Patents by Inventor Daniel J. KLEINBAUM
Daniel J. KLEINBAUM 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: 11955207Abstract: The disclosure provides systems and methods for data analysis of experimental data. The analysis can include reference data that are not directly generated from the present experiment, which reference data may be values of the experimental parameters that were either provided by a user, computed by the system with input from a user, or computed by the system without using any input from a user. Another example of such reference data may be information about the instrument, such as the calibration method of the instrument.Type: GrantFiled: June 30, 2016Date of Patent: April 9, 2024Assignee: Emerald Cloud Lab, Inc.Inventors: Alex M. Yoshikawa, Anand V. Sastry, Asuka Ota, Ben C. Kline, Bradley M. Bond, Brian M. Frezza, Cameron R. Lamoureux, Catherine L. Hofler, Cheri Y. Li, Courtney E. Webster, Daniel J. Kleinbaum, George N. Stanley, George W. Fraser, Guillaume Robichaud, Hayley E. Buchman, James R. McKernan, Jonathan K. Leung, Paul R. Zurek, Robert M. Teed, Ruben E. Valas, Sean M. Fitzgerald, Sergio I. Villarreal, Shayna L. Hilburg, Shivani S. Baisiwala, Srikant Vaithilingam, Wyatt J. Woodson, Yang Choo, Yidan Y. Cong
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Publication number: 20220009956Abstract: Conjugated molecules are prepared that comprise a predetermined number of oligo conjugation components. The conjugated molecules also may comprise one or more detectable labels. Preparation of these molecules can be implemented according to an asymmetric or a symmetric conjugation strategy.Type: ApplicationFiled: April 22, 2021Publication date: January 13, 2022Inventors: Brian M. Frezza, Courtney E. Webster, Daniel J. Kleinbaum
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Publication number: 20210233605Abstract: The disclosure provides systems and methods for conducting and managing integrated laboratory experiments. The system includes a variety of laboratory instruments that are connected to conduct a large number of different types of experiments, and an interface for a user to design experiments and adjust parameters for the experiments. Given the integration, the system can further take data from related samples and instruments for determining or adjusting certain experimental parameters for optimized experimental efficiency and results.Type: ApplicationFiled: April 12, 2021Publication date: July 29, 2021Inventors: Alex M. Yoshikawa, Anand V. Sastry, Asuka Ota, Ben C. Kline, Bradley M. Bond, Brian M. Frezza, Cameron R. Lamoureux, Catherine L. Hofler, Cheri Y. Li, Courtney E. Webster, Daniel J. Kleinbaum, George N. Stanley, George W. Fraser, Guillaume Robichaud, Hayley E. Buchman, James R. McKernan, Jonathan K. Leung, Paul R. Zurek, Robert M. Teed, Ruben E. Valas, Sean M. Fitzgerald, Sergio I. Villarreal, Shayna L. Hilburg, Shivani S. Baisiwala, Srikant Vaithilingam, Wyatt J. Woodson, Yang Choo, Yidan Y. Cong
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Patent number: 10978172Abstract: The disclosure provides systems and methods for conducting and managing integrated laboratory experiments. The system includes a variety of laboratory instruments that are connected to conduct a large number of different types of experiments, and an interface for a user to design experiments and adjust parameters for the experiments. Given the integration, the system can further take data from related samples and instruments for determining or adjusting certain experimental parameters for optimized experimental efficiency and results.Type: GrantFiled: June 30, 2016Date of Patent: April 13, 2021Assignee: Emerald Cloud Lab, Inc.Inventors: Alex M. Yoshikawa, Anand V. Sastry, Asuka Ota, Ben C. Kline, Bradley M. Bond, Brian M. Frezza, Cameron R. Lamoureux, Catherine L. Hofler, Cheri Y. Li, Courtney E. Webster, Daniel J. Kleinbaum, George N. Stanley, George W. Fraser, Guillaume Robichaud, Hayley E. Buchman, James R. McKernan, Jonathan K. Leung, Paul R. Zurek, Robert M. Teed, Ruben E. Valas, Sean M. Fitzgerald, Sergio I. Villarreal, Shayna L. Hilburg, Shivani S. Baisiwala, Srikant Vaithilingam, Wyatt J. Woodson, Yang Choo, Yidan Y. Cong
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Publication number: 20210102207Abstract: Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.Type: ApplicationFiled: November 30, 2020Publication date: April 8, 2021Inventors: Daniel J. Kleinbaum, Brian M. Frezza, Brad Bond, Jonathan Leung, George W. Fraser
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Publication number: 20210034944Abstract: A method is provided for improving a nucleic acid-based molecular computing system comprised of (i) a nucleic acid structure, (ii) at least one polynucleotide displacement molecule that can bind with the nucleic acid structure under hybridizing conditions, and (iii) a clashing polynucleotide molecule that competes with the polynucleotide displacement molecule for binding the nucleic acid structure under the hybridizing conditions The method entails incorporation of chemical modification that inhibits the binding of the clashing molecule and the nucleic acid structure or facilitates the binding of the displacement molecule and the nucleic structure.Type: ApplicationFiled: May 15, 2020Publication date: February 4, 2021Inventor: Daniel J. Kleinbaum
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Patent number: 10883106Abstract: Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.Type: GrantFiled: October 25, 2019Date of Patent: January 5, 2021Assignee: Emerald Therapeutics, Inc.Inventors: Daniel J. Kleinbaum, Brian M. Frezza, Brad Bond, Jonathan Leung, George W. Fraser
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Publication number: 20200056180Abstract: Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.Type: ApplicationFiled: October 25, 2019Publication date: February 20, 2020Inventors: Daniel J. Kleinbaum, Brian M. Frezza, Brad Bond, Jonathan Leung, George W. Fraser
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Publication number: 20200051662Abstract: An approach to designing a polynucleotide probe to hybridize selectively to a target polynucleotide sequence involves calculating the final concentration of the intended binding product between a candidate probe and the target sequence. The calculation takes into consideration the binding reaction between the candidate probe and the target fragment on the target sequence, as well as various other binding reactions, involving either the probe or the target fragment, that interfere with the intended binding reaction. In contrast to the conventional technology, which attempts to determine the entire structure of the target polynucleotide, this approach only needs to determine the binding dynamics that impact on the intended probe-target fragment binding. The approach does not require determination of the structure of the involved sequences.Type: ApplicationFiled: October 25, 2019Publication date: February 13, 2020Inventors: Brian M. Frezza, Bradley M. Bond, Collin A. Melton, Catherine L. Hofler, Daniel J. Kleinbaum
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Patent number: 10504612Abstract: An approach to designing a polynucleotide probe to hybridize selectively to a target polynucleotide sequence involves calculating the final concentration of the intended binding product between a candidate probe and the target sequence. The calculation takes into consideration the binding reaction between the candidate probe and the target fragment on the target sequence, as well as various other binding reactions, involving either the probe or the target fragment, that interfere with the intended binding reaction. In contrast to the conventional technology, which attempts to determine the entire structure of the target polynucleotide, this approach only needs to determine the binding dynamics that impact on the intended probe-target fragment binding. The approach does not require determination of the structure of the involved sequences.Type: GrantFiled: March 13, 2013Date of Patent: December 10, 2019Assignee: EMERALD THERAPEUTICS, INC.Inventors: Brian M. Frezza, Bradley M. Bond, Collin A. Melton, Catherine L. Hofler, Daniel J. Kleinbaum
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Publication number: 20190367554Abstract: Conjugated molecules are prepared that comprise a predetermined number of oligo conjugation components. The conjugated molecules also may comprise one or more detectable labels. Preparation of these molecules can be implemented according to an asymmetric or a symmetric conjugation strategy.Type: ApplicationFiled: April 11, 2019Publication date: December 5, 2019Inventors: Brian M. Frezza, Courtney E. Webster, Daniel J. Kleinbaum
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Patent number: 10479994Abstract: Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.Type: GrantFiled: March 27, 2017Date of Patent: November 19, 2019Assignee: Emerald Therapeutics, Inc.Inventors: Daniel J. Kleinbaum, Brian M. Frezza, Brad Bond, Jonathan Leung, George W. Fraser
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Publication number: 20180196913Abstract: The disclosure provides systems and methods for conducting and managing integrated laboratory experiments. The system includes a variety of laboratory instruments that are connected to conduct a large number of different types of experiments, and an interface for a user to design experiments and adjust parameters for the experiments. Given the integration, the system can further take data from related samples and instruments for determining or adjusting certain experimental parameters for optimized experimental efficiency and results.Type: ApplicationFiled: June 30, 2016Publication date: July 12, 2018Applicant: Emerald Cloud Lab, Inc.Inventors: Alex M. Yoshikawa, Anand V. Sastry, Asuka Ota, Ben C. Kline, Bradley M. Bond, Brian M. Frezza, Cameron R. Lamoureux, Catherine L. Hofler, Cheri Y. Li, Courtney E. Webster, Daniel J. Kleinbaum, George N. Stanley, George W. Fraser, Guillaume Robichaud, Hayley E. Buchman, James R. McKernan, Jonathan K. Leung, Paul R. Zurek, Robert M. Teed, Ruben E. Valas, Sean M. Fitzgerald, Sergio I. Villarreal, Shayna L. Hilburg, Shivani S. Baisiwala, Srikant Vaithilingam, Wyatt J. Woodson, Yang Choo, Yidan Y. Cong
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Publication number: 20180190386Abstract: The disclosure provides systems and methods for data analysis of experimental data. The analysis can include reference data that are not directly generated from the present experiment, which reference data may be values of the experimental parameters that were either provided by a user, computed by the system with input from a user, or computed by the system without using any input from a user. Another example of such reference data may be information about the instrument, such as the calibration method of the instrument.Type: ApplicationFiled: June 30, 2016Publication date: July 5, 2018Inventors: Alex M. Yoshikawa, Anand V. Sastry, Asuka Ota, Ben C. Kline, Bradley M. Bond, Brian M. Frezza, Cameron R. Lamoureux, Catherine L. Hofler, Cheri Y. Li, Courtney E. Webster, Daniel J. Kleinbaum, George N. Stanley, George W. Fraser, Guillaume Robichaud, Hayley E. Buchman, James R. McKernan, Jonathan K. Leung, Paul R. Zurek, Robert M. Teed, Ruben E. Valas, Sean M. Fitzgerald, Sergio I. Villarreal, Shayna L. Hilburg, Shivani S. Baisiwala, Srikant Vaithilingam, Wyatt J. Woodson, Yang Choo, Yidan Y. Cong
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Publication number: 20170220921Abstract: A method is provided for improving a nucleic acid-based molecular computing system comprised of (i) a nucleic acid structure, (ii) at least one polynucleotide displacement molecule that can bind with the nucleic acid structure under hybridizing conditions, and (iii) a clashing polynucleotide molecule that competes with the polynucleotide displacement molecule for binding the nucleic acid structure under the hybridizing conditions The method entails incorporation of chemical modification that inhibits the binding of the clashing molecule and the nucleic acid structure or facilitates the binding of the displacement molecule and the nucleic structure.Type: ApplicationFiled: December 12, 2016Publication date: August 3, 2017Inventor: Daniel J. Kleinbaum
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Publication number: 20170200080Abstract: Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.Type: ApplicationFiled: March 27, 2017Publication date: July 13, 2017Inventors: Daniel J. Kleinbaum, Brian M. Frezza, Brad Bond, Jonathan Leung, George W. Fraser
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Patent number: 9624495Abstract: Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.Type: GrantFiled: May 26, 2015Date of Patent: April 18, 2017Assignee: Emerald Therapeutics, Inc.Inventors: Daniel J. Kleinbaum, Brian M. Frezza, Brad Bond, Jonathan Leung, George W. Fraser
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Patent number: 9547750Abstract: Improvement is effected for a nucleic acid-based molecular computing system that is comprised of (i) a nucleic acid structure, (ii) at least one polynucleotide displacement molecule that can bind with the nucleic acid structure under hybridizing conditions, and (iii) a clashing polynucleotide molecule that competes with the polynucleotide displacement molecule for binding the nucleic acid structure under the hybridizing conditions. The method for such improvement entails incorporating chemical modification that inhibits the binding of the clashing molecule and the nucleic acid structure or facilitating the binding of the displacement molecule and the nucleic structure.Type: GrantFiled: December 27, 2013Date of Patent: January 17, 2017Assignee: Emerald Therapeutics, Inc.Inventor: Daniel J. Kleinbaum
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Publication number: 20160333045Abstract: Conjugated molecules are prepared that comprise a predetermined number of oligo conjugation components. The conjugated molecules also may comprise one or more detectable labels. Preparation of these molecules can be implemented according to an asymmetric or a symmetric conjugation strategy.Type: ApplicationFiled: February 11, 2016Publication date: November 17, 2016Inventors: Brian M. Frezza, Courtney E. Webster, Daniel J. Kleinbaum
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Patent number: 9429547Abstract: A fabrication process for producing, annealing, and conjugating nucleic acid molecules is implemented, under the direction of one or more computer programs, on two or more instruments, for carrying out the process. The process can include: (a) synthesizing, on a solid support and in a plurality of reactions, at least one of a nucleic acid and a peptide nucleic acid, and cleaving the synthesized biomolecule product from the support, providing a sample of synthesized biomolecule product from each reaction of the plurality; (b) measuring, for each sample, the volume of the sample and/or the concentration of the product; (c) subjecting the product from each reaction to chromatography under conditions suitable for achieving single-base-resolution for the product, the conditions being a function of the volume and/or concentration measured in (b); and then (d) collecting and pooling, from the chromatography of (c) for each sample, peaks that correspond to the product.Type: GrantFiled: March 13, 2013Date of Patent: August 30, 2016Assignee: Emerald Therapeutics, Inc.Inventors: Daniel J. Kleinbaum, Brian M. Frezza, Courtney E. Webster, Jonathan K. Leung, Bradley M. Bond, George W. Fraser, Alex M. Yoshikawa, Shayna L. Hilburg, Eric Shyr, Kyla N. Velaer