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Coimmunoprecipitation (co-IP) of Nuclear Proteins and Chromatin Immunoprecipitation (ChIP) from Arabidopsis.

CSH protocols

Fiil BK, Qiu JL, Petersen K, Petersen M, Mundy J.
PMID: 21356918
CSH Protoc. 2008 Sep 01;2008:pdb.prot5049. doi: 10.1101/pdb.prot5049.

INTRODUCTIONTranscriptional reprogramming occurs during development and in response to diverse stimuli and stresses. The isolation and characterization of nuclear proteins, particularly those binding to DNA and chromatin, are therefore important to understanding these processes. Two specific approaches to understanding...

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Fiil BK, Qiu JL, Petersen K, et al. Coimmunoprecipitation (co-IP) of Nuclear Proteins and Chromatin Immunoprecipitation (ChIP) from Arabidopsis. CSH Protoc. 2008;2008:pdb.prot5049doi: 10.1101/pdb.prot5049.
Fiil, B. K., Qiu, J. L., Petersen, K., Petersen, M., & Mundy, J. (2008). Coimmunoprecipitation (co-IP) of Nuclear Proteins and Chromatin Immunoprecipitation (ChIP) from Arabidopsis. CSH protocols, 2008pdb.prot5049. https://doi.org/10.1101/pdb.prot5049
Fiil, Berthe Katrine, et al. "Coimmunoprecipitation (co-IP) of Nuclear Proteins and Chromatin Immunoprecipitation (ChIP) from Arabidopsis." CSH protocols vol. 2008 (2008): pdb.prot5049. doi: https://doi.org/10.1101/pdb.prot5049
Fiil BK, Qiu JL, Petersen K, Petersen M, Mundy J. Coimmunoprecipitation (co-IP) of Nuclear Proteins and Chromatin Immunoprecipitation (ChIP) from Arabidopsis. CSH Protoc. 2008 Sep 01;2008:pdb.prot5049. doi: 10.1101/pdb.prot5049. PMID: 21356918.
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CGDV: a webtool for circular visualization of genomics and transcriptomics data.

BMC genomics

Jha V, Singh G, Kumar S, Sonawane A, Jere A, Anamika K.
PMID: 29065857
BMC Genomics. 2017 Oct 24;18(1):823. doi: 10.1186/s12864-017-4169-5.

BACKGROUND: Interpretation of large-scale data is very challenging and currently there is scarcity of web tools which support automated visualization of a variety of high throughput genomics and transcriptomics data and for a wide variety of model organisms along...

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Jha V, Singh G, Kumar S, et al. CGDV: a webtool for circular visualization of genomics and transcriptomics data. BMC Genomics. 2017;18(1):823doi: 10.1186/s12864-017-4169-5.
Jha, V., Singh, G., Kumar, S., Sonawane, A., Jere, A., & Anamika, K. (2017). CGDV: a webtool for circular visualization of genomics and transcriptomics data. BMC genomics, 18(1), 823. https://doi.org/10.1186/s12864-017-4169-5
Jha, Vineet, et al. "CGDV: a webtool for circular visualization of genomics and transcriptomics data." BMC genomics vol. 18,1 (2017): 823. doi: https://doi.org/10.1186/s12864-017-4169-5
Jha V, Singh G, Kumar S, Sonawane A, Jere A, Anamika K. CGDV: a webtool for circular visualization of genomics and transcriptomics data. BMC Genomics. 2017 Oct 24;18(1):823. doi: 10.1186/s12864-017-4169-5. PMID: 29065857; PMCID: PMC5655900.
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A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in .

Plant methods

Lee JH, Jin S, Kim SY, Kim W, Ahn JH.
PMID: 28539971
Plant Methods. 2017 May 22;13:42. doi: 10.1186/s13007-017-0192-4. eCollection 2017.

BACKGROUND: Binding of transcription factors to their target sequences is a primary step in the regulation of gene expression and largely determines gene regulatory networks. Chromatin immunoprecipitation (ChIP) is an indispensable tool used to investigate the binding of DNA-binding...

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Lee JH, Jin S, Kim SY, et al. A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in . Plant Methods. 2017;13:42doi: 10.1186/s13007-017-0192-4.
Lee, J. H., Jin, S., Kim, S. Y., Kim, W., & Ahn, J. H. (2017). A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in . Plant methods, 1342. https://doi.org/10.1186/s13007-017-0192-4
Lee, Jeong Hwan, et al. "A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in ." Plant methods vol. 13 (2017): 42. doi: https://doi.org/10.1186/s13007-017-0192-4
Lee JH, Jin S, Kim SY, Kim W, Ahn JH. A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in . Plant Methods. 2017 May 22;13:42. doi: 10.1186/s13007-017-0192-4. eCollection 2017. PMID: 28539971; PMCID: PMC5441002.
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Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics.

Chemical science

Nguyen TM, Nakata E, Zhang Z, Saimura M, Dinh H, Morii T.
PMID: 32110294
Chem Sci. 2019 Aug 20;10(40):9315-9325. doi: 10.1039/c9sc02990g. eCollection 2019 Oct 28.

Sequence-selective chemical modification of DNA by synthetic ligands has been a long-standing challenge in the field of chemistry. Even when the ligand consists of a sequence-specific DNA binding domain and reactive group, sequence-selective reactions by these ligands are often...

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Nguyen TM, Nakata E, Zhang Z, et al. Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics. Chem Sci. 2019;10(40):9315-9325doi: 10.1039/c9sc02990g.
Nguyen, T. M., Nakata, E., Zhang, Z., Saimura, M., Dinh, H., & Morii, T. (2019). Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics. Chemical science, 10(40), 9315-9325. https://doi.org/10.1039/c9sc02990g
Nguyen, Thang Minh, et al. "Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics." Chemical science vol. 10,40 (2019): 9315-9325. doi: https://doi.org/10.1039/c9sc02990g
Nguyen TM, Nakata E, Zhang Z, Saimura M, Dinh H, Morii T. Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics. Chem Sci. 2019 Aug 20;10(40):9315-9325. doi: 10.1039/c9sc02990g. eCollection 2019 Oct 28. PMID: 32110294; PMCID: PMC7006624.
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A Model Stacking Framework for Identifying DNA Binding Proteins by Orchestrating Multi-View Features and Classifiers.

Genes

Liu XJ, Gong XJ, Yu H, Xu JH.
PMID: 30071697
Genes (Basel). 2018 Aug 01;9(8). doi: 10.3390/genes9080394.

Nowadays, various machine learning-based approaches using sequence information alone have been proposed for identifying DNA-binding proteins, which are crucial to many cellular processes, such as DNA replication, DNA repair and DNA modification. Among these methods, building a meaningful feature...

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Liu XJ, Gong XJ, Yu H, et al. A Model Stacking Framework for Identifying DNA Binding Proteins by Orchestrating Multi-View Features and Classifiers. Genes (Basel). 2018;9(8)doi: 10.3390/genes9080394.
Liu, X. J., Gong, X. J., Yu, H., & Xu, J. H. (2018). A Model Stacking Framework for Identifying DNA Binding Proteins by Orchestrating Multi-View Features and Classifiers. Genes, 9(8), . https://doi.org/10.3390/genes9080394
Liu, Xiu-Juan, et al. "A Model Stacking Framework for Identifying DNA Binding Proteins by Orchestrating Multi-View Features and Classifiers." Genes vol. 9,8 (2018). doi: https://doi.org/10.3390/genes9080394
Liu XJ, Gong XJ, Yu H, Xu JH. A Model Stacking Framework for Identifying DNA Binding Proteins by Orchestrating Multi-View Features and Classifiers. Genes (Basel). 2018 Aug 01;9(8). doi: 10.3390/genes9080394. PMID: 30071697; PMCID: PMC6116045.
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The evolution of metazoan shelterin.

Genes & development

Myler LR, Kinzig CG, Sasi NK, Zakusilo G, Cai SW, de Lange T.
PMID: 34764137
Genes Dev. 2021 Dec 01;35(23):1625-1641. doi: 10.1101/gad.348835.121. Epub 2021 Nov 11.

The mammalian telomeric shelterin complex-comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1-blocks the DNA damage response at chromosome ends and interacts with telomerase and the CST complex to regulate telomere length. The evolutionary origins of shelterin are unclear,...

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Myler LR, Kinzig CG, Sasi NK, et al. The evolution of metazoan shelterin. Genes Dev. 2021;35(23):1625-1641doi: 10.1101/gad.348835.121.
Myler, L. R., Kinzig, C. G., Sasi, N. K., Zakusilo, G., Cai, S. W., & de Lange, T. (2021). The evolution of metazoan shelterin. Genes & development, 35(23), 1625-1641. https://doi.org/10.1101/gad.348835.121
Myler, Logan R, et al. "The evolution of metazoan shelterin." Genes & development vol. 35,23 (2021): 1625-1641. doi: https://doi.org/10.1101/gad.348835.121
Myler LR, Kinzig CG, Sasi NK, Zakusilo G, Cai SW, de Lange T. The evolution of metazoan shelterin. Genes Dev. 2021 Dec 01;35(23):1625-1641. doi: 10.1101/gad.348835.121. Epub 2021 Nov 11. PMID: 34764137.
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ZEAL: Protein structure alignment based on shape similarity.

Bioinformatics (Oxford, England)

Ljung F, André I.
PMID: 33772587
Bioinformatics. 2021 Mar 27; doi: 10.1093/bioinformatics/btab205. Epub 2021 Mar 27.

MOTIVATION: Most protein-structure superimposition tools consider only Cartesian coordinates. Yet, much of biology happens on the surface of proteins, which is why proteins with shared ancestry and similar function often have comparable surface shapes. Superposition of proteins based on...

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Ljung F, André I. ZEAL: Protein structure alignment based on shape similarity. Bioinformatics. 2021;doi: 10.1093/bioinformatics/btab205.
Ljung, F., & André, I. (2021). ZEAL: Protein structure alignment based on shape similarity. Bioinformatics (Oxford, England), . https://doi.org/10.1093/bioinformatics/btab205
Ljung, Filip, and André, Ingemar. "ZEAL: Protein structure alignment based on shape similarity." Bioinformatics (Oxford, England) vol. (2021). doi: https://doi.org/10.1093/bioinformatics/btab205
Ljung F, André I. ZEAL: Protein structure alignment based on shape similarity. Bioinformatics. 2021 Mar 27; doi: 10.1093/bioinformatics/btab205. Epub 2021 Mar 27. PMID: 33772587.
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Plant transcription factors - being in the right place with the right company.

Current opinion in plant biology

Strader L, Weijers D, Wagner D.
PMID: 34856504
Curr Opin Plant Biol. 2021 Nov 29;65:102136. doi: 10.1016/j.pbi.2021.102136. Epub 2021 Nov 29.

Transcriptional regulation underlies many of the growth and developmental processes that shape plants as well as their adaptation to their environment. Key to transcriptional control are transcription factors, DNA-binding proteins that serve two essential functions: to find the appropriate...

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Strader L, Weijers D, Wagner D. Plant transcription factors - being in the right place with the right company. Curr Opin Plant Biol. 2021;65:102136doi: 10.1016/j.pbi.2021.102136.
Strader, L., Weijers, D., & Wagner, D. (2021). Plant transcription factors - being in the right place with the right company. Current opinion in plant biology, 65102136. https://doi.org/10.1016/j.pbi.2021.102136
Strader, Lucia, et al. "Plant transcription factors - being in the right place with the right company." Current opinion in plant biology vol. 65 (2021): 102136. doi: https://doi.org/10.1016/j.pbi.2021.102136
Strader L, Weijers D, Wagner D. Plant transcription factors - being in the right place with the right company. Curr Opin Plant Biol. 2021 Nov 29;65:102136. doi: 10.1016/j.pbi.2021.102136. Epub 2021 Nov 29. PMID: 34856504.
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Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors.

Microbial pathogenesis

Tavares BADR, Paes JA, Zaha A, Ferreira HB.
PMID: 34864146
Microb Pathog. 2021 Dec 02;162:105344. doi: 10.1016/j.micpath.2021.105344. Epub 2021 Dec 02.

Mycoplasma hyopneumoniae is a bacterium that inhabits the swine respiratory tract, causing porcine enzootic pneumonia, which generates significant economic losses to the swine industry worldwide. The knowledge on M. hyopneumoniae biology and virulence have been significantly increased by genomics...

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Tavares BADR, Paes JA, Zaha A, et al. Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors. Microb Pathog. 2021;162:105344doi: 10.1016/j.micpath.2021.105344.
Tavares, B. A. D. R., Paes, J. A., Zaha, A., & Ferreira, H. B. (2021). Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors. Microbial pathogenesis, 162105344. https://doi.org/10.1016/j.micpath.2021.105344
Tavares, Bryan Augusto da Rosa, et al. "Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors." Microbial pathogenesis vol. 162 (2021): 105344. doi: https://doi.org/10.1016/j.micpath.2021.105344
Tavares BADR, Paes JA, Zaha A, Ferreira HB. Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors. Microb Pathog. 2021 Dec 02;162:105344. doi: 10.1016/j.micpath.2021.105344. Epub 2021 Dec 02. PMID: 34864146.
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Reading the chromatinized genome.

Cell

Michael AK, Thomä NH.
PMID: 34146479
Cell. 2021 Jul 08;184(14):3599-3611. doi: 10.1016/j.cell.2021.05.029. Epub 2021 Jun 18.

Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first...

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Michael AK, Thomä NH. Reading the chromatinized genome. Cell. 2021;184(14):3599-3611doi: 10.1016/j.cell.2021.05.029.
Michael, A. K., & Thomä, N. H. (2021). Reading the chromatinized genome. Cell, 184(14), 3599-3611. https://doi.org/10.1016/j.cell.2021.05.029
Michael, Alicia K, and Thomä, Nicolas H. "Reading the chromatinized genome." Cell vol. 184,14 (2021): 3599-3611. doi: https://doi.org/10.1016/j.cell.2021.05.029
Michael AK, Thomä NH. Reading the chromatinized genome. Cell. 2021 Jul 08;184(14):3599-3611. doi: 10.1016/j.cell.2021.05.029. Epub 2021 Jun 18. PMID: 34146479.
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Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows.

International journal of molecular sciences

Szczepińska T, Mollah AF, Plewczynski D.
PMID: 34769020
Int J Mol Sci. 2021 Oct 27;22(21). doi: 10.3390/ijms222111591.

The nature of genome organization into two basic structural compartments is as yet undiscovered. However, it has been indicated to be a mechanism of gene expression regulation. Using the classification approach, we ranked genomic marks that hint at compartmentalization....

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Szczepińska T, Mollah AF, Plewczynski D. Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows. Int J Mol Sci. 2021;22(21)doi: 10.3390/ijms222111591.
Szczepińska, T., Mollah, A. F., & Plewczynski, D. (2021). Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows. International journal of molecular sciences, 22(21), . https://doi.org/10.3390/ijms222111591
Szczepińska, Teresa, et al. "Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows." International journal of molecular sciences vol. 22,21 (2021). doi: https://doi.org/10.3390/ijms222111591
Szczepińska T, Mollah AF, Plewczynski D. Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows. Int J Mol Sci. 2021 Oct 27;22(21). doi: 10.3390/ijms222111591. PMID: 34769020; PMCID: PMC8584073.
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Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors.

Microbial pathogenesis

Tavares BADR, Paes JA, Zaha A, Ferreira HB.
PMID: 34864146
Microb Pathog. 2021 Dec 02;162:105344. doi: 10.1016/j.micpath.2021.105344. Epub 2021 Dec 02.

Mycoplasma hyopneumoniae is a bacterium that inhabits the swine respiratory tract, causing porcine enzootic pneumonia, which generates significant economic losses to the swine industry worldwide. The knowledge on M. hyopneumoniae biology and virulence have been significantly increased by genomics...

Cite
Tavares BADR, Paes JA, Zaha A, et al. Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors. Microb Pathog. 2021;162:105344doi: 10.1016/j.micpath.2021.105344.
Tavares, B. A. D. R., Paes, J. A., Zaha, A., & Ferreira, H. B. (2021). Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors. Microbial pathogenesis, 162105344. https://doi.org/10.1016/j.micpath.2021.105344
Tavares, Bryan Augusto da Rosa, et al. "Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors." Microbial pathogenesis vol. 162 (2021): 105344. doi: https://doi.org/10.1016/j.micpath.2021.105344
Tavares BADR, Paes JA, Zaha A, Ferreira HB. Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors. Microb Pathog. 2021 Dec 02;162:105344. doi: 10.1016/j.micpath.2021.105344. Epub 2021 Dec 02. PMID: 34864146.
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Showing 25 to 36 of 342 entries