Bruce R Southey

Bruce R Southey

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Bruce R Southey

Publications by authors named "Bruce R Southey"

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Jersey steer ruminal papillae histology and nutrigenomics with diet changes.

J Anim Physiol Anim Nutr (Berl) 2019 Sep 4. Epub 2019 Sep 4.

Department of Animal Sciences, Auburn University, Auburn, AL, USA.

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http://dx.doi.org/10.1111/jpn.13189DOI Listing
September 2019

Bioinformatics for Prohormone and Neuropeptide Discovery.

Methods Mol Biol 2018 ;1719:71-96

Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://dx.doi.org/10.1007/978-1-4939-7537-2_5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5847276PMC
January 2019

Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior.

PLoS One 2018 2;13(8):e0201773. Epub 2018 Aug 2.

Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201773PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6072066PMC
January 2019

Interplay Between Amphetamine and Activity Level in Gene Networks of the Mouse Striatum.

Bioinform Biol Insights 2018 11;12:1177932218815152. Epub 2018 Dec 11.

Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://journals.sagepub.com/doi/10.1177/1177932218815152
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http://dx.doi.org/10.1177/1177932218815152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291885PMC
December 2018

Exploring Exercise- and Context-Induced Peptide Changes in Mice by Quantitative Mass Spectrometry.

ACS Omega 2018 Oct 24;3(10):13817-13827. Epub 2018 Oct 24.

Department of Chemistry, Neuroscience Program, Beckman Institute, Department of Animal Sciences, and Department of Psychology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, 63-5, Urbana, Illinois 61801, United States.

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http://pubs.acs.org/doi/10.1021/acsomega.8b01713
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http://dx.doi.org/10.1021/acsomega.8b01713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6210063PMC
October 2018

Peptide identifications and false discovery rates using different mass spectrometry platforms.

Talanta 2018 May 31;182:456-463. Epub 2018 Jan 31.

Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana 61801, IL, USA. Electronic address:

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http://dx.doi.org/10.1016/j.talanta.2018.01.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5839655PMC
May 2018

Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry.

J Am Soc Mass Spectrom 2018 05 17;29(5):923-934. Epub 2018 Apr 17.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

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http://dx.doi.org/10.1007/s13361-018-1898-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943159PMC
May 2018

Characterization of Genomic Variants Associated with Scout and Recruit Behavioral Castes in Honey Bees Using Whole-Genome Sequencing.

PLoS One 2016 19;11(1):e0146430. Epub 2016 Jan 19.

Department of Animal Sciences, Department of Statistics, Neuroscience Program, and Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146430PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718678PMC
August 2016

Accurate assignment of significance to neuropeptide identifications using Monte Carlo k-permuted decoy databases.

PLoS One 2014 17;9(10):e111112. Epub 2014 Oct 17.

Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111112PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201571PMC
December 2015

Comparative brain transcriptomic analyses of scouting across distinct behavioural and ecological contexts in honeybees.

Proc Biol Sci 2014 Dec;281(1797)

Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

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http://rspb.royalsocietypublishing.org/content/royprsb/281/1
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http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.
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http://dx.doi.org/10.1098/rspb.2014.1868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240991PMC
December 2014

Identification of best indicators of peptide-spectrum match using a permutation resampling approach.

J Bioinform Comput Biol 2014 Oct;12(5):1440001

Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1142/S0219720014400010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243829PMC
October 2014

Comparing label-free quantitative peptidomics approaches to characterize diurnal variation of peptides in the rat suprachiasmatic nucleus.

Anal Chem 2014 Jan 16;86(1):443-52. Epub 2013 Dec 16.

Department of Animal Sciences, ‡Department of Chemistry, §Institute for Genomic Biology, ∥Neuroscience Program, ⊥Department of Cell and Developmental Biology, and ¶Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

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http://dx.doi.org/10.1021/ac4023378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886391PMC
January 2014

Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle.

BMC Genet 2013 Sep 25;14:94. Epub 2013 Sep 25.

Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://dx.doi.org/10.1186/1471-2156-14-94DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819741PMC
September 2013

Quantitative peptidomics for discovery of circadian-related peptides from the rat suprachiasmatic nucleus.

J Proteome Res 2013 Feb 11;12(2):585-93. Epub 2013 Jan 11.

Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA.

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http://dx.doi.org/10.1021/pr300605pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562399PMC
February 2013

Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments.

J Proteomics Bioinform 2013 Jan;6(2):23-29

Department of Animal Sciences, University of Illinois Urbana-Champaign, IL, USA.

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http://dx.doi.org/10.4172/jpb.1000256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768159PMC
January 2013

Evaluation of database search programs for accurate detection of neuropeptides in tandem mass spectrometry experiments.

J Proteome Res 2012 Dec 6;11(12):6044-55. Epub 2012 Nov 6.

Department of Animal Sciences, University of Illinois Urbana-Champaign, Illinois 61801, United States.

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http://dx.doi.org/10.1021/pr3007123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516866PMC
December 2012

Identification and characterization of alternative exon usage linked glioblastoma multiforme survival.

BMC Med Genomics 2012 Dec 4;5:59. Epub 2012 Dec 4.

Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.

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http://dx.doi.org/10.1186/1755-8794-5-59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548711PMC
December 2012

Analyses of pig genomes provide insight into porcine demography and evolution.

Authors:
Martien A M Groenen Alan L Archibald Hirohide Uenishi Christopher K Tuggle Yasuhiro Takeuchi Max F Rothschild Claire Rogel-Gaillard Chankyu Park Denis Milan Hendrik-Jan Megens Shengting Li Denis M Larkin Heebal Kim Laurent A F Frantz Mario Caccamo Hyeonju Ahn Bronwen L Aken Anna Anselmo Christian Anthon Loretta Auvil Bouabid Badaoui Craig W Beattie Christian Bendixen Daniel Berman Frank Blecha Jonas Blomberg Lars Bolund Mirte Bosse Sara Botti Zhan Bujie Megan Bystrom Boris Capitanu Denise Carvalho-Silva Patrick Chardon Celine Chen Ryan Cheng Sang-Haeng Choi William Chow Richard C Clark Christopher Clee Richard P M A Crooijmans Harry D Dawson Patrice Dehais Fioravante De Sapio Bert Dibbits Nizar Drou Zhi-Qiang Du Kellye Eversole João Fadista Susan Fairley Thomas Faraut Geoffrey J Faulkner Katie E Fowler Merete Fredholm Eric Fritz James G R Gilbert Elisabetta Giuffra Jan Gorodkin Darren K Griffin Jennifer L Harrow Alexander Hayward Kerstin Howe Zhi-Liang Hu Sean J Humphray Toby Hunt Henrik Hornshøj Jin-Tae Jeon Patric Jern Matthew Jones Jerzy Jurka Hiroyuki Kanamori Ronan Kapetanovic Jaebum Kim Jae-Hwan Kim Kyu-Won Kim Tae-Hun Kim Greger Larson Kyooyeol Lee Kyung-Tai Lee Richard Leggett Harris A Lewin Yingrui Li Wansheng Liu Jane E Loveland Yao Lu Joan K Lunney Jian Ma Ole Madsen Katherine Mann Lucy Matthews Stuart McLaren Takeya Morozumi Michael P Murtaugh Jitendra Narayan Dinh Truong Nguyen Peixiang Ni Song-Jung Oh Suneel Onteru Frank Panitz Eung-Woo Park Hong-Seog Park Geraldine Pascal Yogesh Paudel Miguel Perez-Enciso Ricardo Ramirez-Gonzalez James M Reecy Sandra Rodriguez-Zas Gary A Rohrer Lauretta Rund Yongming Sang Kyle Schachtschneider Joshua G Schraiber John Schwartz Linda Scobie Carol Scott Stephen Searle Bertrand Servin Bruce R Southey Goran Sperber Peter Stadler Jonathan V Sweedler Hakim Tafer Bo Thomsen Rashmi Wali Jian Wang Jun Wang Simon White Xun Xu Martine Yerle Guojie Zhang Jianguo Zhang Jie Zhang Shuhong Zhao Jane Rogers Carol Churcher Lawrence B Schook

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

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http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
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http://www.nature.com/doifinder/10.1038/nature11622
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http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

First survey and functional annotation of prohormone and convertase genes in the pig.

BMC Genomics 2012 Nov 15;13:582. Epub 2012 Nov 15.

Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1186/1471-2164-13-582DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499383PMC
November 2012

Probing the production of amidated peptides following genetic and dietary copper manipulations.

PLoS One 2011 16;6(12):e28679. Epub 2011 Dec 16.

Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028679PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241674PMC
August 2012

Voluntary wheel running reverses age-induced changes in hippocampal gene expression.

PLoS One 2011 8;6(8):e22654. Epub 2011 Aug 8.

Department of Psychology, Beckman Institute, University of Illinois, Urbana, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022654PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152565PMC
February 2012

A python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites.

Front Neuroinform 2008 16;2. Epub 2008 Dec 16.

Department of Chemistry, University of Illinois Urbana, IL, USA.

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http://dx.doi.org/10.3389/neuro.11.007.2008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2610252PMC
July 2011

Transferase activity function and system development process are critical in cattle embryo development.

Funct Integr Genomics 2011 Mar 16;11(1):139-50. Epub 2010 Sep 16.

Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://dx.doi.org/10.1007/s10142-010-0189-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053413PMC
March 2011

The zebra finch neuropeptidome: prediction, detection and expression.

BMC Biol 2010 Apr 1;8:28. Epub 2010 Apr 1.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA.

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http://dx.doi.org/10.1186/1741-7007-8-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873334PMC
April 2010

Discrete molecular states in the brain accompany changing responses to a vocal signal.

Proc Natl Acad Sci U S A 2009 Jul 18;106(27):11364-9. Epub 2009 Jun 18.

Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.

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http://dx.doi.org/10.1073/pnas.0812998106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708759PMC
July 2009

Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches.

BMC Genomics 2009 May 16;10:228. Epub 2009 May 16.

Department of Chemistry, University of Illinois, Urbana, IL, USA.

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http://dx.doi.org/10.1186/1471-2164-10-228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2698874PMC
May 2009

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Quantitative peptidomics reveal brain peptide signatures of behavior.

Proc Natl Acad Sci U S A 2009 Feb 28;106(7):2383-8. Epub 2009 Jan 28.

Department of Entomology, Neuroscience Program, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1073/pnas.0813021106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632711PMC
February 2009

Meta-analysis of genome-wide expression patterns associated with behavioral maturation in honey bees.

BMC Genomics 2008 Oct 24;9:503. Epub 2008 Oct 24.

Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801, USA.

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http://dx.doi.org/10.1186/1471-2164-9-503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582039PMC
October 2008

Prediction of neuropeptide cleavage sites in insects.

Bioinformatics 2008 Mar 5;24(6):815-25. Epub 2008 Feb 5.

Department of Chemistry and Department of Animal Sciences, University of Illinois, Urbana, IL, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn044DOI Listing
March 2008

Comparative analysis of neuropeptide cleavage sites in human, mouse, rat, and cattle.

Mamm Genome 2008 Feb 23;19(2):106-20. Epub 2008 Jan 23.

Department of Animal Sciences, University of Illinois, Urbana, Illinois, 61801, USA.

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http://dx.doi.org/10.1007/s00335-007-9090-9DOI Listing
February 2008

Semiparametric approach to characterize unique gene expression trajectories across time.

BMC Genomics 2006 Sep 13;7:233. Epub 2006 Sep 13.

Department of Animal Sciences, University of Illinois at Urbana-Champaign, IL 61801, USA.

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http://dx.doi.org/10.1186/1471-2164-7-233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1592090PMC
September 2006

Prediction of neuropeptide prohormone cleavages with application to RFamides.

Peptides 2006 May 21;27(5):1087-98. Epub 2006 Feb 21.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1016/j.peptides.2005.07.026DOI Listing
May 2006