Patents by Inventor Zbyszek Otwinowski
Zbyszek Otwinowski 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: 11697837Abstract: DNA is sequenced by: (a) combining dsDNA fragments with Y-adapters and hairpin adapters comprising an affinity-label under conditions wherein the adapters ligate to fragments forming a mixture of fragment inserts flanked by two Y-adapters, a Y-adapter and a hairpin adapter, and two hairpin adapters; and (b) sequencing the selected fragment inserts with sequencing primers selecting for the Y-adapters.Type: GrantFiled: September 23, 2020Date of Patent: July 11, 2023Assignee: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Publication number: 20230193378Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.Type: ApplicationFiled: December 26, 2022Publication date: June 22, 2023Applicant: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Publication number: 20230197277Abstract: Methods and devices for the prevention, treatment and diagnosis of cancer include assessing and quantifying imperfect dsDNA break repair. The methods may include determining a deletion signal for a DNA-containing sample of a subject, wherein the deletion signal comprises distributions of deletions (frequencies) of deletions with microhomologies of different lengths at the deletion sites in a DNA sequence or genome of the subject or sample thereof. The method may further include decomposing the deletion signal into components corresponding to changes arising from: (1) DNA repair processes, (2) systematic effects due to mapping personal deletion variants to reference genomes, and (3) false positive deletions generated during sample preparation, sequencing, and analysis, and quantifying these components to produce mutational signatures of defective HRR.Type: ApplicationFiled: February 13, 2023Publication date: June 22, 2023Applicant: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek, Raquel Bromberg
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Patent number: 11584964Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.Type: GrantFiled: November 18, 2020Date of Patent: February 21, 2023Assignee: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Publication number: 20220277427Abstract: Methods for correcting one or more image aberrations in an electron microscopy image, including cryo-EM images, are provided. The method includes obtaining a plurality of electron microscope (EM) images of an internal reference grid sample having one or more known properties, the plurality of electron microscope images obtained for a plurality of optical conditions and for a plurality of coordinated beam-image shifts. The method may also include, among other features, determining an aberration correction function that predicts aberrations for every point in the imaged area using kernel canonical correlation analysis (KCCA).Type: ApplicationFiled: August 10, 2020Publication date: September 1, 2022Inventors: Raquel Bromberg, Zbyszek Otwinowski, Dominika Borek
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Publication number: 20210207210Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.Type: ApplicationFiled: November 18, 2020Publication date: July 8, 2021Applicant: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Publication number: 20210002711Abstract: DNA is sequenced by: (a) combining dsDNA fragments with Y-adapters and hairpin adapters comprising an affinity-label under conditions wherein the adapters ligate to fragments forming a mixture of fragment inserts flanked by two Y-adapters, a Y-adapter and a hairpin adapter, and two hairpin adapters; and (b) sequencing the selected fragment inserts with sequencing primers selecting for the Y-adapters.Type: ApplicationFiled: September 23, 2020Publication date: January 7, 2021Applicant: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Patent number: 10870882Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.Type: GrantFiled: May 14, 2018Date of Patent: December 22, 2020Assignee: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Patent number: 10100347Abstract: The invention provides materials and methods to identify and analyze in a genome-wide manner the structural determinants of this organization. Next generation sequencing methods, combined with a novel assay and integrated data analysis, are used to map the long-range interactions in chromatin that are involved in the regulation of transcription.Type: GrantFiled: April 26, 2016Date of Patent: October 16, 2018Assignee: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Publication number: 20180282802Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.Type: ApplicationFiled: May 14, 2018Publication date: October 4, 2018Applicant: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Patent number: 9970054Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.Type: GrantFiled: November 21, 2014Date of Patent: May 15, 2018Assignee: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Publication number: 20160312267Abstract: The invention provides materials and methods to identify and analyze in a genome-wide manner the structural determinants of this organization. Next generation sequencing methods, combined with a novel assay and integrated data analysis, are used to map the long-range interactions in chromatin that are involved in the regulation of transcription.Type: ApplicationFiled: April 26, 2016Publication date: October 27, 2016Applicant: Board of Regents, The University of Texas SystemInventors: Zbyszek Otwinowski, Dominika Borek
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Publication number: 20150275289Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.Type: ApplicationFiled: November 21, 2014Publication date: October 1, 2015Applicant: BOARD OF REGENTS, THE UNIVERSITY OF TEXAS SYSTEMInventors: Zbyszek Otwinowski, Dominika Borek