PanoView: An Iterative Clustering Approach for Analysis of Single-cell RNA-Sequencing Data
Wen Hu MW, Kim DW, Liu S, Zack DJ, Blackshaw S, and Qian J. PLoS Comp Biol, under revision.
ASCOT identifies key regulators of neuronal subtype-specific RNA splicing
Ling JP, Wilks C, Charles R, Ghosh D, Jiang L, Santiago CP, Pang B, Venkataraman A, Clark BS, Nellore A, Langmead B, and Blackshaw S. bioRxiv 2018, 501882.
Decomposing cell identity for transfer learning across platforms, tissues and species
Stein-O’Brien GL, Clark BS, Sherman T, Hu Q, Sealfon R, Wolf A, Zibetti C, Liu S, Qian J, Colantuoni C, Beer M, Blackshaw S, Goff LA, and Fertig EJ. Cell Systems, in press
A toolbox of immunoprecipitation-grade monoclonal antibodies against human transcription factors
Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang K Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Seva G. Khambadkone5, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Anderson S, Myers RM, Boeke JD, Fenyo D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, and Blackshaw S. Nat Methods 2018 doi: 10.1038/nmeth.4632
BPAC: A universal model for prediction of transcription factor binding sites based on chromatin accessibility
Liu S, Zibetti C, Wan J, Wang G, Blackshaw S, and Qian J. BMC Bioinformatics 2017 18:355.
The NIH Protein Capture Reagents Program (PCRP): a standardized affinity reagent toolbox
Blackshaw S, Anderson S, Campbell E, Freeman N, Gatlin C, Pino I, Zhu H and Bader J. Nat Methods 2016 13:805-6.
A human proteome microarray-based pipeline for efficient production of monospecific monoclonal antibodies
Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu S, Woodard C, Vera C, Bayron-Poueymirou D, Rivera-Pacheco ZA, Ramos L, Torres-Castro C, Bonaventura J, Boeke JD, Pino I, Eichinger DJ, Zhu H and Blackshaw S. Mol Cell Proteomics 2012 11:O111.016253.
Yeast one-hybrid assays for high-throughoutput human gene regulatory network mapping
Barutcu1 AR, Reece-Hoyes JS, McCord RP, Jeong J, Jiang L, MacWilliams A, Yang X, Salehi-Ashtiani K, Hill DE, Blackshaw S, Zhu H, Dekker J and Walhout AJM. Nat Methods 2011 8:1050-2
Three-dimensional rapid diffusion tensor microimaging for anatomical characterization and gene expression mapping in mouse brain
Aggarwal M, Mori S, Shimogori T, Blackshaw S, Zhang J. Magnet Res Med 2010 64:249-61.
hPDI: a database of experimental human protein-DNA interactions
Xie Z, Hu S, Blackshaw S, Zhu H, Qian J. Bioinformatics 2010 26:287-89.