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Characterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencing

Author(s): Campbell Joshua D | Luo Lingqi | Liu Gang | Xiao Ji | Gerrein Joseph | Guardela Brenda J | Tedrow John | Aleksyev Yuriy O | Yang Ivana V | Correll Mick | Geraci Mark | Quackenbush John | Sciurba Frank | Schwartz David A | Kaminski Naftali | Lenburg Marc E | Beane Jennifer | Spira Avrum
Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing

Author(s): Brothers John | Kusko Rebecca | Liu Gang | Luo Lingqi | Guardela Brenda | Tedrow John | Alekesyev Yuriy | Yang Ivana V | Correll Mick | Geraci Mark | Quackenbush John | Sciurba Frank | Sebastiani Paola | Lenburg Marc | Kaminski Naftali | Schwartz David A | Spira Avrum | Beane Jennifer
Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq

Author(s): Kusko Rebecca L | Brothers John | Liu Gang | Luo Lingqi | Guardela Brenda | Tedrow John | Aleksyev Yuriy | Yang Ivana V | Correll Mick | Geraci Mark | Quackenbush John | Sciurba Frank | Lenburg Marc | Schwartz David A | Beane Jennifer | Kaminski Naftali | Spira Avrum
POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

Author(s): Ethalinda K. S. Cannon | Scott M. Birkett | Bremen L. Braun | Sateesh Kodavali | Douglas M. Jennewein | Alper Yilmaz | Valentin Antonescu | Corina Antonescu | Lisa C. Harper | Jack M. Gardiner | Mary L. Schaeffer | Darwin A. Campbell | Carson M. Andorf | Destri Andorf | Damon Lisch | Karen E. Koch | Donald R. McCarty | John Quackenbush | Erich Grotewold | Carol M. Lushbough | Taner Z. Sen | Carolyn J. Lawrence
GCOD - GeneChip Oncology Database

Author(s): Liu Fenglong | White Joseph | Antonescu Corina | Gusenleitner Daniel | Quackenbush John
Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old

Author(s): Colak Dilek | Chishti Muhammad | Al-Bakheet Al-Bandary | Al-Qahtani Ahmed | Shoukri Mohamed | Goyns Malcolm | Ozand Pinar | Quackenbush John | Park Ben | Kaya Namik
Data-driven normalization strategies for high-throughput quantitative RT-PCR

Author(s): Mar Jessica | Kimura Yasumasa | Schroder Kate | Irvine Katharine | Hayashizaki Yoshihide | Suzuki Harukazu | Hume David | Quackenbush John
Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

Author(s): Boedigheimer Michael | Wolfinger Russell | Bass Michael | Bushel Pierre | Chou Jeff | Cooper Matthew | Corton J Christopher | Fostel Jennifer | Hester Susan | Lee Janice | Liu Fenglong | Liu Jie | Qian Hui-Rong | Quackenbush John | Pettit Syril | Thompson Karol
A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution

Author(s): Danley Patrick | Mullen Sean | Liu Fenglong | Nene Vishvanath | Quackenbush John | Shaw Kerry
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Author(s): Rayner Tim | Rocca-Serra Philippe | Spellman Paul | Causton Helen | Farne Anna | Holloway Ele | Irizarry Rafael | Liu Junmin | Maier Donald | Miller Michael | Petersen Kjell | Quackenbush John | Sherlock Gavin | Stoeckert Christian | White Joseph | Whetzel Patricia | Wymore Farrell | Parkinson Helen | Sarkans Ugis | Ball Catherine | Brazma Alvis
The molecular portraits of breast tumors are conserved across microarray platforms

Author(s): Hu Zhiyuan | Fan Cheng | Oh Daniel | Marron JS | He Xiaping | Qaqish Bahjat | Livasy Chad | Carey Lisa | Reynolds Evangeline | Dressler Lynn | Nobel Andrew | Parker Joel | Ewend Matthew | Sawyer Lynda | Wu Junyuan | Liu Yudong | Nanda Rita | Tretiakova Maria | Orrico Alejandra | Dreher Donna | Palazzo Juan | Perreard Laurent | Nelson Edward | Mone Mary | Hansen Heidi | Mullins Michael | Quackenbush John | Ellis Matthew | Olopade Olufunmilayo | Bernard Philip | Perou Charles
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.

Author(s): 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
A robust method for the amplification of RNA in the sense orientation

Author(s): Marko Nicholas | Frank Bryan | Quackenbush John | Lee Norman
Submission of Microarray Data to Public Repositories

Author(s): 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
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

Author(s): 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 | Souza Sandro J. de | Debily Marie-Anne | Devignes Marie-Dominique | Dubchak Inna | Endo Toshinori | Estreicher Anne | Eyras Eduardo | Fukami-Kobayashi Kaoru | R. Gopinath Gopal | 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
Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis

Author(s): Ghedin Elodie | Pumfery Anne | de la Fuente Cynthia | Yao Karen | Miller Naomi | Lacoste Vincent | Quackenbush John | Jacobson Steven | Kashanchi Fatah
The limits of log-ratios

Author(s): Sharov Vasily | Kwong Ka | Frank Bryan | Chen Emily | Hasseman Jeremy | Gaspard Renee | Yu Yan | Yang Ivana | Quackenbush John

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