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This is a website for organizing my reading notes of research papers and a few books.
If you have any question about this project, please feel free to contact me: Qian Feng, fengq2@student.unimelb.edu.au.
Paper review
general review papers
Huson 2011
- A survey of combinatorial methods for phylogenetic networks. Huson and Scornavacca, Genome Biol. Evol.2011.
- Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017387/pdf/evq077.pdf
- Note: link
David A.Morrison 2014
- Phylogenetic networks: a review of methods to display evolutionary history David A.Morrison, Annual Research and Review in Biology, 2014
- Paper: http://www.journalrepository.org/media/journals/ARRB_32/2014/Jan/Morrison4102013ARRB8230_1.pdf
- Note: link
Identify recombination
Average PAC likelihood using SNPs
- Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165.4 (2003): 2213-2233.Na Li and Matthew Stephens..
- Paper: http://www.genetics.org/content/genetics/165/4/2213.full.pdf
- Note: link
Integrative Software RDP
- RDP4: Detection and analysis of recombination patterns in virus genomes Virus Evolution, 1(1),(2015)Martin, D. P., Murrell, B., Golden, M., Khoosal, A., & Muhire, B.
- Paper: https://academic.oup.com/ve/article/1/1/vev003/2568683
- Software: http://web.cbio.uct.ac.za/~darren/RDP4Manual.pdf
- Note: link
Lower and upper bound on minimum recombination number
- Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Song, Yun S., Yufeng Wu, and Dan Gusfield. Bioinformatics 21.suppl_1 (2005): i413-i422.
- Paper: https://academic.oup.com/bioinformatics/article/21/suppl_1/i413/203304
- Note: link
Recombination estmation using HMM and PAC
- Hypervariable antigen genes in malaria have ancient roots. Zilversmit, Martine M., et al. BMC evolutionary biology 13.1 (2013): 110..
- Paper: https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-13-110
- Note: link
- Practice:link
Phylogenetic Network construction
Algorithm from a given MUL tree
- Reconstructing the evolutionary history of polyploid from multilabeled trees. Huber, Katharina T, et al. Molecular Biology and Evolution 23.9 (2006): 1784-1791.
- Paper: https://academic.oup.com/mbe/article/23/9/1784/1014292
- Note: link
Joint Baysian Estimation of Alignment and Phylogeny
- 1.Joint Bayesian estimation of alignment and phylogeny. Redelings, Benjamin D., and Marc A. Suchard. Systematic biology 54.3 (2005): 401-418.
- Paper: https://academic.oup.com/sysbio/article/54/3/401/1727336
Note: link
- 2.BayesCAT: Bayesian co‐estimation of alignment and tree. Shim, Heejung, and Bret Larget. Biometrics (2017).
- Paper: https://heejungshim.org/research/#BayesCAT
Note: link
Var biology background knowledge
- 1.Ape parasite origins of human malaria virulence genes. Larremore, D. B. et al. Nat. Commun. 6:8368 doi: 10.1038/ncomms9368 (2015)
- Paper: https://www.nature.com/articles/ncomms9368.pdf
Note: link
- 2.Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer. Rask, Thomas S., et al.PLoS computational biology 6.9 (2010): e1000933.
- Paper: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000933
Note: link
Magic Algorithms
MCMC
- Understanding the metropolis-hastings algorithm. Chib, Siddhartha, and Edward Greenberg.The american statistician 49.4 (1995): 327-335.
- Paper: http://www2.stat.duke.edu/~scs/Courses/Stat376/Papers/Basic/ChibGreenberg1995.pdf
- Note: link
- Random walk example: link
- Simulated annealing: link
- A short and useful video:Gibbs sampling
HMM and PHMM model
Book Review
Book Cover
Plot tools
Computer science
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