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).
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Publication number: 20250174303Abstract: 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: ApplicationFiled: January 6, 2023Publication date: May 29, 2025Inventors: Margaret Donovan, Yingxiang Huang, Jian Wang, Sangtae Kim, John Blume, Asim Siddiqui, Daniel Hornburg, Shadi Roshdiferdosi, Mahdi Zamanighomi, Harendra Guturu, Alexey Stukalov
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Publication number: 20250157570Abstract: 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: ApplicationFiled: February 15, 2023Publication date: May 15, 2025Inventors: Theodore Platt, Iman Mohtashemi, Hugo Kitano, Asim Siddiqui, Amir ALAVI, Harendra GUTURU
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Publication number: 20250093334Abstract: 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: ApplicationFiled: January 13, 2023Publication date: March 20, 2025Inventors: Xiaoyan ZHAO, Ji Won HA, Margaret DONOVAN, Daniel HORNBURG, Asim SIDDIQUI
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Publication number: 20240395362Abstract: 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: ApplicationFiled: August 6, 2024Publication date: November 28, 2024Inventors: John E. BLUME, William C. MANNING, Gregory TROIANO, Asim SIDDIQUI, Philip MA, Omid C. FAROKHZAD
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Publication number: 20240353419Abstract: 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: ApplicationFiled: July 3, 2024Publication date: October 24, 2024Inventors: 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
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Patent number: 12087405Abstract: 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: GrantFiled: April 13, 2022Date of Patent: September 10, 2024Assignee: PrognomIQ, Inc.Inventors: John E. Blume, William C. Manning, Gregory Troiano, Asim Siddiqui, Philip Ma, Omid C. Farokhzad
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Publication number: 20240280558Abstract: 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: ApplicationFiled: July 13, 2022Publication date: August 22, 2024Inventors: Theodore Platt, Iman Mohtashemi, Hugo Kitano, Asim Siddiqui
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Publication number: 20240219400Abstract: 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: ApplicationFiled: April 29, 2022Publication date: July 4, 2024Inventors: Asim Siddiqui, Daniel Hornburg, Craig Stolarczyk, Yina Li, Hongwei Xia
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Publication number: 20240125795Abstract: 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: ApplicationFiled: February 25, 2022Publication date: April 18, 2024Inventors: Daniel Hornburg, Craig Stolarczyk, Behzad Tangeysh, Asim Siddiqui, Tristan Brown, Shadi Roshdiferdosi, Martin Goldberg, Moaraj HASAN
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Patent number: 11817180Abstract: 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: GrantFiled: February 19, 2019Date of Patent: November 14, 2023Assignee: Life Technologies CorporationInventors: Zheng Zhang, Danwei Guo, Yuandan Lou, Asim Siddiqui, Dumitru Brinza
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Publication number: 20230324401Abstract: 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: ApplicationFiled: July 19, 2021Publication date: October 12, 2023Inventors: 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
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Publication number: 20230212647Abstract: 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: ApplicationFiled: May 28, 2021Publication date: July 6, 2023Inventors: Omid C. FAROKHZAD, Philip MA, John E. BLUME, Asim SIDDIQUI
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Patent number: 11664092Abstract: 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: GrantFiled: January 26, 2022Date of Patent: May 30, 2023Assignee: PrognomIQ, Inc.Inventors: John E. Blume, William C. Manning, Gregory Troiano, Asim Siddiqui, Philip Ma, Omid C. Farokhzad
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Patent number: 11600237Abstract: 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: GrantFiled: July 29, 2021Date of Patent: March 7, 2023Assignee: Dell Products L.P.Inventors: Asim Siddiqui, Jong Seo Lee
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Publication number: 20230037248Abstract: 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: ApplicationFiled: July 29, 2021Publication date: February 2, 2023Inventors: Asim Siddiqui, Jong Seo Lee
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Publication number: 20220334118Abstract: 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: ApplicationFiled: April 13, 2022Publication date: October 20, 2022Inventors: John E. Blume, William C. Manning, Gregory Troiano, Asim Siddiqui, Philip Ma, Omid C. Farokhzad
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Publication number: 20220334123Abstract: 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: ApplicationFiled: April 29, 2022Publication date: October 20, 2022Inventors: Omid FAROKHZAD, Asim SIDDIQUI, Margaret DONOVAN, John E. BLUME, Craig STOLARCZYK
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Patent number: 11455924Abstract: 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: GrantFiled: July 30, 2021Date of Patent: September 27, 2022Assignee: Dell Products L.P.Inventors: Jong Seo Lee, Asim Siddiqui
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Publication number: 20220284986Abstract: 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: ApplicationFiled: March 21, 2022Publication date: September 8, 2022Applicant: Life Technologies CorporationInventors: Paolo Vatta, Onur Sakarya, Heinz Breu, Liviu Popescu, Asim Siddiqui, Fiona Hyland
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Publication number: 20220260559Abstract: 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: ApplicationFiled: November 3, 2021Publication date: August 18, 2022Inventors: John BLUME, Ryan BENZ, Asim SIDDIQUI, Philip MA