Patents by Inventor Ruojia Wu

Ruojia Wu 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).

  • Publication number: 20220098642
    Abstract: Provided herein are methods of quantitative amplicon sequencing, for labeling each strand of targeted genomic loci in a DNA sample with an oligonucleotide barcode sequence by polymerase chain reaction, and amplifying the genomic region(s) for high-throughput sequencing. The methods can be used for the simultaneous detection of copy number variation (CNV) in a set of genes of interest, by quantifying the frequency of extra copies of each gene. In addition, these methods provide for the quantitation of the allele ratio of different genetic identities for targeted genomic loci using multiplexed PCR. In addition, these methods provide for the detection of mutations and quantitation of the variant allele frequency.
    Type: Application
    Filed: January 2, 2020
    Publication date: March 31, 2022
    Applicant: William Marsh Rice University
    Inventors: David ZHANG, Peng DAI, Ruojia WU
  • Publication number: 20220090168
    Abstract: The present invention provides an oligonucleotide composition including a blocker and a first primer oligonucleotide. The blocker oligonucleotide includes a first sequence having a target-neutral subsequence and a blocker variable subsequence. The non-target specific subsequence is flanked on its 3? and 5? ends by the target-neutral subsequence and is continuous with the target-neutral subsequence. The first primer oligonucleotide is sufficient to induce enzymatic extension; herein the first primer oligonucleotide includes a second sequence. The second sequence overlaps with the 5? end of the target-neutral subsequence by at least 5 nucleotides; herein the second sequence includes an overlapping subsequence and a non-overlapping subsequence. The second sequence does not include the non-target specific subsequence.
    Type: Application
    Filed: November 29, 2021
    Publication date: March 24, 2022
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Ruojia WU, Juexiao WANG
  • Publication number: 20210230691
    Abstract: Compositions and methods for highly specific nucleic acid probes and primers are provided. The probe system comprises a complement strand and a protector stand that form a partially double-stranded probe. The reaction standard free energy of hybridization between the probe and target nucleic acid as determined by Expression 1 (?G°rxn=?G°t-TC??G°nh-PC+(?G°v-TC??G°h-PC)) is from about ?4 kcal/mol to about +4 kcal/mol. Alternatively, the reaction standard free energy of hybridization between the probe and target nucleic acid is determined by Expression 1 to be within 5 kcal/mol of the standard free energy as determined by Expression 2 (?R?ln(([P]0?[C]0)/[C]0)]), where the [P]0 term of Expression 2 equals the concentration of the protector strand and the [C]0 term of Expression 2 equals the concentration of the complement strand. In addition, a method for on-the-fly fine tuning of a reaction using the present probe is provided.
    Type: Application
    Filed: December 30, 2020
    Publication date: July 29, 2021
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Juexiao WANG, Ruojia WU
  • Publication number: 20210164026
    Abstract: This invention describes a method of controlling the hybridization yield of nucleic acid probes by adjusting the relative concentrations of auxiliary oligonucleotides to the probes and the targets. The auxiliary oligonucleotide is partially or fully complementary to either the probe or the target, and is released upon hybridization of the probe to the target.
    Type: Application
    Filed: February 5, 2021
    Publication date: June 3, 2021
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Ruojia WU, Juexiao WANG
  • Patent number: 10900079
    Abstract: Compositions and methods for highly specific nucleic acid probes and primers are provided. The probe system comprises a complement strand and a protector stand that form a partially double-stranded probe. The reaction standard free energy of hybridization between the probe and target nucleic acid as determined by Expression 1 (?G°rxn=?G°t-TC??G°nh-PC+(?G°v-TC??G°h-PC)) is from about ?4 kcal/mol to about +4 kcal/mol. Alternatively, the reaction standard free energy of hybridization between the probe and target nucleic acid is determined by Expression 1 to be within 5 kcal/mol of the standard free energy as determined by Expression 2 (?R? ln(([P]0?[C]0)/[C]0)]), where the [P]0 term of Expression 2 equals the concentration of the protector strand and the [C]0 term of Expression 2 equals the concentration of the complement strand. In addition, a method for on-the-fly fine tuning of a reaction using the present probe is provided.
    Type: Grant
    Filed: June 6, 2016
    Date of Patent: January 26, 2021
    Assignee: William Marsh Rice University
    Inventors: David Yu Zhang, Juexiao Wang, Ruojia Wu
  • Publication number: 20190333603
    Abstract: Embodiments of methods, systems, and tangible non-transitory computer readable medium having instructions are presented. A method includes calculating a plurality of feature values for a number of bioinformatic features of the desired hybridization reaction; and calculating distances between the plurality of feature values and corresponding database rate constant values stored in a database, the database comprising a plurality of hybridization reactions having known rate constants. The method additionally includes calculating a weighted average of a logarithm of the database rate constant values, with larger weights assigned to value instances having values lower in distance to the plurality of feature values of the desired hybridization reaction; and providing the weighted average as a predicted logarithm of the rate constant of the desired hybridization reaction.
    Type: Application
    Filed: June 7, 2017
    Publication date: October 31, 2019
    Inventors: Xuemeng Zhang, Zheng Fang, Ruojia Wu, Wei Duan, David Zhang
  • Publication number: 20180179588
    Abstract: This invention describes a method of controlling the hybridization yield of nucleic acid probes by adjusting the relative concentrations of auxiliary oligonucleotides to the probes and the targets. The auxiliary oligonucleotide is partially or fully complementary to either the probe or the target, and is released upon hybridization of the probe to the target.
    Type: Application
    Filed: October 16, 2017
    Publication date: June 28, 2018
    Inventors: David Yu Zhang, Ruojia Wu, Juexiao Wang
  • Publication number: 20170067090
    Abstract: The present invention provides an oligonucleotide composition including a blocker and a first primer oligonucleotide. The blocker oligonucleotide includes a first sequence having a target-neutral subsequence and a blocker variable subsequence. The non-target specific subsequence is flanked on its 3? and 5? ends by the target-neutral subsequence and is continuous with the target-neutral subsequence. The first primer oligonucleotide is sufficient to induce enzymatic extension; herein the first primer oligonucleotide includes a second sequence. The second sequence overlaps with the 5? end of the target-neutral subsequence by at least 5 nucleotides; herein the second sequence includes an overlapping subsequence and a non-overlapping subsequence. The second sequence does not include the non-target specific subsequence.
    Type: Application
    Filed: November 18, 2016
    Publication date: March 9, 2017
    Inventors: David Yu Zhang, Ruojia Wu, Juexiao Wang
  • Publication number: 20160340727
    Abstract: Compositions and methods for highly specific nucleic acid probes and primers are provided. The probe system comprises a complement strand and a protector stand that form a partially double-stranded probe. The reaction standard free energy of hybridization between the probe and target nucleic acid as determined by Expression 1 (?G°rxn=?G°t-TC??G°nh-PC+(?G°v-TC??G°h-PC)) is from about ?4 kcal/mol to about +4 kcal/mol. Alternatively, the reaction standard free energy of hybridization between the probe and target nucleic acid is determined by Expression 1 to be within 5 kcal/mol of the standard free energy as determined by Expression 2 (?R? ln(([P]0?[C]0)/[C]0)]), where the [P]0 term of Expression 2 equals the concentration of the protector strand and the [C]0 term of Expression 2 equals the concentration of the complement strand. In addition, a method for on-the-fly fine tuning of a reaction using the present probe is provided.
    Type: Application
    Filed: June 6, 2016
    Publication date: November 24, 2016
    Inventors: David Yu Zhang, Juexiao Wang, Ruojia Wu