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1. The Human Phenotype Ontology in 2024: phenotypes around the world

Author

Gargano, Michael A, primary, Matentzoglu, Nicolas, additional, Coleman, Ben, additional, Addo-Lartey, Eunice B, additional, Anagnostopoulos, Anna V, additional, Anderton, Joel, additional, Avillach, Paul, additional, Bagley, Anita M, additional, Bakštein, Eduard, additional, Balhoff, James P, additional, Baynam, Gareth, additional, Bello, Susan M, additional, Berk, Michael, additional, Bertram, Holli, additional, Bishop, Somer, additional, Blau, Hannah, additional, Bodenstein, David F, additional, Botas, Pablo, additional, Boztug, Kaan, additional, Čady, Jolana, additional, Callahan, Tiffany J, additional, Cameron, Rhiannon, additional, Carbon, Seth J, additional, Castellanos, Francisco, additional, Caufield, J Harry, additional, Chan, Lauren E, additional, Chute, Christopher G, additional, Cruz-Rojo, Jaime, additional, Dahan-Oliel, Noémi, additional, Davids, Jon R, additional, de Dieuleveult, Maud, additional, de Souza, Vinicius, additional, de Vries, Bert B A, additional, de Vries, Esther, additional, DePaulo, J Raymond, additional, Derfalvi, Beata, additional, Dhombres, Ferdinand, additional, Diaz-Byrd, Claudia, additional, Dingemans, Alexander J M, additional, Donadille, Bruno, additional, Duyzend, Michael, additional, Elfeky, Reem, additional, Essaid, Shahim, additional, Fabrizzi, Carolina, additional, Fico, Giovanna, additional, Firth, Helen V, additional, Freudenberg-Hua, Yun, additional, Fullerton, Janice M, additional, Gabriel, Davera L, additional, Gilmour, Kimberly, additional, Giordano, Jessica, additional, Goes, Fernando S, additional, Moses, Rachel Gore, additional, Green, Ian, additional, Griese, Matthias, additional, Groza, Tudor, additional, Gu, Weihong, additional, Guthrie, Julia, additional, Gyori, Benjamin, additional, Hamosh, Ada, additional, Hanauer, Marc, additional, Hanušová, Kateřina, additional, He, Yongqun (Oliver), additional, Hegde, Harshad, additional, Helbig, Ingo, additional, Holasová, Kateřina, additional, Hoyt, Charles Tapley, additional, Huang, Shangzhi, additional, Hurwitz, Eric, additional, Jacobsen, Julius O B, additional, Jiang, Xiaofeng, additional, Joseph, Lisa, additional, Keramatian, Kamyar, additional, King, Bryan, additional, Knoflach, Katrin, additional, Koolen, David A, additional, Kraus, Megan L, additional, Kroll, Carlo, additional, Kusters, Maaike, additional, Ladewig, Markus S, additional, Lagorce, David, additional, Lai, Meng-Chuan, additional, Lapunzina, Pablo, additional, Laraway, Bryan, additional, Lewis-Smith, David, additional, Li, Xiarong, additional, Lucano, Caterina, additional, Majd, Marzieh, additional, Marazita, Mary L, additional, Martinez-Glez, Victor, additional, McHenry, Toby H, additional, McInnis, Melvin G, additional, McMurry, Julie A, additional, Mihulová, Michaela, additional, Millett, Caitlin E, additional, Mitchell, Philip B, additional, Moslerová, Veronika, additional, Narutomi, Kenji, additional, Nematollahi, Shahrzad, additional, Nevado, Julian, additional, Nierenberg, Andrew A, additional, Čajbiková, Nikola Novák, additional, Nurnberger, John I, additional, Ogishima, Soichi, additional, Olson, Daniel, additional, Ortiz, Abigail, additional, Pachajoa, Harry, additional, Perez de Nanclares, Guiomar, additional, Peters, Amy, additional, Putman, Tim, additional, Rapp, Christina K, additional, Rath, Ana, additional, Reese, Justin, additional, Rekerle, Lauren, additional, Roberts, Angharad M, additional, Roy, Suzy, additional, Sanders, Stephan J, additional, Schuetz, Catharina, additional, Schulte, Eva C, additional, Schulze, Thomas G, additional, Schwarz, Martin, additional, Scott, Katie, additional, Seelow, Dominik, additional, Seitz, Berthold, additional, Shen, Yiping, additional, Similuk, Morgan N, additional, Simon, Eric S, additional, Singh, Balwinder, additional, Smedley, Damian, additional, Smith, Cynthia L, additional, Smolinsky, Jake T, additional, Sperry, Sarah, additional, Stafford, Elizabeth, additional, Stefancsik, Ray, additional, Steinhaus, Robin, additional, Strawbridge, Rebecca, additional, Sundaramurthi, Jagadish Chandrabose, additional, Talapova, Polina, additional, Tenorio Castano, Jair A, additional, Tesner, Pavel, additional, Thomas, Rhys H, additional, Thurm, Audrey, additional, Turnovec, Marek, additional, van Gijn, Marielle E, additional, Vasilevsky, Nicole A, additional, Vlčková, Markéta, additional, Walden, Anita, additional, Wang, Kai, additional, Wapner, Ron, additional, Ware, James S, additional, Wiafe, Addo A, additional, Wiafe, Samuel A, additional, Wiggins, Lisa D, additional, Williams, Andrew E, additional, Wu, Chen, additional, Wyrwoll, Margot J, additional, Xiong, Hui, additional, Yalin, Nefize, additional, Yamamoto, Yasunori, additional, Yatham, Lakshmi N, additional, Yocum, Anastasia K, additional, Young, Allan H, additional, Yüksel, Zafer, additional, Zandi, Peter P, additional, Zankl, Andreas, additional, Zarante, Ignacio, additional, Zvolský, Miroslav, additional, Toro, Sabrina, additional, Carmody, Leigh C, additional, Harris, Nomi L, additional, Munoz-Torres, Monica C, additional, Danis, Daniel, additional, Mungall, Christopher J, additional, Köhler, Sebastian, additional, Haendel, Melissa A, additional, and Robinson, Peter N, additional

Published
2023
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3. NPP-669, a Novel Broad-Spectrum Antiviral Therapeutic with Excellent Cellular Uptake, Antiviral Potency, Oral Bioavailability, Preclinical Efficacy, and a Promising Safety Margin

Author

Lipka, Elke, primary, Chadderdon, Aaron M., additional, Harteg, Cheryl C., additional, Doherty, Matthew K., additional, Simon, Eric S., additional, Domagala, John M., additional, Reyna, Dawn M., additional, Hutchings, Kim M., additional, Gan, Xinmin, additional, White, Andrew D., additional, Hartline, Caroll B., additional, Harden, Emma A., additional, Keith, Kathy A., additional, Prichard, Mark N., additional, James, Scott H., additional, Cardin, Rhonda D., additional, Bernstein, David I., additional, Spencer, Jacqueline F., additional, Tollefson, Ann E., additional, Wold, William S. M., additional, and Toth, Karoly, additional

Published
2022
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6. NPP-669, a Novel Broad-Spectrum Antiviral Therapeutic with Excellent Cellular Uptake, Antiviral Potency, Oral Bioavailability, Preclinical Efficacy, and a Promising Safety Margin.

Author

Lipka, Elke, Chadderdon, Aaron M., Harteg, Cheryl C., Doherty, Matthew K., Simon, Eric S., Domagala, John M., Reyna, Dawn M., Hutchings, Kim M., Gan, Xinmin, White, Andrew D., Hartline, Caroll B., Harden, Emma A., Keith, Kathy A., Prichard, Mark N., James, Scott H., Cardin, Rhonda D., Bernstein, David I., Spencer, Jacqueline F., Tollefson, Ann E., and Wold, William S. M.

Published
2023
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10. Insertional inactivation of the methionine S-methyltransferase gene eliminates the S-methylmethionine cycle and increases the methylation ratio (1)

Author

Kocsis, Michael G., Ranocha, Philippe, Gage, Douglas A., Simon, Eric S., Rhodes, David, Peel, Gregory J., Mellema, Stefan, Saito, Kazuki, Awazuhara, Motoko, Li, Changjiang, Meeley, Robert B., Tarczynski, Mitchell C., Wagner, Conrad, and Hanson, Andrew D.

Subjects
Methyltransferases -- Research, Homocysteine -- Research, Arabidopsis -- Physiological aspects, Biological sciences, Science and technology
Published
2003

12. 20/20 hindsight: effectiveness of simulating the impact of federal sentencing legislation on the future prison population

Author

Gaes, Gerald G., Simon, Eric S., and Rhodes, William M.

Subjects
United States. Sentencing Commission -- Models, Prison sentences -- Statistics, Sentences (Criminal procedure) -- Models, Social sciences
Abstract

A computer model to estimate future prison populations based on current legislation trends has proven to be highly accurate. The model, FEDSIM, was created by the United States Sentencing Commission in 1987 to evaluate the effects of sentencing laws. It proved to be wrong in some areas, notably the length of sentences for certain offenses, due chiefly to laws (such as the Anti-Drug Abuse Act) introduced after the model was developed.

Published
1993

14. Organellar Proteomics

Author

Chen, Xuequn, primary, Walker, Angela K., additional, Strahler, John R., additional, Simon, Eric S., additional, Tomanicek-Volk, Sarah L., additional, Nelson, Bradley B., additional, Hurley, Mary C., additional, Ernst, Stephen A., additional, Williams, John A., additional, and Andrews, Philip C., additional

Published
2006
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15. Quantitative Proteomics Analysis of Cell Cycle-regulated Golgi Disassembly and Reassembly.

Author

Xuequn Chen, Simon, Eric S., Yi Xiang, Kachman, Maureen, Andrews, Philip C., and Yanzhuang Wang

Subjects
*GOLGI apparatus, *PROTEOMICS, *CELL membrane formation, *QUANTITATIVE research, *CELL cycle regulation, *LIQUID chromatography, *LABORATORY mice
Abstract

During mitosis, the stacked structure of the Golgi undergoes a continuous fragmentation process. The generated mitotic fragments are evenly distributed into the daughter cells and reassembled into new Golgi stacks. This disassembly and reassembly process is critical for Golgi biogenesis during cell division, but the underlying molecular mechanism is poorly understood. In this study, we have recapitulated this process using an in vitro assay and analyzed the proteins associated with interphase and mitotic Golgi membranes using a proteomic approach. Incubation of purified rat liver Golgi membranes with mitotic HeLa cell cytosol led to fragmentation of the membranes; subsequent treatment of these membranes with interphase cytosol allowed the reassembly of the Golgi fragments into new Golgi stacks. These membranes were then used for quantitative proteomics analyses by combining the isobaric tags for relative and absolute quantification approach with OFFGEL isoelectric focusing separation and liquid chromatography-matrix assisted laser desorption ionization-tandem mass spectrometry. In three independent experiments, a total of 1,193 Golgi-associated proteins were identified and quantified. These included broad functional categories, such as Golgi structural proteins, Golgi resident enzymes, SNAREs, Rab GlPases, cargo, and cytoskeletal proteins. More importantly, the combination of the quantitative approach with Western blotting allowed us to unveil 84 proteins with significant changes in abundance under the mitotic condition compared with the interphase condition. Among these proteins, several COP! coatomer subunits (a, (3, y, and 5) are of particular interest. Altogether, this systematic quantitative proteomic study revealed candidate proteins of the molecular machinery that control the Golgi disassembly and reassembly processes in the cell cycle. [ABSTRACT FROM AUTHOR]

Published
2010
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16. The Human Phenotype Ontology in 2024: phenotypes around the world.

Author

Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon SJ, Castellanos F, Caufield JH, Chan LE, Chute CG, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He YO, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus ML, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI Jr, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts AM, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, and Robinson PN

Subjects
Humans, Phenotype, Genomics, Algorithms, Rare Diseases, Biological Ontologies
Abstract

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2024
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17. Preparation of peptides from yeast cells for iTRAQ analysis.

Author

Simon ES

Subjects
Aerobiosis, Anaerobiosis, Saccharomyces cerevisiae metabolism, Proteome analysis, Proteome isolation & purification, Proteomics methods, Saccharomyces cerevisiae chemistry, Saccharomyces cerevisiae Proteins analysis, Saccharomyces cerevisiae Proteins isolation & purification
Published
2011
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18. Labeling yeast peptides with the iTRAQ reagent.

Author

Simon ES

Subjects
Aerobiosis, Anaerobiosis, Proteome isolation & purification, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins isolation & purification, Proteome analysis, Proteomics methods, Saccharomyces cerevisiae chemistry, Saccharomyces cerevisiae Proteins analysis, Staining and Labeling methods
Published
2011
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19. Isoelectric focusing of iTRAQ-labeled yeast.

Author

Simon ES

Subjects
Aerobiosis, Anaerobiosis, Isoelectric Focusing methods, Proteome isolation & purification, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins isolation & purification, Staining and Labeling methods, Proteome analysis, Proteomics methods, Saccharomyces cerevisiae chemistry, Saccharomyces cerevisiae Proteins analysis
Published
2011
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20. iTRAQ-labeled yeast peptide clean-up using a reversed-phase column.

Author

Simon ES

Subjects
Aerobiosis, Anaerobiosis, Proteome analysis, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins analysis, Staining and Labeling methods, Chromatography, Reverse-Phase methods, Proteome isolation & purification, Proteomics methods, Saccharomyces cerevisiae chemistry, Saccharomyces cerevisiae Proteins isolation & purification
Published
2011
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