Future presentation schedules
Past Presentations
| Date | Presenter | Content |
|---|---|---|
| Charles A. Herring, et al, "Unsupervised trajectory analysis of single-cell RNA-seq and imaging data reveals alternate tuft cell origins in the gut" | ||
| GPFates Tapio Lonnberg, et al, "Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria" |
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| Mpath Jinmiao Chen, et al, "Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development" |
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| SCUBA Eugenio Marco, et al "Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape" |
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| STREAM http://stream.pinellolab.org/ https://www.biorxiv.org/content/early/2018/04/18/302554.1 |
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| Wishbone Setty et al, "Wishbone identifies bifurcating developmental trajectories from single-cell data" |
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| 11/15/2018 | Bruce | |
| 11/08/2018 | Bruce | Clustering of the Self-Organizing Map |
| 11/01/2018 | Congmin | Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study |
| 10/25/2018 | Michael | Mask R-CNN |
| 10/18/2018 | Bridget | Mining TCGA Data Using Boolean Implications |
| 10/11/2018 | Qi | spatialde: identification of spatially variable genes |
| 10/04/2018 | Jenny | Project Presentation |
| 09/27/2018 | Bruce | Automated identification of stratifying signatures in cellular subpopulation |
| 09/20/2018 | Xingyu | Thesis Defense Practice |
| 09/13/2018 | Qinwei | Project Presentation |
| 09/06/2018 | Peng | GDISC extension to methylation and expression |
| 08/16/2018 | Qinwei | SLICER Joshua D. Welch, "SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data" |
| 08/09/2018 | Qi | TSCAN Ji, "TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis." |
| 8/02/2018 | Bruce | Monocle2 Qiu et al, "Reversed graph embedding resolves complex single-cell trajectories" |
| 7/26/2018 | Qinwei | Diffusion Pseudo Time (DPT) Haghverdi, Laleh, et al. “Diffusion pseudotime robustly reconstructs lineage branching.” Nature methods 13.10 (2016): 845. |
| 7/19/2018 | Qi | Diffusion Map Haghverdi, Laleh, Florian Buettner, and Fabian J. Theis. “Diffusion maps for high-dimensional single-cell analysis of differentiation data.” Bioinformatics 31.18 (2015): 2989-2998. |
| 7/11/2018 | QI | PHATE - https://www.biorxiv.org/content/early/2017/12/01/120378 |
| 06/21 | Qi | MAGIC - https://www.biorxiv.org/content/early/2017/02/25/111591 |
| 06/28 | Qinwei | metaVIPER - Ding, Hongxu, et al. “Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.” Nature communications 9.1 (2018): 1471. |
| 06/14/2018 | Qinwei | Welch, Joshua D., Alexander J. Hartemink, and Jan F. Prins. “MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.” Genome biology 18.1 (2017): 138. |
| 6/07/2018 | Bruce | Haghverdi, Laleh, et al. “Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.” Nature biotechnology (2018). |
| 5/31/2018 | Qi | Butler, Andrew, et al. “Integrating single-cell transcriptomic data across different conditions, technologies, and species.” Nature biotechnology (2018). |
| 5/24/2018 | Qinwei | Satija, Rahul, et al. “Spatial reconstruction of single-cell gene expression data.” Nature biotechnology 33.5 (2015): 495. |
| 5/17/2018 | Bruce and Qi | Macosko et al. “Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.” Cell 161.5 (2015): 1202-1214. |
| 5/10/2018 | Qi | scImpute paper from Jessica Li's group at UCLA |