publications.md

Publications

List of reference papers in Computational Biology.

This is a list of publications (or other links) that I use as reference in my research.

A. Academic publications

1A. Bioconductor:

Two main academic papers describing Bioconductor

• 1.1 Original description written when the project was initiated:
  Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biology. 2004 ;5(10):R80.

• 1.2 Update. Future prospects in Bioconductor:
  Huber et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 2015; 12, 115–121.

2A. GRanges / IRanges

• Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118.

3A. Reproducible Research

• Peng. Reproducible Research in Computational Science. Science. 2011; 334(6060) 1226-1227

4A. Batch effects

• Leek JT, Scharpf RB, Corrada Bravo H, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly Km, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Reviews Genetics 11, (2010) 733-739

5A. DNA algorithms

• 5.1 Boyer-Moore: the benchmark for exact matching algorithm.
  Boyer RS, Moore JS. A fast string searching algorithm. Communications of the ACM, (1977) 762-772 doi:10.1145/359842.359859 https://www.cs.utexas.edu/~moore/publications/fstrpos.pdf
• 5.2 Li L, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform. 11, (2010) 473-483 http://www.ncbi.nlm.nih.gov/pubmed/20460430
• Gusfield, D. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. ISBN-13: 978-0521585194 http://www.amazon.com/Algorithms-Strings-Trees-Sequences-Computational/dp/0521585198

B. Reference Links

• Free Science Data Books by William Chen @wzchen
• Bioconductor for Genomic Data Science by Kasper Daniel Hansen @kasperdhansen
• Data Analysis for Genomics This is based on the the PH525 series by Rafael A Irizarry, Michael Love and the the PH525x team from Dana Farber & Harvard School Public Health. http://genomicsclass.github.io/book/
• Plots to avoid:** http://genomicsclass.github.io/book/pages/plots_to_avoid.html

C. Books

Some important books available online for free:

• R for Data Science by Hadley Wickham. Get the book here or read it for free
• Advanced R by Hadley Wickham. Get the book here or read it for free.
• R packages by Hadley Wickham. Get the book here or read it for free.
• Happy Git and GitHub for the useR by Jenny Bryan. Read the book.
• Text Mining with R by Julia Silge and David Robinson. Read the book .

D. R packages

• h-index over years. My first R package. Plotting the h-index over years for a given author.
• Swirl Courses