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

Differential Exon Analysis

  1. Anders S, Reyes A, Huber W (2012) Detecting differential usage of exons from RNA-seq data. Genome Res 22: 2008–2017. PubMed

Sequence Classification

  1. Han S, Liang Y, Ma Q, Xu Y, Zhang Y, Du W, Wang C, Li Y (2019) LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property. Brief Bioinform 20: 2009–2027. PubMed

Clustering and Network Analysis

  1. 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
  2. Abu-Jamous B, Kelly S (2018) Clust: automatic extraction of optimal co-expressed gene clusters from genhttps://pubmed.ncbi.nlm.nih.gov/30359297/e expression data. Genome Biol 19: 172. PubMed

Embedding of High-dimensional scRNA-Seq Data

  1. 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

ChIP-Seq Peak Callers

  1. 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

Drug-Target Analysis

  1. Chen X, Reynolds CH (2002) Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients. J Chem Inf Comput Sci 42: 1407–1414. PubMed
Last modified 2022-05-24: some edits (faccc5591)