2019
- Verbeeck N, Caprioli RM, Van de Plas R. Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. Screen reader support enabled. Mass Spectrom Rev.(2019), pp.245-291. 10/11/2019, https://doi.org/10.1002/mas.21602.
- Spraggins JM, Djambazova KV, Rivera ES, Migas LG, Neumann EK, Fuetterer A, Suetering J, Goedecke N, Ly A, Van de Plas R, Caprioli RM. High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry. Analytical Chemistry.(2019), pp.14552–14560. 10/08/2019, https://doi.org/10.1021/acs.analchem.9b03612.
- Dong R, Yuan GC. GiniClust3: a fast and memory-efficient tool for rare cell type identification. BMC Bioinormatics.(2019), pp.. 10/07/2019, 10.1186/s12859-020-3482-1.
- Sahaf B, Rahman A, Maecker HT, Bendall SC. High-Parameter Immune Profiling with CyTOF. Biomarkers for Immunotherapy of Cancer.(2019), pp.351–368. 09/10/2019, https://doi.org/10.1007/978-1-4939-9773-2_16.
- Pliner HA, Shendure J, Trapnell C. Supervised classification enables rapid annotation of cell atlases. Nature Methods.(2019), pp.983–986. 09/10/2019, https://doi.org/10.1038/s41592-019-0535-3.
- McFaline-Figueroa JL, Hill AJ, Qiu X, Jackson D, Shendure J, Trapnell C. A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. Nature Genetics.(2019), pp.1389–1398. 09/02/2019, https://doi.org/10.1038/s41588-019-0489-5.
- Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P. Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. Nature Biotechnology.(2019), pp.1080–1090. 08/19/2019, https://doi.org/10.1038/s41587-019-0207-y.
- Rockne RC, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, Macklin P, Hormuth DA, Jarrett AM, Lima EABF, Tinsley Oden J, Biros G, Yankeelov TE, Curtius K, Al Bakir I, Wodarz D, Komarova N, Aparicio L, Bordyuh M, Rabadan R, Finley SD, Enderling H, Caudell J, et al. The 2019 mathematical oncology roadmap. Physical Biology.(2019), pp.. 06/19/2019, https://doi.org/10.1088/1478-3975/ab1a09.
- Ryan DJ, Patterson NH, Putnam NE, Wilde AD, Weiss A, Perry WJ, Cassat JE, Skaar EP, Caprioli RM, Spraggins JM. MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies.. Anal Chem..(2019), pp.7578-7585. 06/18/2019, 10.1021/acs.analchem.8b05889.
- HuBMAP Consortium The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Quantitative Biology.(2019), pp.. 06/07/2019, https://10.1038/s41586-019-1629-x.
- Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R. Comprehensive Integration of Single-Cell Data. Cell.(2019), pp.1888-1902. 06/06/2019, https://doi.org/10.1016/j.cell.2019.05.031.
- Ding J, Lin C, Bar-Joseph Z. Cell lineage inference from SNP and scRNA-Seq data. Nucleic Acids Research.(2019), pp.. 06/04/2019, https://doi.org/10.1093/nar/gkz146.
- Ginda M, Richey MC, Cousino M, Börner K. Visualizing learner engagement, performance, and trajectories to evaluate and optimize online course design. PLOS One.(2019), pp.. 05/06/2019, https://doi.org/10.1371/journal.pone.0215964.
- Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P. SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nature Methods.(2019), pp.533–544. 05/01/2019, https://doi.org/10.1038/s41592-019-0404-0.
- Spraggins JM, Schwamborn K, Heeren RMA, Eberlin LS. The Importance of Clinical Tissue Imaging. Clin Mass Spectrom.(2019), pp.47-49. 04/19/2019, https://doi.org/10.1016/j.clinms.2019.04.001.
- Prentice BM, Hart NJ, Phillips N, Haliyur R, Judd A, Armandala R, Spraggins JM, Lowe CL, Boyd KL, Stein RW, Wright CV, Norris JL, Powers AC, Brissova M, Caprioli RM. Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. Diabetologia.(2019), pp.1036-1047. 04/06/2019, https://doi.org/10.1007/s00125-019-4855-8.
- Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature.(2019), pp.235-239. 03/25/2019, https://doi.org/10.1038/s41586-019-1049-y.
- Prentice BM, McMillen JC, Caprioli RM Multiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry. Int J Mass Spectrom ..(2019), pp.30-37. 03/01/2019, https://10.1016/j.ijms.2018.06.006.
- Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C & Shendure J The single-cell transcriptional landscape of mammalian organogenesis. Nature.(2019), pp.496–502. 02/20/2019, https://doi.org/10.1038/s41586-019-0969-x.
- Rashid S, Shah S, Bar-Joseph Z, Pandya R. Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data. Bioinformatics.(2019), pp.. 02/15/2019, https://doi.org/10.1101/183863.
