HuBMAP Publications

2020

• Hartmann FJ, Mrdjen D, McCaffrey E, Glass DR, Greenwald NF, Bharadwaj A, Khair Z, Verberk SGS, Baranski A, Baskar R, Graf W, Van Valen D, Van den Bossche J, Angelo M, Bendall SC Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol.(2020), pp.. 08/31/2020, 10.1038/s41587-020-0651-8.
• Keyes TJ, Domizi P, Lo YC, Nolan GP, Davis KL A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. Journal of Quantitative Cell Science.(2020), pp.. 06/30/2020, https://doi.org/10.1002/cyto.a.24158.
• Zafar H, Lin C, Bar-Joseph Z. Single-cell Lineage Tracing by Integrating CRISPR-Cas9 Mutations With Transcriptomic Data. Nature Communications.(2020), pp.3055. 06/16/2020, https://doi.org/10.1038/s41467-020-16821-5.
• Islam M, Chen B, Spraggins JM, Kelly RT, Lau KS. Use of Single Cell -omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. Gastroenterology.(2020), pp.1-14. 05/14/2020, https://doi.org/10.1053/j.gastro.2020.04.073.
• Hurley K, Ding J, Villacorta-Martin C, Herriges MJ, Jacob A, Vedaie M, Alysandratos KD, Sun YL, Lin C, Werder RB, Huang J, Wilson AA, Mithal A, Mostoslavsky G, Oglesby I, Caballero IS, Guttentag SH, Ahangari F, Kaminski N, Rodriguez-Fraticelli A, Camargo F, Bar-Joseph Z, Kotton DN. Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. Cell Stem Cell.(2020), pp.593-608. 04/02/2020, https://doi.org/10.1016/j.stem.2019.12.009.
• Perry WJ, Weiss A, Van de Plas R, Spraggins JM, Caprioli RM, Skaar EP. Integrated molecular imaging technologies for investigation of metals in biological systems: A brief review. Curr Opin Chem Biol..(2020), pp.127-135. 04/01/2020, https://doi:10.1016/j.cbpa.2020.01.008.
• Weber, GM, Ju, Y, Börner K. Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body. Frontiers in Cardiovascular Medicine.(2020), pp.. 03/13/2020, https://doi.org/10.3389/fcvm.2020.00029.
• Tsai AG, Glass DR, Juntilla M, Hartmann FJ, Oak JS, Fernandez-Pol S, Ohgami RS, Bendall SC. Multiplexed single-cell morphometry for hematopathology diagnostics. Nature Medicine.(2020), pp.408–417. 03/11/2020, https://doi.org/10.1038/s41591-020-0783-x.
• Lin C, Ding J, Bar-Joseph Z. Inferring TF activation order in time series scRNA-Seq studies. PLOS Computational Biology.(2020), pp.. 02/18/2020, https://doi.org/10.1371/journal.pcbi.1007644.
• Piehowski PD, Zhu Y, Bramer LM, Stratton KG, Zhao R, Orton DJ, Moore RJ, Yuan J, Mitchell HD, Gao Y, Webb-Robertson BM, Dey SK, Kelly RT, Burnum-Johnson KE. Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution. Nature Communications volume.(2020), pp.. 01/07/2020, https://doi.org/10.1038/s41467-019-13858-z.

2019

• Hartmann FJ, Bendall SC. Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nat Rev Rheumatol.(2019), pp.87-99. 12/31/2019, https://10.1038/s41584-019-0338-z.
• Yuan Y, Bar-Joseph Z. Deep learning for inferring gene relationships from single-cell expression data. PNAS.(2019), pp.27151-27158. 12/26/2019, https://doi.org/10.1073/pnas.1911536116.
• Hafemeister C, Satija R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biology.(2019), pp.. 12/23/2019, https://doi.org/10.1186/s13059-019-1874-1.
• Perry WJ, Patterson NH, Prentice BM, Neumann EK, Caprioli RM, Spraggins JM. Uncovering matrix effects on lipid analyses in MALDI imaging mass spectrometry experiments. Mass Spectrometry.(2019), pp.. 12/20/2019, https://doi.org/doi:%2010.1002/jms.4491.
• Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G, Marioni JC, Regev A, Satija R. Toward a Common Coordinate Framework for the Human Body. Cell.(2019), pp.1455-1467. 12/12/2019, https://doi.org/10.1016/j.cell.2019.11.019.
• Lin C, Bar-Joseph Z. Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data. Bioinformatics.(2019), pp.4707–4715. 11/15/2019, https://doi.org/10.1093/bioinformatics/btz296.
• Yin R, Burnum-Johnson KE, Sun X, Dey SK & Laskin J High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry. Nature Protocols.(2019), pp.3445–3470. 11/13/2019, https://doi.org/10.1038/s41596-019-0237-4.
• Chen S, Lake BB, Zhang K. High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nature Biotechnology.(2019), pp.1452–1457. 10/14/2019, https://doi.org/10.1038/s41587-019-0290-0.
• 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.