Phylogenetic dependency networks: Inferring patterns of adaptation in HIV

Phylogenetic dependency networks: Inferring patterns of adaptation in HIV (2009)

Cached

Download Links

by Jonathan M. Carlson

Citations:

BibTeX

@MISC{Carlson09phylogeneticdependency,
    author = {Jonathan M. Carlson},
    title = {Phylogenetic dependency networks: Inferring patterns of adaptation in HIV},
    year = {2009}
}

Bookmark

OpenURL

Abstract

Citations

6234	Maximum likelihood from incomplete data via the EM algorithm - Dempster, Laird, et al. - 1977
1393	Controlling the false discovery rate: a practical and powerful approach to multiple testing - Benjamini, Hochberg - 1995
711	A tutorial on learning with Bayesian networks - Heckerman - 1998
541	Evolutionary trees from DNA sequences: a maximum likelihood approach - Felsenstein - 1981
508	PHYLIP (Phylogeny Inference Package) version 3.6, version - Felsenstein
400	A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood - Guindon, Gascuel - 2003
215	Inference of population structure using multilocus genotype data. Genetics. 2000;155: 945–59 - JK, Stephens, et al.
186	Inferring Phylogenies Sinauer Associates - Felsenstein - 2004
184	Tibshirani R: Statistical significance for genomewide studies - JD
152	Gojobori T. Simple methods for estimating the number of synonymous and nonsynonymous substitutions. Mol Biol Evol - Nei - 1986
122	K.: Dependency Networks for Inference, Collaborative Filtering, and Data Visualization - Heckerman, Chickering, et al.
100	Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929–936 - Nielsen, Yang - 1998
86	A direct approach to false discovery rates - JD
74	Phylogenies and the comparative method - Felsenstein - 1985
70	Genomic control for association studies - Devlin, Roeder - 1999
64	The comparative method in evolutionary biology - Harvey, Pagel - 1991
54	L: A stochastic process approach to false discovery control. The Annals of Statistics 2004 - Genovese, Wasserman
51	Ranganathan R: Evolutionarily conserved pathways of energetic connectivity in protein families - SW - 1999
51	Donnelly P: Association mapping in structured populations - JK, Stephens, et al.
44	PLINK: a toolset for whole-genome association and population-based linkage analyses - Purcell, Neale, et al. - 2007
37	Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus - Borrow, Lewicki, et al. - 1997
37	Effective use of sequence correlation and conservation in fold recognition - Olmea, Rost, et al. - 1999
35	The positive false discovery rate: A Bayesian interpretation and the q-value - JD - 2003
32	Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters - Pagel - 1994
28	Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection - Shankarappa, Margolick, et al. - 1999
27	Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904–909 - AL, NJ, et al. - 2006
26	Teukolsky S, Vetterling W, Flannery B - Press - 1992
24	JD: Plant pathogens and integrated defence responses to infection - JL, Jones
23	D: Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach - JD, JE, et al.
22	The Comparative Method in Evolutionary Biology: Oxford University Press. 235 p - PH, MD - 1991
22	How frequent are correlated changes in families of protein sequences - Neher - 1994
21	Assessing the impact of population stratification on genetic association studies - Freedman, Reich, et al. - 2004
20	L: Genomic control, a new approach to genetic-based association studies. Theoretical Population Biology 2001 - Devlin, Roeder, et al.
20	AIDS epidemic update - UNAIDSWHO - 2007
19	Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am Nat 149: 646–667 - Martins, Hansen - 1997
19	Compensating changes in protein multiple sequence alignments. Protein Eng 7 - WR, Hatrick - 1994
19	epidemic update - AIDS - 2007
18	Felsenstein J: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol - MK - 1994
18	Searching for genetic determinants in the new millennium. Nature 405: 847–856 - NJ - 2000
18	ES: A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 2006 - JM, Pressoir, et al.
17	T: Timing the ancestor of the HIV-1 pandemic strains - Korber, Muldoon, et al.
16	Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes. Science 283: 857–860 - JE, MJ, et al. - 1999
15	2005a). Expectation maximization and complex duration distributions for continuous time Bayesian networks - Nodelman, Shelton, et al.
15	Coevolving protein residues: Maximum likelihood identification and relationship to structure - DD, WR, et al. - 1999
14	Influence of conservation on calculations of amino acid covariance in multiple sequence alignments - Fodor, Aldrich - 2004
14	Diversity considerations in HIV-1 vaccine selection - Gaschen, Taylor, et al. - 2002
14	Storey JD: Capturing heterogeneity in gene expression studies by surrogate variable analysis - JT
14	MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat Genet 36: 512–517 - Marchini, LR, et al.
14	Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection - Jr, KM, et al. - 1998
14	Liang K: Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under non-standard conditions - SG - 1987