Patents by Inventor David W. Ruff
David W. Ruff has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11447815Abstract: Various embodiments of methods for analyzing proximity binding assay (PBA) data are disclosed. Proximity binding assays as a class of analyses offer the advantages of the sensitivity and specificity of biorecognition binding, along with the exponential signal amplification offered by a variety of oligonucleotide amplification reactions, such as the polymerase chain reaction (PCR). However, as various proximity binding assays have reaction kinetics governed by an additional step of the binding of a biorecognition probe (BRP) with a target molecule, there is a need for methods for the analysis of PBA data that are particularly suited to the unique characteristics of such data.Type: GrantFiled: December 20, 2018Date of Patent: September 20, 2022Assignee: Life Technologies CorporationInventors: Shiaw-Min Chen, David W. Ruff, Harrison Leong
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Publication number: 20190241942Abstract: Various embodiments of methods for analyzing proximity binding assay (PBA) data are disclosed. Proximity binding assays as a class of analyses offer the advantages of the sensitivity and specificity of biorecognition binding, along with the exponential signal amplification offered by a variety of oligonucleotide amplification reactions, such as the polymerase chain reaction (PCR). However, as various proximity binding assays have reaction kinetics governed by an additional step of the binding of a biorecognition probe (BRP) with a target molecule, there is a need for methods for the analysis of PBA data that are particularly suited to the unique characteristics of such data.Type: ApplicationFiled: December 20, 2018Publication date: August 8, 2019Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Shiaw-Min CHEN, David W. RUFF, Harrison LEONG
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Patent number: 10208335Abstract: Various embodiments of methods for analyzing proximity binding assay (PBA) data are disclosed. Proximity binding assays as a class of analyses offer the advantages of the sensitivity and specificity of biorecognition binding, along with the exponential signal amplification offered by a variety of oligonucleotide amplification reactions, such as the polymerase chain reaction (PCR). However, as various proximity binding assays have reaction kinetics governed by an additional step of the binding of a biorecognition probe (BRP) with a target molecule, there is a need for methods for the analysis of PBA data that are particularly suited to the unique characteristics of such data.Type: GrantFiled: August 5, 2010Date of Patent: February 19, 2019Assignee: Life Technologies CorporationInventors: Shiaw-Min Chen, David W. Ruff, Harrison M. Leong
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Publication number: 20150220685Abstract: A method for determining bias across two domains comprising gene expression data. The method can comprise (a) providing a first domain and a second domain; (b) obtaining information indicative of a bias within the first domain; (c) obtaining information indicative of a bias within the second domain; and (d) using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains.Type: ApplicationFiled: April 16, 2015Publication date: August 6, 2015Inventors: Mark E. Shannon, Mark F. Oldham, David W. Ruff
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Patent number: 9026371Abstract: A method for determining bias across two domains comprising gene expression data. The method can comprise (a) providing a first domain and a second domain; (b) obtaining information indicative of a bias within the first domain; (c) obtaining information indicative of a bias within the second domain; and (d) using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains.Type: GrantFiled: September 11, 2009Date of Patent: May 5, 2015Assignee: Applied Biosystems, LLCInventors: Mark E. Shannon, Mark F. Oldham, David W. Ruff
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Patent number: 8568580Abstract: A system for collecting target nucleic acids from a sample can include at least one sample chamber configured to receive a sample containing target nucleic acids and other material, at least one collection chamber removably mountable relative to the at least one sample chamber and configured to collect target nucleic acids separated from the other material, a filter removably mountable relative to the at least one sample chamber and configured to be disposed between the at least one sample chamber and the at least one collection chamber when the at least one collection chamber is mounted relative to the at least one sample chamber.Type: GrantFiled: July 24, 2008Date of Patent: October 29, 2013Assignee: Applied Biosystems, LLCInventors: Charles S. Vann, Maxim G. Brevnov, David W. Ruff, Kenneth J. Livak
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Patent number: 8535878Abstract: The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.Type: GrantFiled: May 2, 2007Date of Patent: September 17, 2013Assignee: Applied Biosystems, LLCInventors: David W. Ruff, Mark E. Shannon, Kenneth J. Livak, Karl J. Guegler, Kevin M. Hennessy
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Patent number: 8323897Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.Type: GrantFiled: November 26, 2003Date of Patent: December 4, 2012Assignee: Applied Biosystems, LLCInventors: Mark R. Andersen, David W. Ruff
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Publication number: 20110287436Abstract: Methods of detecting at least one analyte and at least one nucleic acid in a sample are provided. Reagents for carrying out the methods are also provided.Type: ApplicationFiled: July 29, 2011Publication date: November 24, 2011Applicant: Applied Biosystems, LLCInventors: Mark E. Shannon, David W. Ruff
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Patent number: 8012685Abstract: Methods of detecting at least one analyte and at least one nucleic acid in a sample are provided. Reagents for carrying out the methods are also provided.Type: GrantFiled: July 31, 2007Date of Patent: September 6, 2011Assignee: Applied Biosystems, LLCInventors: Mark E. Shannon, David W. Ruff
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Publication number: 20110208441Abstract: Various embodiments of methods for analyzing proximity binding assay (PBA) data are disclosed. Proximity binding assays as a class of analyses offer the advantages of the sensitivity and specificity of biorecognition binding, along with the exponential signal amplification offered by a variety of oligonucleotide amplification reactions, such as the polymerase chain reaction (PCR). However, as various proximity binding assays have reaction kinetics governed by an additional step of the binding of a biorecognition probe (BRP) with a target molecule, there is a need for methods for the analysis of PBA data that are particularly suited to the unique characteristics of such data.Type: ApplicationFiled: August 5, 2010Publication date: August 25, 2011Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Shiaw-Min Chen, David W. Ruff, Harrison M. Leong
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Publication number: 20100036616Abstract: A method for determining bias across two domains comprising gene expression data. The method can comprise (a) providing a first domain and a second domain; (b) obtaining information indicative of a bias within the first domain; (c) obtaining information indicative of a bias within the second domain; and (d) using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains.Type: ApplicationFiled: September 11, 2009Publication date: February 11, 2010Applicant: Life Technologies CorporationInventors: Mark E. Shannon, Mark F. Oldham, David W. Ruff
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Publication number: 20090071830Abstract: A system for collecting target nucleic acids from a sample can include at least one sample chamber configured to receive a sample containing target nucleic acids and other material, at least one collection chamber removably mountable relative to the at least one sample chamber and configured to collect target nucleic acids separated from the other material, a filter removably mountable relative to the at least one sample chamber and configured to be disposed between the at least one sample chamber and the at least one collection chamber when the at least one collection chamber is mounted relative to the at least one sample chamber.Type: ApplicationFiled: July 24, 2008Publication date: March 19, 2009Applicant: Applied Biosystems Inc.Inventors: Charles S. Vann, Maxim G. Brevnov, David W. Ruff, Kenneth J. Livak
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Publication number: 20040245163Abstract: A device, system, kit, and method are provided for filtering relatively large volumes of whole blood to recover purified RNA for analysis. The device can include: a filter including a body having an interior, a first filter connector in communication with the interior of the body, a ribonucleic acid-capturing (RNA-capturing) membrane disposed within the interior, and an optional filter frit disposed within the interior adjacent the RNA-capturing membrane. The system can include a vacuum adapter plate including a substrate having a first surface, a second surface, and one or more through-holes each extending at least from the first surface to the second surface. The first filter connector can connect to a respective through-hole to form a fluid communication between the filter and the vacuum adapter plate. The system can include a collection vessel in fluid communication with the filter.Type: ApplicationFiled: January 15, 2004Publication date: December 9, 2004Inventors: Gary Lim, David W. Ruff, Michael A. Tanner, Somaya L. Bit
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Publication number: 20040175733Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.Type: ApplicationFiled: November 26, 2003Publication date: September 9, 2004Inventors: Mark R. Andersen, David W. Ruff