2006

Oncopeltus fasciatus zen is essential for serosal tissue function in katatrepsis.

Dev Biol 2006 Apr 7;292(1):226-43. Epub 2006 Feb 7.

University Museum of Zoology, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK.

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http://dx.doi.org/10.1016/j.ydbio.2005.12.028DOI Listing
April 2006

Short and long germ segmentation: unanswered questions in the evolution of a developmental mode.

Evol Dev 2005 Nov-Dec;7(6):629-46

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1111/j.1525-142X.2005.05066.xDOI Listing
February 2006

Comparative developmental genetics and the evolution of arthropod body plans.

Annu Rev Genet 2005 ;39:95-119

Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269-3043, USA. david.angeliniguconn.edu

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http://dx.doi.org/10.1146/annurev.genet.39.073003.112310DOI Listing
February 2006

Hox gene function and interaction in the milkweed bug Oncopeltus fasciatus (Hemiptera).

Dev Biol 2005 Nov 23;287(2):440-55. Epub 2005 Sep 23.

Department of Biology, Indiana University, 1001 E. Third St., Bloomington, IN 47405-7005, USA.

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http://dx.doi.org/10.1016/j.ydbio.2005.08.010DOI Listing
November 2005

Insect appendages and comparative ontogenetics.

Dev Biol 2005 Oct;286(1):57-77

Department of Biology, Indiana University, 1001 E. Third St., Bloomington, IN 47405-7005, USA.

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http://dx.doi.org/10.1016/j.ydbio.2005.07.006DOI Listing
October 2005

Functional analyses in the milkweed bug Oncopeltus fasciatus (Hemiptera) support a role for Wnt signaling in body segmentation but not appendage development.

Dev Biol 2005 Jul;283(2):409-23

Department of Biology, Indiana University, Bloomington, 47405-7005, USA.

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http://dx.doi.org/10.1016/j.ydbio.2005.04.034DOI Listing
July 2005

even-skipped is not a pair-rule gene but has segmental and gap-like functions in Oncopeltus fasciatus, an intermediate germband insect.

Development 2005 May 23;132(9):2081-92. Epub 2005 Mar 23.

Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1242/dev.01807DOI Listing
May 2005

Research resources for Drosophila: the expanding universe.

Nat Rev Genet 2005 Mar;6(3):179-93

Department of Biology, Indiana University, Bloomington, Indiana 47405-3700, USA.

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http://dx.doi.org/10.1038/nrg1554DOI Listing
March 2005

Expression patterns of the rogue Hox genes Hox3/zen and fushi tarazu in the apterygote insect Thermobia domestica.

Evol Dev 2004 Nov-Dec;6(6):393-401

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1111/j.1525-142X.2004.04048.xDOI Listing
May 2005

Kruppel is a gap gene in the intermediate germband insect Oncopeltus fasciatus and is required for development of both blastoderm and germband-derived segments.

Development 2004 Sep;131(18):4567-79

Department of Biology, Indiana University, 1001 East Third Street, Bloomington IN, 47405, USA.

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http://dx.doi.org/10.1242/dev.01311DOI Listing
September 2004

Functional analyses in the hemipteran Oncopeltus fasciatus reveal conserved and derived aspects of appendage patterning in insects.

Dev Biol 2004 Jul;271(2):306-21

Department of Biology, Indiana University, Bloomington, IN 47405-3700, USA.

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http://dx.doi.org/10.1016/j.ydbio.2004.04.005DOI Listing
July 2004

Hox gene cross-regulatory interactions in the embryonic brain of Drosophila.

Mech Dev 2004 Jun;121(6):527-36

Institute of Zoology, Biocenter/Pharmacenter University of Basel, Klingelbergstr.50, CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1016/j.mod.2004.04.009DOI Listing
June 2004

hunchback is required for suppression of abdominal identity, and for proper germband growth and segmentation in the intermediate germband insect Oncopeltus fasciatus.

Development 2004 Apr 3;131(7):1515-27. Epub 2004 Mar 3.

Howard Hughes Medical Institute, Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1242/dev.01046DOI Listing
April 2004

Hox genes and the evolution of the arthropod body plan.

Evol Dev 2002 Nov-Dec;4(6):459-99

Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1046/j.1525-142x.2002.02034.xDOI Listing
May 2003

The centrosome is a dynamic structure that ejects PCM flares.

J Cell Sci 2002 Dec;115(Pt 23):4707-18

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1242/jcs.00134DOI Listing
December 2002

The Anopheles genome and comparative insect genomics.

Science 2002 Oct;298(5591):97-8

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1126/science.1077901DOI Listing
October 2002

Customized microinjection glass capillary needles for P-element transformations in Drosophila melanogaster.

Biotechniques 2002 Aug;33(2):366-7, 369-70, 372 passim

Indiana University, Bloomington 47405, USA.

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http://dx.doi.org/10.2144/02332rr03DOI Listing
August 2002

Exploring myriapod segmentation: the expression patterns of even-skipped, engrailed, and wingless in a centipede.

Dev Biol 2002 Jul;247(1):47-61

Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington 47405, USA.

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http://dx.doi.org/10.1006/dbio.2002.0683DOI Listing
July 2002

The development and evolution of insect mouthparts as revealed by the expression patterns of gnathocephalic genes.

Evol Dev 2002 Mar-Apr;4(2):96-110

Department of Biology, HHMI, Indiana University, Bloomington 47405, USA.

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http://dx.doi.org/10.1046/j.1525-142x.2002.01065.xDOI Listing
January 2003

Exploring the myriapod body plan: expression patterns of the ten Hox genes in a centipede.

Development 2002 Mar;129(5):1225-38

Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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March 2002