Editorial: The Future of Publishing Microarray Data. - Paul T. Spellman (Briefings Bioinform., 2001)

The Stanford Microarray Database. - Gavin Sherlock; Tina Hernandez-Boussard; Andrew Kasarskis; Gail Binkley; John C. Matese; Selina S. Dwight; Miroslava Kaloper; Shuai Weng; Heng Jin; Catherine A. Ball; Michael B. Eisen; Paul T. Spellman; et al. (Nucleic Acids Res., 2001)

An open letter to the scientific journals. - Catherine A. Ball; Gavin Sherlock; Helen E. Parkinson; Philippe Rocca-Serra; Catherine Brooksbank; Helen C. Causton; Duccio Cavalieri; Terry Gaasterland; Pascal Hingamp; Frank C. P. Holstege; Martin Ringwald; Paul T. Spellman; et al. (Bioinform., 2002)

A Status Report on Mage. - Paul T. Spellman (Bioinform., 2005)

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. - Tim F. Rayner; Philippe Rocca-Serra; Paul T. Spellman; Helen C. Causton; Anna Farne; Ele Holloway; Rafael A. Irizarry; Junmin Liu; Donald Maier; Michael Miller 001; Kjell Petersen; John Quackenbush; et al. (BMC Bioinform., 2006)

Spectral Decomposition of Signaling Networks. - Bahram Parvin; Nirmalya Ghosh; Laura Heiser; Merrill Knapp; Carolyn L. Talcott; Keith Laderoute; Joe W. Gray; Paul T. Spellman (CIBCB, 2007)

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. - Henrik Bengtsson; Amrita Ray; Paul T. Spellman; Terence P. Speed (Bioinform., 2009)

Sparse combinatorial inference with an application in cancer biology. - Sach Mukherjee; Steven Pelech; Richard M. Neve; Wen-Lin Kuo; Safiyyah Ziyad; Paul T. Spellman; Joe W. Gray; Terence P. Speed (Bioinform., 2009)

GenomeGraphs: integrated genomic data visualization with R. - Steffen Durinck; James H. Bullard; Paul T. Spellman; Sandrine Dudoit (BMC Bioinform., 2009)

Prediction of epigenetically regulated genes in breast cancer cell lines. - Leandro A. Loss; Anguraj Sadanandam; Steffen Durinck; Shivani Nautiya; Diane Flaucher; Victoria E. H. Carlton; Martin Moorhead; Yontao Lu; Joe W. Gray; Malek Faham; Paul T. Spellman; Bahram Parvin (BMC Bioinform., 2010)

Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma multiforme. - Ju Han; Hang Chang; Leandro A. Loss; Kai Zhang 001; Frederick L. Baehner; Joe W. Gray; Paul T. Spellman; Bahram Parvin (ISBI, 2011)

Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. - Adam B. Olshen; Henrik Bengtsson; Pierre Neuvial; Paul T. Spellman; Richard A. Olshen; Venkatraman E. Seshan (Bioinform., 2011)

Morphometic analysis of TCGA glioblastoma multiforme. - Hang Chang; Gerald Fontenay; Ju Han; Ge Cong; Frederick L. Baehner; Joe W. Gray; Paul T. Spellman; Bahram Parvin (BMC Bioinform., 2011)

Batch-invariant nuclear segmentation in whole mount histology sections. - Hang Chang; Leandro A. Loss; Paul T. Spellman; Alexander Borowsky; Bahram Parvin (ISBI, 2012)

Molecular bases of morphometric composition in Glioblastoma multiforme. - Ju Han; Hang Chang; Gerald Fontenay; Paul T. Spellman; Alexander Borowsky; Bahram Parvin (ISBI, 2012)

Learning invariant features of tumor signatures. - Quoc V. Le; Ju Han; Joe W. Gray; Paul T. Spellman; Alexander Borowsky; Bahram Parvin (ISBI, 2012)

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line. - Steven M. Hill; Yiling Lu; Jennifer Molina; Laura Heiser; Paul T. Spellman; Terence P. Speed; Joe W. Gray; Gordon B. Mills; Sach Mukherjee (Bioinform., 2012)

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. - Steven M. Hill; Richard M. Neve; Nora Bayani; Wen-Lin Kuo; Safiyyah Ziyad; Paul T. Spellman; Joe W. Gray; Sach Mukherjee (BMC Bioinform., 2012)

Multireference Level Set for the Characterization of Nuclear Morphology in Glioblastoma Multiforme. - Hang Chang; Ju Han; Paul T. Spellman; Bahram Parvin (IEEE Trans. Biomed. Eng., 2012)

Classification of Tumor Histology via Morphometric Context. - Hang Chang; Alexander Borowsky; Paul T. Spellman; Bahram Parvin (CVPR, 2013)

Stacked Predictive Sparse Coding for Classification of Distinct Regions in Tumor Histopathology. - Hang Chang; Yin Zhou; Paul T. Spellman; Bahram Parvin (ICCV, 2013)

Classification of tumor histopathology via sparse feature learning. - Nandita Nayak; Hang Chang; Alexander Borowsky; Paul T. Spellman; Bahram Parvin (ISBI, 2013)

Characterization of Tissue Histopathology via Predictive Sparse Decomposition and Spatial Pyramid Matching. - Hang Chang; Nandita Nayak; Paul T. Spellman; Bahram Parvin (MICCAI (2), 2013)

Methods and challenges in timing chromosomal abnormalities within cancer samples. - Elizabeth Purdom; Christine Ho; Catherine S. Grasso; Michael Quist; Raymond J. Cho; Paul T. Spellman (Bioinform., 2013)

Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association. - Hang Chang; Ju Han; Alexander Borowsky; Leandro A. Loss; Joe W. Gray; Paul T. Spellman; Bahram Parvin (IEEE Trans. Medical Imaging, 2013)

Classification of Histology Sections via Multispectral Convolutional Sparse Coding. - Yin Zhou; Hang Chang; Kenneth E. Barner; Paul T. Spellman; Bahram Parvin (CVPR, 2014)

Predictive sparse morphometric context for classification of histology sections. - Hang Chang; Paul T. Spellman; Bahram Parvin (ISBI, 2015)

Stacked Predictive Sparse Decomposition for Classification of Histology Sections. - Hang Chang; Yin Zhou; Alexander Borowsky; Kenneth E. Barner; Paul T. Spellman; Bahram Parvin (Int. J. Comput. Vis., 2015)

The evolutionary history of 2,658 cancers. - Moritz Gerstung; Clemency Jolly; Ignaty Leshchiner; Stefan C. Dentro; Santiago Gonzalez; Thomas J. Mitchell; Yulia Rubanova; Pavana Anur; Kaixian Yu; Maxime Tarabichi; Amit G. Deshwar; Jeff Wintersinger; et al. (Nat., 2020)

Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. - Özgün Babur; Augustin Luna; Anil Korkut; Funda Durupinar; Metin Can Siper; Ugur Dogrusoz; Alvaro Sebastian Vaca Jacome; Ryan Peckner; Karen E. Christianson; Jacob D. Jaffe; Paul T. Spellman; Joseph E. Aslan; et al. (Patterns, 2021)

Supervised learning of high-confidence phenotypic subpopulations from single-cell data. - Tao Ren; Canping Chen; Alexey V. Danilov; Susan Liu; Xiangnan Guan; Shunyi Du; Xiwei Wu; Mara H. Sherman; Paul T. Spellman; Lisa M. Coussens; Andrew C. Adey; Gordon B. Mills; et al. (Nat. Mac. Intell., 2023)

Author Correction: Supervised learning of high-confidence phenotypic subpopulations from single-cell data. - Tao Ren; Canping Chen; Alexey V. Danilov; Susan Liu; Xiangnan Guan; Shunyi Du; Xiwei Wu; Mara H. Sherman; Paul T. Spellman; Lisa M. Coussens; Andrew C. Adey; Gordon B. Mills; et al. (Nat. Mac. Intell., 2023)