Literature DB >> 16964224

Data quality in genomics and microarrays.

Hanlee Ji1, Ronald W Davis.   

Abstract

Mesh:

Year:  2006        PMID: 16964224      PMCID: PMC2943412          DOI: 10.1038/nbt0906-1112

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  13 in total

1.  Evaluation of gene expression measurements from commercial microarray platforms.

Authors:  Paul K Tan; Thomas J Downey; Edward L Spitznagel; Pin Xu; Dadin Fu; Dimiter S Dimitrov; Richard A Lempicki; Bruce M Raaka; Margaret C Cam
Journal:  Nucleic Acids Res       Date:  2003-10-01       Impact factor: 16.971

2.  Are data from different gene expression microarray platforms comparable?

Authors:  Anna-Kaarina Järvinen; Sampsa Hautaniemi; Henrik Edgren; Petri Auvinen; Janna Saarela; Olli-P Kallioniemi; Outi Monni
Journal:  Genomics       Date:  2004-06       Impact factor: 5.736

Review 3.  Maximizing the potential of functional genomics.

Authors:  Lars M Steinmetz; Ronald W Davis
Journal:  Nat Rev Genet       Date:  2004-03       Impact factor: 53.242

Review 4.  In control: systematic assessment of microarray performance.

Authors:  Harm van Bakel; Frank C P Holstege
Journal:  EMBO Rep       Date:  2004-10       Impact factor: 8.807

5.  Multiple-laboratory comparison of microarray platforms.

Authors:  Rafael A Irizarry; Daniel Warren; Forrest Spencer; Irene F Kim; Shyam Biswal; Bryan C Frank; Edward Gabrielson; Joe G N Garcia; Joel Geoghegan; Gregory Germino; Constance Griffin; Sara C Hilmer; Eric Hoffman; Anne E Jedlicka; Ernest Kawasaki; Francisco Martínez-Murillo; Laura Morsberger; Hannah Lee; David Petersen; John Quackenbush; Alan Scott; Michael Wilson; Yanqin Yang; Shui Qing Ye; Wayne Yu
Journal:  Nat Methods       Date:  2005-04-21       Impact factor: 28.547

6.  Immune signatures in follicular lymphoma.

Authors:  Robert Tibshirani
Journal:  N Engl J Med       Date:  2005-04-07       Impact factor: 91.245

7.  The External RNA Controls Consortium: a progress report.

Authors:  Shawn C Baker; Steven R Bauer; Richard P Beyer; James D Brenton; Bud Bromley; John Burrill; Helen Causton; Michael P Conley; Rosalie Elespuru; Michael Fero; Carole Foy; James Fuscoe; Xiaolian Gao; David Lee Gerhold; Patrick Gilles; Federico Goodsaid; Xu Guo; Joe Hackett; Richard D Hockett; Pranvera Ikonomi; Rafael A Irizarry; Ernest S Kawasaki; Tamma Kaysser-Kranich; Kathleen Kerr; Gretchen Kiser; Walter H Koch; Kathy Y Lee; Chunmei Liu; Z Lewis Liu; Anne Lucas; Chitra F Manohar; Garry Miyada; Zora Modrusan; Helen Parkes; Raj K Puri; Laura Reid; Thomas B Ryder; Marc Salit; Raymond R Samaha; Uwe Scherf; Timothy J Sendera; Robert A Setterquist; Leming Shi; Richard Shippy; Jesus V Soriano; Elizabeth A Wagar; Janet A Warrington; Mickey Williams; Frederike Wilmer; Mike Wilson; Paul K Wolber; Xiaoning Wu; Renata Zadro
Journal:  Nat Methods       Date:  2005-10       Impact factor: 28.547

8.  The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Authors:  Leming Shi; Laura H Reid; Wendell D Jones; Richard Shippy; Janet A Warrington; Shawn C Baker; Patrick J Collins; Francoise de Longueville; Ernest S Kawasaki; Kathleen Y Lee; Yuling Luo; Yongming Andrew Sun; James C Willey; Robert A Setterquist; Gavin M Fischer; Weida Tong; Yvonne P Dragan; David J Dix; Felix W Frueh; Frederico M Goodsaid; Damir Herman; Roderick V Jensen; Charles D Johnson; Edward K Lobenhofer; Raj K Puri; Uwe Schrf; Jean Thierry-Mieg; Charles Wang; Mike Wilson; Paul K Wolber; Lu Zhang; Shashi Amur; Wenjun Bao; Catalin C Barbacioru; Anne Bergstrom Lucas; Vincent Bertholet; Cecilie Boysen; Bud Bromley; Donna Brown; Alan Brunner; Roger Canales; Xiaoxi Megan Cao; Thomas A Cebula; James J Chen; Jing Cheng; Tzu-Ming Chu; Eugene Chudin; John Corson; J Christopher Corton; Lisa J Croner; Christopher Davies; Timothy S Davison; Glenda Delenstarr; Xutao Deng; David Dorris; Aron C Eklund; Xiao-hui Fan; Hong Fang; Stephanie Fulmer-Smentek; James C Fuscoe; Kathryn Gallagher; Weigong Ge; Lei Guo; Xu Guo; Janet Hager; Paul K Haje; Jing Han; Tao Han; Heather C Harbottle; Stephen C Harris; Eli Hatchwell; Craig A Hauser; Susan Hester; Huixiao Hong; Patrick Hurban; Scott A Jackson; Hanlee Ji; Charles R Knight; Winston P Kuo; J Eugene LeClerc; Shawn Levy; Quan-Zhen Li; Chunmei Liu; Ying Liu; Michael J Lombardi; Yunqing Ma; Scott R Magnuson; Botoul Maqsodi; Tim McDaniel; Nan Mei; Ola Myklebost; Baitang Ning; Natalia Novoradovskaya; Michael S Orr; Terry W Osborn; Adam Papallo; Tucker A Patterson; Roger G Perkins; Elizabeth H Peters; Ron Peterson; Kenneth L Philips; P Scott Pine; Lajos Pusztai; Feng Qian; Hongzu Ren; Mitch Rosen; Barry A Rosenzweig; Raymond R Samaha; Mark Schena; Gary P Schroth; Svetlana Shchegrova; Dave D Smith; Frank Staedtler; Zhenqiang Su; Hongmei Sun; Zoltan Szallasi; Zivana Tezak; Danielle Thierry-Mieg; Karol L Thompson; Irina Tikhonova; Yaron Turpaz; Beena Vallanat; Christophe Van; Stephen J Walker; Sue Jane Wang; Yonghong Wang; Russ Wolfinger; Alex Wong; Jie Wu; Chunlin Xiao; Qian Xie; Jun Xu; Wen Yang; Liang Zhang; Sheng Zhong; Yaping Zong; William Slikker
Journal:  Nat Biotechnol       Date:  2006-09       Impact factor: 54.908

9.  Independence and reproducibility across microarray platforms.

Authors:  Jennie E Larkin; Bryan C Frank; Haralambos Gavras; Razvan Sultana; John Quackenbush
Journal:  Nat Methods       Date:  2005-04-21       Impact factor: 28.547

10.  Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains.

Authors:  Robert G Eason; Nader Pourmand; Waraporn Tongprasit; Zelek S Herman; Kevin Anthony; Olufisayo Jejelowo; Ronald W Davis; Viktor Stolc
Journal:  Proc Natl Acad Sci U S A       Date:  2004-07-16       Impact factor: 11.205

View more
  9 in total

1.  The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Authors:  Leming Shi; Laura H Reid; Wendell D Jones; Richard Shippy; Janet A Warrington; Shawn C Baker; Patrick J Collins; Francoise de Longueville; Ernest S Kawasaki; Kathleen Y Lee; Yuling Luo; Yongming Andrew Sun; James C Willey; Robert A Setterquist; Gavin M Fischer; Weida Tong; Yvonne P Dragan; David J Dix; Felix W Frueh; Frederico M Goodsaid; Damir Herman; Roderick V Jensen; Charles D Johnson; Edward K Lobenhofer; Raj K Puri; Uwe Schrf; Jean Thierry-Mieg; Charles Wang; Mike Wilson; Paul K Wolber; Lu Zhang; Shashi Amur; Wenjun Bao; Catalin C Barbacioru; Anne Bergstrom Lucas; Vincent Bertholet; Cecilie Boysen; Bud Bromley; Donna Brown; Alan Brunner; Roger Canales; Xiaoxi Megan Cao; Thomas A Cebula; James J Chen; Jing Cheng; Tzu-Ming Chu; Eugene Chudin; John Corson; J Christopher Corton; Lisa J Croner; Christopher Davies; Timothy S Davison; Glenda Delenstarr; Xutao Deng; David Dorris; Aron C Eklund; Xiao-hui Fan; Hong Fang; Stephanie Fulmer-Smentek; James C Fuscoe; Kathryn Gallagher; Weigong Ge; Lei Guo; Xu Guo; Janet Hager; Paul K Haje; Jing Han; Tao Han; Heather C Harbottle; Stephen C Harris; Eli Hatchwell; Craig A Hauser; Susan Hester; Huixiao Hong; Patrick Hurban; Scott A Jackson; Hanlee Ji; Charles R Knight; Winston P Kuo; J Eugene LeClerc; Shawn Levy; Quan-Zhen Li; Chunmei Liu; Ying Liu; Michael J Lombardi; Yunqing Ma; Scott R Magnuson; Botoul Maqsodi; Tim McDaniel; Nan Mei; Ola Myklebost; Baitang Ning; Natalia Novoradovskaya; Michael S Orr; Terry W Osborn; Adam Papallo; Tucker A Patterson; Roger G Perkins; Elizabeth H Peters; Ron Peterson; Kenneth L Philips; P Scott Pine; Lajos Pusztai; Feng Qian; Hongzu Ren; Mitch Rosen; Barry A Rosenzweig; Raymond R Samaha; Mark Schena; Gary P Schroth; Svetlana Shchegrova; Dave D Smith; Frank Staedtler; Zhenqiang Su; Hongmei Sun; Zoltan Szallasi; Zivana Tezak; Danielle Thierry-Mieg; Karol L Thompson; Irina Tikhonova; Yaron Turpaz; Beena Vallanat; Christophe Van; Stephen J Walker; Sue Jane Wang; Yonghong Wang; Russ Wolfinger; Alex Wong; Jie Wu; Chunlin Xiao; Qian Xie; Jun Xu; Wen Yang; Liang Zhang; Sheng Zhong; Yaping Zong; William Slikker
Journal:  Nat Biotechnol       Date:  2006-09       Impact factor: 54.908

2.  A ratiometric lectin microarray approach to analysis of the dynamic mammalian glycome.

Authors:  Kanoelani T Pilobello; Deepika E Slawek; Lara K Mahal
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-02       Impact factor: 11.205

3.  BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.

Authors:  Archana N Rao; David W Grainger
Journal:  Biomater Sci       Date:  2014-04-01       Impact factor: 6.843

4.  PCR-free quantification of multiple splice variants in a cancer gene by surface-enhanced Raman spectroscopy.

Authors:  Lan Sun; Joseph Irudayaraj
Journal:  J Phys Chem B       Date:  2009-10-22       Impact factor: 2.991

5.  Development of Potential Pharmacodynamic and Diagnostic Markers for Anti-IFN-α Monoclonal Antibody Trials in Systemic Lupus Erythematosus.

Authors:  Yihong Yao; Brandon W Higgs; Chris Morehouse; Melissa de Los Reyes; Wendy Trigona; Philip Brohawn; Wendy White; Jianliang Zhang; Barbara White; Anthony J Coyle; Peter A Kiener; Bahija Jallal
Journal:  Hum Genomics Proteomics       Date:  2009-11-17

6.  Detecting and correcting systematic variation in large-scale RNA sequencing data.

Authors:  Sheng Li; Paweł P Łabaj; Paul Zumbo; Peter Sykacek; Wei Shi; Leming Shi; John Phan; Po-Yen Wu; May Wang; Charles Wang; Danielle Thierry-Mieg; Jean Thierry-Mieg; David P Kreil; Christopher E Mason
Journal:  Nat Biotechnol       Date:  2014-08-24       Impact factor: 54.908

7.  Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples.

Authors:  Xiaoqiang Sun; Ji Zhang; Qing Nie
Journal:  PLoS Comput Biol       Date:  2021-03-05       Impact factor: 4.475

8.  Quality control in microarray assessment of gene expression in human airway epithelium.

Authors:  Tina Raman; Timothy P O'Connor; Neil R Hackett; Wei Wang; Ben-Gary Harvey; Marc A Attiyeh; David T Dang; Matthew Teater; Ronald G Crystal
Journal:  BMC Genomics       Date:  2009-10-24       Impact factor: 3.969

9.  Gene expression profiling for molecular distinction and characterization of laser captured primary lung cancers.

Authors:  Astrid Rohrbeck; Judith Neukirchen; Michael Rosskopf; Guillermo G Pardillos; Helene Geddert; Andreas Schwalen; Helmut E Gabbert; Arndt von Haeseler; Gerald Pitschke; Matthias Schott; Ralf Kronenwett; Rainer Haas; Ulrich-Peter Rohr
Journal:  J Transl Med       Date:  2008-11-07       Impact factor: 5.531

  9 in total

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