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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
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Posts
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Blog Post number 4
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Blog Post number 1
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portfolio
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publications
Acyl-Lipid Metabolism Permalink
Published in The Arabidopsis Book, 2010
Recommended citation: Li-Beisson, Yonghua, Basil Shorrosh, Fred Beisson, Mats X. Andersson, Vincent Arondel, Philip D. Bates, Sébastien Baud, David Bird, Allan DeBono, Timothy P. Durrett, Rochus B. Franke, Ian A. Graham, Kenta Katayama, Amélie A. Kelly, Tony Larson, Jonathan E. Markham, Martine Miquel, Isabel Molina, Ikuo Nishida, Owen Rowland, Lacey Samuels, Katherine M. Schmid, Hajime Wada, Ruth Welti, Changcheng Xu, Rémi Zallot, and John Ohlrogge. 2010. ‘Acyl-Lipid Metabolism’. The Arabidopsis Book 8:e0133. doi: 10.1199/tab.0133.
Polyphosphoinositides Are Enriched in Plant Membrane Rafts and Form Microdomains in the Plasma Membrane Permalink
Published in Plant Physiology, 2010
Recommended citation: Furt, Fabienne, Sabine König, Jean-Jacques Bessoule, Françoise Sargueil, Rémi Zallot, Thomas Stanislas, Elodie Noirot, Jeanine Lherminier, Françoise Simon-Plas, Ingo Heilmann, and Sébastien Mongrand. 2010. ‘Polyphosphoinositides Are Enriched in Plant Membrane Rafts and Form Microdomains in the Plasma Membrane’. Plant Physiology 152(4):2173–87. doi: 10.1104/pp.109.149823.
Acyl-Lipid Metabolism Permalink
Published in The Arabidopsis Book, 2013
Recommended citation: Li-Beisson, Yonghua, Basil Shorrosh, Fred Beisson, Mats X. Andersson, Vincent Arondel, Philip D. Bates, Sébastien Baud, David Bird, Allan DeBono, Timothy P. Durrett, Rochus B. Franke, Ian A. Graham, Kenta Katayama, Amélie A. Kelly, Tony Larson, Jonathan E. Markham, Martine Miquel, Isabel Molina, Ikuo Nishida, Owen Rowland, Lacey Samuels, Katherine M. Schmid, Hajime Wada, Ruth Welti, Changcheng Xu, Rémi Zallot, and John Ohlrogge. 2013. ‘Acyl-Lipid Metabolism’. The Arabidopsis Book 11:e0161. doi: 10.1199/tab.0161.
Identification of Mitochondrial Coenzyme A Transporters from Maize and Arabidopsis Permalink
Published in Plant Physiology, 2013
Recommended citation: Zallot, Rémi, Gennaro Agrimi, Claudia Lerma-Ortiz, Howard J. Teresinski, Océane Frelin, Kenneth W. Ellens, Alessandra Castegna, Annamaria Russo, Valérie de Crécy-Lagard, Robert T. Mullen, Ferdinando Palmieri, and Andrew D. Hanson. 2013. ‘Identification of Mitochondrial Coenzyme A Transporters from Maize and Arabidopsis’. Plant Physiology 162(2):581–88. doi: 10.1104/pp.113.218081.
Identification of the thiamin salvage enzyme thiazole kinase in Arabidopsis and maize Permalink
Published in Phytochemistry, 2013
Recommended citation: Yazdani, Mohammad, Rémi Zallot, Meral Tunc-Ozdemir, Valérie de Crécy-Lagard, David K. Shintani, and Andrew D. Hanson. 2013. ‘Identification of the Thiamin Salvage Enzyme Thiazole Kinase in Arabidopsis and Maize’. Phytochemistry 94:68–73. doi: 10.1016/j.phytochem.2013.05.017.
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource Permalink
Published in Proceedings of the National Academy of Sciences, 2014
Recommended citation: Seaver, Samuel M. D., Svetlana Gerdes, Océane Frelin, Claudia Lerma-Ortiz, Louis M. T. Bradbury, Rémi Zallot, Ghulam Hasnain, Thomas D. Niehaus, Basma El Yacoubi, Shiran Pasternak, Robert Olson, Gordon Pusch, Ross Overbeek, Rick Stevens, Valérie de Crécy-Lagard, Doreen Ware, Andrew D. Hanson, and Christopher S. Henry. 2014. ‘High-Throughput Comparison, Functional Annotation, and Metabolic Modeling of Plant Genomes Using the PlantSEED Resource’. Proceedings of the National Academy of Sciences 111(26):9645–50. doi: 10.1073/pnas.1401329111.
Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine Permalink
Published in Biochemical Journal, 2014
Recommended citation: Zallot, Rémi, Mohammad Yazdani, Aymeric Goyer, Michael J. Ziemak, Jiahn-Chou Guan, Donald R. McCarty, Valérie de Crécy-Lagard, Svetlana Gerdes, Timothy J. Garrett, Jordi Benach, John F. Hunt, David K. Shintani, and Andrew D. Hanson. 2014. ‘Salvage of the Thiamin Pyrimidine Moiety by Plant TenA Proteins Lacking an Active-Site Cysteine’. Biochemical Journal 463(1):145–55. doi: 10.1042/BJ20140522.
Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae Permalink
Published in Journal of Biological Chemistry, 2015
Recommended citation: Kuznetsova, Ekaterina, Boguslaw Nocek, Greg Brown, Kira S. Makarova, Robert Flick, Yuri I. Wolf, Anna Khusnutdinova, Elena Evdokimova, Ke Jin, Kemin Tan, Andrew D. Hanson, Ghulam Hasnain, Rémi Zallot, Valérie de Crécy-Lagard, Mohan Babu, Alexei Savchenko, Andrzej Joachimiak, Aled M. Edwards, Eugene V. Koonin, and Alexander F. Yakunin. 2015. ‘Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces Cerevisiae’. Journal of Biological Chemistry 290(30):18678–98. doi: 10.1074/jbc.M115.657916.
Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis Permalink
Published in Biochemical Journal, 2016
Recommended citation: Hasnain, Ghulam, Sanja Roje, Na Sa, Rémi Zallot, Michael J. Ziemak, Valérie de Crécy-Lagard, Jesse F. Gregory, and Andrew D. Hanson. 2016. ‘Bacterial and Plant HAD Enzymes Catalyse a Missing Phosphatase Step in Thiamin Diphosphate Biosynthesis’. Biochemical Journal 473(2):157–66. doi: 10.1042/BJ20150805.
A family of metal-dependent phosphatases implicated in metabolite damage-control Permalink
Published in Nature Chemical Biology, 2016
Recommended citation: Huang, Lili, Anna Khusnutdinova, Boguslaw Nocek, Greg Brown, Xiaohui Xu, Hong Cui, Pierre Petit, Robert Flick, Rémi Zallot, Kelly Balmant, Michael J. Ziemak, John Shanklin, Valérie de Crécy-Lagard, Oliver Fiehn, Jesse F. Gregory, Andrzej Joachimiak, Alexei Savchenko, Alexander F. Yakunin, and Andrew D. Hanson. 2016. ‘A Family of Metal-Dependent Phosphatases Implicated in Metabolite Damage-Control’. Nature Chemical Biology 12(8):621–27. doi: 10.1038/nchembio.2108.
Functional Annotations of Paralogs: A Blessing and a Curse Permalink
Published in Life, 2016
Recommended citation: Zallot, Rémi, Katherine Harrison, Bryan Kolaczkowski, and Valérie de Crécy-Lagard. 2016. ‘Functional Annotations of Paralogs: A Blessing and a Curse’. Life 6(3):39. doi: 10.3390/life6030039.
Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase Permalink
Published in The Plant Cell, 2016
Recommended citation: Mimura, Manaki, Rémi Zallot, Thomas D. Niehaus, Ghulam Hasnain, Satinder K. Gidda, Thuy N. D. Nguyen, Erin M. Anderson, Robert T. Mullen, Greg Brown, Alexander F. Yakunin, Valérie de Crécy-Lagard, Jesse F. Gregory, Donald R. McCarty, and Andrew D. Hanson. 2016. ‘Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase’. The Plant Cell 28(10):2683–96. doi: 10.1105/tpc.16.00600.
Systematic identification and analysis of frequent gene fusion events in metabolic pathways Permalink
Published in BMC Genomics, 2016
Recommended citation: Henry, Christopher S., Claudia Lerma-Ortiz, Svetlana Y. Gerdes, Jeffrey D. Mullen, Ric Colasanti, Aleksey Zhukov, Océane Frelin, Jennifer J. Thiaville, Rémi Zallot, Thomas D. Niehaus, Ghulam Hasnain, Neal Conrad, Andrew D. Hanson, and Valérie de Crécy-Lagard. 2016. ‘Systematic Identification and Analysis of Frequent Gene Fusion Events in Metabolic Pathways’. BMC Genomics 17(1):473. doi: 10.1186/s12864-016-2782-3.
Plant, Animal, and Fungal Micronutrient Queuosine Is Salvaged by Members of the DUF2419 Protein Family Permalink
Published in ACS Chemical Biology, 2017
Recommended citation: Zallot, Rémi, Céline Brochier-Armanet, Kirk W. Gaston, Farhad Forouhar, Patrick A. Limbach, John F. Hunt, and Valérie de Crécy-Lagard. 2014. ‘Plant, Animal, and Fungal Micronutrient Queuosine Is Salvaged by Members of the DUF2419 Protein Family’. ACS Chemical Biology 9(8):1812–25. doi: 10.1021/cb500278k.
The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ0) Transport Permalink
Published in Biomolecules, 2017
Recommended citation: Zallot, Rémi, Yifeng Yuan, and Valérie de Crécy-Lagard. 2017. ‘The Escherichia Coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (PreQ0) Transport’. Biomolecules 7(4):12. doi: 10.3390/biom7010012.
Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics Permalink
Published in ACS Chemical Biology, 2017
Recommended citation: Zallot, Rémi, Robert Ross, Wei-Hung Chen, Steven D. Bruner, Patrick A. Limbach, and Valérie de Crécy-Lagard. 2017. ‘Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics’. ACS Chemical Biology 12(3):844–51. doi: 10.1021/acschembio.6b01100.
Gene Graphics: a genomic neighborhood data visualization web application Permalink
Published in Bioinformatics, 2018
Recommended citation: Harrison, Katherine J., Valérie de Crécy-Lagard, and Rémi Zallot. 2018. ‘Gene Graphics: A Genomic Neighborhood Data Visualization Web Application’ edited by J. Hancock. Bioinformatics 34(8):1406–8. doi: 10.1093/bioinformatics/btx793.
Functional assignment of multiple catabolic pathways for d-apiose Permalink
Published in Nature Chemical Biology, 2018
Recommended citation: Carter, Michael S., Xinshuai Zhang, Hua Huang, Jason T. Bouvier, Brian San Francisco, Matthew W. Vetting, Nawar Al-Obaidi, Jeffrey B. Bonanno, Agnidipta Ghosh, Rémi G. Zallot, Harvey M. Andersen, Steven C. Almo, and John A. Gerlt. 2018. ‘Functional Assignment of Multiple Catabolic Pathways for D-Apiose’. Nature Chemical Biology 14(7):696–705. doi: 10.1038/s41589-018-0067-7.
‘Democratized’ genomic enzymology web tools for functional assignment Permalink
Published in Current Opinion in Chemical Biology, 2018
Recommended citation: Zallot, Rémi, Nils O. Oberg, and John A. Gerlt. 2018. ‘“Democratized” Genomic Enzymology Web Tools for Functional Assignment’. Current Opinion in Chemical Biology 47:77–85. doi: 10.1016/j.cbpa.2018.09.009.
Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens Permalink
Published in Proceedings of the National Academy of Sciences, 2019
Recommended citation: Yuan, Yifeng, Rémi Zallot, Tyler L. Grove, Daniel J. Payan, Isabelle Martin-Verstraete, Sara Šepić, Seetharamsingh Balamkundu, Ramesh Neelakandan, Vinod K. Gadi, Chuan-Fa Liu, Manal A. Swairjo, Peter C. Dedon, Steven C. Almo, John A. Gerlt, and Valérie de Crécy-Lagard. 2019. ‘Discovery of Novel Bacterial Queuine Salvage Enzymes and Pathways in Human Pathogens’. Proceedings of the National Academy of Sciences 116(38):19126–35. doi: 10.1073/pnas.1909604116.
The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways Permalink
Published in Biochemistry, 2019
Recommended citation: Zallot, Rémi, Nils Oberg, and John A. Gerlt. 2019. ‘The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways’. Biochemistry 58(41):4169–82. doi: 10.1021/acs.biochem.9b00735.
Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools Permalink
Published in Current Opinion in Biotechnology, 2021
Recommended citation: Zallot, Rémi, Nils Oberg, and John A. Gerlt. 2021. ‘Discovery of New Enzymatic Functions and Metabolic Pathways Using Genomic Enzymology Web Tools’. Current Opinion in Biotechnology 69:77–90. doi: 10.1016/j.copbio.2020.12.004.
Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme Permalink
Published in Biochemistry, 2021
Recommended citation: Li, Qiang, Rémi Zallot, Brian S. MacTavish, Alvaro Montoya, Daniel J. Payan, You Hu, John A. Gerlt, Alexander Angerhofer, Valérie de Crécy-Lagard, and Steven D. Bruner. 2021. ‘Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to TRNA Queuosine Is a Unique Metalloenzyme’. Biochemistry 60(42):3152–61. doi: 10.1021/acs.biochem.1c00164.
Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases Permalink
Published in ACS Catalysis, 2022
Recommended citation: Zhang, Zhen, Mochen Dong, Rémi Zallot, George Michael Blackburn, Nini Wang, Chengjian Wang, Long Chen et al. "Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases." ACS Catalysis 13 (2022): 824-836.
EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools Permalink
Published in Journal of Molecular Biology, 2023
Recommended citation: Oberg, Nils, Rémi Zallot, and John A. Gerlt. "EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools." Journal of Molecular Biology (2023): 168018.
talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
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