Student Paper Presentations

2 minute read

Overview

Each student has been assigned one journal publication to present in class. The expected structure of the paper presentations is outlined in this Slideshow Template. A detailed presentation schedule is available on the internal Course Schedule. The following lists the assigned papers organized by course project topics.

Publications organized by course projects

All references in Paperpile

RNA-Seq Aligners

  1. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12: 357–360. PubMed

DEG Methods

  1. Zhou X, Lindsay H, Robinson MD (2014) Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Res 42: e91. PubMed
  2. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550. PubMed

Clustering and Network Analysis

  1. Langfelder P, Luo R, Oldham MC, Horvath S (2011) Is my network module preserved and reproducible? PLoS Comput Biol 7: e1001057. PubMed
  2. Rodriguez MZ, Comin CH, Casanova D, Bruno OM, Amancio DR, Costa L da F, Rodrigues FA (2019) Clustering algorithms: A comparative approach. PLoS One 14: e0210236. PubMed

Embedding of High-dimensional scRNA-Seq Data

  1. Shulse CN, Cole BJ, Ciobanu D, Lin J, Yoshinaga Y, Gouran M, Turco GM, Zhu Y, O’Malley RC, Brady SM, et al (2019) High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types. Cell Rep 27: 2241–2247.e4. PubMed
  2. Sun S, Zhu J, Ma Y, Zhou X (2019) Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis. Genome Biol 20: 269. PubMed
  3. McInnes L, Healy J, Melville J (2018) UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. arXiv

ChIP-Seq Peak Callers

  1. Wilbanks EG, Facciotti MT (2010) Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One. doi: 10.1371/journal.pone.0011471. PubMed
  2. Feng J, Liu T, Qin B, Zhang Y, Liu XS (2012) Identifying ChIP-seq enrichment using MACS. Nat Protoc 7: 1728–1740. PubMed

Functional Enrichment Analysis

  1. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545–15550. PubMed

Motif Enrichment Analysis

  1. McLeay, Robert C, and Timothy L Bailey. 2010. “Motif Enrichment Analysis: A Unified Framework and an Evaluation on ChIP Data.” BMC Bioinformatics 11: 165. PubMed

Programmable Genome Summary Graphics

  1. Zhang H, Meltzer P, Davis S (2013) RCircos: an R package for Circos 2D track plots. BMC Bioinformatics 14: 244–244. PubMed
Last modified 2021-04-27: some edits (a9ca982b8)