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Paul Spellman

Research Profile

Devices

Oligonucleotide Array Sequence Analysis

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Gene Expression Profiling

Disorders

Anatomy

Tumor Cell Line

Physiology

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Chemicals & Drugs

RNA, Messenger

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Genes & Molecular Sequences

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Saccharomyces cerevisiae

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TOP 3
Anguraj Sadanandam; Gary Scott; Paul Spellman; Fred Waldman; Stephen C Benz; Serenella Eppenberger-Castori; Joe W Gray; Aseem Lal; Christopher C Benz
Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells?
Steven M Hill; Yiling Lu; Gordon B Mills; Jennifer Molina; Joe W Gray; Laura M Heiser; Terence P Speed; Paul Spellman; Sach Mukherjee
Bayesian inference of signaling network topology in a cancer cell line.
Eric A Collisson; David Dankort; Joe W Gray; Shenda Gu; Byron Hann; Laura M Heiser; James E Korkola; Wayne A Phillips; Brian A Rabinovich; Jillian M Silva; Paul Spellman; Christy L Trejo; Roch-Philippe Charles; Martin McMahon
A central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma.

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2012: Anguraj Sadanandam; Gary Scott; Paul Spellman; Fred Waldman; Stephen C Benz; Serenella Eppenberger-Castori; Joe W Gray; Aseem Lal; Christopher C Benz
Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells?
Breast cancer research and treatment 2012;136(3):693-703.
2012: Steven M Hill; Yiling Lu; Gordon B Mills; Jennifer Molina; Joe W Gray; Laura M Heiser; Terence P Speed; Paul Spellman; Sach Mukherjee
Bayesian inference of signaling network topology in a cancer cell line.
Bioinformatics (Oxford, England) 2012;28(21):2804-10.
2012: Eric A Collisson; David Dankort; Joe W Gray; Shenda Gu; Byron Hann; Laura M Heiser; James E Korkola; Wayne A Phillips; Brian A Rabinovich; Jillian M Silva; Paul Spellman; Christy L Trejo; Roch-Philippe Charles; Martin McMahon
A central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma.
Cancer discovery 2012;2(8):685-93.
2012: Ellen Ordinario; Francis Rodier; Paul Spellman; Mina J Bissell; Judith Campisi; Saori Furuta; Joe W Gray; Hye-Jung Han; Laura M Heiser; Lakshmi R Jakkula; Yoshinori Kohwi; Terumi Kohwi-Shigematsu
ATM suppresses SATB1-induced malignant progression in breast epithelial cells.
PloS one 2012;7(12):e51786.
2012: Steven M Hill; Wen-Lin Kuo; Nora Bayani; Joe W Gray; Richard M Neve; Paul Spellman; Safiyyah Ziyad; Sach Mukherjee
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology.
BMC bioinformatics 2012;13():94.
2011: Adam B Olshen; Richard A Olshen; Henrik Bengtsson; Pierre Neuvial; Paul Spellman; Venkatraman E Seshan
Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.
Bioinformatics (Oxford, England) 2011;27(15):2038-46.
2011: Paul Spellman; Joe Gray
A new treasure in the breast cancer gene hunt.
Nature medicine 2011;17(4):422-3.
2011: Eric A Collisson; Anguraj Sadanandam; Peter Olson; William J Gibb; Morgan Truitt; Shenda Gu; Janine Cooc; Jennifer Weinkle; Grace E Kim; Lakshmi Jakkula; Heidi S Feiler; Andrew H Ko; Adam B Olshen; Kathleen L Danenberg; Margaret A Tempero; Paul Spellman; Douglas Hanahan; Joe Gray
Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy.
Nature medicine 2011;17(4):500-3.
2011: Nima Nabavizadeh; C Klifa; David Newitt; Ying Lu; Yunn-Yi Chen; Howard Hsu; Clark Fisher; Taku Tokayasu; Adam B Olshen; Paul Spellman; Joe Gray; Nola M Hylton; Catherine Park
Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI.
Integrative biology : quantitative biosciences from nano to macro 2011;3(4):490-6.
2011: Hang Chang; Ge Cong; Gerald V Fontenay; Joe W Gray; Ju Han; Frederick L Baehner; Paul Spellman; Bahram Parvin
Morphometic analysis of TCGA glioblastoma multiforme.
BMC bioinformatics 2011;12():484.
2011: Xin Victoria Wang; Roel G W Verhaak; Elizabeth Purdom; Paul Spellman; Terence P Speed
Unifying gene expression measures from multiple platforms using factor analysis.
PloS one 2011;6(3):e17691.
2010: Shivani Nautiyal; Victoria E H Carlton; Yontao Lu; James S Ireland; Diane Flaucher; Martin Moorhead; Joe Gray; Paul Spellman; Michael Mindrinos; Paul Berg; Malek Faham
High-throughput method for analyzing methylation of CpGs in targeted genomic regions.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(28):12587-92.
2010: Anna Lapuk; Henry Marr; Lakshmi Jakkula; Helder Pedro; Sanchita Bhattacharya; Elizabeth Purdom; Zhi Hu; Ken Simpson; Lior Pachter; Steffen Durinck; Nicholas Wang; Bahram Parvin; Gerald Fontenay; Terence P Speed; James Garbe; Martha Stampfer; Hovig Bayandorian; Shannon Dorton; Tyson A Clark; Anthony Schweitzer; Andrew Wyrobek; Heidi Feiler; Paul Spellman; John G Conboy; Joe Gray
Exon-level microarray analyses identify alternative splicing programs in breast cancer.
Molecular cancer research : MCR 2010;8(7):961-74.
2010: Thomas J Hudson; Warwick Anderson; Axel Artez; Anna D Barker; Cindy Bell; Rosa R Bernabé; M K Bhan; Fabien Calvo; Iiro Eerola; Daniela S Gerhard; Alan Guttmacher; Mark Guyer; Fiona M Hemsley; Jennifer L Jennings; David Kerr; Peter Klatt; Patrik Kolar; Jun Kusada; David P Lane; Frank Laplace; Lu Youyong; Gerd Nettekoven; Brad Ozenberger; Jane Peterson; T S Rao; Jacques Remacle; Alan J Schafer; Tatsuhiro Shibata; Michael R Stratton; Joseph G Vockley; Koichi Watanabe; Huanming Yang; Matthew M F Yuen; Bartha M Knoppers; Martin Bobrow; Anne Cambon-Thomsen; Lynn G Dressler; Stephanie O M Dyke; Yann Joly; Kazuto Kato; Karen L Kennedy; Pilar Nicolás; Michael J Parker; Emmanuelle Rial-Sebbag; Carlos M Romeo-Casabona; Kenna M Shaw; Susan Wallace; Georgia L Wiesner; Nikolajs Zeps; Peter Lichter; Andrew V Biankin; Christian Chabannon; Lynda Chin; Bruno Clément; Enrique de Alava; Françoise Degos; Martin L Ferguson; Peter Geary; D Neil Hayes; Thomas J Hudson; Amber L Johns; Arek Kasprzyk; Hidewaki Nakagawa; Robert J Penny; Miguel A Piris; Rajiv Sarin; Aldo Scarpa; Tatsuhiro Shibata; Marc van de Vijver; P Andrew Futreal; Hiroyuki Aburatani; Mónica Bayés; David D L Botwell; Peter J Campbell; Xavier Estivill; Daniela S Gerhard; Sean M Grimmond; Ivo Gut; Martin Hirst; Carlos López-Otín; Partha Majumder; Marco Marra; John D McPherson; Hidewaki Nakagawa; Zemin Ning; Xose S Puente; Yijun Ruan; Tatsuhiro Shibata; Michael R Stratton; Hendrik G Stunnenberg; Harold Swerdlow; Victor E Velculescu; Richard K Wilson; Hong H Xue; Liu Yang; Paul Spellman; Gary D Bader; Paul C Boutros; Peter J Campbell; Paul Flicek; Gad Getz; Roderic Guigó; Guangwu Guo; David Haussler; Simon Heath; Tim J Hubbard; Tao Jiang; Steven M Jones; Qibin Li; Nuria López-Bigas; Ruibang Luo; Lakshmi Muthuswamy; B F Francis Ouellette; John Pearson; Xose S Puente; Victor Quesada; Benjamin J Raphael; Chris Sander; Tatsuhiro Shibata; Terence P Speed; Lincoln D Stein; Joshua M Stuart; Jon W Teague; Yasushi Totoki; Tatsuhiko Tsunoda; Alfonso Valencia; David A Wheeler; Honglong Wu; Shancen Zhao; Guangyu Zhou; Lincoln D Stein; Roderic Guigó; Tim J Hubbard; Yann Joly; Steven M Jones; Arek Kasprzyk; Mark Lathrop; Nuria López-Bigas; B F Francis Ouellette; Paul T Spellman; Jon W Teague; Gilles Thomas; Alfonso Valencia; Teruhiko Yoshida; Karen L Kennedy; Myles Axton; Stephanie O M Dyke; P Andrew Futreal; Daniela S Gerhard; Chris Gunter; Mark Guyer; Thomas J Hudson; John D McPherson; Linda J Miller; Brad Ozenberger; Kenna M Shaw; Arek Kasprzyk; Lincoln D Stein; Junjun Zhang; Syed A Haider; Jianxin Wang; Christina K Yung; Anthony Cross; Yong Liang; Saravanamuttu Gnaneshan; Jonathan Guberman; Jack Hsu; Martin Bobrow; Don R C Chalmers; Karl W Hasel; Yann Joly; Terry S H Kaan; Karen L Kennedy; Bartha M Knoppers; William W Lowrance; Tohru Masui; Pilar Nicolás; Emmanuelle Rial-Sebbag; Laura Lyman Rodriguez; Catherine Vergely; Teruhiko Yoshida; Sean M Grimmond; Andrew V Biankin; David D L Bowtell; Nicole Cloonan; Anna deFazio; James R Eshleman; Dariush Etemadmoghadam; Brooke A Gardiner; James G Kench; Aldo Scarpa; Robert L Sutherland; Margaret A Tempero; Nicola J Waddell; Peter J Wilson; John D McPherson; Steve Gallinger; Ming-Sound Tsao; Patricia A Shaw; Gloria M Petersen; Debabrata Mukhopadhyay; Lynda Chin; Ronald A DePinho; Sarah Thayer; Lakshmi Muthuswamy; Kamran Shazand; Timothy Beck; Michelle Sam; Lee Timms; Vanessa Ballin; Youyong Lu; Jiafu Ji; Xiuqing Zhang; Feng Chen; Xueda Hu; Guangyu Zhou; Qi Yang; Geng Tian; Lianhai Zhang; Xiaofang Xing; Xianghong Li; Zhenggang Zhu; Yingyan Yu; Jun Yu; Huanming Yang; Mark Lathrop; Jörg Tost; Paul Brennan; Ivana Holcatova; David Zaridze; Alvis Brazma; Lars Egevard; Egor Prokhortchouk; Rosamonde Elizabeth Banks; Mathias Uhlén; Anne Cambon-Thomsen; Juris Viksna; Fredrik Ponten; Konstantin Skryabin; Michael R Stratton; P Andrew Futreal; Ewan Birney; Ake Borg; Anne-Lise Børresen-Dale; Carlos Caldas; John A Foekens; Sancha Martin; Jorge S Reis-Filho; Andrea L Richardson; Christos Sotiriou; Hendrik G Stunnenberg; Giles Thoms; Marc van de Vijver; Laura van't Veer; Fabien Calvo; Daniel Birnbaum; Hélène Blanche; Pascal Boucher; Sandrine Boyault; Christian Chabannon; Ivo Gut; Jocelyne D Masson-Jacquemier; Mark Lathrop; Iris Pauporté; Xavier Pivot; Anne Vincent-Salomon; Eric Tabone; Charles Theillet; Gilles Thomas; Jörg Tost; Isabelle Treilleux; Fabien Calvo; Paulette Bioulac-Sage; Bruno Clément; Thomas Decaens; Françoise Degos; Dominique Franco; Ivo Gut; Marta Gut; Simon Heath; Mark Lathrop; Didier Samuel; Gilles Thomas; Jessica Zucman-Rossi; Peter Lichter; Roland Eils; Benedikt Brors; Jan O Korbel; Andrey Korshunov; Pablo Landgraf; Hans Lehrach; Stefan Pfister; Bernhard Radlwimmer; Guido Reifenberger; Michael D Taylor; Christof von Kalle; Partha P Majumder; Rajiv Sarin; T S Rao; M K Bhan; Aldo Scarpa; Paolo Pederzoli; Rita A Lawlor; Massimo Delledonne; Alberto Bardelli; Andrew V Biankin; Sean M Grimmond; Thomas Gress; David S Klimstra; Giuseppe Zamboni; Tatsuhiro Shibata; Yusuke Nakamura; Hidewaki Nakagawa; Jun Kusada; Tatsuhiko Tsunoda; Satoru Miyano; Hiroyuki Aburatani; Kazuto Kato; Akihiro Fujimoto; Teruhiko Yoshida; Elias Campo; Carlos López-Otín; Xavier Estivill; Roderic Guigó; Silvia de Sanjosé; Miguel A Piris; Emili Montserrat; Marcos González-Díaz; Xose S Puente; Pedro Jares; Alfonso Valencia; Heinz Himmelbaue; Victor Quesada; Silvia Bea; Michael R Stratton; P Andrew Futreal; Peter J Campbell; Anne Vincent-Salomon; Andrea L Richardson; Jorge S Reis-Filho; Marc van de Vijver; Gilles Thomas; Jocelyne D Masson-Jacquemier; Samuel Aparicio; Ake Borg; Anne-Lise Børresen-Dale; Carlos Caldas; John A Foekens; Hendrik G Stunnenberg; Laura van't Veer; Douglas F Easton; Paul T Spellman; Sancha Martin; Anna D Barker; Lynda Chin; Francis S Collins; Carolyn Corlies Compton; Martin L Ferguson; Daniela S Gerhard; Gad Getz; Chris Gunter; Alan Guttmacher; Mark Guyer; D Neil Hayes; Eric S Lander; Brad Ozenberger; Robert Penny; Jane Peterson; Chris Sander; Kenna M Shaw; Terence P Speed; Paul T Spellman; Joseph G Vockley; David A Wheeler; Richard K Wilson; Thomas J Hudson; Lynda Chin; Bartha M Knoppers; Eric S Lander; Peter Lichter; Lincoln D Stein; Michael R Stratton; Warwick Anderson; Anna D Barker; Cindy Bell; Martin Bobrow; Wylie Burke; Francis S Collins; Carolyn C Compton; Ronald A DePinho; Douglas F Easton; P Andrew Futreal; Daniela S Gerhard; Anthony R Green; Mark Guyer; Stanley R Hamilton; Tim J Hubbard; Olli P Kallioniemi; Karen L Kennedy; Timothy J Ley; Edison T Liu; Youyong Lu; Partha Majumder; Marco Marra; Brad Ozenberger; Jane Peterson; Alan J Schafer; Paul T Spellman; Hendrik G Stunnenberg; Brandon J Wainwright; Richard K Wilson; Anthony Cros; Brooke B Gardiner; Heinz Himmelbauer; Huanming Yang
International network of cancer genome projects.
Nature 2010;464(7291):993-8.
2010: Roel G W Verhaak; Katherine A Hoadley; Elizabeth Purdom; Victoria Wang; Yuan Qi; Matthew D Wilkerson; Ryan Miller; Li Ding; Todd Golub; Jill P Mesirov; Gabriele Alexe; Michael Lawrence; Michael O'Kelly; Pablo Tamayo; Barbara A Weir; Stacey Gabriel; Wendy Winckler; Supriya Gupta; Lakshmi Jakkula; Heidi S Feiler; J Graeme Hodgson; C David James; Jann N Sarkaria; Cameron Brennan; Ari Kahn; Paul Spellman; Richard K Wilson; Terence P Speed; Joe Gray; Matthew Meyerson; Gad Getz; Charles M Perou; David Hayes
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.
Cancer cell 2010;17(1):98-110.
2010: Leandro A Loss; Anguraj Sadanandam; Steffen Durinck; Shivani Nautiyal; Diane Flaucher; Victoria E H Carlton; Martin Moorhead; Yontao Lu; Joe Gray; Malek Faham; Paul Spellman; Bahram Parvin
Prediction of epigenetically regulated genes in breast cancer cell lines.
BMC bioinformatics 2010;11():305.
2009: J Graeme Hodgson; Ru-Fang Yeh; Amrita Ray; Nicholas J Wang; Ivan Smirnov; Mamie Yu; Sujatmi Hariono; Joachim Silber; Heidi S Feiler; Joe Gray; Paul Spellman; Scott R Vandenberg; Mitchel S Berger; C David James
Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts.
Neuro-oncology 2009;11(5):477-87.
2009: Henrik Bengtsson; Amrita Ray; Paul Spellman; Terence P Speed
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.
Bioinformatics (Oxford, England) 2009;25(7):861-7.
2009: Olga K Mirzoeva; Debopriya Das; Laura M Heiser; Sanchita Bhattacharya; Doris Siwak; Rina Gendelman; Nora Bayani; Nicholas J Wang; Richard M Neve; Yinghui Guan; Zhi Hu; Zachary A Knight; Heidi S Feiler; Philippe Gascard; Bahram Parvin; Paul Spellman; Kevan M Shokat; Andrew J Wyrobek; Mina J Bissell; Frank McCormick; Wen-Lin Kuo; Gordon B Mills; Joe Gray; W Michael Korn
Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition.
Cancer research 2009;69(2):565-72.
2009: Sach Mukherjee; Steven Pelech; Richard M Neve; Wen-Lin Kuo; Safiyyah Ziyad; Paul Spellman; Joe Gray; Terence P Speed
Sparse combinatorial inference with an application in cancer biology.
Bioinformatics (Oxford, England) 2009;25(2):265-71.
2009: Wen-Lin Kuo; Debopriya Das; Safiyyah Ziyad; Sanchita Bhattacharya; William J Gibb; Laura M Heiser; Anguraj Sadanandam; Gerald V Fontenay; Zhi Hu; Nicholas J Wang; Nora Bayani; Heidi S Feiler; Richard M Neve; Andrew J Wyrobek; Paul Spellman; Laurence J Marton; Joe Gray
A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047.
BMC medicine 2009;7():77.
2009: Steffen Durinck; Paul Spellman; Ewan Birney; Wolfgang Huber
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Nature protocols 2009;4(8):1184-91.
2009: Laura M Heiser; Nicholas J Wang; Carolyn L Talcott; Keith R Laderoute; Merrill Knapp; Yinghui Guan; Zhi Hu; Safiyyah Ziyad; Barbara L Weber; Sylvie Laquerre; Jeffrey R Jackson; Richard F Wooster; Wen Lin Kuo; Joe Gray; Paul Spellman
Integrated analysis of breast cancer cell lines reveals unique signaling pathways.
Genome biology 2009;10(3):R31.
2009: Yuker Wang; Victoria E H Carlton; George Karlin-Neumann; Ronald Sapolsky; Li Zhang; Martin Moorhead; Zhigang C Wang; Andrea L Richardson; Robert Warren; Axel Walther; Melissa Bondy; Aysegul Sahin; Ralf Krahe; Musaffe Tuna; Patricia A Thompson; Paul Spellman; Joe Gray; Gordon B Mills; Malek Faham
High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays.
BMC medical genomics 2009;2():8.
2009: Steffen Durinck; James Bullard; Paul Spellman; Sandrine Dudoit
GenomeGraphs: integrated genomic data visualization with R.
BMC bioinformatics 2009;10():2.
2008: Lindsay A Brown; Steve Kalloger; Melinda A Miller; Ie-Ming Shih; Steven E McKinney; Jennifer L Santos; Ken Swenerton; Paul Spellman; Joe Gray; C Blake Gilks; David Huntsman
Amplification of 11q13 in ovarian carcinoma.
Genes, chromosomes & cancer 2008;47(6):481-9.
2008: Joshua Z Press; Alessandro De Luca; Niki Boyd; Sean Young; Armelle Troussard; Yolanda Ridge; Pardeep Kaurah; Steve Kalloger; Katherine A Blood; Margaret Smith; Paul Spellman; Yuker Wang; Dianne M Miller; Douglas E Horsman; Malek Faham; C Blake Gilks; Joe Gray; David Huntsman
Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities.
BMC cancer 2008;8():17.
2007: Andrew R Jones; Michael Miller; Ruedi Aebersold; Rolf Apweiler; Catherine A Ball; Alvis Brazma; James Degreef; Nigel Hardy; Henning Hermjakob; Simon Hubbard; Peter Hussey; Mark Igra; Helen Jenkins; Randall K Julian; Kent Laursen; Stephen G Oliver; Norman W Paton; Susanna-Assunta Sansone; Ugis Sarkans; Christian J Stoeckert; Christopher Taylor; Patricia L Whetzel; Joseph A White; Paul Spellman; Angel Pizarro
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Nature biotechnology 2007;25(10):1127-33.
2007: Paraic Kenny; Genee Y Lee; connie anne myers; Richard M Neve; Jeremy R Semeiks; Paul Spellman; Katrin Lorenz; Eva H Lee; Mary Helen Barcellos-Hoff; Ole W Petersen; Joe Gray; Mina J Bissell
The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression.
Molecular oncology 2007;1(1):84-96.
2007: Yuker Wang; Martin Moorhead; George Karlin-Neumann; Nicholas J Wang; James Ireland; Steven Lin; Chunnuan Chen; Laura M Heiser; Koei Chin; Laura Esserman; Joe Gray; Paul Spellman; Malek Faham
Analysis of molecular inversion probe performance for allele copy number determination.
Genome biology 2007;8(11):R246.
2006: Koei Chin; Sandy Devries; Jane Fridlyand; Paul Spellman; Ritu Roydasgupta; Wen-Lin Kuo; Anna Lapuk; Richard M Neve; Zuwei Qian; Tom Ryder; Fanqing Chen; Heidi Feiler; Taku Tokuyasu; Christopher Kingsley; Shanaz H Dairkee; Zhenhang Meng; Karen L Chew; Daniel Pinkel; Ajay Jain; Britt-Marie Ljung; Laura Esserman; Donna G Albertson; Frederic M Waldman; Joe Gray
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies.
Cancer cell 2006;10(6):529-41.
2006: Richard M Neve; Koei Chin; Jane Fridlyand; Jennifer Yeh; Frederick L Baehner; Tea Fevr; Laura Clark; Nora Bayani; Jean-Philippe Coppe; Frances Tong; Terence P Speed; Paul Spellman; Sandy Devries; Anna Lapuk; Nick J Wang; Wen-Lin Kuo; Jackie L Stilwell; Daniel Pinkel; Donna G Albertson; Frederic M Waldman; Frank McCormick; Robert B Dickson; Michael D Johnson; Marc Lippman; Stephen Ethier; Adi F Gazdar; Joe Gray
A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.
Cancer cell 2006;10(6):515-27.
2006: Sylvain Brun; Sheila Vidal; Paul Spellman; Kuniaki Takahashi; Hervé Tricoire; Bruno Lemaitre
The MAPKKK Mekk1 regulates the expression of Turandot stress genes in response to septic injury in Drosophila.
Genes to cells : devoted to molecular & cellular mechanisms 2006;11(4):397-407.
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: 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: Andrew R Jones; Angel Pizarro; Paul Spellman; Michael Miller
FuGE: Functional Genomics Experiment Object Model.
Omics : a journal of integrative biology 2006;10(2):179-84.
2005: Paul Spellman
A status report on MAGE.
Bioinformatics (Oxford, England) 2005;21(17):3459-60.
2005: nicolas vodovar; Marisa Vinals; Peter Liehl; Alan Basset; Jeril Degrouard; Paul Spellman; Frédéric Boccard; Bruno Lemaitre
Drosophila host defense after oral infection by an entomopathogenic Pseudomonas species.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(32):11414-9.
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: 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: Paul Spellman; Gavin Sherlock
Final words: cell age and cell cycle are unlinked.
Trends in biotechnology 2004;22(6):277-8.
2004: Paul Spellman; Gavin Sherlock
Reply: whole-culture synchronization - effective tools for cell cycle studies.
Trends in biotechnology 2004;22(6):270-3.
2003: Lori Ann Pile; Paul Spellman; Rebeccah J Katzenberger; David A Wassarman
The SIN3 deacetylase complex represses genes encoding mitochondrial proteins: implications for the regulation of energy metabolism.
The Journal of biological chemistry 2003;278(39):37840-8.
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: 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: Paul Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Design and implementation of microarray gene expression markup language (MAGE-ML).
Genome biology 2002;3(9):RESEARCH0046.
2002: Ennio De Gregorio; Paul Spellman; Phoebe Tzou; Gerald M Rubin; Bruno Lemaitre
The Toll and Imd pathways are the major regulators of the immune response in Drosophila.
The EMBO journal 2002;21(11):2568-79.
2002: Paul Spellman; Gerald M Rubin
Evidence for large domains of similarly expressed genes in the Drosophila genome.
Journal of biology 2002;1(1):5.
2001: Paul Spellman
The future of publishing microarray data.
Briefings in bioinformatics 2001;2(4):316-8.
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: Ennio De Gregorio; Paul Spellman; Gerald M Rubin; Bruno Lemaitre
Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(22):12590-5.
2001: Reed A George; J P Woolley; Paul Spellman
Ceramic capillaries for use in microarray fabrication.
Genome research 2001;11(10):1780-3.
2001: Gavin Sherlock; Tina Hernandez-Boussard; A Kasarskis; Gail Binkley; John Matese; Selina S Dwight; Miroslava Kaloper; Shuai Weng; Heng Jin; Catherine A Ball; Michael B Eisen; Paul Spellman; Patrick O Brown; David Botstein; J Michael Cherry
The Stanford Microarray Database.
Nucleic acids research 2001;29(1):152-5.
2000: Audrey P Gasch; Paul Spellman; C M Kao; O Carmel-Harel; Michael B Eisen; Gisela Storz; David Botstein; Patrick O Brown
Genomic expression programs in the response of yeast cells to environmental changes.
Molecular biology of the cell 2000;11(12):4241-57.
2000: G Zhu; Paul Spellman; Tom Volpe; Patrick O Brown; David Botstein; Trisha Davis; Bruce Futcher
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth.
Nature 2000;406(6791):90-4.
2000: Douglas T Ross; Uwe Scherf; Michael B Eisen; Charles M Perou; C Rees; Paul Spellman; V Iyer; Stefanie S Jeffrey; Matt van de Rijn; Mark Waltham; A Pergamenschikov; JC Lee; DA Lashkari; D Shalon; Timothy G Myers; John N Weinstein; David Botstein; Patrick O Brown
Systematic variation in gene expression patterns in human cancer cell lines.
Nature genetics 2000;24(3):227-35.
1998: Michael B Eisen; Paul Spellman; Patrick O Brown; David Botstein
Cluster analysis and display of genome-wide expression patterns.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(25):14863-8.
1998: Paul Spellman; Gavin Sherlock; M Q Zhang; Vishwanath R Iyer; K Anders; Michael B Eisen; Patrick O Brown; David Botstein; Bruce Futcher
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
Molecular biology of the cell 1998;9(12):3273-97.