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Showing 1 to 12 of 15 entries
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A home-brew real-time PCR assay for reliable detection and quantification of mature miR-122.

Applied immunohistochemistry & molecular morphology : AIMM

Naderi M, Abdul Tehrani H, Soleimani M, Shabani I, Hashemi SM.
PMID: 25075470
Appl Immunohistochem Mol Morphol. 2015 Sep;23(8):601-6. doi: 10.1097/PAI.0000000000000125.

miR-122 is a liver-specific miRNA that has significant gene expression alterations in response to specific pathophysiological circumstances of liver such as drug-induced liver injury, hepatocellular carcinoma, and hepatitis B and C virus infections. Therefore, accurate and precise quantification of...

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Naderi M, Abdul Tehrani H, Soleimani M, et al. A home-brew real-time PCR assay for reliable detection and quantification of mature miR-122. Appl Immunohistochem Mol Morphol. 2015;23(8):601-6doi: 10.1097/PAI.0000000000000125.
Naderi, M., Abdul Tehrani, H., Soleimani, M., Shabani, I., & Hashemi, S. M. (2015). A home-brew real-time PCR assay for reliable detection and quantification of mature miR-122. Applied immunohistochemistry & molecular morphology : AIMM, 23(8), 601-6. https://doi.org/10.1097/PAI.0000000000000125
Naderi, Mahmood, et al. "A home-brew real-time PCR assay for reliable detection and quantification of mature miR-122." Applied immunohistochemistry & molecular morphology : AIMM vol. 23,8 (2015): 601-6. doi: https://doi.org/10.1097/PAI.0000000000000125
Naderi M, Abdul Tehrani H, Soleimani M, Shabani I, Hashemi SM. A home-brew real-time PCR assay for reliable detection and quantification of mature miR-122. Appl Immunohistochem Mol Morphol. 2015 Sep;23(8):601-6. doi: 10.1097/PAI.0000000000000125. PMID: 25075470.
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Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells.

Journal of the American Chemical Society

Lee SY, Kang MG, Shin S, Kwak C, Kwon T, Seo JK, Kim JS, Rhee HW.
PMID: 28156110
J Am Chem Soc. 2017 Mar 15;139(10):3651-3662. doi: 10.1021/jacs.6b10418. Epub 2017 Mar 03.

The inner mitochondrial membrane (IMM) proteome plays a central role in maintaining mitochondrial physiology and cellular metabolism. Various important biochemical reactions such as oxidative phosphorylation, metabolite production, and mitochondrial biogenesis are conducted by the IMM proteome, and mitochondria-targeted therapeutics...

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Lee SY, Kang MG, Shin S, et al. Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells. J Am Chem Soc. 2017;139(10):3651-3662doi: 10.1021/jacs.6b10418.
Lee, S. Y., Kang, M. G., Shin, S., Kwak, C., Kwon, T., Seo, J. K., Kim, J. S., & Rhee, H. W. (2017). Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells. Journal of the American Chemical Society, 139(10), 3651-3662. https://doi.org/10.1021/jacs.6b10418
Lee, Song-Yi, et al. "Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells." Journal of the American Chemical Society vol. 139,10 (2017): 3651-3662. doi: https://doi.org/10.1021/jacs.6b10418
Lee SY, Kang MG, Shin S, Kwak C, Kwon T, Seo JK, Kim JS, Rhee HW. Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells. J Am Chem Soc. 2017 Mar 15;139(10):3651-3662. doi: 10.1021/jacs.6b10418. Epub 2017 Mar 03. PMID: 28156110.
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Single-Nucleotide-Resolution Computing and Memory in Living Cells.

Molecular cell

Farzadfard F, Gharaei N, Higashikuni Y, Jung G, Cao J, Lu TK.
PMID: 31442423
Mol Cell. 2019 Aug 22;75(4):769-780.e4. doi: 10.1016/j.molcel.2019.07.011.

The ability to process and store information in living cells is essential for developing next-generation therapeutics and studying biology in situ. However, existing strategies have limited recording capacity and are challenging to scale. To overcome these limitations, we developed...

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Farzadfard F, Gharaei N, Higashikuni Y, et al. Single-Nucleotide-Resolution Computing and Memory in Living Cells. Mol Cell. 2019;75(4):769-780.e4doi: 10.1016/j.molcel.2019.07.011.
Farzadfard, F., Gharaei, N., Higashikuni, Y., Jung, G., Cao, J., & Lu, T. K. (2019). Single-Nucleotide-Resolution Computing and Memory in Living Cells. Molecular cell, 75(4), 769-780.e4. https://doi.org/10.1016/j.molcel.2019.07.011
Farzadfard, Fahim, et al. "Single-Nucleotide-Resolution Computing and Memory in Living Cells." Molecular cell vol. 75,4 (2019): 769-780.e4. doi: https://doi.org/10.1016/j.molcel.2019.07.011
Farzadfard F, Gharaei N, Higashikuni Y, Jung G, Cao J, Lu TK. Single-Nucleotide-Resolution Computing and Memory in Living Cells. Mol Cell. 2019 Aug 22;75(4):769-780.e4. doi: 10.1016/j.molcel.2019.07.011. PMID: 31442423; PMCID: PMC7001763.
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Crystal structure of the human NLRP9 pyrin domain suggests a distinct mode of inflammasome assembly.

FEBS letters

Marleaux M, Anand K, Latz E, Geyer M.
PMID: 32542665
FEBS Lett. 2020 Aug;594(15):2383-2395. doi: 10.1002/1873-3468.13865. Epub 2020 Jul 06.

Inflammasomes are cytosolic multimeric signaling complexes of the innate immune system that induce activation of caspases. The NOD-like receptor NLRP9 recruits the adaptor protein ASC to form an ASC-dependent inflammasome to limit rotaviral replication in intestinal epithelial cells, but...

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Marleaux M, Anand K, Latz E, et al. Crystal structure of the human NLRP9 pyrin domain suggests a distinct mode of inflammasome assembly. FEBS Lett. 2020;594(15):2383-2395doi: 10.1002/1873-3468.13865.
Marleaux, M., Anand, K., Latz, E., & Geyer, M. (2020). Crystal structure of the human NLRP9 pyrin domain suggests a distinct mode of inflammasome assembly. FEBS letters, 594(15), 2383-2395. https://doi.org/10.1002/1873-3468.13865
Marleaux, Michael, et al. "Crystal structure of the human NLRP9 pyrin domain suggests a distinct mode of inflammasome assembly." FEBS letters vol. 594,15 (2020): 2383-2395. doi: https://doi.org/10.1002/1873-3468.13865
Marleaux M, Anand K, Latz E, Geyer M. Crystal structure of the human NLRP9 pyrin domain suggests a distinct mode of inflammasome assembly. FEBS Lett. 2020 Aug;594(15):2383-2395. doi: 10.1002/1873-3468.13865. Epub 2020 Jul 06. PMID: 32542665.
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Low-voltage electrical cell lysis using a microfluidic device.

Biomedical microdevices

Wei XY, Li JH, Wang L, Yang F.
PMID: 30790126
Biomed Microdevices. 2019 Feb 21;21(1):22. doi: 10.1007/s10544-019-0369-x.

Cell lysis, where cellular material is released, is the basis for the separation and purification of cell contents, biochemical analysis, and other related experiments. It is also a key step in molecular, real-time, and cancer diagnoses as well as...

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Wei XY, Li JH, Wang L, et al. Low-voltage electrical cell lysis using a microfluidic device. Biomed Microdevices. 2019;21(1):22doi: 10.1007/s10544-019-0369-x.
Wei, X. Y., Li, J. H., Wang, L., & Yang, F. (2019). Low-voltage electrical cell lysis using a microfluidic device. Biomedical microdevices, 21(1), 22. https://doi.org/10.1007/s10544-019-0369-x
Wei, Xiao-Yu, et al. "Low-voltage electrical cell lysis using a microfluidic device." Biomedical microdevices vol. 21,1 (2019): 22. doi: https://doi.org/10.1007/s10544-019-0369-x
Wei XY, Li JH, Wang L, Yang F. Low-voltage electrical cell lysis using a microfluidic device. Biomed Microdevices. 2019 Feb 21;21(1):22. doi: 10.1007/s10544-019-0369-x. PMID: 30790126.
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Broad spectral excitation of opsin for enhanced stimulation of cells.

Optics letters

Satpathy S, Batabyal S, Dhakal KR, Lin J, Kim YT, Mohanty SK.
PMID: 26030533
Opt Lett. 2015 Jun 01;40(11):2465-8. doi: 10.1364/OL.40.002465.

Optical stimulation of cells expressing light-sensitive proteins (opsins) has allowed targeted activation with cellular specificity. However, since narrow-band light has been used for excitation of these optogenetic probes, only active stimulation strategies are being attempted for clinical applications such...

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Satpathy S, Batabyal S, Dhakal KR, et al. Broad spectral excitation of opsin for enhanced stimulation of cells. Opt Lett. 2015;40(11):2465-8doi: 10.1364/OL.40.002465.
Satpathy, S., Batabyal, S., Dhakal, K. R., Lin, J., Kim, Y. T., & Mohanty, S. K. (2015). Broad spectral excitation of opsin for enhanced stimulation of cells. Optics letters, 40(11), 2465-8. https://doi.org/10.1364/OL.40.002465
Satpathy, Sarmishtha, et al. "Broad spectral excitation of opsin for enhanced stimulation of cells." Optics letters vol. 40,11 (2015): 2465-8. doi: https://doi.org/10.1364/OL.40.002465
Satpathy S, Batabyal S, Dhakal KR, Lin J, Kim YT, Mohanty SK. Broad spectral excitation of opsin for enhanced stimulation of cells. Opt Lett. 2015 Jun 01;40(11):2465-8. doi: 10.1364/OL.40.002465. PMID: 26030533.
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Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.

Cell

Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, Golbazi A, Maenpaa E, Stricker K, Guha Thakurta S, Zhang T, Rad R, Pan J, Nusinow DP, Paulo JA, Schweppe DK, Vaites LP, Harper JW, Gygi SP.
PMID: 33961781
Cell. 2021 May 27;184(11):3022-3040.e28. doi: 10.1016/j.cell.2021.04.011. Epub 2021 May 06.

Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. The first, BioPlex 3.0, results from affinity purification of 10,128...

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Huttlin EL, Bruckner RJ, Navarrete-Perea J, et al. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell. 2021;184(11):3022-3040.e28doi: 10.1016/j.cell.2021.04.011.
Huttlin, E. L., Bruckner, R. J., Navarrete-Perea, J., Cannon, J. R., Baltier, K., Gebreab, F., Gygi, M. P., Thornock, A., Zarraga, G., Tam, S., Szpyt, J., Gassaway, B. M., Panov, A., Parzen, H., Fu, S., Golbazi, A., Maenpaa, E., Stricker, K., Guha Thakurta, S., Zhang, T., Rad, R., Pan, J., Nusinow, D. P., Paulo, J. A., Schweppe, D. K., Vaites, L. P., Harper, J. W., & Gygi, S. P. (2021). Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell, 184(11), 3022-3040.e28. https://doi.org/10.1016/j.cell.2021.04.011
Huttlin, Edward L, et al. "Dual proteome-scale networks reveal cell-specific remodeling of the human interactome." Cell vol. 184,11 (2021): 3022-3040.e28. doi: https://doi.org/10.1016/j.cell.2021.04.011
Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, Golbazi A, Maenpaa E, Stricker K, Guha Thakurta S, Zhang T, Rad R, Pan J, Nusinow DP, Paulo JA, Schweppe DK, Vaites LP, Harper JW, Gygi SP. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell. 2021 May 27;184(11):3022-3040.e28. doi: 10.1016/j.cell.2021.04.011. Epub 2021 May 06. PMID: 33961781; PMCID: PMC8165030.
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Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins.

Nature communications

Chen L, Park JE, Paa P, Rajakumar PD, Prekop HT, Chew YT, Manivannan SN, Chew WL.
PMID: 33654077
Nat Commun. 2021 Mar 02;12(1):1384. doi: 10.1038/s41467-021-21559-9.

Many genetic diseases are caused by single-nucleotide polymorphisms. Base editors can correct these mutations at single-nucleotide resolution, but until recently, only allowed for transition edits, addressing four out of twelve possible DNA base substitutions. Here, we develop a class...

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Chen L, Park JE, Paa P, et al. Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins. Nat Commun. 2021;12(1):1384doi: 10.1038/s41467-021-21559-9.
Chen, L., Park, J. E., Paa, P., Rajakumar, P. D., Prekop, H. T., Chew, Y. T., Manivannan, S. N., & Chew, W. L. (2021). Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins. Nature communications, 12(1), 1384. https://doi.org/10.1038/s41467-021-21559-9
Chen, Liwei, et al. "Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins." Nature communications vol. 12,1 (2021): 1384. doi: https://doi.org/10.1038/s41467-021-21559-9
Chen L, Park JE, Paa P, Rajakumar PD, Prekop HT, Chew YT, Manivannan SN, Chew WL. Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins. Nat Commun. 2021 Mar 02;12(1):1384. doi: 10.1038/s41467-021-21559-9. PMID: 33654077; PMCID: PMC7925527.
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Increasing the targeting scope and efficiency of base editing with Proxy-BE strategy.

FEBS letters

Liu Y, Li G, Yang G, Gu H, Huang S, Yu W, Qin G, Liu X, Zhou F, Huang X, Wei Y.
PMID: 31837228
FEBS Lett. 2020 Apr;594(8):1319-1328. doi: 10.1002/1873-3468.13719. Epub 2019 Dec 29.

Base editors (BEs) are widely used in precise gene editing due to their simplicity and versatility. However, their efficiencies are hindered by various obstacles. Considering the chromatin microenvironment as a possible obstacle, here, we demonstrate a further development of...

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Liu Y, Li G, Yang G, et al. Increasing the targeting scope and efficiency of base editing with Proxy-BE strategy. FEBS Lett. 2019;594(8):1319-1328doi: 10.1002/1873-3468.13719.
Liu, Y., Li, G., Yang, G., Gu, H., Huang, S., Yu, W., Qin, G., Liu, X., Zhou, F., Huang, X., & Wei, Y. (2020). Increasing the targeting scope and efficiency of base editing with Proxy-BE strategy. FEBS letters, 594(8), 1319-1328. https://doi.org/10.1002/1873-3468.13719
Liu, Yin, et al. "Increasing the targeting scope and efficiency of base editing with Proxy-BE strategy." FEBS letters vol. 594,8 (2020): 1319-1328. doi: https://doi.org/10.1002/1873-3468.13719
Liu Y, Li G, Yang G, Gu H, Huang S, Yu W, Qin G, Liu X, Zhou F, Huang X, Wei Y. Increasing the targeting scope and efficiency of base editing with Proxy-BE strategy. FEBS Lett. 2020 Apr;594(8):1319-1328. doi: 10.1002/1873-3468.13719. Epub 2019 Dec 29. PMID: 31837228.
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Imaging Protein-Protein Interactions by Förster Resonance Energy Transfer (FRET) Microscopy in Live Cells.

Current protocols in protein science

Manzella-Lapeira J, Brzostowski JA.
PMID: 29984911
Curr Protoc Protein Sci. 2018 Aug;93(1):e58. doi: 10.1002/cpps.58. Epub 2018 Jul 09.

This updated unit compares three methods to acquire Förster Resonance Energy Transfer (FRET) data in living cells using a confocal microscope: Acceptor photobleaching, Acceptor-sensitized emission FRET, and Donor fluorescence lifetime imaging. Detailed protocols for live cell husbandry, image acquisition,...

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Manzella-Lapeira J, Brzostowski JA. Imaging Protein-Protein Interactions by Förster Resonance Energy Transfer (FRET) Microscopy in Live Cells. Curr Protoc Protein Sci. 2018;93(1):e58doi: 10.1002/cpps.58.
Manzella-Lapeira, J., & Brzostowski, J. A. (2018). Imaging Protein-Protein Interactions by Förster Resonance Energy Transfer (FRET) Microscopy in Live Cells. Current protocols in protein science, 93(1), e58. https://doi.org/10.1002/cpps.58
Manzella-Lapeira, Javier, and Brzostowski, Joseph A. "Imaging Protein-Protein Interactions by Förster Resonance Energy Transfer (FRET) Microscopy in Live Cells." Current protocols in protein science vol. 93,1 (2018): e58. doi: https://doi.org/10.1002/cpps.58
Manzella-Lapeira J, Brzostowski JA. Imaging Protein-Protein Interactions by Förster Resonance Energy Transfer (FRET) Microscopy in Live Cells. Curr Protoc Protein Sci. 2018 Aug;93(1):e58. doi: 10.1002/cpps.58. Epub 2018 Jul 09. PMID: 29984911.
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Proteomic Analysis of the Human Tankyrase Protein Interaction Network Reveals Its Role in Pexophagy.

Cell reports

Li X, Han H, Zhou MT, Yang B, Ta AP, Li N, Chen J, Wang W.
PMID: 28723574
Cell Rep. 2017 Jul 18;20(3):737-749. doi: 10.1016/j.celrep.2017.06.077.

Tankyrase 1 (TNKS) and tankyrase 2 (TNKS2) belong to the poly(ADP-ribose) polymerase family of proteins, which use nicotinamide adenine dinucleotide to modify substrate proteins with ADP-ribose modifications. Emerging evidence has revealed the pathological relevance of TNKS and TNKS2, and...

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Li X, Han H, Zhou MT, et al. Proteomic Analysis of the Human Tankyrase Protein Interaction Network Reveals Its Role in Pexophagy. Cell Rep. 2017;20(3):737-749doi: 10.1016/j.celrep.2017.06.077.
Li, X., Han, H., Zhou, M. T., Yang, B., Ta, A. P., Li, N., Chen, J., & Wang, W. (2017). Proteomic Analysis of the Human Tankyrase Protein Interaction Network Reveals Its Role in Pexophagy. Cell reports, 20(3), 737-749. https://doi.org/10.1016/j.celrep.2017.06.077
Li, Xu, et al. "Proteomic Analysis of the Human Tankyrase Protein Interaction Network Reveals Its Role in Pexophagy." Cell reports vol. 20,3 (2017): 737-749. doi: https://doi.org/10.1016/j.celrep.2017.06.077
Li X, Han H, Zhou MT, Yang B, Ta AP, Li N, Chen J, Wang W. Proteomic Analysis of the Human Tankyrase Protein Interaction Network Reveals Its Role in Pexophagy. Cell Rep. 2017 Jul 18;20(3):737-749. doi: 10.1016/j.celrep.2017.06.077. PMID: 28723574.
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Non-canonical targets play an important role in microRNA stability control mechanisms.

BMB reports

Park JH, Shin C.
PMID: 28228216
BMB Rep. 2017 Apr;50(4):158-159. doi: 10.5483/bmbrep.2017.50.4.029.

MicroRNAs (miRNAs) regulate gene expression by guiding the Argonaute (Ago)-containing RNA-induced silencing complex (RISC) to specific target mRNA molecules. It is well established that miRNAs are stabilized by Ago proteins, but the molecular features that trigger miRNA destabilization from...

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Park JH, Shin C. Non-canonical targets play an important role in microRNA stability control mechanisms. BMB Rep. 2017;50(4):158-159doi: 10.5483/bmbrep.2017.50.4.029.
Park, J. H., & Shin, C. (2017). Non-canonical targets play an important role in microRNA stability control mechanisms. BMB reports, 50(4), 158-159. https://doi.org/10.5483/bmbrep.2017.50.4.029
Park, June Hyun, and Shin, Chanseok. "Non-canonical targets play an important role in microRNA stability control mechanisms." BMB reports vol. 50,4 (2017): 158-159. doi: https://doi.org/10.5483/bmbrep.2017.50.4.029
Park JH, Shin C. Non-canonical targets play an important role in microRNA stability control mechanisms. BMB Rep. 2017 Apr;50(4):158-159. doi: 10.5483/bmbrep.2017.50.4.029. PMID: 28228216; PMCID: PMC5437957.
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