US 4792520A
· Stambrook et al.
· 1988
[cited by applicant]
US 6218122B1
· Friend et al.
· 2001
[cited by applicant]
US 6365367B1
· Friedman et al.
· 2002
[cited by applicant]
US 7271952B2
· Suzuki et al.
· 2007
[cited by applicant]
US 7390463B2
· He et al.
· 2008
[cited by applicant]
US 8551710B2
· Bernitz et al.
· 2013
[cited by applicant]
US 9371598B2
· Chee
· 2016
[cited by applicant]
US 9556473B2
· Bernitz et al.
· 2017
[cited by applicant]
US 9593365B2
· Frisen et al.
· 2017
[cited by applicant]
US 9598723B2
· Ammann et al.
· 2017
[cited by applicant]
US 20010053519A1
· Fodor et al.
· 2001
[cited by applicant]
US 20030032024A1
· Lizardi et al.
· 2003
[cited by applicant]
US 20030082556A1
· Kaufman et al.
· 2003
[cited by applicant]
US 20030143536A1
· Lizardi
· 2003
[cited by applicant]
US 20050089860A1
· Arita
· 2005
[cited by applicant]
US 20050208644A1
· Takiguchi et al.
· 2005
[cited by applicant]
US 20050287578A1
· Davis
· 2005
[cited by applicant]
US 20060050376A1
· Houston et al.
· 2006
[cited by applicant]
US 20060292559A1
· Reddy et al.
· 2006
[cited by applicant]
US 20090298718A1
· Denman et al.
· 2009
[cited by applicant]
US 20110223585A1
· Gullberg et al.
· 2011
[cited by applicant]
US 20120301886A1
· Farrell et al.
· 2012
[cited by applicant]
US 20140056811A1
· Jacob et al.
· 2014
[cited by applicant]
US 20140057799A1
· Johnson et al.
· 2014
[cited by applicant]
US 20160257993A1
· Boyden et al.
· 2016
[cited by applicant]
US 20160369329A1
· Cai et al.
· 2016
[cited by applicant]
US 20170107563A1
· Samusik et al.
· 2017
[cited by applicant]
US 20190017106A1
· Frisen et al.
· 2019
[cited by applicant]
US 20190071668A1
· Schmidt et al.
· 2019
[cited by applicant]
US 20190113423A1
· Goodman et al.
· 2019
[cited by applicant]
US 20190155835A1
· Daugharthy et al.
· 2019
[cited by applicant]
US 20190241945A1
· Malyshev
· 2019
[cited by examiner]
US 20190376123A1
· Bobrow et al.
· 2019
[cited by applicant]
US 20200277663A1
· Ramachandran Iyer et al.
· 2020
[cited by applicant]
US 20200277664A1
· Frenz
· 2020
[cited by applicant]
US 20200362334A1
· Regev et al.
· 2020
[cited by applicant]
US 20210017596A1
· Tong et al.
· 2021
[cited by applicant]
US 20210039062A1
· Mirkin et al.
· 2021
[cited by applicant]
US 20210108195A1
· Bernate et al.
· 2021
[cited by applicant]
US 20210382033A1
· Mir
· 2021
[cited by applicant]
US 20210388424A1
· Bava
· 2021
[cited by applicant]
US 20230088043A1
· Kovacs et al.
· 2023
[cited by applicant]
US 20230100215A1
· Glezer et al.
· 2023
[cited by applicant]
JP 2005265627A
· 2005
[cited by applicant]
JP 5970959B2
· 2016
[cited by applicant]
WO WO2005039389A2
· 2005
[cited by applicant]
WO WO2008042067A2
· 2008
[cited by applicant]
WO WO2013090360A2
· 2013
[cited by applicant]
WO WO2013090360A3
· 2013
[cited by applicant]
WO WO2014030066A2
· 2014
[cited by applicant]
WO WO2014030066A3
· 2014
[cited by applicant]
WO WO2017079382A1
· 2017
[cited by applicant]
WO WO2018091676A1
· 2018
[cited by applicant]
WO WO2019068880A1
· 2019
[cited by applicant]
WO WO2019084062A1
· 2019
[cited by applicant]
WO WO2019199579A1
· 2019
[cited by applicant]
WO WO2019222284A1
· 2019
[cited by applicant]
WO WO2020028194A1
· 2020
[cited by applicant]
WO WO2020076976A1
· 2020
[cited by applicant]
WO WO2020076979A1
· 2020
[cited by applicant]
WO WO2020096687A1
· 2020
[cited by applicant]
WO WO2020099640A1
· 2020
[cited by applicant]
WO WO2020123309A1
· 2020
[cited by applicant]
WO WO2020160044A1
· 2020
[cited by applicant]
WO WO2022032194A1
· 2022
[cited by applicant]
WO WO2022032195A2
· 2022
[cited by applicant]
WO WO2022032195A3
· 2022
[cited by applicant]
WO WO2022235764A1
· 2022
[cited by applicant]
Ambardar et al., High Throughput Sequencing: An Overview of Sequencing Chemistry. Indian J. of Microbiology 56(4) :394 (Year: 2016).
[cited by examiner]
Krywkowski et al., Chpt. 14 : Padlock Probes to detect Single Nucleotide Polymorphisms. Methods in Molecular Biology 1649 :209 (Year: 2018).
[cited by examiner]
You et al., Design of LNA probes that improve mismatch discrimination. Nucleic Acids Research 34(8) : e60 (Year: 2006).
[cited by examiner]
Zhang et al., Amplification of circularizable probes for the detection of target nucleic acids and proteins. Clinical Chemistry Acta 363: 61 (Year: 2006).
[cited by examiner]
Wahlestedt et al. Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. PNAS 97(10) : 5633-5638 (Year: 2000).
[cited by examiner]
Payne A., MIT Master Thesis Towards Sequencing by synthesis in situ (Year: 2017).
[cited by examiner]
Krywkowski et al.Methods in Molecular Biology 1649:209 (Year: 2018).
[cited by examiner]
Agrawal, S. et al. (Nov. 15, 2016). “Nivolumab dose selection: challenges, opportunities, and lessons learned for cancer immunotherapy,”
[cited by applicant]
Ahern, H. (1995) “Biochemical, reagent kits offer scientists good return on investment,”
[cited by applicant]
Alon, S. et al. (2020). “Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems,”
[cited by applicant]
Arce, S. et al. (2013). “Fast and accurate automated cell boundary determination for fluorescence microscopy,”
[cited by applicant]
Banér, J. et al. (April 1, 005). “Analysis of T-cell receptor vβ gene repertoires after immune stimulation and in malignancy by use of padlock probes and microarrays,”
[cited by applicant]
Bullinger, L. et al. (Apr. 15, 2004). “Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia,”
[cited by applicant]
Carow, B. et al. (2019). “Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma,”
[cited by applicant]
Carpenter, A. E. et al (2006, e-published Oct. 31, 2016). “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,”
[cited by applicant]
Catuogno, S. et al. (Apr. 8, 2011). “Recent advance in biosensors for microRNAs detection in cancer,”
[cited by applicant]
Chen, F. et al. (Jan. 30, 2015, e-published Jan. 15, 2015). “Optical imaging. Expansion microscopy,”
[cited by applicant]
Chen, K. H. et al. (Apr. 24, 2015, e-published Apr. 9, 2015). “RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells,”
[cited by applicant]
Chen, X. et al. (Feb. 28, 2018, e-published Nov. 28, 2017). “Efficient in situ barcode sequencing using padlock probe-based BaristaSeq,”
[cited by applicant]
Christian, A.T. et al. (Dec. 4, 2001, e-published Nov. 27, 2001). “Detection of DNA point mutations and mRNA expression levels by rolling circle amplification in individual cells,”
[cited by applicant]
Costea, P. I. et al. (Mar. 4, 2013). “TagGD: fast and accurate software for DNA Tag generation and demultiplexing,”
[cited by applicant]
Daigeler, A. et al. (Jul. 6, 2006). “Clinicopathological findings in a case series of extrathoracic solitary fibrous tumors of soft tissues,”
[cited by applicant]
Denkert, C. et al. (Nov. 1, 2015, e-published Aug. 14, 2015). “Strategies for developing Ki67 as a useful biomarker in breast cancer,”
[cited by applicant]
Edelman, M. J. et al. (May 1997, e-published Feb. 28, 2002). “The utility of follow-up testing after curative cancer therapy: a critical review and economic analysis,”
[cited by applicant]
El-Sagheer, A. H. et al. (Aug. 21, 2012, e-published Mar. 22, 2012).“Click nucleic acid ligation: applications in biology and nanotechnology,”
[cited by applicant]
Extended European Search Report mailed Mar. 18, 2024, for EP Application No. 21852670.5, 13 pages.
[cited by applicant]
Fijnvandraat, A. C. et al. (Sep. 1, 2002, e-published Sep. 10, 2002). “Nonradioactive in situ detection of mRNA in ES cell-derived cardiomyocytes and in the developing heart,”
[cited by applicant]
Frank, D. N. (Oct. 29, 2009). “BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing,”
[cited by applicant]
Fredriksson, S. et al. (Apr. 2007, e-published Mar. 18, 2007). “Multiplexed protein detection by proximity ligation for cancer biomarker validation,”
[cited by applicant]
Fredriksson, S. et al. (May 1, 2002). “Protein detection using proximity-dependent DNA ligation assays,”
[cited by applicant]
Gao, H. et al. (Dec. 2019, e-published Oct. 17, 2019). “Rolling circle amplification for single cell analysis and in situ sequencing,”
[cited by applicant]
Garmendia, C. et al. (Feb. 1992). “The bacteriophage phi 29 DNA polymerase, a proofreading enzyme,”
[cited by applicant]
Gelali, E. et al. (Apr. 9, 2019). “iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture,”
[cited by applicant]
Gore, A. et al. (Mar. 3, 2011). “Somatic coding mutations in human induced pluripotent stem cells,”
[cited by applicant]
Gullberg, M. et al. (May 21, 2004). “Cytokine detection by antibody-based proximity ligation,”
[cited by applicant]
Guo, J. et al. (Jul. 8, 2008, e-published Jun. 30, 2008). “Four-color DNA sequencing with 3′- O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides,”
[cited by applicant]
Gyllborg, D. et al. (Nov. 4, 2020). “Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue,”
[cited by applicant]
Hagai, T. et al. (Nov. 2018, e-published Oct. 24, 2018). “Gene expression variability across cells and species shapes innate immunity,”
[cited by applicant]
Hamaday, M. et al. (Mar. 2008) “Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex,”
[cited by applicant]
Hamilton, N. (2009) “Quantification and its applications in fluorescent microscopy imaging.”
[cited by applicant]
Hardenbol, P. et al. (2003) “Multiplexed genotyping with sequence-tagged molecular inversion probes.”
[cited by applicant]
Heintzmann, R. et al. (Dec. 13, 2017, e-published Nov. 10, 2017). “Super-Resolution Structured Illumination Microscopy,”
[cited by applicant]
Hu, Y. et al. (2014) “Sensitive quantification of messenger RNA with a real-time ligase chain reaction by using a ribonucleotide-modified DNA probe.”
[cited by applicant]
International Search Report and Written Opinion mailed on Nov. 23, 2021, for PCT Application No. PCT/US2021/045104, filed Aug. 6, 2021, 15 pages.
[cited by applicant]
International Search Report & Written Opinion mailed on Jan. 31, 2022, for PCT Application No. PCT/US2021/045105, filed Aug. 6, 2022, 18 pages.
[cited by applicant]
International Search Report & Written Opinion mailed on Sep. 19, 2022, for PCT Application No. PCT/US2022/027630, filed May 4, 2022, 14 pages.
[cited by applicant]
Jeong, S. et al. (Apr. 2020, e-published Jan. 30, 2020). “Current immunoassay methods and their applications to clinically used biomarkers of breast cancer,”
[cited by applicant]
Kappler, K. et al. (Aug. 2020, e-published Aug. 5, 2020). “Emergence and significance of carbohydrate-specific antibodies,”
[cited by applicant]
Ke, R. et al. (Sep. 2013, e-published Jul. 14, 2013) “In situ sequencing for RNA analysis in preserved tissue and cells.”
[cited by applicant]
Klein A.M., et al. (Jul. 25, 2017). “InDrops and Drop-seq technologies for single-cell sequencing,”
[cited by applicant]
Kobori, T. et al. (2014) “Expanding possibilities of rolling circle amplification as a biosensing platform,”
[cited by applicant]
Kohman, R. E. et al. (Apr. 28, 2020). “Fluorescent in situ sequencing of DNA barcoded antibodies,”
[cited by applicant]
Lareau, C. A., et al. (Feb. 13, 2020). “Inference and effects of barcode multiplets in droplet-based single-cell assays,”
[cited by applicant]
Larsson, C. et al., (May 2010, e-published Apr. 11, 2010). “In situ detection and genotyping of individual mRNA molecules,”
[cited by applicant]
Lee, J. H. et al. (e-published Feb. 12, 2015). “Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues,”
[cited by applicant]
Lee, J. H. et al. (Feb. 27, 2014, e-published Feb. 20, 2014). “Highly multiplexed subcellular RNA sequencing in situ,”
[cited by applicant]
Li, J. B. et al. (Sep. 2009, e-published Jun. 12, 2009). Multiplex padlock targeted sequencing reveals human hypermutable CpG variations,
[cited by applicant]
Li, J. B. et al. (May 29, 2009). “Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing,”
[cited by applicant]
Li, N. et al. (May 21, 2009) “Stand-alone rolling circle amplification combined with capillary electrophoresis for specific detection of small RNA.”
[cited by applicant]
Lubeck, E. et al. (Jul. 2012, e-published Jun. 3, 2012). “Single-cell systems biology by super-resolution imaging and combinatorial labeling,”
[cited by applicant]
Lubeck, E. et al. (Apr. 2014, e-published Mar. 28, 2014). “Single-cell in situ RNA profiling by sequential hybridization,”
[cited by applicant]
Manuguerra I. et al. (May 1, 2018). “Gene assembly via one-pot chemical ligation of DNA promoted by DNA nanostructures,”
[cited by applicant]
Mignardi, M. et al. (Apr. 28, 2014). “Fourth-generation sequencing in the cell and the clinic,”
[cited by applicant]
Mitra, R.D. et al. (2003) “Fluorescent in situ sequencing on polymerase colonies.”
[cited by applicant]
Mohammadi-Kambs, M. et al. (2017) “Hamming distance as a concept in DNA molecular recognition.”
[cited by applicant]
Nilsson, M. et al. (Sep. 30, 1994). “Padlock probes: circularizing oligonucleotides for localized DNA detection,”
[cited by applicant]
Nitta, H. et al. (Aug. 2013, e-published Nov. 15, 2015). “New methods for ALK status diagnosis in non-small-Cell lung Cancer: an improved ALK immunohistochemical assay and a new, Brightfield, dual ALK IHC-In situ hybrid…
[cited by applicant]
Odeh, F., et al. (Dec. 18, 2019). “Aptamers Chemistry: Chemical Modifications and Conjugation Strategies,”
[cited by applicant]
Ouladan, S. et al. (Jun. 2015, e-published Apr. 20, 2015). “Differential diagnosis of solitary fibrous tumors: A study of 454 soft tissue tumors indicating the diagnostic value of nuclear STAT6 relocation and ALDH1 expr…
[cited by applicant]
Park, M. S. et al. (May 11, 2013). “The role of chemotherapy in advanced solitary fibrous tumors: a retrospective analysis,”
[cited by applicant]
Patel, A.P. et al. (Jun. 20, 2014, e-published Jun. 12, 2014). “Single-cell RNA—seq highlights intratumoral heterogeneity in primary glioblastoma,”
[cited by applicant]
Pearson, A. et al. (Aug. 2016, e-published May 13, 2016). “High-Level Clonal FGFR Amplification and Response to FGFR Inhibition in a Translational Clinical Trial,”
[cited by applicant]
Peerzade, S.A. et al. (May 8, 2020). “Ultrabright Fluorescent Silica Nanoparticles for Multiplexed Detection,”
[cited by applicant]
Peters, J.M. et al. (Jan. 2011). “Multiparameter flow cytometry in the diagnosis and management of acute leukemia,”
[cited by applicant]
Porreca, G. J. et al. (Nov. 2007, e-published Oct. 14, 2007). “Multiplex amplification of large sets of human exons,”
[cited by applicant]
Rouhanifard, S. H., et al. (2018) “Exponential fluorescent amplification of individual RNAs using clampFISH probes.”
[cited by applicant]
Sansone, A. (Jun. 2019). “Spatial transcriptomics levels up,”
[cited by applicant]
Sapoznik, E. et al. (Nov. 12, 2020). “A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics,”
[cited by applicant]
Schallmeiner, E. et al. (Feb. 1, 2007, e-published Dec. 17, 2006). “Sensitive protein detection via triple-binder proximity ligation assays,”
[cited by applicant]
Schlachter, S. et al. (2009). “A method to unmix multiple fluorophores in microscopy images with minimal a priori information,”
[cited by applicant]
Shirakawa, H. et al. (Mar. 2004). “Blind spectral decomposition of single-cell fluorescence by parallel factor analysis,”
[cited by applicant]
Stratagene Catalog, The (1988). p. 39.
[cited by applicant]
Strell, C. et al. (Apr. 2019, e-published Mar. 14, 2019). “Placing RNA in context and space—methods for spatially resolved transcriptomics,”
[cited by applicant]
Suzuki, A. et al. (Dec. 20, 2019). “Characterization of cancer omics and drug perturbations in panels of lung cancer cells,”
[cited by applicant]
Takahashi, H. et al. (2018) “RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection.”
[cited by applicant]
Tang, S. et al. (Aug. 2, 2016). “Suppression of rolling circle amplification by nucleotide analogs in circular template for three DNA polymerases,”
[cited by applicant]
Turczyk, B. M. et al. (Jul. 2020). “Spatial sequencing: a perspective,”
[cited by applicant]
Vickovic, S. et al. (Oct. 2019, e-published Sep. 9, 2019). “High-definition spatial transcriptomics for in situ tissue profiling,”
[cited by applicant]
Wang, G. et al. (Mar. 19, 2018). “Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy,”
[cited by applicant]
Wang X. et al. (Jul. 27, 2018, e-published Jun. 21, 2018). “Three-dimensional intact-tissue sequencing of single-cell transcriptional states,”
[cited by applicant]
Wassie, A. T. et al. (e-published Dec. 20, 2018). “Expansion microscopy: principles and uses in biological research,”
[cited by applicant]
Weibrecht, I. et al. (Jan. 2013) “In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay.”
[cited by applicant]
Wilson, C.S. et al. (Jul. 15, 2006, e-published Apr. 4, 2006). “Gene expression profiling of adult acute myeloid leukemia identifies novel biologic clusters for risk classification and outcome prediction,”
[cited by applicant]
Xu, Q. et al. (2009) “Design of 240,000 orthogonal 25mer DNA barcode probes.”
[cited by applicant]
York, A.G. et al. (Nov. 2013, e-published Oct. 6, 2013). “Instant super-resolution imaging in live cells and embryos via analog image processing,”
[cited by applicant]
Zhang, K. et al. (Aug. 2009, e-published Jul. 20, 2009). “Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human,”
[cited by applicant]
Zheng, G. X. et al. (Jan. 16, 2017). “Massively parallel digital transcriptional profiling of single cells,”
[cited by applicant]
Ambardar, S. et al. (Dec. 2016, e-published Jul. 9, 2016). “High throughput sequencing: an overview of sequencing chemistry,”
[cited by applicant]
Borkamo, E. D. et al. (Dec. 1, 2009, e-published Nov. 19, 2009). “cDNA microarray analysis of serially sampled cervical cancer specimens from patients treated with thermochemoradiotherapy,”
[cited by applicant]
Conze, T. et al. (Jul. 2009, e-published Feb. 19, 2009). “Analysis of genes, transcripts, and proteins via DNA ligation,”
[cited by applicant]
Frances-Soriano, L. et al. (Jan. 26, 2021, e-published Dec. 28, 2020). “In Situ rolling circle amplification Forster resonance energy transfer (RCA-FRET) for washing-free real-time single-protein imaging,”
[cited by applicant]
Krzywkowski, T. et al. (Oct. 2018). “Chimeric padlock and iLock probes for increased efficiency of targeted RNA detection,”
[cited by applicant]
Roussis, I. M. et al. (Mar. 3, 2017). “RNA whole-mount in situ hybridization proximity ligation assay (rISH-PLA), an assay for detecting RNA-protein complexes in intact cells,”
[cited by applicant]
Söderberg, O. et al. (Dec. 2006, e-published Oct. 29, 2006). “Direct observation of individual endogenous protein complexes in situ by proximity ligation,”
[cited by applicant]
You, Y. et al. (Apr. 1, 2006, e-published Jan. 1, 2006). “Design of LNA probes that improve mismatch discrimination,”
[cited by applicant]
Zhang, D. et al. (Jan. 2006, e-published Aug. 24, 2005). “Amplification of circularizable probes for the detection of target nucleic acids and proteins,”
[cited by applicant]
Konry, T. et al. (Feb. 7, 2011, e-published Dec. 27, 2010). “Ultrasensitive detection of low-abundance surface-marker protein using isothermal rolling circle amplification in a microfluidic nanoliter platform,”
[cited by applicant]
Payne, A. C. (Jun. 2017, e-published Jul. 31, 2017). “Towards sequencing by synthesis in situ. Doctoral Dissertation.”
[cited by applicant]