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John Quackenbush
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14
Pertea, Geo
12
Karamycheva, Svetlana
10
Stoeckert, Christian
10
Yeatman, Timothy
9
Sherlock, Gavin
9
White, Joseph
9
Sultana, Razvan
9
Brazma, Alvis
8
Causton, Helen
8
Cheung, Foo
8
Parkinson, Helen
8
Spellman, Paul
8
Liang, Frank
7
Lee, Yuandan
7
Lee, Norman
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All Publications
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2009: Culhane Aedín C; Quackenbush John
Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".
Cancer research 2009;69(18):7480-5.
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2009: Fedorov Vadim B; Goropashnaya Anna V; Tøien Oivind; Stewart Nathan C; Gracey Andrew Y; Chang Celia; Qin Shizhen; Pertea Geo; Quackenbush John; Showe Louise C; Showe Michael K; Boyer Bert B; Barnes Brian M
Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus).
Physiological genomics 2009;37(2):108-18.
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2009: Dutta Bhaskar; Kanani Harin; Quackenbush John; Klapa Maria I
Time-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures.
Biotechnology and bioengineering 2009;102(1):264-79.
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2009: Mar Jessica C; Kimura Yasumasa; Schroder Kate; Irvine Katharine M; Hayashizaki Yoshihide; Suzuki Harukazu; Hume David; Quackenbush John
Data-driven normalization strategies for high-throughput quantitative RT-PCR.
BMC bioinformatics 2009;10():110.
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2008: Taylor Chris F; Field Dawn; Sansone Susanna-Assunta; Aerts Jan; Apweiler Rolf; Ashburner Michael; Ball Catherine A; Binz Pierre-Alain; Bogue Molly; Booth Tim; Brazma Alvis; Brinkman Ryan R; Michael Clark Adam; Deutsch Eric W; Fiehn Oliver; Fostel Jennifer; Ghazal Peter; Gibson Frank; Gray Tanya; Grimes Graeme; Hancock John M; Hardy Nigel W; Hermjakob Henning; Julian Randall K; Kane Matthew; Kettner Carsten; Kinsinger Christopher; Kolker Eugene; Kuiper Martin; Le Novère Nicolas; Leebens-Mack Jim; Lewis Suzanna E; Lord Phillip; Mallon Ann-Marie; Marthandan Nishanth; Masuya Hiroshi; McNally Ruth; Mehrle Alexander; Morrison Norman; Orchard Sandra; Quackenbush John; Reecy James M; Robertson Donald G; Rocca-Serra Philippe; Rodriguez Henry; Rosenfelder Heiko; Santoyo-Lopez Javier; Scheuermann Richard H; Schober Daniel; Smith Barry; Snape Jason; Stoeckert Christian J; Tipton Keith; Sterk Peter; Untergasser Andreas; Vandesompele Jo; Wiemann Stefan
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Nature biotechnology 2008;26(8):889-96.
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2008: Chittenden Thomas W; Howe Eleanor A; Culhane Aedin C; Sultana Razvan; Taylor Jennifer M; Holmes Chris; Quackenbush John
Functional classification analysis of somatically mutated genes in human breast and colorectal cancers.
Genomics 2008;91(6):508-11.
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2008: Taoufik Era; Petit Edwige; Divoux Didier; Tseveleki Vivian; Mengozzi Manuela; Roberts Michael L; Valable Samuel; Ghezzi Pietro; Quackenbush John; Brines Michael; Cerami Anthony; Probert Lesley
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.
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2008: Cheng Alfred S L; Culhane Aedín C; Chan Michael W Y; Venkataramu Chinnambally R; Ehrich Mathias; Nasir Aejaz; Rodriguez Benjamin A T; Liu Joseph; Yan Pearlly S; Quackenbush John; Nephew Kenneth P; Yeatman Timothy J; Huang Tim H-M
Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome.
Cancer research 2008;68(6):1786-96.
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2008: Deutsch Eric W; Ball Catherine A; Berman Jules J; Bova G Steven; Brazma Alvis; Bumgarner Roger E; Campbell David; Causton Helen C; Christiansen Jeffrey H; Daian Fabrice; Dauga Delphine; Davidson Duncan R; Gimenez Gregory; Goo Young Ah; Grimmond Sean; Henrich Thorsten; Herrmann Bernhard G; Johnson Michael H; Korb Martin; Mills Jason C; Oudes Asa J; Parkinson Helen E; Pascal Laura E; Pollet Nicolas; Quackenbush John; Ramialison Mirana; Ringwald Martin; Salgado David; Sansone Susanna-Assunta; Sherlock Gavin; Stoeckert Christian J; Swedlow Jason; Taylor Ronald C; Walashek Laura; Warford Anthony; Wilkinson David G; Zhou Yi; Zon Leonard I; Liu Alvin Y; True Lawrence D
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
Nature biotechnology 2008;26(3):305-12.
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2008: Djebbari Amira; Quackenbush John
Seeded Bayesian Networks: constructing genetic networks from microarray data.
BMC systems biology 2008;2():57.
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2008: Boedigheimer Michael J; Wolfinger Russell D; Bass Michael B; Bushel Pierre R; Chou Jeff W; Cooper Matthew; Corton J Christopher; Fostel Jennifer; Hester Susan; Lee Janice S; Liu Fenglong; Liu Jie; Qian Hui-Rong; Quackenbush John; Pettit Syril; Thompson Karol L
Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories.
BMC genomics 2008;9():285.
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2007: Hollingsworth John W; Whitehead Gregory; Berman Katherine Gray; Tekippe Erin McElvania; Gilmour M Ian; Larkin Jennie E; Quackenbush John; Schwartz David A
Genetic basis of murine antibacterial defense to streptococcal lung infection.
Immunogenetics 2007;59(9):713-24.
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2007: Raj J Usha; Aliferis Constantin; Caprioli Richard M; Cowley Allen W; Davies Peter F; Duncan Mark W; Erle David J; Erzurum Serpil C; Finn Patricia W; Ischiropoulos Harry; Kaminski Naftali; Kleeberger Steven R; Leikauf George D; Loyd James E; Martin Thomas R; Matalon Sadis; Moore Jason H; Quackenbush John; Sabo-Attwood Tara; Shapiro Steve D; Schnitzer Jan E; Schwartz David A; Schwiebert Lisa M; Sheppard Dean; Ware Lorraine B; Weiss Scott T; Whitsett Jeff A; Wurfel Mark M; Matthay Michael A
Genomics and proteomics of lung disease: conference summary.
American journal of physiology. Lung cellular and molecular physiology 2007;293(1):L45-51.
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2007: Quackenbush John
Extracting biology from high-dimensional biological data.
The Journal of experimental biology 2007;210(Pt 9):1507-17.
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2007: Song Jun S; Maghsoudi Kaveh; Li Wei; Fox Edward; Quackenbush John; Shirley Liu X
Microarray blob-defect removal improves array analysis.
Bioinformatics (Oxford, England) 2007;23(8):966-71.
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2007: Chan Agnes P; Rabinowicz Pablo D; Quackenbush John; Buell C Robin; Town Chris D
Plant database resources at The Institute for Genomic Research.
Methods in molecular biology (Clifton, N.J.) 2007;406():113-36.
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2007: Danley Patrick D; Mullen Sean P; Liu Fenglong; Nene Vishvanath; Quackenbush John; Shaw Kerry L
A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution.
BMC genomics 2007;8():109.
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2006: Maher Elizabeth A; Brennan Cameron; Wen Patrick Y; Durso Laura; Ligon Keith L; Richardson Aaron; Khatry Deepak; Feng Bin; Sinha Raktim; Louis David N; Quackenbush John; Black Peter McL; Chin Lynda; DePinho Ronald A
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.
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2006: Chan Vera S F; Chau Suk-Yi; Tian Lina; Chen Yan; Kwong Simon K Y; Quackenbush John; Dallman Margaret; Lamb Jonathan; Tam Paul K H
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.
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2006: Bruggmann Rémy; Bharti Arvind K; Gundlach Heidrun; Lai Jinsheng; Young Sarah; Pontaroli Ana C; Wei Fusheng; Haberer Georg; Fuks Galina; Du Chunguang; Raymond Christina; Estep Matt C; Liu Renyi; Bennetzen Jeffrey L; Chan Agnes P; Rabinowicz Pablo D; Quackenbush John; Barbazuk W Brad; Wing Rod A; Birren Bruce; Nusbaum Chad; Rounsley Steve; Mayer Klaus F X; Messing Joachim
Uneven chromosome contraction and expansion in the maize genome.
Genome research 2006;16(10):1241-51.
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2006: Quackenbush John; Irizarry Rafael A
Response to Shields: 'MIAME, we have a problem'.
Trends in genetics : TIG 2006;22(9):471-2.
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2006: Quackenbush J
From 'omes to biology.
Animal genetics 2006;37 Suppl 1():48-56.
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2006: Quackenbush John; Salzberg Steven L
It is time to end the patenting of software.
Bioinformatics (Oxford, England) 2006;22(12):1416-7.
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2006: Quackenbush John
Microarray analysis and tumor classification.
The New England journal of medicine 2006;354(23):2463-72.
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2006: Walker Julia K L; Ahumada Adriana; Frank Bryan; Gaspard Renee; Berman Katherine; Quackenbush John; Schwartz David A
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.
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2006: Maeda Norihiro; Kasukawa Takeya; Oyama Rieko; Gough Julian; Frith Martin; Engström Pär G; Lenhard Boris; Aturaliya Rajith N; Batalov Serge; Beisel Kirk W; Bult Carol J; Fletcher Colin F; Forrest Alistair R R; Furuno Masaaki; Hill David; Itoh Masayoshi; Kanamori-Katayama Mutsumi; Katayama Shintaro; Katoh Masaru; Kawashima Tsugumi; Quackenbush John; Ravasi Timothy; Ring Brian Z; Shibata Kazuhiro; Sugiura Koji; Takenaka Yoichi; Teasdale Rohan D; Wells Christine A; Zhu Yunxia; Kai Chikatoshi; Kawai Jun; Hume David A; Carninci Piero; Hayashizaki Yoshihide
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
PLoS genetics 2006;2(4):e62.
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2006: Quackenbush John; Stoeckert Christian; Ball Catherine; Brazma Alvis; Gentleman Robert; Huber Wolfgang; Irizarry Rafael; Salit Marc; Sherlock Gavin; Spellman Paul; Winegarden Neil
Top-down standards will not serve systems biology.
Nature 2006;440(7080):24.
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2006: Malek Renae L; Wang Hong-ying; Kwitek Anne E; Greene Andrew S; Bhagabati Nirmal; Borchardt Gretta; Cahill Lisa; Currier Tracey; Frank Bryan; Fu Xianping; Hasinoff Michael; Howe Eleanor; Letwin Noah; Luu Truong V; Saeed Alexander; Sajadi Hedieh; Salzberg Steven L; Sultana Razvan; Thiagarajan Mathangi; Tsai Jennifer; Veratti Kathleen; White Joseph; Quackenbush John; Jacob Howard J; Lee Norman H
Physiogenomic resources for rat models of heart, lung and blood disorders.
Nature genetics 2006;38(2):234-9.
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2006: Frith Martin C; Bailey Timothy L; Kasukawa Takeya; Mignone Flavio; Kummerfeld Sarah K; Madera Martin; Sunkara Sirisha; Furuno Masaaki; Bult Carol J; Quackenbush John; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Pesole Graziano; Mattick John S
Discrimination of non-protein-coding transcripts from protein-coding mRNA.
RNA biology 2006;3(1):40-8.
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2006: Stoeckert Christian; Ball Catherine; Brazma Alvis; Brinkman Ryan; Causton Helen; Fan Liju; Fostel Jennifer; Fragoso Gilberto; Heiskanen Mervi; Holstege Frank; Morrison Norman; Parkinson Helen; Quackenbush John; Rocca-Serra Philippe; Sansone Susanna-Assunta; Sarkans Ugis; Sherlock Gavin; Stevens Robert; Taylor Chris; Taylor Ronald; Whetzel Patricia; White Joseph
Wrestling with SUMO and bio-ontologies.
Nature biotechnology 2006;24(1):21-2; author reply 23.
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2006: Chan Agnes P; Pertea Geo; Cheung Foo; Lee Dan; Zheng Li; Whitelaw Cathy; Pontaroli Ana C; SanMiguel Phillip; Yuan Yinan; Bennetzen Jeffrey; Barbazuk William Brad; Quackenbush John; Rabinowicz Pablo D
The TIGR Maize Database.
Nucleic acids research 2006;34(Database issue):D771-6.
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2006: Mar Jessica C; Rubio Renee; Quackenbush John
Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples.
Genome biology 2006;7(12):R119.
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2006: Quackenbush John
Weighing our measures of gene expression.
Molecular systems biology 2006;2():63.
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2006: Rayner Tim F; Rocca-Serra Philippe; Spellman Paul T; Causton Helen C; Farne Anna; Holloway Ele; Irizarry Rafael A; Liu Junmin; Maier Donald S; Miller Michael; Petersen Kjell; Quackenbush John; Sherlock Gavin; Stoeckert Christian J; White Joseph; Whetzel Patricia L; Wymore Farrell; Parkinson Helen; Sarkans Ugis; Ball Catherine A; Brazma Alvis
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC bioinformatics 2006;7():489.
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2006: Quackenbush J
Computational approaches to analysis of DNA microarray data.
Yearbook of medical informatics 2006;():91-103.
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2006: Saeed Alexander I; Bhagabati Nirmal K; Braisted John C; Liang Wei; Sharov Vasily; Howe Eleanor A; Li Jianwei; Thiagarajan Mathangi; White Joseph A; Quackenbush John
TM4 microarray software suite.
Methods in enzymology 2006;411():134-93.
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2006: Deutsch Eric W; Ball Catherine A; Bova G Steven; Brazma Alvis; Bumgarner Roger E; Campbell David; Causton Helen C; Christiansen Jeff; Davidson Duncan; Eichner Lillian J; Goo Young Ah; Grimmond Sean; Henrich Thorsten; Johnson Michael H; Korb Martin; Mills Jason C; Oudes Asa; Parkinson Helen E; Pascal Laura E; Quackenbush John; Ramialison Mirana; Ringwald Martin; Sansone Susanna-A; Sherlock Gavin; Stoeckert Christian J; Swedlow Jason; Taylor Ronald C; Walashek Laura; Zhou Yi; Liu Alvin Y; True Lawrence D
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.
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2006: Brooksbank Cath; Quackenbush John
Data standards: a call to action.
Omics : a journal of integrative biology 2006;10(2):94-9.
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2006: Quackenbush John
Standardizing the standards.
Molecular systems biology 2006;2():2006.0010.
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2006: Hu Valerie W; Frank Bryan C; Heine Shannon; Lee Norman H; Quackenbush John
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.
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2005: Cui Liwang; Fan Qi; Hu Yi; Karamycheva Svetlana A; Quackenbush John; Khuntirat Benjawan; Sattabongkot Jetsumon; Carlton Jane M
Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages.
Molecular and biochemical parasitology 2005;144(1):1-9.
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2005: Carninci P; Kasukawa T; Katayama S; Gough J; Frith M C; Maeda N; Oyama R; Ravasi T; Lenhard B; Wells C; Kodzius R; Shimokawa K; Bajic V B; Brenner S E; Batalov S; Forrest A R R; Zavolan M; Davis M J; Wilming L G; Aidinis V; Allen J E; Ambesi-Impiombato A; Apweiler R; Aturaliya R N; Bailey T L; Bansal M; Baxter L; Beisel K W; Bersano T; Bono H; Chalk A M; Chiu K P; Choudhary V; Christoffels A; Clutterbuck D R; Crowe M L; Dalla E; Dalrymple B P; de Bono B; Della Gatta G; di Bernardo D; Down T; Engstrom P; Fagiolini M; Faulkner G; Fletcher C F; Fukushima T; Furuno M; Futaki S; Gariboldi M; Georgii-Hemming P; Gingeras T R; Gojobori T; Green R E; Gustincich S; Harbers M; Hayashi Y; Hensch T K; Hirokawa N; Hill D; Huminiecki L; Iacono M; Ikeo K; Iwama A; Ishikawa T; Jakt M; Kanapin A; Katoh M; Kawasawa Y; Kelso J; Kitamura H; Kitano H; Kollias G; Krishnan S P T; Kruger A; Kummerfeld S K; Kurochkin I V; Lareau L F; Lazarevic D; Lipovich L; Liu J; Liuni S; McWilliam S; Madan Babu M; Madera M; Marchionni L; Matsuda H; Matsuzawa S; Miki H; Mignone F; Miyake S; Morris K; Mottagui-Tabar S; Mulder N; Nakano N; Nakauchi H; Ng P; Nilsson R; Nishiguchi S; Nishikawa S; Nori F; Ohara O; Okazaki Y; Orlando V; Pang K C; Pavan W J; Pavesi G; Pesole G; Petrovsky N; Piazza S; Reed J; Reid J F; Ring B Z; Ringwald M; Rost B; Ruan Y; Salzberg S L; Sandelin A; Schneider C; Schönbach C; Sekiguchi K; Semple C A M; Seno S; Sessa L; Sheng Y; Shibata Y; Shimada H; Shimada K; Silva D; Sinclair B; Sperling S; Stupka E; Sugiura K; Sultana R; Takenaka Y; Taki K; Tammoja K; Tan S L; Tang S; Taylor M S; Tegner J; Teichmann S A; Ueda H R; van Nimwegen E; Verardo R; Wei C L; Yagi K; Yamanishi H; Zabarovsky E; Zhu S; Zimmer A; Hide W; Bult C; Grimmond S M; Teasdale R D; Liu E T; Brusic V; Quackenbush J; Wahlestedt C; Mattick J S; Hume D A; Kai C; Sasaki D; Tomaru Y; Fukuda S; Kanamori-Katayama M; Suzuki M; Aoki J; Arakawa T; Iida J; Imamura K; Itoh M; Kato T; Kawaji H; Kawagashira N; Kawashima T; Kojima M; Kondo S; Konno H; Nakano K; Ninomiya N; Nishio T; Okada M; Plessy C; Shibata K; Shiraki T; Suzuki S; Tagami M; Waki K; Watahiki A; Okamura-Oho Y; Suzuki H; Kawai J; Hayashizaki Y;
The transcriptional landscape of the mammalian genome.
Science (New York, N.Y.) 2005;309(5740):1559-63.
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2005: Quackenbush John
Extracting meaning from functional genomics experiments.
Toxicology and applied pharmacology 2005;207(2 Suppl):195-9.
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2005: Kwong Ka Yin; Bloom Gregory C; Yang Ivana; Boulware David; Coppola Domenico; Haseman Jeremy; Chen Emily; McGrath Andrew; Makusky A James; Taylor John; Steiner Sandra; Zhou Jeffery; Yeatman Timothy J; Quackenbush John
Synchronous global assessment of gene and protein expression in colorectal cancer progression.
Genomics 2005;86(2):142-58.
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2005: Djebbari Amira; Karamycheva Svetlana; Howe Eleanor; Quackenbush John
MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.
Bioinformatics (Oxford, England) 2005;21(15):3324-6.
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2005: Pinent M; Bladé M C; Salvadó M J; Arola L; Hackl H; Quackenbush J; Trajanoski Z; Ardévol A
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.
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2005: Margolin Adam A; Greshock Joel; Naylor Tara L; Mosse Yael; Maris John M; Bignell Graham; Saeed Alexander I; Quackenbush John; Weber Barbara L
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.
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2005: Guerrero F D; Miller R J; Rousseau M-E; Sunkara S; Quackenbush J; Lee Y; Nene V
BmiGI: a database of cDNAs expressed in Boophilus microplus, the tropical/southern cattle tick.
Insect biochemistry and molecular biology 2005;35(6):585-95.
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2005: Eschrich Steven; Yang Ivana; Bloom Greg; Kwong Ka Yin; Boulware David; Cantor Alan; Coppola Domenico; Kruhøffer Mogens; Aaltonen Lauri; Orntoft Torben F; Quackenbush John; Yeatman Timothy J
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.
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2005: Irizarry Rafael A; Warren Daniel; Spencer Forrest; Kim Irene F; Biswal Shyam; Frank Bryan C; Gabrielson Edward; Garcia Joe G N; Geoghegan Joel; Germino Gregory; Griffin Constance; Hilmer Sara C; Hoffman Eric; Jedlicka Anne E; Kawasaki Ernest; Martínez-Murillo Francisco; Morsberger Laura; Lee Hannah; Petersen David; Quackenbush John; Scott Alan; Wilson Michael; Yang Yanqin; Ye Shui Qing; Yu Wayne
Multiple-laboratory comparison of microarray platforms.
Nature methods 2005;2(5):345-50.
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2005: Larkin Jennie E; Frank Bryan C; Gavras Haralambos; Sultana Razvan; Quackenbush John
Independence and reproducibility across microarray platforms.
Nature methods 2005;2(5):337-44.
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2005: Liu Fenglong; Vantoai Tara; Moy Linda P; Bock Geoffrey; Linford Lara D; Quackenbush John
Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis.
Plant physiology 2005;137(3):1115-29.
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2005: Bergman Nicholas H; Passalacqua Karla D; Gaspard Renee; Shetron-Rama Lynne M; Quackenbush John; Hanna Philip C
Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication.
Infection and immunity 2005;73(2):1069-80.
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2005: Stanley Kim H; Yu Yan; Snesrud Erik C; Moy Linda P; Linford Lara D; Haas Brian J; Nierman William C; Quackenbush John
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.
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2005: Lee Y; Tsai J; Sunkara S; Karamycheva S; Pertea G; Sultana R; Antonescu V; Chan A; Cheung F; Quackenbush J
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.
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2005: Hackl Hubert; Burkard Thomas Rainer; Sturn Alexander; Rubio Renee; Schleiffer Alexander; Tian Sun; Quackenbush John; Eisenhaber Frank; Trajanoski Zlatko
Molecular processes during fat cell development revealed by gene expression profiling and functional annotation.
Genome biology 2005;6(13):R108.
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2005: Marko Nicholas F; Frank Bryan; Quackenbush John; Lee Norman H
A robust method for the amplification of RNA in the sense orientation.
BMC genomics 2005;6(1):27.
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2004: Ball Catherine; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Icahn Carl; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Christian; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil;
An open letter on microarray data from the MGED Society.
Microbiology (Reading, England) 2004;150(Pt 11):3522-4.
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2004: Nene Vishvanath; Lee Dan; Kang'a Simon; Skilton Robert; Shah Trushar; de Villiers Etienne; Mwaura Stephen; Taylor David; Quackenbush John; Bishop Richard
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.
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2004: Ball Catherine A; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Chris; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil
Submission of microarray data to public repositories.
PLoS biology 2004;2(9):E317.
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2004: Ball Catherine; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Christian; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil;
Standards for microarray data: an open letter.
Environmental health perspectives 2004;112(12):A666-7.
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2004: Cronin Maureen; Ghosh Krishna; Sistare Frank; Quackenbush John; Vilker Vincent; O'Connell Catherine
Universal RNA reference materials for gene expression.
Clinical chemistry 2004;50(8):1464-71.
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2004: Larkin Jennie E; Frank Bryan C; Gaspard Renee M; Duka Irena; Gavras Haralambos; Quackenbush John
Cardiac transcriptional response to acute and chronic angiotensin II treatments.
Physiological genomics 2004;18(2):152-66.
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2004: Cook Donald N; Wang Shuibang; Wang Yonghong; Howles Gabriel P; Whitehead Gregory S; Berman Katherine G; Church Tony D; Frank Bryan C; Gaspard Renee M; Yu Yan; Quackenbush John; Schwartz David A
Genetic regulation of endotoxin-induced airway disease.
Genomics 2004;83(6):961-9.
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2004: Imanishi Tadashi; Itoh Takeshi; Suzuki Yutaka; O'Donovan Claire; Fukuchi Satoshi; Koyanagi Kanako O; Barrero Roberto A; Tamura Takuro; Yamaguchi-Kabata Yumi; Tanino Motohiko; Yura Kei; Miyazaki Satoru; Ikeo Kazuho; Homma Keiichi; Kasprzyk Arek; Nishikawa Tetsuo; Hirakawa Mika; Thierry-Mieg Jean; Thierry-Mieg Danielle; Ashurst Jennifer; Jia Libin; Nakao Mitsuteru; Thomas Michael A; Mulder Nicola; Karavidopoulou Youla; Jin Lihua; Kim Sangsoo; Yasuda Tomohiro; Lenhard Boris; Eveno Eric; Suzuki Yoshiyuki; Yamasaki Chisato; Takeda Jun-ichi; Gough Craig; Hilton Phillip; Fujii Yasuyuki; Sakai Hiroaki; Tanaka Susumu; Amid Clara; Bellgard Matthew; Bonaldo Maria de Fatima; Bono Hidemasa; Bromberg Susan K; Brookes Anthony J; Bruford Elspeth; Carninci Piero; Chelala Claude; Couillault Christine; de Souza Sandro J; Debily Marie-Anne; Devignes Marie-Dominique; Dubchak Inna; Endo Toshinori; Estreicher Anne; Eyras Eduardo; Fukami-Kobayashi Kaoru; Gopinath Gopal R; Graudens Esther; Hahn Yoonsoo; Han Michael; Han Ze-Guang; Hanada Kousuke; Hanaoka Hideki; Harada Erimi; Hashimoto Katsuyuki; Hinz Ursula; Hirai Momoki; Hishiki Teruyoshi; Hopkinson Ian; Imbeaud Sandrine; Inoko Hidetoshi; Kanapin Alexander; Kaneko Yayoi; Kasukawa Takeya; Kelso Janet; Kersey Paul; Kikuno Reiko; Kimura Kouichi; Korn Bernhard; Kuryshev Vladimir; Makalowska Izabela; Makino Takashi; Mano Shuhei; Mariage-Samson Regine; Mashima Jun; Matsuda Hideo; Mewes Hans-Werner; Minoshima Shinsei; Nagai Keiichi; Nagasaki Hideki; Nagata Naoki; Nigam Rajni; Ogasawara Osamu; Ohara Osamu; Ohtsubo Masafumi; Okada Norihiro; Okido Toshihisa; Oota Satoshi; Ota Motonori; Ota Toshio; Otsuki Tetsuji; Piatier-Tonneau Dominique; Poustka Annemarie; Ren Shuang-Xi; Saitou Naruya; Sakai Katsunaga; Sakamoto Shigetaka; Sakate Ryuichi; Schupp Ingo; Servant Florence; Sherry Stephen; Shiba Rie; Shimizu Nobuyoshi; Shimoyama Mary; Simpson Andrew J; Soares Bento; Steward Charles; Suwa Makiko; Suzuki Mami; Takahashi Aiko; Tamiya Gen; Tanaka Hiroshi; Taylor Todd; Terwilliger Joseph D; Unneberg Per; Veeramachaneni Vamsi; Watanabe Shinya; Wilming Laurens; Yasuda Norikazu; Yoo Hyang-Sook; Stodolsky Marvin; Makalowski Wojciech; Go Mitiko; Nakai Kenta; Takagi Toshihisa; Kanehisa Minoru; Sakaki Yoshiyuki; Quackenbush John; Okazaki Yasushi; Hayashizaki Yoshihide; Hide Winston; Chakraborty Ranajit; Nishikawa Ken; Sugawara Hideaki; Tateno Yoshio; Chen Zhu; Oishi Michio; Tonellato Peter; Apweiler Rolf; Okubo Kousaku; Wagner Lukas; Wiemann Stefan; Strausberg Robert L; Isogai Takao; Auffray Charles; Nomura Nobuo; Gojobori Takashi; Sugano Sumio
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
PLoS biology 2004;2(6):e162.
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2004: Quackenbush John
Data standards for 'omic' science.
Nature biotechnology 2004;22(5):613-4.
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2004: Sharov Vasily; Kwong Ka Yin; Frank Bryan; Chen Emily; Hasseman Jeremy; Gaspard Renee; Yu Yan; Yang Ivana; Quackenbush John
The limits of log-ratios.
BMC biotechnology 2004;4():3.
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2004: Bloom Greg; Yang Ivana V; Boulware David; Kwong Ka Yin; Coppola Domenico; Eschrich Steven; Quackenbush John; Yeatman Timothy J
Multi-platform, multi-site, microarray-based human tumor classification.
The American journal of pathology 2004;164(1):9-16.
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2004: Ghedin Elodie; Pumfery Anne; de la Fuente Cynthia; Yao Karen; Miller Naomi; Lacoste Vincent; Quackenbush John; Jacobson Steven; Kashanchi Fatah
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.
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2004: Grigoryev Dmitry N; Ma Shwu-Fan; Irizarry Rafael A; Ye Shui Qing; Quackenbush John; Garcia Joe G N
Orthologous gene-expression profiling in multi-species models: search for candidate genes.
Genome biology 2004;5(5):R34.
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2003: Klapa Maria I; Quackenbush John
The quest for the mechanisms of life.
Biotechnology and bioengineering 2003;84(7):739-42.
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2003: Whitelaw C A; Barbazuk W B; Pertea G; Chan A P; Cheung F; Lee Y; Zheng L; van Heeringen S; Karamycheva S; Bennetzen J L; SanMiguel P; Lakey N; Bedell J; Yuan Y; Budiman M A; Resnick A; Van Aken S; Utterback T; Riedmuller S; Williams M; Feldblyum T; Schubert K; Beachy R; Fraser C M; Quackenbush J
Enrichment of gene-coding sequences in maize by genome filtration.
Science (New York, N.Y.) 2003;302(5653):2118-20.
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2003: Lee Yuandan; Quackenbush John
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.
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2003: Agrawal Deepak; Chen Tingan; Irby Rosalyn; Quackenbush John; Chambers Ann F; Szabo Marianna; Cantor Alan; Coppola Domenico; Yeatman Timothy J
Osteopontin identified as colon cancer tumor progression marker.
Comptes rendus biologies 2003;326(10-11):1041-3.
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2003: Quackenbush John
Genomics. Microarrays--guilt by association.
Science (New York, N.Y.) 2003;302(5643):240-1.
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2003: Chen Tingan; Yang Ivana; Irby Rosalyn; Shain Kenneth H; Wang Hong Gang; Quackenbush John; Coppola Domenico; Cheng Jin Q; Yeatman Timothy J
Regulation of caspase expression and apoptosis by adenomatous polyposis coli.
Cancer research 2003;63(15):4368-74.
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2003: Abulencia James P; Gaspard Renee; Healy Zachary R; Gaarde William A; Quackenbush John; Konstantopoulos Konstantinos
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.
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2003: Kasukawa Takeya; Furuno Masaaki; Nikaido Itoshi; Bono Hidemasa; Hume David A; Bult Carol; Hill David P; Baldarelli Richard; Gough Julian; Kanapin Alexander; Matsuda Hideo; Schriml Lynn M; Hayashizaki Yoshihide; Okazaki Yasushi; Quackenbush John
Development and evaluation of an automated annotation pipeline and cDNA annotation system.
Genome research 2003;13(6B):1542-51.
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2003: Wells Christine A; Ravasi Timothy; Sultana Razvan; Yagi Ken; Carninci Piero; Bono Hidemasa; Faulkner Geoffrey; Okazaki Yasushi; Quackenbush John; Hume David A; Lyons Paul A;
Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.
Genome research 2003;13(6B):1360-5.
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2003: Merrick Joseph M; Osman Ahmed; Tsai Jennifer; Quackenbush John; LoVerde Philip T; Lee Norman H
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.
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2003: Dudoit Sandrine; Gentleman Robert C; Quackenbush John
Open source software for the analysis of microarray data.
BioTechniques 2003;Suppl():45-51.
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2003: Pertea Geo; Huang Xiaoqiu; Liang Feng; Antonescu Valentin; Sultana Razvan; Karamycheva Svetlana; Lee Yuandan; White Joseph; Cheung Foo; Parvizi Babak; Tsai Jennifer; Quackenbush John
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
Bioinformatics (Oxford, England) 2003;19(5):651-2.
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2003: Cook Donald N; Wang Shuibang; Howles Gabriel P; Speer Marcy; Churchhill Gary; Quackenbush John; Schwartz David A
The genetics of innate immunity in the lung.
Chest 2003;123(3 Suppl):369S.
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2003: Kim Heenam; Snesrud Erik C; Haas Brian; Cheung Foo; Town Christopher D; Quackenbush John
Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.
Genome research 2003;13(3):327-40.
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2003: Saeed A I; Sharov V; White J; Li J; Liang W; Bhagabati N; Braisted J; Klapa M; Currier T; Thiagarajan M; Sturn A; Snuffin M; Rezantsev A; Popov D; Ryltsov A; Kostukovich E; Borisovsky I; Liu Z; Vinsavich A; Trush V; Quackenbush J
TM4: a free, open-source system for microarray data management and analysis.
BioTechniques 2003;34(2):374-8.
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2003: Ronning Catherine M; Stegalkina Svetlana S; Ascenzi Robert A; Bougri Oleg; Hart Amy L; Utterbach Teresa R; Vanaken Susan E; Riedmuller Steve B; White Joseph A; Cho Jennifer; Pertea Geo M; Lee Yuandan; Karamycheva Svetlana; Sultana Razvan; Tsai Jennifer; Quackenbush John; Griffiths Helen M; Restrepo Silvia; Smart Christine D; Fry William E; Van Der Hoeven Rutger; Tanksley Steve; Zhang Peifen; Jin Hailing; Yamamoto Miki L; Baker Barbara J; Buell C Robin
Comparative analyses of potato expressed sequence tag libraries.
Plant physiology 2003;131(2):419-29.
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2003: Yuan Qiaoping; Ouyang Shu; Liu Jia; Suh Bernard; Cheung Foo; Sultana Razvan; Lee Dan; Quackenbush John; Buell C Robin
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.
Nucleic acids research 2003;31(1):229-33.
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2003: Quackenbush John
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.
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2003: Rexroad C E; Lee Y; Keele J W; Karamycheva S; Brown G; Koop B; Gahr S A; Palti Y; Quackenbush J
Sequence analysis of a rainbow trout cDNA library and creation of a gene index.
Cytogenetic and genome research 2003;102(1-4):347-54.
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2003: Quackenbush John
Open-source software accelerates bioinformatics.
Genome biology 2003;4(9):336.
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2003: Zhu Yunxia; King Benjamin L; Parvizi Babak; Brunk Brian P; Stoeckert Christian J; Quackenbush John; Richardson Joel; Bult Carol J
Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database.
Genome biology 2003;4(2):R16.
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2003: Wang Hong-Ying; Malek Renae L; Kwitek Anne E; Greene Andrew S; Luu Truong V; Behbahani Babak; Frank Bryan; Quackenbush John; Lee Norman H
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays.
Genome biology 2003;4(1):R5.
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2002: Okazaki Y; Furuno M; Kasukawa T; Adachi J; Bono H; Kondo S; Nikaido I; Osato N; Saito R; Suzuki H; Yamanaka I; Kiyosawa H; Yagi K; Tomaru Y; Hasegawa Y; Nogami A; Schönbach C; Gojobori T; Baldarelli R; Hill D P; Bult C; Hume D A; Quackenbush J; Schriml L M; Kanapin A; Matsuda H; Batalov S; Beisel K W; Blake J A; Bradt D; Brusic V; Chothia C; Corbani L E; Cousins S; Dalla E; Dragani T A; Fletcher C F; Forrest A; Frazer K S; Gaasterland T; Gariboldi M; Gissi C; Godzik A; Gough J; Grimmond S; Gustincich S; Hirokawa N; Jackson I J; Jarvis E D; Kanai A; Kawaji H; Kawasawa Y; Kedzierski R M; King B L; Konagaya A; Kurochkin I V; Lee Y; Lenhard B; Lyons P A; Maglott D R; Maltais L; Marchionni L; McKenzie L; Miki H; Nagashima T; Numata K; Okido T; Pavan W J; Pertea G; Pesole G; Petrovsky N; Pillai R; Pontius J U; Qi D; Ramachandran S; Ravasi T; Reed J C; Reed D J; Reid J; Ring B Z; Ringwald M; Sandelin A; Schneider C; Semple C A M; Setou M; Shimada K; Sultana R; Takenaka Y; Taylor M S; Teasdale R D; Tomita M; Verardo R; Wagner L; Wahlestedt C; Wang Y; Watanabe Y; Wells C; Wilming L G; Wynshaw-Boris A; Yanagisawa M; Yang I; Yang L; Yuan Z; Zavolan M; Zhu Y; Zimmer A; Carninci P; Hayatsu N; Hirozane-Kishikawa T; Konno H; Nakamura M; Sakazume N; Sato K; Shiraki T; Waki K; Kawai J; Aizawa K; Arakawa T; Fukuda S; Hara A; Hashizume W; Imotani K; Ishii Y; Itoh M; Kagawa I; Miyazaki A; Sakai K; Sasaki D; Shibata K; Shinagawa A; Yasunishi A; Yoshino M; Waterston R; Lander E S; Rogers J; Birney E; Hayashizaki Y;
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Nature 2002;420(6915):563-73.
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2002: Quackenbush John
Microarray data normalization and transformation.
Nature genetics 2002;32 Suppl():496-501.
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2002: Ball Catherine A; Sherlock Gavin; Parkinson Helen; Rocca-Sera Philippe; Brooksbank Catherine; Causton Helen C; Cavalieri Duccio; Gaasterland Terry; Hingamp Pascal; Holstege Frank; Ringwald Martin; Spellman Paul; Stoeckert Christian J; Stewart Jason E; Taylor Ronald; Brazma Alvis; Quackenbush John;
The underlying principles of scientific publication.
Bioinformatics (Oxford, England) 2002;18(11):1409.
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2002: Nene Vishvanath; Lee Dan; Quackenbush John; Skilton Robert; Mwaura Stephen; Gardner Malcolm J; Bishop Richard
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.
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2002: Yang Ivana V; Chen Emily; Hasseman Jeremy P; Liang Wei; Frank Bryan C; Wang Shuibang; Sharov Vasily; Saeed Alexander I; White Joseph; Li Jerry; Lee Norman H; Yeatman Timothy J; Quackenbush John
Within the fold: assessing differential expression measures and reproducibility in microarray assays.
Genome biology 2002;3(11):research0062.
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2002: Kim H; Zhao B; Snesrud E C; Haas B J; Town C D; Quackenbush J
Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses.
BioTechniques 2002;33(4):924-30.
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2002: Ball Catherine A; Sherlock Gavin; Parkinson Helen; Rocca-Sera Philippe; Brooksbank Catherine; Causton Helen C; Cavalieri Duccio; Gaasterland Terry; Hingamp Pascal; Holstege Frank; Ringwald Martin; Spellman Paul; Stoeckert Christian J; Stewart Jason E; Taylor Ronald; Brazma Alvis; Quackenbush John;
Standards for microarray data.
Science (New York, N.Y.) 2002;298(5593):539.
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2002: Malek Renae L; Irby Rosalyn B; Guo Qingbin M; Lee Kerry; Wong Sylvia; He Mei; Tsai Jennifer; Frank Bryan; Liu Edison T; Quackenbush John; Jove Richard; Yeatman Timothy J; Lee Norman H
Identification of Src transformation fingerprint in human colon cancer.
Oncogene 2002;21(47):7256-65.
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2002: Carlton Jane M; Angiuoli Samuel V; Suh Bernard B; Kooij Taco W; Pertea Mihaela; Silva Joana C; Ermolaeva Maria D; Allen Jonathan E; Selengut Jeremy D; Koo Hean L; Peterson Jeremy D; Pop Mihai; Kosack Daniel S; Shumway Martin F; Bidwell Shelby L; Shallom Shamira J; van Aken Susan E; Riedmuller Steven B; Feldblyum Tamara V; Cho Jennifer K; Quackenbush John; Sedegah Martha; Shoaibi Azadeh; Cummings Leda M; Florens Laurence; Yates John R; Raine J Dale; Sinden Robert E; Harris Michael A; Cunningham Deirdre A; Preiser Peter R; Bergman Lawrence W; Vaidya Akhil B; van Lin Leo H; Janse Chris J; Waters Andrew P; Smith Hamilton O; White Owen R; Salzberg Steven L; Venter J Craig; Fraser Claire M; Hoffman Stephen L; Gardner Malcolm J; Carucci Daniel J
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.
Nature 2002;419(6906):512-9.
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2002: Fahrenkrug Scott C; Smith Timothy P L; Freking Brad A; Cho Jennifer; White Joseph; Vallet Jeff; Wise Tommy; Rohrer Gary; Pertea Geo; Sultana Razvan; Quackenbush John; Keele John W
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.
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2002: Sonstegard Tad S; Capuco Anthony V; White Joseph; Van Tassell Curtis P; Connor Erin E; Cho Jennifer; Sultana Razvan; Shade Larry; Wray James E; Wells Kevin D; Quackenbush John
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.
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2002: Andersson T; Unneberg P; Nilsson P; Odeberg J; Quackenbush J; Lundeberg J
Monitoring of representational difference analysis subtraction procedures by global microarrays.
BioTechniques 2002;32(6):1348-50, 1352, 1354-6, 1358.
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2002: Agrawal Deepak; Chen Tingan; Irby Rosalyn; Quackenbush John; Chambers Ann F; Szabo Marianna; Cantor Alan; Coppola Domenico; Yeatman Timothy J
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.
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2002: Lee Yuandan; Sultana Razvan; Pertea Geo; Cho Jennifer; Karamycheva Svetlana; Tsai Jennifer; Parvizi Babak; Cheung Foo; Antonescu Valentin; White Joseph; Holt Ingeborg; Liang Feng; Quackenbush John
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).
Genome research 2002;12(3):493-502.
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2002: Sturn Alexander; Quackenbush John; Trajanoski Zlatko
Genesis: cluster analysis of microarray data.
Bioinformatics (Oxford, England) 2002;18(1):207-8.
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2001: Brazma A; Hingamp P; Quackenbush J; Sherlock G; Spellman P; Stoeckert C; Aach J; Ansorge W; Ball C A; Causton H C; Gaasterland T; Glenisson P; Holstege F C; Kim I F; Markowitz V; Matese J C; Parkinson H; Robinson A; Sarkans U; Schulze-Kremer S; Stewart J; Taylor R; Vilo J; Vingron M
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Nature genetics 2001;29(4):365-71.
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2001: Hegde P; Qi R; Gaspard R; Abernathy K; Dharap S; Earle-Hughes J; Gay C; Nwokekeh N U; Chen T; Saeed A I; Sharov V; Lee N H; Yeatman T J; Quackenbush J
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.
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2001: Quackenbush J
The power of public access: the human genome project and the scientific process.
Nature genetics 2001;29(1):4-6.
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2001: Kappe S H; Gardner M J; Brown S M; Ross J; Matuschewski K; Ribeiro J M; Adams J H; Quackenbush J; Cho J; Carucci D J; Hoffman S L; Nussenzweig V
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.
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2001: Huang J; Qi R; Quackenbush J; Dauway E; Lazaridis E; Yeatman T
Effects of ischemia on gene expression.
The Journal of surgical research 2001;99(2):222-7.
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2001: Gaspard R; Dharap S; Malek J; Qi R; Quackenbush J
Optimized growth conditions for direct amplification of cDNA clone inserts from culture.
BioTechniques 2001;31(1):35-6.
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2001: Flores-Morales A; Ståhlberg N; Tollet-Egnell P; Lundeberg J; Malek R L; Quackenbush J; Lee N H; Norstedt G
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.
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2001: Quackenbush J
Computational analysis of microarray data.
Nature reviews. Genetics 2001;2(6):418-27.
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2001: Smith T P; Grosse W M; Freking B A; Roberts A J; Stone R T; Casas E; Wray J E; White J; Cho J; Fahrenkrug S C; Bennett G L; Heaton M P; Laegreid W W; Rohrer G A; Chitko-McKown C G; Pertea G; Holt I; Karamycheva S; Liang F; Quackenbush J; Keele J W
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.
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2001: Yuan Q; Quackenbush J; Sultana R; Pertea M; Salzberg S L; Buell C R
Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species.
Plant physiology 2001;125(3):1166-74.
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2001: Kawai J; Shinagawa A; Shibata K; Yoshino M; Itoh M; Ishii Y; Arakawa T; Hara A; Fukunishi Y; Konno H; Adachi J; Fukuda S; Aizawa K; Izawa M; Nishi K; Kiyosawa H; Kondo S; Yamanaka I; Saito T; Okazaki Y; Gojobori T; Bono H; Kasukawa T; Saito R; Kadota K; Matsuda H; Ashburner M; Batalov S; Casavant T; Fleischmann W; Gaasterland T; Gissi C; King B; Kochiwa H; Kuehl P; Lewis S; Matsuo Y; Nikaido I; Pesole G; Quackenbush J; Schriml L M; Staubli F; Suzuki R; Tomita M; Wagner L; Washio T; Sakai K; Okido T; Furuno M; Aono H; Baldarelli R; Barsh G; Blake J; Boffelli D; Bojunga N; Carninci P; de Bonaldo M F; Brownstein M J; Bult C; Fletcher C; Fujita M; Gariboldi M; Gustincich S; Hill D; Hofmann M; Hume D A; Kamiya M; Lee N H; Lyons P; Marchionni L; Mashima J; Mazzarelli J; Mombaerts P; Nordone P; Ring B; Ringwald M; Rodriguez I; Sakamoto N; Sasaki H; Sato K; Schönbach C; Seya T; Shibata Y; Storch K F; Suzuki H; Toyo-oka K; Wang K H; Weitz C; Whittaker C; Wilming L; Wynshaw-Boris A; Yoshida K; Hasegawa Y; Kawaji H; Kohtsuki S; Hayashizaki Y;
Functional annotation of a full-length mouse cDNA collection.
Nature 2001;409(6821):685-90.
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2001: Quackenbush J; Cho J; Lee D; Liang F; Holt I; Karamycheva S; Parvizi B; Pertea G; Sultana R; White J
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
Nucleic acids research 2001;29(1):159-64.
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2001: Tsai J; Sultana R; Lee Y; Pertea G; Karamycheva S; Antonescu V; Cho J; Parvizi B; Cheung F; Quackenbush J
RESOURCERER: a database for annotating and linking microarray resources within and across species.
Genome biology 2001;2(11):SOFTWARE0002.
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2000: Quackenbush J
Viva la revolution! A report from the FANTOM meeting.
Nature genetics 2000;26(3):255-6.
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2000: Hegde P; Qi R; Abernathy K; Gay C; Dharap S; Gaspard R; Hughes J E; Snesrud E; Lee N; Quackenbush J
A concise guide to cDNA microarray analysis.
BioTechniques 2000;29(3):548-50, 552-4, 556 passim.
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2000: Liang F; Holt I; Pertea G; Karamycheva S; Salzberg S L; Quackenbush J
An optimized protocol for analysis of EST sequences.
Nucleic acids research 2000;28(18):3657-65.
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2000: Yuan Q; Liang F; Hsiao J; Zismann V; Benito M I; Quackenbush J; Wing R; Buell R
Anchoring of rice BAC clones to the rice genetic map in silico.
Nucleic acids research 2000;28(18):3636-41.
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2000: Liang F; Holt I; Pertea G; Karamycheva S; Salzberg S L; Quackenbush J
Gene index analysis of the human genome estimates approximately 120,000 genes.
Nature genetics 2000;25(2):239-40.
-
2000: El-Sayed N M; Hegde P; Quackenbush J; Melville S E; Donelson J E
The African trypanosome genome.
International journal for parasitology 2000;30(4):329-45.
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2000: Quackenbush J; Liang F; Holt I; Pertea G; Upton J
The TIGR gene indices: reconstruction and representation of expressed gene sequences.
Nucleic acids research 2000;28(1):141-5.
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1997: Fraser C M; Casjens S; Huang W M; Sutton G G; Clayton R; Lathigra R; White O; Ketchum K A; Dodson R; Hickey E K; Gwinn M; Dougherty B; Tomb J F; Fleischmann R D; Richardson D; Peterson J; Kerlavage A R; Quackenbush J; Salzberg S; Hanson M; van Vugt R; Palmer N; Adams M D; Gocayne J; Weidman J; Utterback T; Watthey L; McDonald L; Artiach P; Bowman C; Garland S; Fuji C; Cotton M D; Horst K; Roberts K; Hatch B; Smith H O; Venter J C
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.
Nature 1997;390(6660):580-6.
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1997: Klenk H P; Clayton R A; Tomb J F; White O; Nelson K E; Ketchum K A; Dodson R J; Gwinn M; Hickey E K; Peterson J D; Richardson D L; Kerlavage A R; Graham D E; Kyrpides N C; Fleischmann R D; Quackenbush J; Lee N H; Sutton G G; Gill S; Kirkness E F; Dougherty B A; McKenney K; Adams M D; Loftus B; Peterson S; Reich C I; McNeil L K; Badger J H; Glodek A; Zhou L; Overbeek R; Gocayne J D; Weidman J F; McDonald L; Utterback T; Cotton M D; Spriggs T; Artiach P; Kaine B P; Sykes S M; Sadow P W; D'Andrea K P; Bowman C; Fujii C; Garland S A; Mason T M; Olsen G J; Fraser C M; Smith H O; Woese C R; Venter J C
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.
Nature 1997;390(6658):364-70.
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1997: Tomb J F; White O; Kerlavage A R; Clayton R A; Sutton G G; Fleischmann R D; Ketchum K A; Klenk H P; Gill S; Dougherty B A; Nelson K; Quackenbush J; Zhou L; Kirkness E F; Peterson S; Loftus B; Richardson D; Dodson R; Khalak H G; Glodek A; McKenney K; Fitzegerald L M; Lee N; Adams M D; Hickey E K; Berg D E; Gocayne J D; Utterback T R; Peterson J D; Kelley J M; Cotton M D; Weidman J M; Fujii C; Bowman C; Watthey L; Wallin E; Hayes W S; Borodovsky M; Karp P D; Smith H O; Fraser C M; Venter J C
The complete genome sequence of the gastric pathogen Helicobacter pylori.
Nature 1997;388(6642):539-47.
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1997: Inoue I; Nakajima T; Williams C S; Quackenbush J; Puryear R; Powers M; Cheng T; Ludwig E H; Sharma A M; Hata A; Jeunemaitre X; Lalouel J M
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.
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1997: Doyle D J; Quackenbush J
Symposium on Genomic Medicine, University of Maryland, Shady Grove Campus, Rockville, Maryland, March 17-18, 1997.
Microbial & comparative genomics 1997;2(2):99-102.
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1997: Korenberg J R; Aaltonen J; Brahe C; Cabin D; Creau N; Delabar J M; Doering J; Gardiner K; Hubert R S; Ives J; Kessling A; Kudoh J; Lafrenière R; Murakami Y; Ohira M; Ohki M; Patterson D; Potier M C; Quackenbush J; Reeves R H; Sakaki Y; Shimizu N; Soeda E; Van Broeckhoven C; Yaspo M L
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.
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1996: Schuler G D; Boguski M S; Stewart E A; Stein L D; Gyapay G; Rice K; White R E; Rodriguez-Tomé P; Aggarwal A; Bajorek E; Bentolila S; Birren B B; Butler A; Castle A B; Chiannilkulchai N; Chu A; Clee C; Cowles S; Day P J; Dibling T; Drouot N; Dunham I; Duprat S; East C; Edwards C; Fan J B; Fang N; Fizames C; Garrett C; Green L; Hadley D; Harris M; Harrison P; Brady S; Hicks A; Holloway E; Hui L; Hussain S; Louis-Dit-Sully C; Ma J; MacGilvery A; Mader C; Maratukulam A; Matise T C; McKusick K B; Morissette J; Mungall A; Muselet D; Nusbaum H C; Page D C; Peck A; Perkins S; Piercy M; Qin F; Quackenbush J; Ranby S; Reif T; Rozen S; Sanders C; She X; Silva J; Slonim D K; Soderlund C; Sun W L; Tabar P; Thangarajah T; Vega-Czarny N; Vollrath D; Voyticky S; Wilmer T; Wu X; Adams M D; Auffray C; Walter N A; Brandon R; Dehejia A; Goodfellow P N; Houlgatte R; Hudson J R; Ide S E; Iorio K R; Lee W Y; Seki N; Nagase T; Ishikawa K; Nomura N; Phillips C; Polymeropoulos M H; Sandusky M; Schmitt K; Berry R; Swanson K; Torres R; Venter J C; Sikela J M; Beckmann J S; Weissenbach J; Myers R M; Cox D R; James M R; Bentley D; Deloukas P; Lander E S; Hudson T J
A gene map of the human genome.
Science (New York, N.Y.) 1996;274(5287):540-6.
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1995: Quackenbush J; Davies C; Bailis J M; Khristich J V; Diggle K; Marchuck Y; Tobin J; Clark S P; Rodkins A; Marcano S
An STS content map of human chromosome 11: localization of 910 YAC clones and 109 islands.
Genomics 1995;29(2):512-25.
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1995: Kupfer K; Smith M W; Quackenbush J; Evans G A
Physical mapping of complex genomes by sampled sequencing: a theoretical analysis.
Genomics 1995;27(1):90-100.
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1994: Khristich J V; Bailis J; Diggle K; Rodkins A; Romo A; Quackenbush J; Evans G A
Large-scale screening of yeast artificial chromosome libraries using PCR.
BioTechniques 1994;17(3):498-501.
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1994: Selleri L; Giovannini M; Hermanson G G; Romo A; Quackenbush J; Penny L; Khristich J V; Evans G A
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.
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