Patents by Inventor Kok-Hao Chen
Kok-Hao Chen 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: 11959075Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: GrantFiled: March 16, 2023Date of Patent: April 16, 2024Assignee: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang
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Publication number: 20230323338Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: ApplicationFiled: March 16, 2023Publication date: October 12, 2023Applicant: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang
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Publication number: 20230323339Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: ApplicationFiled: March 16, 2023Publication date: October 12, 2023Applicant: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang
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Publication number: 20230279387Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: ApplicationFiled: April 7, 2023Publication date: September 7, 2023Applicant: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang
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Publication number: 20230279383Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: ApplicationFiled: October 13, 2022Publication date: September 7, 2023Applicant: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang
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Publication number: 20230083623Abstract: The present invention relates to a pair of non-naturally occurring nucleic acid probes for detecting a polynucleotide analyte for fluorescence in situ hybridization (FISH) wherein the probes comprise a first nucleic acid probe comprising a first probe binding arm that is complementary to a first probe target region of a bridge probe and a first polynucleotide analyte binding arm that is complementary to a first analyte target region of a polynucleotide analyte and a second nucleic acid probe comprising a second probe binding arm that is complementary to a second probe target region of the bridge probe. The binding of the pair of probes to target polynucleotides permits the binding of the bridge probe to allow detection of the polynucleotide analyte. It also provides a probe system comprising said pair of nucleic acid probes and methods of detecting polynucleotide analytes in a sample.Type: ApplicationFiled: June 24, 2020Publication date: March 16, 2023Inventors: Kok Hao Chen, Jie Lin Jolene GOH, Shijie Nigel Chou, Wan Yi Seow, Norbert Ha, Ziqing Zhao, Christabelle Goh
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Publication number: 20220375546Abstract: Exemplary embodiments provide methods, mediums, and systems for processing multiplexed image data from a fluorescence in-situ hybridization (FISH) experiment. According to exemplary embodiments, a convolutional neural network (CNN) may be applied to the image data to localize and identify hybridization spots in images corresponding to different sets of targeting probes. The CNN is configured in such a way that it is able to discriminate hybridization spots in situations that are difficult for conventional techniques. The CNN may be trained on a relatively small amount of data by exploiting the nature of the FISH codebook.Type: ApplicationFiled: May 24, 2021Publication date: November 24, 2022Applicant: Applied Materials, Inc.Inventors: Mike Jin-An Huang, Yun-Ching Chang, Dan Xie, Kok Hao Chen, Shijie Nigel Chou
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Publication number: 20220025442Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: ApplicationFiled: July 13, 2021Publication date: January 27, 2022Applicant: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang
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Patent number: 11098303Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: GrantFiled: July 29, 2015Date of Patent: August 24, 2021Assignee: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang
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Publication number: 20170220733Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: ApplicationFiled: July 29, 2015Publication date: August 3, 2017Applicant: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang