title: Epigraph: A Vaccine Design Tool Applied to an HIV Therapeutic Vaccine and a Pan-Filovirus Vaccine.
abstract: Epigraph is an efficient graph-based algorithm for designing vaccine antigens to optimize potential T-cell epitope (PTE) coverage. Epigraph vaccine antigens are functionally similar to Mosaic vaccines, which have demonstrated effectiveness in preliminary HIV non-human primate studies. In contrast to the Mosaic algorithm, Epigraph is substantially faster, and in restricted cases, provides a mathematically optimal solution. Epigraph furthermore has new features that enable enhanced vaccine design flexibility. These features include the ability to exclude rare epitopes from a design, to optimize population coverage based on inexact epitope matches, and to apply the code to both aligned and unaligned input sequences. Epigraph was developed to provide practical design solutions for two outstanding vaccine problems. The first of these is a personalized approach to a therapeutic T-cell HIV vaccine that would provide antigens with an excellent match to an individual's infecting strain, intended to contain or clear a chronic infection. The second is a pan-filovirus vaccine, with the potential to protect against all known viruses in the Filoviradae family, including ebolaviruses. A web-based interface to run the Epigraph tool suite is available (http://www.hiv.lanl.gov/content/sequence/EPIGRAPH/epigraph.html).
authors.affiliation: Los Alamos National Laboratory, Los Alamos, NM 87545, USA.|New Mexico Consortium, Los Alamos, NM 87544, USA.
authors.forename: James
authors.initials: J
authors.lastname: Theiler
authors.affiliation: Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: Hyejin
authors.initials: H
authors.lastname: Yoon
authors.affiliation: Los Alamos National Laboratory, Los Alamos, NM 87545, USA.|New Mexico Consortium, Los Alamos, NM 87544, USA.
authors.forename: Karina
authors.initials: K
authors.lastname: Yusim
authors.affiliation: Oregon Health and Science University, Portland, OR 97239, USA.
authors.forename: Louis J
authors.initials: LJ
authors.lastname: Picker
authors.affiliation: Oregon Health and Science University, Portland, OR 97239, USA.
authors.forename: Klaus
authors.initials: K
authors.lastname: Fruh
authors.affiliation: Los Alamos National Laboratory, Los Alamos, NM 87545, USA.|New Mexico Consortium, Los Alamos, NM 87544, USA.
authors.forename: Bette
authors.initials: B
authors.lastname: Korber
mesh_terms: D016915:AIDS Vaccines / Q000235:genetics / Q000276:immunology; D000939:Epitopes / Q000235:genetics / Q000276:immunology; D016563:Filoviridae / Q000235:genetics / Q000276:immunology; D018702:Filoviridae Infections / Q000235:genetics / Q000276:immunology / Q000628:therapy; D015658:HIV Infections / Q000235:genetics / Q000276:immunology / Q000628:therapy; D015497:HIV-1 / Q000235:genetics / Q000276:immunology; D006801:Humans; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D016915:AIDS Vaccines; D000939:Epitopes