Patents by Inventor Jeffrey Clark Mellen
Jeffrey Clark Mellen 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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Publication number: 20230394790Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.Type: ApplicationFiled: July 20, 2023Publication date: December 7, 2023Inventors: Jeffrey Clark MELLEN, Jasper STAAB, Kevin J. WU, Neil Ira WEISENFELD, Florian BAUMGARTNER, Brynn CLAYPOOLE
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Publication number: 20230287486Abstract: Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.Type: ApplicationFiled: November 14, 2022Publication date: September 14, 2023Applicant: Bio-Rad Laboratories, Inc.Inventors: John F. REGAN, Serge SAXONOV, Michael Y. LUCERO, Benjamin J. HINDSON, Phillip BELGRADER, Simant DUBE, Austin SO, Jeffrey Clark MELLEN, Nicholas Jack HEREDIA, Kevin D. NESS, Billy W. COLSTON, Jr.
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Patent number: 11756286Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.Type: GrantFiled: October 18, 2022Date of Patent: September 12, 2023Assignee: 10X GENOMICS, INC.Inventors: Jeffrey Clark Mellen, Jasper Staab, Kevin J. Wu, Neil Ira Weisenfeld, Florian Baumgartner, Brynn Claypoole
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Publication number: 20230081613Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.Type: ApplicationFiled: October 18, 2022Publication date: March 16, 2023Inventors: Jeffrey Clark MELLEN, Jasper STAAB, Kevin J. WU, Neil Ira WEISENFELD, Florian BAUMGARTNER, Brynn CLAYPOOLE
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Patent number: 11514575Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.Type: GrantFiled: September 30, 2020Date of Patent: November 29, 2022Assignee: 10X GENOMICS, INC.Inventors: Jeffrey Clark Mellen, Jasper Staab, Kevin J. Wu, Neil Ira Weisenfeld, Florian Baumgartner, Brynn Claypoole
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Publication number: 20220362764Abstract: The present disclosure provides methods and compositions for detecting polynucleotides in a sample and for quantifying polynucleotide load in a sample. The polynucleotides can be associated with a disease, disorder, or condition. In some applications, methylated DNA is quantified, e.g., in order to determine the load of polynucleotides in a sample. The present disclosure also provides methods and compositions for determining the load of fetal polynucleotides in a biological sample, e.g., the load of fetal polynucleotides (e.g., DNA, RNA) in maternal plasma. The present disclosure provides methods and compositions for detecting cellular processes such as cellular viability, growth rates, and infection rates. This disclosure also provides compositions and methods for detecting differences in copy number of a target polynucleotide. In some embodiments, the methods and compositions provided herein are useful for diagnosis of fetal genetic abnormalities, when the starting sample is maternal tissue (e.g.Type: ApplicationFiled: May 20, 2022Publication date: November 17, 2022Applicant: Bio-Rad Laboratories, Inc.Inventors: Benjamin J. HINDSON, Serge SAXONOV, Phillip BELGRADER, Kevin D. NESS, Michael Y. LUCERO, Billy W. COLSTON, JR., Shawn Paul HODGES, Nicholas J. HEREDIA, Jeffrey Clark MELLEN, Camille Bodley TROUP, Paul WYATT
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Publication number: 20210155982Abstract: Systems and methods for spatial analysis of analytes include placing a sample on a substrate having fiducial markers and capture spots. Then, an image of the sample is acquired and sequence reads are obtained from the capture spots. Each capture probe plurality in a set of capture probe pluralities is (i) at a different capture spot, (ii) directly or indirectly associates with analytes from the sample and (iii) has a unique spatial barcode. The sequencing reads serve to detect the analytes. Sequencing reads include a spatial barcode of the corresponding capture probe plurality. Spatial barcodes localize reads to corresponding capture spots, thereby dividing them into subsets, each subset for a respective capture spot. Fiducial markers facilitate a composite representation comprising (i) the image aligned to the capture spots and (ii) a representation of each subset of sequence reads at respective positions within the image mapping to the corresponding capture spots.Type: ApplicationFiled: November 18, 2020Publication date: May 27, 2021Inventors: Yifeng Yin, Zachary Bent, Stephen Williams, Ian Fiddes, Jeffrey Clark Mellen, Jasper Staab, Kevin J. Wu, Neil Ira Weisenfeld, Florian Baumgartner, Brynn Claypoole, Preyas Shah, Narek Dshkhunyan, Erik Leonard Henrik Borgstrom, Benjamin McCreath
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Publication number: 20210097684Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.Type: ApplicationFiled: September 30, 2020Publication date: April 1, 2021Inventors: Jeffrey Clark MELLEN, Jasper STAAB, Kevin J. WU, Neil Ira WEISENFELD, Florian BAUMGARTNER, Brynn CLAYPOOLE
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Patent number: 9127312Abstract: Provided herein are improved methods, compositions, and kits for analysis of nucleic acids. The improved methods, compositions, and kits can enable copy number estimation of a nucleic acid in a sample. Also provided herein are methods, compositions, and kits for determining the linkage of two or more copies of a target nucleic acid in a sample (e.g., whether the two or more copies are on the same chromosome or different chromosomes) or for phasing alleles.Type: GrantFiled: February 9, 2012Date of Patent: September 8, 2015Assignee: Bio-Rad Laboratories, Inc.Inventors: John Frederick Regan, Serge Saxonov, Mike Lucero, Ben Hindson, Phil Belgrader, Simant Dube, Austin So, Jeffrey Clark Mellen, Nicholas Jack Heredia, Kevin Ness, Bill Colston
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Publication number: 20120322058Abstract: Provided herein are improved methods, compositions, and kits for analysis of nucleic acids. The improved methods, compositions, and kits can enable copy number estimation of a nucleic acid in a sample. Also provided herein are methods, compositions, and kits for determining the linkage of two or more copies of a target nucleic acid in a sample (e.g., whether the two or more copies are on the same chromosome or different chromosomes) or for phasing alleles.Type: ApplicationFiled: February 9, 2012Publication date: December 20, 2012Applicant: Bio-Rad LaboratoriesInventors: John Frederick Regan, Serge Saxonov, Mike Lucero, Ben Hindson, Phil Belgrader, Simant Dube, Austin So, Jeffrey Clark Mellen, Nicholas Jack Heredia, Kevin Ness, Bill Colston
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Publication number: 20120252015Abstract: The present disclosure provides methods and compositions for detecting polynucleotides in a sample and for quantifying polynucleotide load in a sample. The polynucleotides can be associated with a disease, disorder, or condition. In some applications, methylated DNA is quantified, e.g., in order to determine the load of polynucleotides in a sample. The present disclosure also provides methods and compositions for determining the load of fetal polynucleotides in a biological sample, e.g., the load of fetal polynucleotides (e.g., DNA, RNA) in maternal plasma. The present disclosure provides methods and compositions for detecting cellular processes such as cellular viability, growth rates, and infection rates. This disclosure also provides compositions and methods for detecting differences in copy number of a target polynucleotide. In some embodiments, the methods and compositions provided herein are useful for diagnosis of fetal genetic abnormalities, when the starting sample is maternal tissue (e.g.Type: ApplicationFiled: February 17, 2012Publication date: October 4, 2012Applicant: Bio-Rad LaboratoriesInventors: Benjamin Hindson, Serge Saxonov, Philip Belgrader, Kevin Ness, Michael Lucero, Billy Colston, Shawn Paul Hodges, Nicholas J. Heredia, Jeffrey Clark Mellen, Camille Bodley Troup, Paul Wyatt