Emory University

Beckman Coulter, Inc.

Beth Israel Deaconess Medical Center, Inc.

Pharmasset, Inc.

Agencourt Bioscience Corporation

Erik Alan Gustafson

Raymond F Schinazi

Junxing Shi

Jiuliu Lu

Zihua Wang

John Riley

Antonio Arevalo Reyes

Joyce D Fingeroth

Kevin J McKernan

Adrianne D Brand

A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element, a plurality of second input values associated with a second genetic element, and a plurality of third input values associated with a third genetic element associated with a plurality of samples. The method also includes determining a threshold value associated with the third genetic element, separating the samples using the threshold value into a first set of samples and a second set of samples, clustering the first set of samples in a feature space defined by the first genetic element and the second genetic element, defining a first boundary space using the first set of samples, and defining a second boundary space using the second set of samples.

Systems and methods for detecting the presence of a biological status using clustering

A method and composition for the treatment, prevention and/or prophylaxis of a host, and in particular, a human, infected with Epstein-Barr virus (EBV), is provided that includes administering an effective amount of a 5-substituted uracil nucleoside or its pharmaceutically acceptable salt or prodrug, optionally in a pharmaceutically acceptable diluent or excipient.

Treatment of EBV and KHSV infection and associated abnormal cellular proliferation

Systems and methods for identifying Methicillin resistant strains of(MRSA) in a sample are used that are based on the fact that an MRSA positive sample should have roughly the same copy numbers of mecA, SCCmec, and a-specific target gene sequence. The systems and methods may further present the three assays simultaneously on a 2-D plot with each axis of the plot 120 degrees apart. According to one embodiment, a Y plot is used for the 2-D display. If a given sample has similar readings of mecA, SCCmec, and a-specific target gene sequence, the sample's measured copy numbers of mecA, SCCmec, and the-specific target gene sequence can plot close to the origin regardless of the sample's absolute assay readings. With the help of this transformation, a boundary function can be defined that can be used to distinguish MRSA-positive samples from MRSA-negative samples.

Systems and methods for detecting the presence of a biological status using plot

A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element (e.g., mecA), a plurality of second input values associated with a second genetic element (femA), and a plurality of third input values associated with a third genetic element (e.g., orfX) associated with a plurality of samples. Each sample includes a first input value in the plurality of first input values, a second input value in the plurality of second input values, and a third input value in the plurality of third input values. The method also includes determining a threshold value associated with the third genetic element, separating the samples using the threshold value into a first set of samples and a second set of samples, clustering the first set of samples in a feature space defined by the first genetic element and the second genetic element, defining a first boundary space using the first set of samples, and defining a second boundary space using the second set of samples. The first and second boundary spaces differentiate a biological entity from other biological statuses. Other embodiments may also include the use of a genetic element such as SCCmec.

The present invention is directed to a method of isolating a target species (e.g., target nucleic acid species) from a mixture. In the methods of the present invention, the mixture is combined with solid phase carriers having a surface comprising multiple functional groups one of which reversibly and selectively binds the target species. In a particular embodiment, the mixture is combined with solid phase carriers having a first functional group which reversibly binds nucleic acids and a second functional group which selectively and reversibly binds the target nucleic acid species, thereby producing a first combination. The first combination is maintained under conditions appropriate for binding of the nucleic acids to the first functional group and binding of the target nucleic acid species to the second functional group. The solid phase carriers are separated from the first combination, and combined with an agent (e.g., buffer) that selectively removes (e.g., elutes) either the nucleic acid from the first functional group or the target nucleic acid species from the second functional group of the solid phase carriers, thereby isolating a target nucleic acid species from a mixture comprising a plurality of nucleic acid species.

Methods of isolating nucleic acids using multifunctional group-coated solid phase carriers

Treatment of EBV and KHSV infection

Growing community of inventors

Norwood, MA, United States of America

Erik Alan Gustafson