Lab Meetings and Presentations

Future presentation schedules

Past Presentations

Charles A. Herring, et al, "Unsupervised trajectory analysis of single-cell RNA-seq and imaging data reveals alternate tuft cell origins in the gut"
Tapio Lonnberg, et al, "Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria"
Jinmiao Chen, et al, "Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development"
Eugenio Marco, et al "Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape"

Setty et al, "Wishbone identifies bifurcating developmental trajectories from single-cell data"
11/08/2018BruceClustering of the Self-Organizing Map
11/01/2018CongminAge-related changes in gut microbiota
composition from newborn to centenarian:
a cross-sectional study
10/25/2018MichaelMask R-CNN
10/18/2018BridgetMining TCGA Data Using Boolean Implications
10/11/2018Qispatialde: identification of spatially variable genes
10/04/2018JennyProject Presentation
09/27/2018BruceAutomated identification of stratifying signatures in cellular subpopulation
09/20/2018XingyuThesis Defense Practice
09/13/2018QinweiProject Presentation
09/06/2018PengGDISC extension to methylation and expression
Joshua D. Welch, "SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data"

Ji, "TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis."
Qiu et al, "Reversed graph embedding resolves complex single-cell trajectories"
7/26/2018QinweiDiffusion Pseudo Time (DPT)
Haghverdi, Laleh, et al. “Diffusion pseudotime robustly reconstructs lineage branching.” Nature methods 13.10 (2016): 845.
7/19/2018QiDiffusion 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.
7/11/2018QIPHATE -
06/21QiMAGIC -
06/28QinweimetaVIPER - 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.
06/14/2018QinweiWelch, 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.
6/07/2018BruceHaghverdi, Laleh, et al. “Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.” Nature biotechnology (2018).
5/31/2018QiButler, Andrew, et al. “Integrating single-cell transcriptomic data across different conditions, technologies, and species.” Nature biotechnology (2018).
5/24/2018QinweiSatija, Rahul, et al. “Spatial reconstruction of single-cell gene expression data.” Nature biotechnology 33.5 (2015): 495.
5/17/2018Bruce and QiMacosko et al. “Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.” Cell 161.5 (2015): 1202-1214.
5/10/2018QiscImpute paper from Jessica Li's group at UCLA