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John Quackenbush

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Oligonucleotide Array Sequence Analysis

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Chemicals & Drugs

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Mouse

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Physiology

Transcription, Genetic

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Mick Correll; Giovanni Ferrari; Mariano Brizzio; Christopher K Johnson; Andrew W C Mak; John Quackenbush; Richard E Shaw; Alex Zapolanski; Juan B Grau
Mutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting.
Matthew Schwede; Dimitrios Spentzos; Stefan Bentink; Benjamin Haibe-Kains; David Harrington; Oliver Hofmann; John Quackenbush; Aedín C Culhane
Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis.
Daniel Gusenleitner; Eleanor A Howe; John Quackenbush; Stefan Bentink; Aedín C Culhane
iBBiG: iterative binary bi-clustering of gene sets.

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2013: Mick Correll; Giovanni Ferrari; Mariano Brizzio; Christopher K Johnson; Andrew W C Mak; John Quackenbush; Richard E Shaw; Alex Zapolanski; Juan B Grau
Mutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting.
Genomics 2013;101(6):313-7.
2013: Matthew Schwede; Dimitrios Spentzos; Stefan Bentink; Benjamin Haibe-Kains; David Harrington; Oliver Hofmann; John Quackenbush; Aedín C Culhane
Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis.
PloS one 2013;8(3):e57799.
2012: Daniel Gusenleitner; Eleanor A Howe; John Quackenbush; Stefan Bentink; Aedín C Culhane
iBBiG: iterative binary bi-clustering of gene sets.
Bioinformatics (Oxford, England) 2012;28(19):2484-92.
2012: Thomas W Chittenden; Harold Gómez; Martin J Aryee; John Braisted; Eleanor A Howe; Jessica C Mar; Sarita J Nair; John Quackenbush; Razvan Sultana; Jennifer M Taylor; Chris Holmes
nEASE: a method for gene ontology subclassification of high-throughput gene expression data.
Bioinformatics (Oxford, England) 2012;28(5):726-8.
2012: Benjamin Haibe-Kains; Sherene Loi; John Quackenbush; Gianluca Bontempi; Aedín C Culhane; Christine Desmedt; Christos Sotiriou
A three-gene model to robustly identify breast cancer molecular subtypes.
Journal of the National Cancer Institute 2012;104(4):311-25.
2012: Stefan Bentink; Jing Chen; Aedín C Culhane; Ronny Drapkin; Jian-Bing Fan; Benjamin Haibe-Kains; Michelle S Hirsch; Kristina Holton; Joyce Liu; John Quackenbush; Thomas Risch; Renee Rubio; Eliza Wickham-Garcia; Craig April; Ursula Matulonis
Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer.
PloS one 2012;7(2):e30269.
2012: Benjamin Haibe-Kains; Catharina Olsen; Gianluca Bontempi; Christopher Bouton; Mick Correll; Amira Djebbari; John Quackenbush
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.
Nucleic acids research 2012;40(Database issue):D866-75.
2011: Eleanor A Howe; Daniel Schlauch; Raktim Sinha; John Quackenbush
RNA-Seq analysis in MeV.
Bioinformatics (Oxford, England) 2011;27(22):3209-10.
2011: Markus Schröder; John Quackenbush; Aedín C Culhane; Benjamin Haibe-Kains
survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.
Bioinformatics (Oxford, England) 2011;27(22):3206-8.
2011: Jarupon Fah Sathirapongsasuti; John Quackenbush; Scott Binder; Georg Brunner; Alistair J Cochran; Basil A J Horst; Hane Lee; Stanley F Nelson
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Bioinformatics (Oxford, England) 2011;27(19):2648-54.
2011: Jessica C Mar; Christine A Wells; John Quackenbush
Defining an informativeness metric for clustering gene expression data.
Bioinformatics (Oxford, England) 2011;27(8):1094-100.
2011: Jessica C Mar; Nicholas A Matigian; John Quackenbush; Christine A Wells
attract: A method for identifying core pathways that define cellular phenotypes.
PloS one 2011;6(10):e25445.
2011: Fenglong Liu; Joseph A White; Corina Antonescu; Daniel Gusenleitner; John Quackenbush
GCOD - GeneChip Oncology Database.
BMC bioinformatics 2011;12():46.
2010: Vivian Tseveleki; Renee Rubio; Sotiris-Spyros Vamvakas; Joseph White; Era Taoufik; Edwige Petit; John Quackenbush; Lesley Probert
Comparative gene expression analysis in mouse models for multiple sclerosis, Alzheimer's disease and stroke for identifying commonly regulated and disease-specific gene changes.
Genomics 2010;96(2):82-91.
2010: Corina Antonescu; Valentin Antonescu; Razvan Sultana; John Quackenbush
Using the DFCI gene index databases for biological discovery.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2010;Chapter 1():Unit1.6.1-36.
2010: Thomas W Chittenden; Jane Pak; Renee Rubio; Hailing Cheng; Kristina Holton; Niall Prendergast; Vladimir Glinskii; Yi Cai; Aedin Culhane; Stefan Bentink; Mathew Schwede; Jessica C Mar; Eleanor A Howe; Martin Aryee; Razvan Sultana; Anthony A Lanahan; Jennifer M Taylor; Chris Holmes; William C Hahn; Jean J Zhao; J Dirk Iglehart; John Quackenbush
Therapeutic implications of GIPC1 silencing in cancer.
PloS one 2010;5(12):e15581.
2010: Aedín C Culhane; Thomas Schwarzl; Razvan Sultana; Kermshlise C Picard; Shaita C Picard; Tim H Lu; Katherine R Franklin; Simon J French; Gerald Papenhausen; Mick Correll; John Quackenbush
GeneSigDB--a curated database of gene expression signatures.
Nucleic acids research 2010;38(Database issue):D716-25.
2009: Jessica C Mar; John Quackenbush
Decomposition of gene expression state space trajectories.
PLoS computational biology 2009;5(12):e1000626.
2009: Aedín C Culhane; John Quackenbush
Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".
Cancer research 2009;69(18):7480-5.
2009: Vadim B Fedorov; Anna V Goropashnaya; Oivind Tøien; Nathan C Stewart; Andrew Y Gracey; Celia Chang; Shizhen Qin; Geo Pertea; John Quackenbush; Louise C Showe; Michael K Showe; Bert Boyer; Brian Barnes
Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus).
Physiological genomics 2009;37(2):108-18.
2009: Martin Aryee; José A Gutiérrez-Pabello; Igor Kramnik; Tapabrata Maiti; John Quackenbush
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).
BMC bioinformatics 2009;10():409.
2009: Jessica C Mar; Yasumasa Kimura; Kate Schroder; Katharine M Irvine; Yoshihide Hayashizaki; Harukazu Suzuki; David Hume; John Quackenbush
Data-driven normalization strategies for high-throughput quantitative RT-PCR.
BMC bioinformatics 2009;10():110.
2009: Bhaskar Dutta; Harin Kanani; John Quackenbush; Maria I Klapa
Time-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures.
Biotechnology and bioengineering 2009;102(1):264-79.
2008: Christopher Taylor; Dawn Field; Susanna-Assunta Sansone; Jan Aerts; Rolf Apweiler; Michael Ashburner; Catherine A Ball; Pierre-Alain Binz; Molly Bogue; Tim Booth; Alvis Brazma; Ryan R Brinkman; Adam Michael Clark; Eric W Deutsch; Oliver Fiehn; Jennifer Fostel; Peter Ghazal; Frank Gibson; Tanya Gray; Graeme Grimes; John M Hancock; Nigel W Hardy; Henning Hermjakob; Randall K Julian; Matthew Kane; Carsten Kettner; Christopher Kinsinger; Eugene Kolker; Martin Kuiper; Nicolas Le Novère; Jim Leebens-Mack; Suzanna E Lewis; Phillip Lord; Ann-Marie Mallon; Nishanth Marthandan; Hiroshi Masuya; ruth mcnally; Alexander Mehrle; Norman Morrison; Sandra Orchard; John Quackenbush; James Reecy; Donald G Robertson; Philippe Rocca-Serra; Henry Rodriguez; Heiko Rosenfelder; Javier Santoyo-Lopez; Richard Scheuermann; Daniel Schober; Barry Smith; Jason Snape; Christian J Stoeckert; Keith Tipton; Peter Sterk; Andreas Untergasser; Jo Vandesompele; Stefan Wiemann
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Nature biotechnology 2008;26(8):889-96.
2008: Thomas W Chittenden; Eleanor A Howe; Aedin C Culhane; Razvan Sultana; Jennifer M Taylor; Chris Holmes; John Quackenbush
Functional classification analysis of somatically mutated genes in human breast and colorectal cancers.
Genomics 2008;91(6):508-11.
2008: Era Taoufik; Edwige Petit; Didier Divoux; Vivian Tseveleki; Manuela Mengozzi; Michael Leslie Roberts; Samuel Valable; Pietro Ghezzi; John Quackenbush; Michael Brines; Anthony Cerami; Lesley Probert
TNF receptor I sensitizes neurons to erythropoietin- and VEGF-mediated neuroprotection after ischemic and excitotoxic injury.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(16):6185-90.
2008: Alfred S L Cheng; Aedín C Culhane; Michael W Y Chan; Chinnambally R Venkataramu; Mathias Ehrich; Aejaz Nasir; Benjamin A T Rodriguez; Joseph Liu; Pearlly S Yan; John Quackenbush; Kenneth P Nephew; Timothy J Yeatman; Hui-Ming (Tim) Huang
Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome.
Cancer research 2008;68(6):1786-96.
2008: Eric W Deutsch; Catherine A Ball; Jules J Berman; G Steven Bova; Alvis Brazma; Roger Bumgarner; David Campbell; Helen C Causton; Jeffrey Christiansen; Fabrice Daian; Delphine Dauga; Duncan R Davidson; Gregory Gimenez; Young Ah Goo; Sean Grimmond; Thorsten Henrich; Bernhard G Herrmann; Michael H Johnson; Martin Korb; Jason C Mills; Asa J Oudes; Helen E Parkinson; Laura E Pascal; Nicolas Pollet; John Quackenbush; Mirana Ramialison; Martin Ringwald; David Salgado; Susanna-Assunta Sansone; Gavin Sherlock; Christian J Stoeckert; Jason Swedlow; Ronald C Taylor; Laura Walashek; Anthony Warford; David George Wilkinson; Yi Zhou; Leonard I Zon; Alvin Y Liu; Lawrence True
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
Nature biotechnology 2008;26(3):305-12.
2008: Amira Djebbari; John Quackenbush
Seeded Bayesian Networks: constructing genetic networks from microarray data.
BMC systems biology 2008;2():57.
2008: Michael J Boedigheimer; Russell D Wolfinger; Michael B Bass; Pierre R Bushel; Jeff W Chou; Matthew Cooper; J Christopher Corton; Jennifer Fostel; Susan Hester; Janice S Lee; Fenglong Liu; Jie Liu; Hui-Rong Qian; John Quackenbush; Syril Pettit; Karol L Thompson
Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories.
BMC genomics 2008;9():285.
2007: John W Hollingsworth; gregory whitehead; Katherine G Berman; Erin McElvania Tekippe; M Ian Gilmour; Jennie E Larkin; John Quackenbush; David A Schwartz
Genetic basis of murine antibacterial defense to streptococcal lung infection.
Immunogenetics 2007;59(9):713-24.
2007: J Usha Raj; Constantin F Aliferis; Richard M Caprioli; Allen W Cowley; Peter F Davies; Mark W Duncan; David J Erle; Serpil C Erzurum; Patricia W Finn; Harry Ischiropoulos; Naftali Kaminski; Steven R Kleeberger; George Leikauf; James E Loyd; Thomas R Martin; Sadis Matalon; Jason Moore; John Quackenbush; Tara Sabo- Attwood; Steven D Shapiro; Jan E Schnitzer; David A Schwartz; Lisa M Schwiebert; Dean Sheppard; Lorraine B Ware; Scott Weiss; Jeff A Whitsett; Mark M Wurfel; Michael A Matthay
Genomics and proteomics of lung disease: conference summary.
American journal of physiology. Lung cellular and molecular physiology 2007;293(1):L45-51.
2007: John Quackenbush
Extracting biology from high-dimensional biological data.
The Journal of experimental biology 2007;210(Pt 9):1507-17.
2007: Jun S Song; Kaveh Maghsoudi; Wei Li; Edward Fox; John Quackenbush; X Shirley Liu
Microarray blob-defect removal improves array analysis.
Bioinformatics (Oxford, England) 2007;23(8):966-71.
2007: Agnes P Chan; Pablo D Rabinowicz; John Quackenbush; C Robin Buell; Chris D Town
Plant database resources at The Institute for Genomic Research.
Methods in molecular biology (Clifton, N.J.) 2007;406():113-36.
2007: Patrick D Danley; Sean P Mullen; Fenglong Liu; Vishvanath Nene; John Quackenbush; Kerry L Shaw
A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution.
BMC genomics 2007;8():109.
2006: Elizabeth A Maher; Cameron Brennan; Patrick Y Wen; Laura Durso; Keith L Ligon; Aaron Richardson; Deepak Khatry; Bin Feng; Raktim Sinha; David N Louis; John Quackenbush; Peter Black; Lynda Chin; Ronald A DePinho
Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities.
Cancer research 2006;66(23):11502-13.
2006: Vera S F Chan; Suk-Yi Chau; Lina Tian; Yan Chen; Simon K Y Kwong; John Quackenbush; Margaret Dallman; Jonathan Lamb; Paul K H Tam
Sonic hedgehog promotes CD4+ T lymphocyte proliferation and modulates the expression of a subset of CD28-targeted genes.
International immunology 2006;18(12):1627-36.
2006: Rémy Bruggmann; Arvind K Bharti; Heidrun Gundlach; Jinsheng Lai; Sarah Young; Ana C Pontaroli; Fusheng Wei; Georg Haberer; Galina Fuks; Chunguang Du; Christina Raymond; Matt C Estep; Renyi Liu; Jeffrey L Bennetzen; Agnes P Chan; Pablo D Rabinowicz; John Quackenbush; W Brad Barbazuk; Rod A Wing; Bruce Birren; Chad Nusbaum; Steve Rounsley; Klaus F X Mayer; Joachim Messing
Uneven chromosome contraction and expansion in the maize genome.
Genome research 2006;16(10):1241-51.
2006: John Quackenbush; Rafael A Irizarry
Response to Shields: 'MIAME, we have a problem'.
Trends in genetics : TIG 2006;22(9):471-2.
2006: John Quackenbush
From 'omes to biology.
Animal genetics 2006;37 Suppl 1():48-56.
2006: John Quackenbush; Steven L Salzberg
It is time to end the patenting of software.
Bioinformatics (Oxford, England) 2006;22(12):1416-7.
2006: John Quackenbush
Microarray analysis and tumor classification.
The New England journal of medicine 2006;354(23):2463-72.
2006: Julia K L Walker; Adriana Ahumada; Bryan Frank; Renee Gaspard; Katherine G Berman; John Quackenbush; David A Schwartz
Multistrain genetic comparisons reveal CCR5 as a receptor involved in airway hyperresponsiveness.
American journal of respiratory cell and molecular biology 2006;34(6):711-8.
2006: Norihiro Maeda; Takeya Kasukawa; Rieko Oyama; Julian Gough; Martin Frith; Pär G Engström; Boris Lenhard; Rajith N Aturaliya; Serge Batalov; Kirk W Beisel; Carol Bult; Colin F Fletcher; Alistair Forrest; Masaaki Furuno; David Hill; Masayoshi Itoh; Mutsumi Kanamori-Katayama; Shintaro Katayama; Masaru Katoh; Tsugumi Kawashima; John Quackenbush; Timothy Ravasi; Brian Z Ring; Kazuhiro Shibata; Koji Sugiura; Yoichi Takenaka; Rohan Teasdale; Christine A Wells; Yunxia Zhu; Chikatoshi Kai; Jun Kawai; David A Hume; piero carninci; Yoshihide Hayashizaki
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
PLoS genetics 2006;2(4):e62.
2006: John Quackenbush; Christian J Stoeckert; Catherine Ball; Alvis Brazma; Robert Gentleman; Wolfgang Huber; Rafael A Irizarry; Marc Salit; Gavin Sherlock; Paul Spellman; Neil Winegarden
Top-down standards will not serve systems biology.
Nature 2006;440(7080):24.
2006: Renae L Malek; Hong-ying Wang; Anne E Kwitek; Andrew S Greene; Nirmal K Bhagabati; Gretta Borchardt; Lisa Cahill; Tracey Currier; Bryan Frank; Xianping Fu; Michael Hasinoff; Eleanor Howe; Noah E Letwin; Truong V Luu; Alexander Saeed; Hedieh Sajadi; Steven L Salzberg; Razvan Sultana; Mathangi Thiagarajan; Jennifer Tsai; Kathleen Veratti; Joseph White; John Quackenbush; Howard J Jacob; Norman H Lee
Physiogenomic resources for rat models of heart, lung and blood disorders.
Nature genetics 2006;38(2):234-9.
2006: Jessica C Mar; Renee Rubio; John Quackenbush
Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples.
Genome biology 2006;7(12):R119.
2006: Martin C Frith; Timothy Lawrence Bailey; Takeya Kasukawa; Flavio Mignone; Sarah K Kummerfeld; Martin Madera; Sirisha Sunkara; Masaaki Furuno; Carol Bult; John Quackenbush; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Graziano Pesole; John S Mattick
Discrimination of non-protein-coding transcripts from protein-coding mRNA.
RNA biology 2006;3(1):40-8.
2006: John Quackenbush
Weighing our measures of gene expression.
Molecular systems biology 2006;2():63.
2006: Tim Rayner; Philippe Rocca-Serra; Paul Spellman; Helen C Causton; Anna Farne; Ele Holloway; Rafael A Irizarry; Junmin Liu; Donald S Maier; Michael Miller; Kjell Petersen; John Quackenbush; Gavin Sherlock; Christian J Stoeckert; Joseph White; Patricia L Whetzel; Farrell Wymore; Helen Parkinson; Ugis Sarkans; Catherine A Ball; Alvis Brazma
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC bioinformatics 2006;7():489.
2006: John Quackenbush
Computational approaches to analysis of DNA microarray data.
Yearbook of medical informatics 2006;():91-103.
2006: Alexander I Saeed; Nirmal K Bhagabati; John C Braisted; Wei Liang; Vasily Sharov; Eleanor A Howe; Jianwei Li; Mathangi Thiagarajan; Joseph A White; John Quackenbush
TM4 microarray software suite.
Methods in enzymology 2006;411():134-93.
2006: Eric W Deutsch; Catherine A Ball; G Steven Bova; Alvis Brazma; Roger Bumgarner; David Campbell; Helen C Causton; Jeff Christiansen; Duncan Davidson; Lillian J Eichner; Young Ah Goo; Sean Grimmond; Thorsten Henrich; Michael H Johnson; Martin Korb; Jason C Mills; Asa Oudes; Helen E Parkinson; Laura E Pascal; John Quackenbush; Mirana Ramialison; Martin Ringwald; Susanna-A Sansone; Gavin Sherlock; Christian J Stoeckert; Jason Swedlow; Ronald C Taylor; Laura Walashek; Yi Zhou; Alvin Y Liu; Lawrence True
Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).
Omics : a journal of integrative biology 2006;10(2):205-8.
2006: Cath Brooksbank; John Quackenbush
Data standards: a call to action.
Omics : a journal of integrative biology 2006;10(2):94-9.
2006: John Quackenbush
Standardizing the standards.
Molecular systems biology 2006;2():2006.0010.
2006: Valerie W Hu; Bryan C Frank; Shannon Heine; Norman H Lee; John Quackenbush
Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes.
BMC genomics 2006;7():118.
2006: Christian J Stoeckert; Catherine Ball; Alvis Brazma; Ryan Brinkman; Helen C Causton; Liju Fan; Jennifer Fostel; Gilberto Fragoso; Mervi Heiskanen; Frank C P Holstege; Norman Morrison; Helen Parkinson; John Quackenbush; Philippe Rocca-Serra; Susanna-Assunta Sansone; Ugis Sarkans; Gavin Sherlock; Robert Stevens; Chris Taylor; Ronald Taylor; Patricia L Whetzel; Joseph White
Wrestling with SUMO and bio-ontologies.
Nature biotechnology 2006;24(1):21-2; author reply 23.
2006: Agnes P Chan; Geo Pertea; Foo Cheung; Dan Lee; Li Zheng; Catherine A Whitelaw; Ana C Pontaroli; Phillip SanMiguel; Yinan Yuan; Jeffrey L Bennetzen; W Brad Barbazuk; John Quackenbush; Pablo D Rabinowicz
The TIGR Maize Database.
Nucleic acids research 2006;34(Database issue):D771-6.
2005: Liwang Cui; Qi Fan; Yi Hu; Svetlana A Karamycheva; John Quackenbush; Benjawan Khuntirat; Jetsumon Sattabongkot; Jane M Carlton
Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages.
Molecular and biochemical parasitology 2005;144(1):1-9.
2005: piero carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; Vladimir Bajic; S E Brenner; S Batalov; Alistair Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; Timothy Lawrence Bailey; M Bansal; L Baxter; K W Beisel; Tom Bersano; H Bono; Alistair Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; manuela gariboldi; P Georgii-Hemming; Thomas Gingeras; Takashi Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; Kazuho Ikeo; A Iwama; T Ishikawa; M Jakt; Alexander Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; george kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; Leonard Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; LUIGI MARCHIONNI; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Yasushi Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; Nikolai Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; Steven L Salzberg; A Sandelin; C Schneider; Christian Schönbach; K Sekiguchi; Colin Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; Elia Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; Martin Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; Winston Hide; Carol Bult; S M Grimmond; Rohan Teasdale; Edison Liu; V Brusic; John Quackenbush; Claes Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; Masayoshi Itoh; T Kato; Hideya Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; Kazunori Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
The transcriptional landscape of the mammalian genome.
Science (New York, N.Y.) 2005;309(5740):1559-63.
2005: John Quackenbush
Extracting meaning from functional genomics experiments.
Toxicology and applied pharmacology 2005;207(2 Suppl):195-9.
2005: Ka Yin Kwong; Gregory C Bloom; Ivana Yang; David Boulware; Domenico Coppola; Jeremy Haseman; Emily Chen; Andrew M McGrath; Anthony J Makusky; John Taylor; Sandra Steiner; Jeffery Zhou; Timothy J Yeatman; John Quackenbush
Synchronous global assessment of gene and protein expression in colorectal cancer progression.
Genomics 2005;86(2):142-58.
2005: Amira Djebbari; Svetlana Karamycheva; Eleanor Howe; John Quackenbush
MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.
Bioinformatics (Oxford, England) 2005;21(15):3324-6.
2005: Montse Pinent; M Cinta Bladé; M Josepa Salvadó; Lluís Arola; Hubert Hackl; John Quackenbush; Zlatko Trajanoski; Anna Ardévol
Grape-seed derived procyanidins interfere with adipogenesis of 3T3-L1 cells at the onset of differentiation.
International journal of obesity (2005) 2005;29(8):934-41.
2005: Adam Margolin; Joel Greshock; Tara L Naylor; Yael Mosse; John M Maris; Graham R Bignell; Alexander I Saeed; John Quackenbush; Barbara L Weber
CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.
Bioinformatics (Oxford, England) 2005;21(15):3308-11.
2005: F D Guerrero; R J Miller; M-E Rousseau; S Sunkara; John Quackenbush; Y Lee; Vishvanath Nene
BmiGI: a database of cDNAs expressed in Boophilus microplus, the tropical/southern cattle tick.
Insect biochemistry and molecular biology 2005;35(6):585-95.
2005: Steven Eschrich; Ivana Yang; Gregory C Bloom; Ka Yin Kwong; David Boulware; Alan Cantor; Domenico Coppola; Mogens Kruhøffer; Lauri Aaltonen; Torben F Orntoft; John Quackenbush; Timothy J Yeatman
Molecular staging for survival prediction of colorectal cancer patients.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2005;23(15):3526-35.
2005: Rafael A Irizarry; Daniel S Warren; Forrest Spencer; Irene F Kim; Shyam Biswal; Bryan C Frank; Edward Gabrielson; Joe G. N. Garcia; Joel Geoghegan; Gregory G Germino; Constance A Griffin; Sara C Hilmer; Eric Hoffman; Anne E Jedlicka; Ernest Kawasaki; Francisco Martínez-Murillo; Laura Morsberger; Hannah Lee; David Petersen; John Quackenbush; Alan L Scott; Michael Wilson; Yanqin Yang; Shui Q Ye; Wayne Yu
Multiple-laboratory comparison of microarray platforms.
Nature methods 2005;2(5):345-50.
2005: Jennie E Larkin; Bryan C Frank; Haralambos Gavras; Razvan Sultana; John Quackenbush
Independence and reproducibility across microarray platforms.
Nature methods 2005;2(5):337-44.
2005: Fenglong Liu; Tara Vantoai; Linda P Moy; Geoffrey Bock; Lara D Linford; John Quackenbush
Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis.
Plant physiology 2005;137(3):1115-29.
2005: Nicholas H Bergman; Karla D Passalacqua; Renee Gaspard; Lynne M Shetron-Rama; John Quackenbush; Philip C Hanna
Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication.
Infection and immunity 2005;73(2):1069-80.
2005: Hubert Hackl; Thomas Rainer Burkard; Alexander Sturn; Renee Rubio; Alexander Schleiffer; Sun Tian; John Quackenbush; Frank Eisenhaber; Zlatko Trajanoski
Molecular processes during fat cell development revealed by gene expression profiling and functional annotation.
Genome biology 2005;6(13):R108.
2005: Nicholas F Marko; Bryan Frank; John Quackenbush; Norman H Lee
A robust method for the amplification of RNA in the sense orientation.
BMC genomics 2005;6():27.
2005: H Stanley Kim; Yan Yu; Erik C Snesrud; Linda P Moy; Lara D Linford; Brian J Haas; William C Nierman; John Quackenbush
Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome.
The Plant journal : for cell and molecular biology 2005;41(2):212-20.
2005: Yuandan Lee; Jennifer Tsai; S Sunkara; Svetlana Karamycheva; Geo Pertea; Razvan Sultana; Valentin Antonescu; A Chan; Foo Cheung; John Quackenbush
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
Nucleic acids research 2005;33(Database issue):D71-4.
2004: Catherine Ball; Alvis Brazma; Helen C Causton; Steve Chervitz; Ron Edgar; Pascal Hingamp; John Matese; Carl Icahn; Helen Parkinson; John Quackenbush; Martin Ringwald; Susanna-Assunta Sansone; Gavin Sherlock; Paul Spellman; Christian J Stoeckert; Yoshio Tateno; Ronald Taylor; Joseph White; Neil Winegarden
An open letter on microarray data from the MGED Society.
Microbiology (Reading, England) 2004;150(Pt 11):3522-4.
2004: Vishvanath Nene; Dan Lee; Simon Kang'a; Robert Skilton; Trushar Shah; Etienne de Villiers; Stephen Mwaura; David Taylor; John Quackenbush; Richard Bishop
Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva.
Insect biochemistry and molecular biology 2004;34(10):1117-28.
2004: Catherine A Ball; Alvis Brazma; Helen C Causton; Steve Chervitz; Ron Edgar; Pascal Hingamp; John Matese; Helen Parkinson; John Quackenbush; Martin Ringwald; Susanna-Assunta Sansone; Gavin Sherlock; Paul Spellman; Christian J Stoeckert; Yoshio Tateno; Ronald Taylor; Joseph White; Neil Winegarden
Submission of microarray data to public repositories.
PLoS biology 2004;2(9):E317.
2004: Catherine Ball; Alvis Brazma; Helen C Causton; Steve Chervitz; Ron Edgar; Pascal Hingamp; John Matese; Helen Parkinson; John Quackenbush; Martin Ringwald; Susanna-Assunta Sansone; Gavin Sherlock; Paul Spellman; Christian J Stoeckert; Yoshio Tateno; Ronald Taylor; Joseph White; Neil Winegarden
Standards for microarray data: an open letter.
Environmental health perspectives 2004;112(12):A666-7.
2004: Maureen Cronin; Krishna Ghosh; Frank D Sistare; John Quackenbush; Vincent Vilker; Catherine O'Connell
Universal RNA reference materials for gene expression.
Clinical chemistry 2004;50(8):1464-71.
2004: Jennie E Larkin; Bryan C Frank; Renee M Gaspard; Irena Duka; Haralambos Gavras; John Quackenbush
Cardiac transcriptional response to acute and chronic angiotensin II treatments.
Physiological genomics 2004;18(2):152-66.
2004: Donald N Cook; Shuibang Wang; Yonghong Wang; Gabriel P Howles; gregory whitehead; Katherine G Berman; Tony D Church; Bryan C Frank; Renee M Gaspard; Yan Yu; John Quackenbush; David A Schwartz
Genetic regulation of endotoxin-induced airway disease.
Genomics 2004;83(6):961-9.
2004: Tadashi Imanishi; Takeshi Itoh; Yutaka Suzuki; Claire O'Donovan; Satoshi Fukuchi; Kanako O Koyanagi; Roberto A Barrero; Takuro Tamura; Yumi Yamaguchi-Kabata; Motohiko Tanino; Kei Yura; Satoru Miyazaki; Kazuho Ikeo; Keiichi Homma; Arek Kasprzyk; Tetsuo Nishikawa; Mika Hirakawa; Jean Thierry-Mieg; Danielle Thierry-Mieg; Jennifer Ashurst; Libin Jia; Mitsuteru Nakao; Michael A Thomas; Nicola Mulder; Youla Karavidopoulou; Lihua Jin; Sangsoo Kim; Tomohiro Yasuda; Boris Lenhard; Eric Eveno; Yoshiyuki Suzuki; Chisato Yamasaki; Jun-ichi Takeda; Craig Gough; Phillip Hilton; Yasuyuki Fujii; Hiroaki Sakai; Susumu Tanaka; Clara Amid; Matthew Bellgard; Maria de Fatima Bonaldo; Hidemasa Bono; Susan K Bromberg; Anthony J Brookes; Elspeth Bruford; piero carninci; Claude Chelala; Christine Couillault; Sandro J de Souza; Marie-Anne Debily; Marie-Dominique Devignes; Inna Dubchak; Toshinori Endo; Anne Estreicher; Eduardo Eyras; Kaoru Fukami-Kobayashi; Gopal R Gopinath; Esther Graudens; Yoonsoo Hahn; Michael Han; Ze-Guang Han; Kousuke Hanada; Hideki Hanaoka; Erimi Harada; Katsuyuki Hashimoto; Ursula Hinz; Momoki Hirai; Teruyoshi Hishiki; Ian Hopkinson; Sandrine Imbeaud; Hidetoshi Inoko; Alexander Kanapin; Yayoi Kaneko; Takeya Kasukawa; Janet Kelso; Paul Kersey; Reiko Kikuno; Kouichi Kimura; Bernhard Korn; Vladimir Kuryshev; Izabela Makalowska; Takashi Makino; Shuhei Mano; Regine Mariage-Samson; Jun Mashima; Hideo Matsuda; Hans-Werner Mewes; Shinsei Minoshima; Keiichi Nagai; Hideki Nagasaki; Naoki Nagata; Rajni Nigam; Osamu Ogasawara; Osamu Ohara; Masafumi Ohtsubo; Norihiro Okada; Toshihisa Okido; Satoshi Oota; Motonori Ota; Toshio Ota; Tetsuji Otsuki; Dominique Piatier-Tonneau; Annemarie Poustka; Shuang-Xi Ren; Naruya Saitou; Katsunaga Sakai; Shigetaka Sakamoto; Ryuichi Sakate; Ingo Schupp; Florence Servant; Stephen Sherry; Rie Shiba; Nobuyoshi Shimizu; Mary Shimoyama; Andrew J Simpson; Bento Soares; Charles Steward; Makiko Suwa; Mami Suzuki; Aiko Takahashi; Gen Tamiya; Hiroshi Tanaka; Todd Taylor; Joseph D Terwilliger; Per Unneberg; Vamsi Veeramachaneni; Shinya Watanabe; Laurens Wilming; Norikazu Yasuda; Hyang-Sook Yoo; Marvin Stodolsky; Wojciech Makalowski; Mitiko Go; Kenta Nakai; Toshihisa Takagi; Minoru Kanehisa; Yoshiyuki Sakaki; John Quackenbush; Yasushi Okazaki; Yoshihide Hayashizaki; Winston Hide; Ranajit Chakraborty; Ken Nishikawa; Hideaki Sugawara; Yoshio Tateno; Zhu Chen; Michio Oishi; Peter Tonellato; Rolf Apweiler; Kousaku Okubo; Lukas Wagner; Stefan Wiemann; Robert L Strausberg; Takao Isogai; Charles Auffray; Nobuo Nomura; Takashi Gojobori; Sumio Sugano
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
PLoS biology 2004;2(6):e162.
2004: John Quackenbush
Data standards for 'omic' science.
Nature biotechnology 2004;22(5):613-4.
2004: Vasily Sharov; Ka Yin Kwong; Bryan Frank; Emily Chen; Jeremy Hasseman; Renee Gaspard; Yan Yu; Ivana Yang; John Quackenbush
The limits of log-ratios.
BMC biotechnology 2004;4():3.
2004: Elodie Ghedin; Anne Pumfery; Cynthia de la Fuente; Karen Yao; Naomi Miller; Vincent Lacoste; John Quackenbush; Steven Jacobson; Fatah Kashanchi
Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis.
Retrovirology 2004;1():10.
2004: Dmitry N Grigoryev; Shwu-Fan Ma; Rafael A Irizarry; Shui Q Ye; John Quackenbush; Joe G. N. Garcia
Orthologous gene-expression profiling in multi-species models: search for candidate genes.
Genome biology 2004;5(5):R34.
2004: Gregory C Bloom; Ivana V Yang; David Boulware; Ka Yin Kwong; Domenico Coppola; Steven Eschrich; John Quackenbush; Timothy J Yeatman
Multi-platform, multi-site, microarray-based human tumor classification.
The American journal of pathology 2004;164(1):9-16.
2003: Maria I Klapa; John Quackenbush
The quest for the mechanisms of life.
Biotechnology and bioengineering 2003;84(7):739-42.
2003: Catherine A Whitelaw; W Brad Barbazuk; Geo Pertea; Agnes P Chan; Foo Cheung; Yuandan Lee; Li Zheng; S van Heeringen; Svetlana Karamycheva; Jeffrey L Bennetzen; Phillip SanMiguel; Nathan Lakey; Joseph A Bedell; Y Yuan; Muhammad A Budiman; A Resnick; S Van Aken; Teresa Utterback; S Riedmuller; M Williams; Tamara Feldblyum; K Schubert; R Beachy; Claire M Fraser-Liggett; John Quackenbush
Enrichment of gene-coding sequences in maize by genome filtration.
Science (New York, N.Y.) 2003;302(5653):2118-20.
2003: Yuandan Lee; John Quackenbush
Using the TIGR gene index databases for biological discovery.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2003;Chapter 1():Unit 1.6.
2003: John Quackenbush
Genomics. Microarrays--guilt by association.
Science (New York, N.Y.) 2003;302(5643):240-1.
2003: Deepak Agrawal; Tingan Chen; Rosalyn B Irby; John Quackenbush; Ann F Chambers; Marianna Szabo; Alan Cantor; Domenico Coppola; Timothy J Yeatman
Osteopontin identified as colon cancer tumor progression marker.
Comptes rendus biologies 2003;326(10-11):1041-3.
2003: Tingan Chen; Ivana Yang; Rosalyn B Irby; Kenneth H Shain; Hong-Gang Wang; John Quackenbush; Domenico Coppola; Jin Q Cheng; Timothy J Yeatman
Regulation of caspase expression and apoptosis by adenomatous polyposis coli.
Cancer research 2003;63(15):4368-74.
2003: James P Abulencia; Renee Gaspard; Zachary R Healy; William A Gaarde; John Quackenbush; Konstantinos Konstantopoulos
Shear-induced cyclooxygenase-2 via a JNK2/c-Jun-dependent pathway regulates prostaglandin receptor expression in chondrocytic cells.
The Journal of biological chemistry 2003;278(31):28388-94.
2003: Takeya Kasukawa; Masaaki Furuno; Itoshi Nikaido; Hidemasa Bono; David A Hume; Carol Bult; David P Hill; Richard Baldarelli; Julian Gough; Alexander Kanapin; Hideo Matsuda; Lynn M Schriml; Yoshihide Hayashizaki; Yasushi Okazaki; John Quackenbush
Development and evaluation of an automated annotation pipeline and cDNA annotation system.
Genome research 2003;13(6B):1542-51.
2003: Christine A Wells; Timothy Ravasi; Razvan Sultana; Ken Yagi; piero carninci; Hidemasa Bono; Geoffrey J Faulkner; Yasushi Okazaki; John Quackenbush; David A Hume; Paul A Lyons
Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.
Genome research 2003;13(6B):1360-5.
2003: Joseph M Merrick; Ahmed Osman; Jennifer Tsai; John Quackenbush; Philip T LoVerde; Norman H Lee
The Schistosoma mansoni gene index: gene discovery and biology by reconstruction and analysis of expressed gene sequences.
The Journal of parasitology 2003;89(2):261-9.
2003: Geo Pertea; Xiaoqiu Huang; Frank Liang; Valentin Antonescu; Razvan Sultana; Svetlana Karamycheva; Yuandan Lee; Joseph White; Foo Cheung; Babak Parvizi; Jennifer Tsai; John Quackenbush
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
Bioinformatics (Oxford, England) 2003;19(5):651-2.
2003: Sandrine Dudoit; Robert Gentleman; John Quackenbush
Open source software for the analysis of microarray data.
BioTechniques 2003;Suppl():45-51.
2003: Donald N Cook; Shuibang Wang; Gabriel P Howles; Marcy C Speer; Gary Churchhill; John Quackenbush; David A Schwartz
The genetics of innate immunity in the lung.
Chest 2003;123(3 Suppl):369S.
2003: Heenam Stanley Kim; Erik C Snesrud; Brian Haas; Foo Cheung; Christopher D Town; John Quackenbush
Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.
Genome research 2003;13(3):327-40.
2003: Alexander I Saeed; Vasily Sharov; Joseph White; J Li; Wei Liang; Nirmal K Bhagabati; John C Braisted; M Klapa; T Currier; Mathangi Thiagarajan; A Sturn; M Snuffin; A Rezantsev; D Popov; A Ryltsov; E Kostukovich; I Borisovsky; Z Liu; A Vinsavich; V Trush; John Quackenbush
TM4: a free, open-source system for microarray data management and analysis.
BioTechniques 2003;34(2):374-8.
2003: Catherine M Ronning; Svetlana Stegalkina; Robert A Ascenzi; Oleg Bougri; Amy L Hart; Teresa R Utterbach; Susan E Vanaken; Steve B Riedmuller; Joseph A White; Jennifer Cho; Geo Pertea; Yuandan Lee; Svetlana Karamycheva; Razvan Sultana; Jennifer Tsai; John Quackenbush; Helen M Griffiths; Silvia Restrepo; Christine D Smart; William E Fry; Rutger Van der Hoeven; Steven D Tanksley; Peifen Zhang; Hailing Jin; Miki L Yamamoto; Barbara J Baker; C Robin Buell
Comparative analyses of potato expressed sequence tag libraries.
Plant physiology 2003;131(2):419-29.
2003: John Quackenbush
John Quackenbush talks about the clinical promise of genetic microarrays. Interviewed by Brian Vastag.
JAMA : the journal of the American Medical Association 2003;289(2):159-60, 163.
2003: Caird E Rexroad; Y Lee; J W Keele; Svetlana Karamycheva; G Brown; B Koop; Scott A Gahr; Yniv Palti; John Quackenbush
Sequence analysis of a rainbow trout cDNA library and creation of a gene index.
Cytogenetic and genome research 2003;102(1-4):347-54.
2003: John Quackenbush
Open-source software accelerates bioinformatics.
Genome biology 2003;4(9):336.
2003: Yunxia Zhu; Benjamin L King; Babak Parvizi; Brian P Brunk; Christian J Stoeckert; John Quackenbush; Joel Richardson; Carol Bult
Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database.
Genome biology 2003;4(2):R16.
2003: Hong-Ying Wang; Renae L Malek; Anne E Kwitek; Andrew S Greene; Truong V Luu; Babak Behbahani; Bryan Frank; John Quackenbush; Norman H Lee
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays.
Genome biology 2003;4(1):R5.
2003: Qiaoping Yuan; Shu Ouyang; Jia Liu; Bernard Suh; Foo Cheung; Razvan Sultana; Dan Lee; John Quackenbush; C Robin Buell
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.
Nucleic acids research 2003;31(1):229-33.
2002: Yasushi Okazaki; M Furuno; T Kasukawa; J Adachi; H Bono; S Kondo; I Nikaido; N Osato; R Saito; H Suzuki; I Yamanaka; H Kiyosawa; K Yagi; Y Tomaru; Y Hasegawa; A Nogami; Christian Schönbach; Takashi Gojobori; R Baldarelli; D P Hill; Carol Bult; D A Hume; John Quackenbush; Lynn M Schriml; Alexander Kanapin; H Matsuda; S Batalov; K W Beisel; J A Blake; D Bradt; V Brusic; C Chothia; L E Corbani; S Cousins; E Dalla; T A Dragani; C F Fletcher; Alistair Forrest; K S Frazer; T Gaasterland; manuela gariboldi; C Gissi; A Godzik; J Gough; S Grimmond; S Gustincich; N Hirokawa; I J Jackson; E D Jarvis; A Kanai; Hideya Kawaji; Y Kawasawa; R M Kedzierski; B L King; A Konagaya; I V Kurochkin; Y Lee; B Lenhard; P A Lyons; D R Maglott; L Maltais; LUIGI MARCHIONNI; L McKenzie; H Miki; T Nagashima; K Numata; T Okido; W J Pavan; G Pertea; G Pesole; Nikolai Petrovsky; R Pillai; J U Pontius; D Qi; S Ramachandran; T Ravasi; J C Reed; D J Reed; J Reid; B Z Ring; M Ringwald; A Sandelin; C Schneider; Colin Semple; M Setou; K Shimada; R Sultana; Y Takenaka; Martin Taylor; Rohan Teasdale; M Tomita; R Verardo; L Wagner; Claes Wahlestedt; Y Wang; Y Watanabe; C Wells; L G Wilming; A Wynshaw-Boris; M Yanagisawa; I Yang; L Yang; Z Yuan; M Zavolan; Y Zhu; A Zimmer; piero carninci; N Hayatsu; T Hirozane-Kishikawa; H Konno; M Nakamura; N Sakazume; K Sato; T Shiraki; Kazunori Waki; J Kawai; K Aizawa; T Arakawa; S Fukuda; A Hara; W Hashizume; K Imotani; Y Ishii; Masayoshi Itoh; I Kagawa; A Miyazaki; K Sakai; D Sasaki; K Shibata; A Shinagawa; A Yasunishi; M Yoshino; R Waterston; E S Lander; J Rogers; E Birney; Y Hayashizaki
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Nature 2002;420(6915):563-73.
2002: John Quackenbush
Microarray data normalization and transformation.
Nature genetics 2002;32 Suppl():496-501.
2002: Catherine A Ball; Gavin Sherlock; Helen Parkinson; Philippe Rocca-Sera; Catherine Brooksbank; Helen C Causton; Duccio Cavalieri; Terry Gaasterland; Pascal Hingamp; Frank C P Holstege; Martin Ringwald; Paul Spellman; Christian J Stoeckert; Jason E Stewart; Ronald Taylor; Alvis Brazma; John Quackenbush
The underlying principles of scientific publication.
Bioinformatics (Oxford, England) 2002;18(11):1409.
2002: Vishvanath Nene; Dan Lee; John Quackenbush; Robert Skilton; Stephen Mwaura; Malcolm J Gardner; Richard Bishop
AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum.
International journal for parasitology 2002;32(12):1447-56.
2002: Ivana V Yang; Emily Chen; Jeremy P Hasseman; Wei Liang; Bryan C Frank; Shuibang Wang; Vasily Sharov; Alexander I Saeed; Joseph White; Jerry Li; Norman H Lee; Timothy J Yeatman; John Quackenbush
Within the fold: assessing differential expression measures and reproducibility in microarray assays.
Genome biology 2002;3(11):research0062.
2002: Catherine A Ball; Gavin Sherlock; Helen Parkinson; Philippe Rocca-Sera; Catherine Brooksbank; Helen C Causton; Duccio Cavalieri; Terry Gaasterland; Pascal Hingamp; Frank C P Holstege; Martin Ringwald; Paul Spellman; Christian J Stoeckert; Jason E Stewart; Ronald Taylor; Alvis Brazma; John Quackenbush
Standards for microarray data.
Science (New York, N.Y.) 2002;298(5593):539.
2002: Renae L Malek; Rosalyn B Irby; Qingbin M Guo; Kerry Lee; Sylvia Wong; Mei He; Jennifer Tsai; Bryan Frank; Edison Liu; John Quackenbush; Richard Jove; Timothy J Yeatman; Norman H Lee
Identification of Src transformation fingerprint in human colon cancer.
Oncogene 2002;21(47):7256-65.
2002: Jane M Carlton; Samuel V Angiuoli; Bernard B Suh; Taco W Kooij; Mihaela Pertea; Joana Carneiro Da Silva; Maria D Ermolaeva; Jonathan E Allen; Jeremy D Selengut; Hean L Koo; Jeremy D Peterson; Mihai Pop; Daniel S Kosack; Martin F Shumway; Shelby L Bidwell; Shamira J Shallom; Susan E van Aken; Steven B Riedmuller; Tamara V Feldblyum; Jennifer K Cho; John Quackenbush; Martha Sedegah; Azadeh Shoaibi; Leda M Cummings; Laurence Florens; John R Yates; J Dale Raine; Robert E Sinden; Michael A Harris; Deirdre A Cunningham; Peter R Preiser; Lawrence W Bergman; Akhil B Vaidya; Leo H van Lin; Chris J Janse; Andrew P Waters; Hamilton O Smith; Owen R White; Steven L Salzberg; J Craig Venter; Claire M Fraser-Liggett; Stephen L Hoffman; Malcolm J Gardner; Daniel J Carucci
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.
Nature 2002;419(6906):512-9.
2002: Heenam Stanley Kim; B Zhao; Erik C Snesrud; Brian J Haas; Christopher D Town; John Quackenbush
Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses.
BioTechniques 2002;33(4):924-30.
2002: Scott C Fahrenkrug; Timothy P L Smith; Brad A Freking; Jennifer Cho; Joseph White; Jeff Vallet; Tommy Wise; Gary A Rohrer; Geo Pertea; Razvan Sultana; John Quackenbush; John W Keele
Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly.
Mammalian genome : official journal of the International Mammalian Genome Society 2002;13(8):475-8.
2002: Tad S Sonstegard; Anthony V Capuco; Joseph White; Curtis Van Tassell; Erin E Connor; Jennifer Cho; Razvan Sultana; Larry L Shade; James E Wray; Kevin D Wells; John Quackenbush
Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index.
Mammalian genome : official journal of the International Mammalian Genome Society 2002;13(7):373-9.
2002: Tove Andersson; Per Unneberg; Peter Nilsson; Jacob Odeberg; John Quackenbush; Joakim Lundeberg
Monitoring of representational difference analysis subtraction procedures by global microarrays.
BioTechniques 2002;32(6):1348-50, 1352, 1354-6, 1358.
2002: Deepak Agrawal; Tingan Chen; Rosalyn B Irby; John Quackenbush; Ann F Chambers; Marianna Szabo; Alan Cantor; Domenico Coppola; Timothy J Yeatman
Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling.
Journal of the National Cancer Institute 2002;94(7):513-21.
2002: Yuandan Lee; Razvan Sultana; Geo Pertea; Jennifer Cho; Svetlana Karamycheva; Jennifer Tsai; Babak Parvizi; Foo Cheung; Valentin Antonescu; Joseph White; Ingeborg Holt; Frank Liang; John Quackenbush
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).
Genome research 2002;12(3):493-502.
2002: Alexander Sturn; John Quackenbush; Zlatko Trajanoski
Genesis: cluster analysis of microarray data.
Bioinformatics (Oxford, England) 2002;18(1):207-8.
2001: Alvis Brazma; Pascal Hingamp; John Quackenbush; Gavin Sherlock; Paul Spellman; Christian J Stoeckert; J Aach; W Ansorge; Catherine A Ball; Helen C Causton; Terry Gaasterland; P Glenisson; Frank C P Holstege; I F Kim; V Markowitz; John Matese; Helen Parkinson; Alan Robinson; Ugis Sarkans; S Schulze-Kremer; J Stewart; R Taylor; Jaak Vilo; Martin Vingron
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Nature genetics 2001;29(4):365-71.
2001: P Hegde; R Qi; Renee Gaspard; K Abernathy; S Dharap; J Earle-Hughes; C Gay; N U Nwokekeh; T Chen; Alexander I Saeed; Vasily Sharov; Norman H Lee; Timothy J Yeatman; John Quackenbush
Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray.
Cancer research 2001;61(21):7792-7.
2001: John Quackenbush
The power of public access: the human genome project and the scientific process.
Nature genetics 2001;29(1):4-6.
2001: Stefan Kappe; Malcolm J Gardner; S M Brown; Jessica Ross; Kai Matuschewski; J M Ribeiro; John H Adams; John Quackenbush; J Cho; Daniel J Carucci; Stephen L Hoffman; Victor Nussenzweig
Exploring the transcriptome of the malaria sporozoite stage.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(17):9895-900.
2001: J Huang; R Qi; John Quackenbush; E Dauway; E Lazaridis; T Yeatman
Effects of ischemia on gene expression.
The Journal of surgical research 2001;99(2):222-7.
2001: Renee Gaspard; S Dharap; J Malek; R Qi; John Quackenbush
Optimized growth conditions for direct amplification of cDNA clone inserts from culture.
BioTechniques 2001;31(1):35-6.
2001: Amilcar Flores-Morales; Nina Ståhlberg; Petra Tollet-Egnell; J Lundeberg; R L Malek; John Quackenbush; Norman H Lee; Gunnar Norstedt
Microarray analysis of the in vivo effects of hypophysectomy and growth hormone treatment on gene expression in the rat.
Endocrinology 2001;142(7):3163-76.
2001: John Quackenbush
Computational analysis of microarray data.
Nature reviews. Genetics 2001;2(6):418-27.
2001: Timothy P L Smith; William M Grosse; Brad A Freking; A J Roberts; Roger T Stone; E Casas; James E Wray; Joseph White; Jennifer Cho; Scott C Fahrenkrug; Gary L Bennett; Michael P Heaton; William W Laegreid; Gary A Rohrer; Carol Chitko-McKown; Geo Pertea; Ingeborg Holt; Svetlana Karamycheva; Frank Liang; John Quackenbush; John W Keele
Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle.
Genome research 2001;11(4):626-30.
2001: Qiaoping Yuan; John Quackenbush; Razvan Sultana; Mihaela Pertea; Steven L Salzberg; C Robin Buell
Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species.
Plant physiology 2001;125(3):1166-74.
2001: J Kawai; A Shinagawa; K Shibata; M Yoshino; Masayoshi Itoh; Y Ishii; T Arakawa; A Hara; Y Fukunishi; H Konno; J Adachi; S Fukuda; K Aizawa; M Izawa; K Nishi; H Kiyosawa; S Kondo; I Yamanaka; T Saito; Yasushi Okazaki; Takashi Gojobori; H Bono; T Kasukawa; R Saito; K Kadota; H Matsuda; Michael Ashburner; S Batalov; T Casavant; W Fleischmann; T Gaasterland; C Gissi; B King; H Kochiwa; P Kuehl; S Lewis; Y Matsuo; I Nikaido; G Pesole; John Quackenbush; Lynn M Schriml; F Staubli; R Suzuki; M Tomita; L Wagner; T Washio; K Sakai; T Okido; M Furuno; H Aono; R Baldarelli; G Barsh; J Blake; D Boffelli; N Bojunga; piero carninci; M F de Bonaldo; M J Brownstein; Carol Bult; C Fletcher; M Fujita; manuela gariboldi; S Gustincich; D Hill; Martin Hofmann-Apitius; D A Hume; M Kamiya; N H Lee; P Lyons; LUIGI MARCHIONNI; J Mashima; J Mazzarelli; P Mombaerts; P Nordone; B Ring; M Ringwald; ivan rodriguez; N Sakamoto; H Sasaki; K Sato; Christian Schönbach; Tsukasa Seya; Y Shibata; K F Storch; H Suzuki; K Toyo-oka; K H Wang; C Weitz; C Whittaker; L Wilming; A Wynshaw-Boris; K Yoshida; Y Hasegawa; Hideya Kawaji; S Kohtsuki; Y Hayashizaki
Functional annotation of a full-length mouse cDNA collection.
Nature 2001;409(6821):685-90.
2001: Jennifer Tsai; Razvan Sultana; Yuandan Lee; Geo Pertea; Svetlana Karamycheva; Valentin Antonescu; Jennifer Cho; Babak Parvizi; Foo Cheung; John Quackenbush
RESOURCERER: a database for annotating and linking microarray resources within and across species.
Genome biology 2001;2(11):SOFTWARE0002.
2001: John Quackenbush; Jennifer Cho; Dan Lee; Frank Liang; Ingeborg Holt; Svetlana Karamycheva; Babak Parvizi; Geo Pertea; Razvan Sultana; Joseph White
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
Nucleic acids research 2001;29(1):159-64.
2000: John Quackenbush
Viva la revolution! A report from the FANTOM meeting.
Nature genetics 2000;26(3):255-6.
2000: Frank Liang; Ingeborg Holt; Geo Pertea; Svetlana Karamycheva; Steven L Salzberg; John Quackenbush
An optimized protocol for analysis of EST sequences.
Nucleic acids research 2000;28(18):3657-65.
2000: Qiaoping Yuan; Frank Liang; Joseph Hsiao; Victoria L Zismann; M I Benito; John Quackenbush; Rod A Wing; R Buell
Anchoring of rice BAC clones to the rice genetic map in silico.
Nucleic acids research 2000;28(18):3636-41.
2000: P Hegde; R Qi; K Abernathy; C Gay; S Dharap; Renee Gaspard; J E Hughes; Erik C Snesrud; N Lee; John Quackenbush
A concise guide to cDNA microarray analysis.
BioTechniques 2000;29(3):548-50, 552-4, 556 passim.
2000: Frank Liang; Ingeborg Holt; Geo Pertea; Svetlana Karamycheva; Steven L Salzberg; John Quackenbush
Gene index analysis of the human genome estimates approximately 120,000 genes.
Nature genetics 2000;25(2):239-40.
2000: Najib M El-Sayed; P Hegde; John Quackenbush; Sara E Melville; John E Donelson
The African trypanosome genome.
International journal for parasitology 2000;30(4):329-45.
2000: John Quackenbush; Frank Liang; Ingeborg Holt; Geo Pertea; J Upton
The TIGR gene indices: reconstruction and representation of expressed gene sequences.
Nucleic acids research 2000;28(1):141-5.
1997: Claire M Fraser-Liggett; S Casjens; W M Huang; G G Sutton; R Clayton; Raju Lathigra; Owen R White; K A Ketchum; R Dodson; E K Hickey; Michelle G Giglio; B Dougherty; J F Tomb; R D Fleischmann; D Richardson; J Peterson; A R Kerlavage; John Quackenbush; Steven L Salzberg; Mark S Hanson; R van Vugt; N Palmer; M D Adams; J Gocayne; J Weidman; T Utterback; L Watthey; L McDonald; P Artiach; C Bowman; S Garland; C Fuji; M D Cotton; K Horst; K Roberts; B Hatch; Hamilton O Smith; J C Venter
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.
Nature 1997;390(6660):580-6.
1997: H P Klenk; R A Clayton; J F Tomb; Owen R White; K E Nelson; K A Ketchum; R J Dodson; Michelle G Giglio; E K Hickey; J D Peterson; D L Richardson; A R Kerlavage; D E Graham; Nikos Kyrpides; R D Fleischmann; John Quackenbush; N H Lee; G G Sutton; S Gill; E F Kirkness; B A Dougherty; keith h mckenney; M D Adams; B Loftus; S Peterson; C I Reich; Leslie Klis McNeil; J H Badger; A Glodek; L Zhou; R Overbeek; J D Gocayne; J F Weidman; L McDonald; T Utterback; M D Cotton; T Spriggs; P Artiach; B P Kaine; S M Sykes; P W Sadow; K P D'Andrea; C Bowman; C Fujii; S A Garland; T M Mason; G J Olsen; Claire M Fraser-Liggett; Hamilton O Smith; C R Woese; J C Venter
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.
Nature 1997;390(6658):364-70.
1997: J F Tomb; Owen R White; A R Kerlavage; R A Clayton; G G Sutton; R D Fleischmann; K A Ketchum; H P Klenk; S Gill; B A Dougherty; K Nelson; John Quackenbush; L Zhou; E F Kirkness; S Peterson; B Loftus; D Richardson; R Dodson; Hanif Khalak; A Glodek; keith h mckenney; L M Fitzegerald; N Lee; M D Adams; E K Hickey; D E Berg; J D Gocayne; T R Utterback; J D Peterson; J M Kelley; M D Cotton; J M Weidman; C Fujii; C Bowman; L Watthey; E Wallin; W S Hayes; Mark Borodovsky; Peter Karp; Hamilton O Smith; Claire M Fraser-Liggett; J C Venter
The complete genome sequence of the gastric pathogen Helicobacter pylori.
Nature 1997;388(6642):539-47.
1997: Ituro Inoue; Toshiaki Nakajima; Christopher Williams; John Quackenbush; R Puryear; M Powers; Tong Cheng; Erwin H Ludwig; Arya Sharma; A Hata; Xavier Jeunemaitre; Jean-Marc Lalouel
A nucleotide substitution in the promoter of human angiotensinogen is associated with essential hypertension and affects basal transcription in vitro.
The Journal of clinical investigation 1997;99(7):1786-97.
1997: D J Doyle; John Quackenbush
Symposium on Genomic Medicine, University of Maryland, Shady Grove Campus, Rockville, Maryland, March 17-18, 1997.
Microbial & comparative genomics 1997;2(2):99-102.
1997: Julie R Korenberg; Jaakko Aaltonen; C Brahe; Deborah E Cabin; N Creau; Jean-Maurice Delabar; J Doering; Katheleen Gardiner; RS Hubert; JH Ives; AM Kessling; J Kudoh; R Lafrenière; Y Murakami; M Ohira; M Ohki; D Patterson; Marie-Claude Potier; John Quackenbush; Roger H Reeves; Y Sakaki; N Shimizu; E Soeda; Christine Van Broeckhoven; Marie-Laure Yaspo
Report and abstracts of the Sixth International Workshop on Human Chromosome 21 Mapping 1996. Cold Spring Harbor, New York, USA. May 6-8,1996.
Cytogenetics and cell genetics 1997;79(1-2):21-52.
1996: Gerold Schuler; Mark S Boguski; E A Stewart; L D Stein; Gabor Gyapay; K Rice; R E White; P Rodriguez-Tomé; A Aggarwal; E Bajorek; S Bentolila; B B Birren; A Butler; A B Castle; N Chiannilkulchai; A Chu; C Clee; S Cowles; Philip Day; T Dibling; N Drouot; Carl Bruder; S Duprat; C East; C Edwards; Jian-Bing Fan; N Fang; C Fizames; C Garrett; L Green; D Hadley; M Harris; P Harrison; S Brady; A Hicks; E Holloway; L Hui; S Hussain; C Louis-Dit-Sully; J Ma; A MacGilvery; C Mader; A Maratukulam; TC Matise; K B McKusick; J Morissette; Andrew Mungall; D Muselet; H C Nusbaum; David C Page; A Peck; S Perkins; M Piercy; F Qin; John Quackenbush; S Ranby; T Reif; Steve Rozen; C Sanders; X She; J Silva; DK Slonim; CA Soderlund; W L Sun; P Tabar; T Thangarajah; N Vega-Czarny; D Vollrath; S Voyticky; T Wilmer; X Wu; Mark D Adams; Charles Auffray; Nicole Walter; R Brandon; AM Dehejia; PN Goodfellow; R Houlgatte; J R Hudson; S E Ide; K R Iorio; W Y Lee; N Seki; T Nagase; K Ishikawa; N Nomura; C Phillips; Mihael H Polymeropoulos; M Sandusky; K Schmitt; R Berry; K Swanson; R Torres; J Craig Venter; James M Sikela; Jacques Beckmann; Jean Weissenbach; Richard Myers; D R Cox; M R James; D Bentley; Panos Deloukas; Eric S Lander; Thomas J Hudson
A gene map of the human genome.
Science (New York, N.Y.) 1996;274(5287):540-6.
1995: John Quackenbush; C Davies; J M Bailis; J V Khristich; K Diggle; Y Marchuck; J Tobin; S P Clark; A Rodkins; S Marcano
An STS content map of human chromosome 11: localization of 910 YAC clones and 109 islands.
Genomics 1995;29(2):512-25.
1995: K Kupfer; M W Smith; John Quackenbush; Glen A Evans
Physical mapping of complex genomes by sampled sequencing: a theoretical analysis.
Genomics 1995;27(1):90-100.
1994: J V Khristich; J Bailis; K Diggle; A Rodkins; A Romo; John Quackenbush; Glen A Evans
Large-scale screening of yeast artificial chromosome libraries using PCR.
BioTechniques 1994;17(3):498-501.
1994: L Selleri; M Giovannini; G G Hermanson; A Romo; John Quackenbush; L Penny; J V Khristich; Glen A Evans
Yeast artificial chromosome cloning of 3.2 megabases within chromosomal band 11q24 closely linking c-ets 1 and Fli-1 and encompassing the Ewing sarcoma breakpoint.
Genomics 1994;22(1):137-47.