Patents by Inventor Asim Siddiqui

Asim Siddiqui 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: 20250174303
    Abstract: The present disclosure describes a method for assaying a biological sample. In some cases, the method comprises assaying a set of nucleic acids from the biological sample to obtain genotypic information of the biological sample. In some cases, the method comprises generating, based at least in part on the genotypic information, a set of expressible proteoforms that can be expressed from the set of nucleic acids. In some cases, the method comprises assaying a set of polyamino acids from the biological sample to generate proteomic information of the biological sample, wherein the proteomic information comprises a set of identifications for the set of polyamino acids. In some cases, the method comprises mapping the set of identifications to the set of expressible proteoforms, thereby determining a set of expressed proteoforms in the biological sample.
    Type: Application
    Filed: January 6, 2023
    Publication date: May 29, 2025
    Inventors: Margaret Donovan, Yingxiang Huang, Jian Wang, Sangtae Kim, John Blume, Asim Siddiqui, Daniel Hornburg, Shadi Roshdiferdosi, Mahdi Zamanighomi, Harendra Guturu, Alexey Stukalov
  • Publication number: 20250157570
    Abstract: In some aspects, the present disclosure provides a method for determining a polyamino acid descriptor associated with a biological state. The method can comprise removing technical variation from a proteomic dataset to generate a refined proteomic dataset, the technical variation arising from a predetermined non-biological factor, by training a neural network using a loss function. The loss function can be configured to increase a similarity between a first set of latent embeddings that are based on a first subset of polyamino acid descriptors in the proteomic dataset, wherein the first subset of polyamino acid descriptors are obtained from the same sample. The loss function can be configured to decrease the similarity between a second set of latent embeddings that are based on a second subset of polyamino acid descriptors in the proteomic dataset, wherein the second subset of polyamino acid descriptors are obtained from different samples.
    Type: Application
    Filed: February 15, 2023
    Publication date: May 15, 2025
    Inventors: Theodore Platt, Iman Mohtashemi, Hugo Kitano, Asim Siddiqui, Amir ALAVI, Harendra GUTURU
  • Publication number: 20250093334
    Abstract: In some aspects, the present disclosure provides a method for identifying one or more biomolecules. In some embodiments, the method comprises generating a set of biomolecules by incubating a cell in a supplemented medium under conditions sufficient for the cell to generate the set of biomolecules. In some embodiments, the method comprises contacting at least a portion of the supplemented medium with one or more surfaces to adsorb the set of biomolecules. In some embodiments, the method comprises removing the one or more surfaces and the set of biomolecules from the at least the portion of the supplemented medium to produce a separated sample. In some embodiments, the method comprises releasing, in the separated sample, the set of biomolecules from the one or more surfaces. In some embodiments, the method comprises detecting at least a subset of the set of biomolecules, thereby identifying one or more biomolecules.
    Type: Application
    Filed: January 13, 2023
    Publication date: March 20, 2025
    Inventors: Xiaoyan ZHAO, Ji Won HA, Margaret DONOVAN, Daniel HORNBURG, Asim SIDDIQUI
  • Publication number: 20240395362
    Abstract: Disclosed herein are methods and compositions for processing biofluid samples. Some such methods may include obtaining a biofluid sample from a subject having a disease state such as lung cancer. The biofluid sample may be contacted with a nanoparticles to adsorb proteins. The proteins may then be ionized or contacted with a detection reagent. Also disclosed herein are compositions comprising proteins coupled to a nanoparticle upon contact of the nanoparticle with a biofluid sample from a subject having a disease.
    Type: Application
    Filed: August 6, 2024
    Publication date: November 28, 2024
    Inventors: John E. BLUME, William C. MANNING, Gregory TROIANO, Asim SIDDIQUI, Philip MA, Omid C. FAROKHZAD
  • Publication number: 20240353419
    Abstract: Disclosed herein are particles and methods of using said particles in assays for detection of biomolecules in a sample. Various methods of the present disclosure utilize particles for biomolecule adsorption. In some aspects, the present disclosure provides methods which utilize multiple particle concentrations to differentially fractionate biological samples. In further aspects, the present disclosure provides methods which utilize low particle concentrations to enhance adsorbed biomolecule diversity.
    Type: Application
    Filed: July 3, 2024
    Publication date: October 24, 2024
    Inventors: Omid C. FAROKHZAD, Craig STOLARCZYK, John E. BLUME, Xiaoyan ZHAO, Martin GOLDBERG, Michael FIGA, Asim SIDDIQUI, Daniel HORNBURG, Damian HARRIS, Philip MA, Theodore PLATT, Shadi ROSHDIFERDOSI
  • Patent number: 12087405
    Abstract: Disclosed herein are methods and compositions for processing biofluid samples. Some such methods may include obtaining a biofluid sample from a subject having a disease state such as lung cancer. The biofluid sample may be contacted with a nanoparticles to adsorb proteins. The proteins may then be ionized or contacted with a detection reagent. Also disclosed herein are compositions comprising proteins coupled to a nanoparticle upon contact of the nanoparticle with a biofluid sample from a subject having a disease.
    Type: Grant
    Filed: April 13, 2022
    Date of Patent: September 10, 2024
    Assignee: PrognomIQ, Inc.
    Inventors: John E. Blume, William C. Manning, Gregory Troiano, Asim Siddiqui, Philip Ma, Omid C. Farokhzad
  • Publication number: 20240280558
    Abstract: In some aspects, the present disclosure provides a method for normalizing and processing mass spectrometry datasets. In some embodiments, the method comprises loading a plurality of mass spectrometry data obtained from a plurality of samples into a memory of a computing node to generate a cached dataset. In some embodiments, the method comprises transmitting a copy of the cached dataset to a plurality of cache memories of a plurality of computing nodes. In some embodiments, the method comprises determining, using the plurality of computing nodes, a plurality of feature values for the plurality of mass spectrometry data. In some embodiments, the method comprises normalizing, using the plurality of computing nodes, across the plurality of mass spectrometry datasets using the plurality of feature values to generate a plurality of normalized mass spectrometry data.
    Type: Application
    Filed: July 13, 2022
    Publication date: August 22, 2024
    Inventors: Theodore Platt, Iman Mohtashemi, Hugo Kitano, Asim Siddiqui
  • Publication number: 20240219400
    Abstract: The present disclosure provides a range of compositions and methods for enriching subsets of complex biological samples. Aspects of the present disclosure provide peptide-functionalized particles comprising affinities for subsets of biomolecules from complex biological samples. The present disclosure further provides methods for utilizing functionalized particles to fractionate and analyze complex biological samples.
    Type: Application
    Filed: April 29, 2022
    Publication date: July 4, 2024
    Inventors: Asim Siddiqui, Daniel Hornburg, Craig Stolarczyk, Yina Li, Hongwei Xia
  • Publication number: 20240125795
    Abstract: Disclosed herein are methods for identifying physicochemical properties associated with protein corona formation at the level of proteins and NP-functionalization. Further disclosed herein are compositions comprising combinations of particles configured for low abundance protein collection and deep proteomic analysis.
    Type: Application
    Filed: February 25, 2022
    Publication date: April 18, 2024
    Inventors: Daniel Hornburg, Craig Stolarczyk, Behzad Tangeysh, Asim Siddiqui, Tristan Brown, Shadi Roshdiferdosi, Martin Goldberg, Moaraj HASAN
  • Patent number: 11817180
    Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.
    Type: Grant
    Filed: February 19, 2019
    Date of Patent: November 14, 2023
    Assignee: Life Technologies Corporation
    Inventors: Zheng Zhang, Danwei Guo, Yuandan Lou, Asim Siddiqui, Dumitru Brinza
  • Publication number: 20230324401
    Abstract: Disclosed herein are particles and methods of using said particles in assays for detection of biomolecules in a sample. Various methods of the present disclosure utilize particles for biomolecule adsorption. In some aspects, the present disclosure provides methods which utilize multiple particle concentrations to differentially fractionate biological samples. In further aspects, the present disclosure provides methods which utilize low particle concentrations to enhance adsorbed biomolecule diversity.
    Type: Application
    Filed: July 19, 2021
    Publication date: October 12, 2023
    Inventors: Omid C. FAROKHZAD, Craig STOLARCZYK, John E. BLUME, Xiaoyan ZHAO, Martin GOLDBERG, Michael FIGA, Asim SIDDIQUI, Daniel HORNBURG, Damian HARRIS, Philip MA, Theodore PLATT, Shadi ROSHDIFERDOSI
  • Publication number: 20230212647
    Abstract: Disclosed herein are systems and methods of use thereof for coupling affinity reagents (e.g., in solution affinity reagents such as proteins, peptides, and nucleic acids and libraries of affinity reagents) with particles having coronas for rapid detection of proteins in a sample.
    Type: Application
    Filed: May 28, 2021
    Publication date: July 6, 2023
    Inventors: Omid C. FAROKHZAD, Philip MA, John E. BLUME, Asim SIDDIQUI
  • Patent number: 11664092
    Abstract: Disclosed herein are biomarkers associated with a disease state such as lung cancer, and methods of discovering or using biomarkers. Also disclosed herein are classifiers built on biomarkers and methods of detecting the disease state in samples from subjects. The method may include obtaining a data set that includes protein information from a biofluid sample, and may involve using a classifier to identify the sample as indicative of a healthy state, a disease state, or a comorbidity.
    Type: Grant
    Filed: January 26, 2022
    Date of Patent: May 30, 2023
    Assignee: PrognomIQ, Inc.
    Inventors: John E. Blume, William C. Manning, Gregory Troiano, Asim Siddiqui, Philip Ma, Omid C. Farokhzad
  • Patent number: 11600237
    Abstract: A liquid crystal display (LCD) device includes an LCD panel with a number (N) of pixel elements for displaying an image. A dimming panel includes N dimming elements. The dimming panel has a first mode to apply a uniform dimming to the N dimming elements to provide a privacy function for the LCD device. The dimming panel further has a second mode to a apply a per-element dimming to provide a local dimming function for the LCD device.
    Type: Grant
    Filed: July 29, 2021
    Date of Patent: March 7, 2023
    Assignee: Dell Products L.P.
    Inventors: Asim Siddiqui, Jong Seo Lee
  • Publication number: 20230037248
    Abstract: A liquid crystal display (LCD) device includes an LCD panel with a number (N) of pixel elements for displaying an image. A dimming panel includes N dimming elements. The dimming panel has a first mode to apply a uniform dimming to the N dimming elements to provide a privacy function for the LCD device. The dimming panel further has a second mode to a apply a per-element dimming to provide a local dimming function for the LCD device.
    Type: Application
    Filed: July 29, 2021
    Publication date: February 2, 2023
    Inventors: Asim Siddiqui, Jong Seo Lee
  • Publication number: 20220334118
    Abstract: Disclosed herein are methods and compositions for processing biofluid samples. Some such methods may include obtaining a biofluid sample from a subject having a disease state such as lung cancer. The biofluid sample may be contacted with a nanoparticles to adsorb proteins. The proteins may then be ionized or contacted with a detection reagent. Also disclosed herein are compositions comprising proteins coupled to a nanoparticle upon contact of the nanoparticle with a biofluid sample from a subject having a disease.
    Type: Application
    Filed: April 13, 2022
    Publication date: October 20, 2022
    Inventors: John E. Blume, William C. Manning, Gregory Troiano, Asim Siddiqui, Philip Ma, Omid C. Farokhzad
  • Publication number: 20220334123
    Abstract: Described herein are methods and systems for identifying protein-protein interactions using particle panels and protein corona formation. Also disclosed herein are systems and methods for enrichment analysis between protein annotations and particle biophysicochemical properties.
    Type: Application
    Filed: April 29, 2022
    Publication date: October 20, 2022
    Inventors: Omid FAROKHZAD, Asim SIDDIQUI, Margaret DONOVAN, John E. BLUME, Craig STOLARCZYK
  • Patent number: 11455924
    Abstract: A liquid crystal display (LCD) device includes a LCD panel and a source driver. The LCD panel includes pixel data inputs and a failure sensing circuit. The pixel data inputs are coupled to columns of pixel elements. The failure sensing circuit provides a failure indication on an output of the LCD panel. In a test mode, the source driver drives a first voltage onto all of the first pixel data inputs. The failure indication includes the first voltage when the LCD panel has no failures on any of the first pixel elements, and the failure indication includes any other second voltage when the LCD panel has at least one failing pixel element.
    Type: Grant
    Filed: July 30, 2021
    Date of Patent: September 27, 2022
    Assignee: Dell Products L.P.
    Inventors: Jong Seo Lee, Asim Siddiqui
  • Publication number: 20220284986
    Abstract: Identification of exon junctions includes obtaining a first read sequence based on a detected plurality of signals of a first sequence. A list of exon prefix and suffix sequences are generated by identifying exons of the human genome with a prefix sequence mapping to a suffix sequence of the first read sequence and by identifying exons with a suffix sequence mapping to a prefix sequence of the first read sequence. A pair of exon sequences is selected, with a first exon sequence being one of the exon suffix sequences and a second exon sequence being one of the exon prefix sequences. Summing a number of sequence elements of the first exon sequence that overlap the prefix of the first read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the first read sequence, and a constant is used to identify a fusion junction.
    Type: Application
    Filed: March 21, 2022
    Publication date: September 8, 2022
    Applicant: Life Technologies Corporation
    Inventors: Paolo Vatta, Onur Sakarya, Heinz Breu, Liviu Popescu, Asim Siddiqui, Fiona Hyland
  • Publication number: 20220260559
    Abstract: Disclosed herein are compositions, systems, and methods for identifying neurological diseases from biological sample analysis. A biological sample from a subject may be contacted to a particle to form a biomolecule corona, which may contain a subset of biomolecules from the biological sample and which can have utility for diagnosing a neurological disease state. Further disclosed herein are machine learning algorithms and trained classifiers for distinguishing neurological disease states based on biological data.
    Type: Application
    Filed: November 3, 2021
    Publication date: August 18, 2022
    Inventors: John BLUME, Ryan BENZ, Asim SIDDIQUI, Philip MA