Our Publications
2020 |
- Zafar H, Lin C, Bar-Joseph Z. Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data. Nat Commun. 2020;11(1):3055. Published 2020 Jun 16. doi: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), doi: https://doi.org/10.1053/j.gastro.2020.04.073.
- Dong R, Yuan GC. GiniClust3: a fast and memory-efficient tool for rare cell type identification. BMC Bioinformatics. 2020;21(1):158. Published 2020 Apr 25. doi:10.1186/s12859-020-3482-1
- Hurley K, Ding J, Villacorta-Martin C, et al. Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. Cell Stem Cell. 2020;26(4):593-608.e8. doi: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: Current Opinion in Chemical Biology, Volume 55, 2020, Pages 127-135, ISSN 1367-5931, https://doi.org/10.1016/j.cbpa.2020.01.008.
- Weber GM, Ju Y and Börner K (2020) Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body. Front. Cardiovasc. Med. 7:29. doi: 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 volume 26, pages408–417(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 Comput Biol. 2020;16(2):e1007644. Published 2020 Feb 18. doi: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 11, Article number: 8 (2020) https://doi.org/10.1038/s41467-019-13858-z.
- Sahaf B., Rahman A., Maecker H.T., Bendall S.C. (2020) High-Parameter Immune Profiling with CyTOF. In: Thurin M., Cesano A., Marincola F. (eds) Biomarkers for Immunotherapy of Cancer. Methods in Molecular Biology, vol 2055. Humana, New York, NY
2019 |
- Hartmann FJ, Bendall SC. Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nature Reviews Rheumatology volume 16, pages87–99(2020). https://doi.org/10.1038/s41584-019-0338-z.
- Yuan Y, Bar-Joseph Z. Deep learning for inferring gene relationships from single-cell expression data Proceedings of the National Academy of Sciences Dec 2019, 116 (52) 27151-27158; DOI: 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 volume 20, Article number: 296 (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. J Mass Spectrom. 2020; 55:e4491. https://doi.org/10.1002/jms.4491
- Rood JE, Stuart T, Ghazanfar S, et al. Toward a Common Coordinate Framework for the Human Body Cell. 2019;179(7):1455-1467. doi:10.1016/j.cell.2019.11.019
- Chen S, Lake BB, Zhang K. High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell Nature Biotechnology volume 37, pages1452–1457(2019) https://doi.org/10.1038/s41587-019-0290-0.
- 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 volume 14, pages3445–3470(2019) https://doi.org/10.1038/s41596-019-0237-4.
- Lin C, Bar-Joseph Z. Continuous-state HMMs for modeling time-series single-cell RNA-Seq data. Bioinformatics. 2019;35(22):4707-4715. doi:10.1093/bioinformatics/btz296
- Verbeeck N, Caprioli RM, Van de Plas R. Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. Mass Spectrom Rev. 2020;39(3):245-291. doi:10.1002/mas.21602.
- HuBMAP Consortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 2019;574(7777):187-192. doi:10.1038/s41586-019-1629-x