Patents Assigned to Cold Spring Harbor Laboratory
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Publication number: 20240238326Abstract: Disclosed herein are compounds, compositions and methods for modulating splicing of SMN2 mRNA in a subject. Also provided are uses of disclosed compounds and compositions in the manufacture of a medicament for treatment of diseases and disorders, including spinal muscular atrophy.Type: ApplicationFiled: October 25, 2023Publication date: July 18, 2024Applicants: Biogen MA Inc., Cold Spring Harbor LaboratoryInventors: C. Frank Bennett, Gene Hung, Frank Rigo, Adrian R. Krainer, Yimin Hua, Marco A. Passini, Lamya Shihabuddin, Seng H. Cheng, Katherine W. Klinger
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Patent number: 12031127Abstract: The present invention provides a composition comprising a plurality of labeled neurons, each of which is labeled by an expression construct that encodes a unique barcoded nucleic acid.Type: GrantFiled: April 5, 2017Date of Patent: July 9, 2024Assignee: COLD SPRING HARBOR LABORATORYInventors: Anthony Zador, Justus Kebschull
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Publication number: 20240199561Abstract: Provided is a compound, including a compound of Formula I: or a pharmaceutically acceptable salt thereof, wherein W is a direct bond or an optionally substituted C, and if W is a direct bond, then X1, X2, X3, and X4 are each independently H, OH, or an electrophile, and optionally one pair selected from X1 and X2, X2 and X3, and X3 and X4 forms a five-membered ring including one or more heteroatom, wherein the one or more heteroatom is selected from O, N, and S, and the five-membered ring is optionally substituted with a ?C, an ?S, or an electrophile, and Y1, Y2, Y3, Y4 and Y5 are each independently selected from H, CH3, OH, O—CH3, and NO2, and an electrophile, and optionally Y2 and Y3 form a five-membered ring including one or more heteroatom, wherein the one or more heteroatom is selected from O, N, and S, and the five-membered ring is optionally substituted with a ?C, ?S, or an electrophile.Type: ApplicationFiled: January 19, 2022Publication date: June 20, 2024Applicants: COLD SPRING HARBOR LABORATORY, VICHEM CHEMIE RESEARCH, LTD., THE FEINSTEIN INSTITUTES FOR MEDICAL RESEARCHInventors: Nicholas TONKS, Carla-Maria GAUSS, Prabhadevi VENKATARAMANI, Leemor JOSHUA-TOR, Elad ELKAYAM, Yousef Al ABED, Kai Fan CHENG, Ahmad ALTITI, Laszlo ORFI, Istvan SZABADKAI, Balint SZOKOL, Zoltan HORVATH
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Publication number: 20240102010Abstract: Provided is an improved design of shRNA based on structural mimics of miR-451 precursors. These miR-451 shRNA mimics are channeled through a novel small RNA biogenesis pathway, require AGO2 catalysis and are processed by Drosha but are independent of DICER processing. This miRNA pathway feeds active elements only into Ago2 because of its unique catalytic activity. These data demonstrate that this newly identified small RNA biogenesis pathway can be exploited in vivo to produce active molecules.Type: ApplicationFiled: August 4, 2023Publication date: March 28, 2024Applicant: Cold Spring Harbor LaboratoryInventors: Gregory J. Hannon, Sihem Cheloufi
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Patent number: 11753641Abstract: Provided is an improved design of shRNA based on structural mimics of miR-451 precursors. These miR-451 shRNA mimics are channeled through a novel small RNA biogenesis pathway, require AGO2 catalysis and are processed by Drosha but are independent of DICER processing. This miRNA pathway feeds active elements only into Ago2 because of its unique catalytic activity. These data demonstrate that this newly identified small RNA biogenesis pathway can be exploited in vivo to produce active molecules.Type: GrantFiled: February 8, 2021Date of Patent: September 12, 2023Assignee: Cold Spring Harbor LaboratoryInventors: Gregory J. Hannon, Sihem Cheloufi
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Patent number: 11739315Abstract: The present invention, SMASH (Short Multiply Aggregated Sequence Homologies), is a technique designed to pack multiple independent mappings into every read. Specifically, the invention relates to a composition comprising a first mixture of different chimeric genomic nucleic acid fragments, wherein each different fragment in the mixture comprises randomly ligated DNA segments, wherein each DNA segment in the fragment is a nucleic acid molecule at least 27 base pairs in length resulting from random fragmentation of a single genome. The invention also relates to methods for generating said composition and use of said composition to obtain genomic information, for example, copy number variation.Type: GrantFiled: May 3, 2019Date of Patent: August 29, 2023Assignee: COLD SPRING HARBOR LABORATORYInventors: Michael H. Wigler, Dan Levy, Zihua Wang
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Publication number: 20230235348Abstract: The present disclosure provides methods for increasing meiotic recombination in crop plants, as well as plants and seeds produced by such methods.Type: ApplicationFiled: July 19, 2022Publication date: July 27, 2023Applicants: Cold Spring Harbor Laboratory, Cambridge Enterprise LimitedInventors: Robert Martienssen, Charles Underwood, Ian Henderson
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Patent number: 11660306Abstract: The present invention relates to agents and methods for treating autism spectrum disorders, such as Rett Syndrome.Type: GrantFiled: April 8, 2019Date of Patent: May 30, 2023Assignee: Cold Spring Harbor LaboratoryInventors: Nicholas Tonks, Navasona Krishnan
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Patent number: 11643665Abstract: Methods and compositions for modulating shoot apical meristem size are provided. Methods are provided for modulating the expression of fea3 sequence in a host plant or plant cell to modulate agronomic characteristics such as altered size and number of organs, including plant seeds.Type: GrantFiled: February 6, 2020Date of Patent: May 9, 2023Assignees: CORTEVA AGRISCIENCE LLC, COLD SPRING HARBOR LABORATORYInventors: Stephen M Allen, David Peter Jackson, Byoung Il Je, Mai Komatsu, Young Koung Lee, Hajime Sakai
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Mutations in solanaceae plants that modulate shoot architecture and enhance yield-related phenotypes
Patent number: 11624074Abstract: Provided herein are genetically-altered Solanaceae plants, compositions related to the Solanaceae plants, and methods of making the Solanaceae plants.Type: GrantFiled: November 19, 2013Date of Patent: April 11, 2023Assignee: Cold Spring Harbor LaboratoryInventors: Zachary Lippman, Soon-Ju Park -
Publication number: 20230030373Abstract: Recently, advances in next-generation sequencing have arisen from the spatial isolation of each molecule into a small volume, enabling many single-molecule sequencing reactions to run in parallel. The fundamental limit to throughput with this technique is the need to isolate individual molecules on a spatial scale, so that sequencing signals are not mixed. Here we disrupt this limit, by observing that, in many cases, it is possible to accurately sequence complex mixtures of DNA and RNA species by exploiting the toolkit of modern compressed sensing and incorporating additional relational information about the relationship between many sequencing problems. This approach thus provides a dramatic increase in the density of DNA molecules in the sequencing reaction for both in-vitro and in-situ techniques.Type: ApplicationFiled: December 23, 2020Publication date: February 2, 2023Applicant: Cold Spring Harbor LaboratoryInventors: Alexander G. VAUGHAN, Anthony M. ZADOR
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Publication number: 20220411809Abstract: Aspects of the disclosure relate to plants containing one or more of a mutant sler (Solyc08g061560) gene or a homolog thereof, a mutant sp5g (Solyc05g053850) gene or a homolog thereof and a mutant sp (Solyc06g074350) gene or a homolog thereof, as well as methods of producing such plants. In some aspects, such plants have one or more improved traits, such as modified stem length and modified time for flowering and fruit production.Type: ApplicationFiled: November 20, 2020Publication date: December 29, 2022Applicant: Cold Spring Harbor LaboratoryInventors: Zachary Lippman, Choon-Tak Kwon
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Publication number: 20220370479Abstract: Provided is a method of forming a copper-containing complex, including contacting a sample containing copper with a compound of Formula I: wherein R is —OH or —O—CH3. Also provided is a method of inhibiting enzymatic activity of a kinase in a sample, including contacting the sample with a compound of Formula I. Further provided is a method of administering to a subject a pharmaceutical composition including a compound of Formula I optionally complexed with copper. Also provided is a pharmaceutical composition including copper complexed with a compound of Formula I.Type: ApplicationFiled: July 18, 2022Publication date: November 24, 2022Applicants: COLD SPRING HARBOR LABORATORY, DEPYMED, INC.Inventors: Nicholas TONKS, Navasona KRISHNAN, Andreas GRILL, Howard SARD
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Patent number: 11406647Abstract: Provided is a method of forming a copper-containing complex, including contacting a sample containing copper with a compound of Formula I: wherein R is —OH or —O—CH3. Also provided is a method of inhibiting enzymatic activity of a kinase in a sample, including contacting the sample with a compound of Formula I. Further provided is a method of administering to a subject a pharmaceutical composition including a compound of Formula I optionally complexed with copper. Also provided is a pharmaceutical composition including copper complexed with a compound of Formula I.Type: GrantFiled: November 6, 2018Date of Patent: August 9, 2022Assignees: COLD SPRING HARBOR LABORATORY, DEPYMED, INC.Inventors: Nicholas Tonks, Navasona Krishnan, Andreas Grill, Howard Sard
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Patent number: 11352624Abstract: The present disclosure relates to compositions and methods for inhibiting nonsense-mediated mRNA decay in a gene-specific manner, for example in the treatment of diseases or disorders caused by nonsense mutations.Type: GrantFiled: April 2, 2020Date of Patent: June 7, 2022Assignee: Cold Spring Harbor LaboratoryInventors: Adrian Krainer, Isabel Aznarez, Tomoki Nomakuchi
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Publication number: 20220042090Abstract: A method for determining the presence or absence of variant ribonucleic acid molecules in a population of ribonucleic acid molecules, wherein the reference sequence of the variant ribonucleic acid molecules is known, the method comprising: (a) interrogating the population of ribonucleic acid molecules with a plurality of primer molecules and a plurality of probes so as to saturate the population of ribonucleic acid molecules with the probes and primer molecules such that the probes and primer molecules are adjacent to one another when hybridized to their respective complimentary sequences on the ribonucleic acid molecules, (b) ligating the probes to their respective adjacent primer molecules so as to form ligated nucleic acid molecules, and (c) detecting the presence of ligated nucleic acid molecules that are complementary to a sequence that differs from the reference sequence, thereby determining the presence or absence of one or more variant ribonucleic acid molecules in the population of ribonucleic acid mType: ApplicationFiled: September 13, 2019Publication date: February 10, 2022Applicant: Cold Spring Harbor LaboratoryInventors: Je H. Lee, David Chitty, Ahmed Elewa, Debarati Ghosh, Simone Weinmann, Daniel Fuerth, Chengxiang Yuan
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Patent number: 11236330Abstract: The present invention provides compounds comprising oligonucleotides complementary to a pyruvate kinase M transcript. Certain such compounds are useful for hybridizing to a pyruvate kinase M transcript, including but not limited to a pyruvate kinase M transcript in a cell. In certain embodiments, such hybridization results in modulation of splicing of the pyruvate kinase M transcript. In certain embodiments, such compounds are used to treat one or more symptoms associated with cancer.Type: GrantFiled: October 2, 2018Date of Patent: February 1, 2022Assignees: Ionis Pharmaceuticals, Inc., Cold Spring Harbor LaboratoryInventors: Frank Rigo, C. Frank Bennett, Adrian R. Krainer, Zhenxun Wang
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Publication number: 20220002740Abstract: Aspects of the disclosure relate to plants, such as Solanaceae plants containing one or more of a mutant Solyc04g005320 gene (or a homolog thereof), a mutant Solycl2g038510 gene (or a homolog thereof), and a mutant Solyc03gl14840 gene (or a homolog thereof), as well as methods of producing such plants. In some aspects, such plants have one or more improved traits, such as modified inflorescence architecture, modified flower number, modified fruit number, higher yield, higher quality products, and higher fruit productivity.Type: ApplicationFiled: May 17, 2018Publication date: January 6, 2022Applicant: Cold Spring Harbor LaboratoryInventors: Zachary Lippman, Sebastian Soyk, Zachary Hartford Lemmon
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Patent number: 11179379Abstract: Methods and compositions for producing fetal hemoglobin and treating a hemoglobinopathy or thalassemia are disclosed.Type: GrantFiled: January 30, 2018Date of Patent: November 23, 2021Assignees: THE CHILDREN'S HOSPITAL OF PHILADELPHIA, THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, COLD SPRING HARBOR LABORATORYInventors: Gerd Blobel, Jeremy Grevet, Junwei Shi, Christopher Vakoc
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Publication number: 20210340604Abstract: A method for determining the number of nucleic acid molecules (NAMs) in a group of NAMs, comprising i) obtaining an amplified and mutagenized group of NAMs that was produced by a. subjecting the group of NAMs to a chemical mutagenesis which mutates only select nucleic acid bases in the group of NAMs at a rate of 10% to 90% thus forming a group of mutagenized NAMs (mNAMs), and b. amplifying the group of mNAMs; ii) obtaining sequences of the mNAMs in the group of amplified mNAMs; and iii) counting the number of different sequences obtained in step (ii) to determine the number of unique mNAMs in the group of mNAMS, thereby determining the number of NAMs in the group of NAMs.Type: ApplicationFiled: May 14, 2021Publication date: November 4, 2021Applicant: Cold Spring Harbor LaboratoryInventors: Michael Wigler, Dan Levy