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Susan C. Athey: John Bates Clark Award Winner 2007

John Roberts
2008 Journal of Economic Perspectives  
Those characteristics were not criteria for the award of the John Bates Clark medal, but they are central to understanding why Susan is held in such high regard.  ...  Athey differentiable context, they amount to the various cross partials being non-negative.  ...  Athey (photo credit: Tanit Sakakini) economics department, Susan's first real involvement in economics.  ... 
doi:10.1257/jep.22.4.181 fatcat:e5xvjg6iwbbjhluzpx6ylzvksa

Organizational Design: Decision Rights and Incentive Contracts

Susan Athey, John John Roberts
2001 Social Science Research Network  
We discuss bargaining at greater length in Athey and Roberts (2001) .  ...  The analysis is similar but more complicated when these assumptions are relaxed, as discussed in Susan Athey and Roberts (2001) .  ... 
doi:10.2139/ssrn.261773 fatcat:6dls7jzx4vbvxpzyqmvvvboe3a

Organizational Design: Decision Rights and Incentive Contracts

Susan Athey, John Roberts
2001 The American Economic Review  
We discuss bargaining at greater length in Athey and Roberts (2001) .  ...  The analysis is similar but more complicated when these assumptions are relaxed, as discussed in Susan Athey and Roberts (2001) .  ... 
doi:10.1257/aer.91.2.200 fatcat:e5uv2zzunnfgpcrdiwrv7vxdie

An Evaluation of Research Productivity in Academic IT

Susan Athey, John Plotnicki
2000 Communications of the Association for Information Systems  
Athey And J. Plotnicki is next to impossible if the "premier" journals are the only acceptable ones at a university.  ...  Athey And J.  ...  Athey And J. Plotnicki IV.  ... 
doi:10.17705/1cais.00307 fatcat:vqxmkbkq5ze77ewyf6zzvrlu4y

Predation on stink bugs (Hemiptera: Pentatomidae) in cotton and soybean agroecosystems

Kacie J. Athey, John R. Ruberson, Dawn M. Olson, James D. Harwood, Antonio Biondi
2019 PLoS ONE  
Acknowledgments We thank Jen White, John Obrycki, and Ric Bessin and two reviewers for helpful comments in preparing this manuscript.  ...  Athey [46] , and then frozen at -20˚C until subsequent DNA analysis.  ... 
doi:10.1371/journal.pone.0214325 pmid:30913247 pmcid:PMC6435312 fatcat:3iqw6wqzirhl3ejc3b5syihvbu

A new and updated resource for codon usage tables

John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V. Santana-Quintero, Upendra Katneni, Vahan Simonyan, Chava Kimchi-Sarfaty
2017 BMC Bioinformatics  
Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codons may affect protein expression, structure, and function. Recombinant gene technologies commonly take advantage of the former effect by implementing a technique termed codon optimization, in which codons are replaced with synonymous ones in order to increase protein expression. This
more » ... que relies on the accurate knowledge of codon usage frequencies. Accurately quantifying codon usage bias for different organisms is useful not only for codon optimization, but also for evolutionary and translation studies: phylogenetic relations of organisms, and host-pathogen co-evolution relationships, may be explored through their codon usage similarities. Furthermore, codon usage has been shown to affect protein structure and function through interfering with translation kinetics, and cotranslational protein folding. Results: Despite the obvious need for accurate codon usage tables, currently available resources are either limited in scope, encompassing only organisms from specific domains of life, or greatly outdated. Taking advantage of the exponential growth of GenBank and the creation of NCBI's RefSeq database, we have developed a new database, the High-performance Integrated Virtual Environment-Codon Usage Tables (HIVE-CUTs), to present and analyse codon usage tables for every organism with publicly available sequencing data. Compared to existing databases, this new database is more comprehensive, addresses concerns that limited the accuracy of earlier databases, and provides several new functionalities, such as the ability to view and compare codon usage between individual organisms and across taxonomical clades, through graphical representation or through commonly used indices. In addition, it is being routinely updated to keep up with the continuous flow of new data in GenBank and RefSeq. Conclusion: Given the impact of codon usage bias on recombinant gene technologies, this database will facilitate effective development and review of recombinant drug products and will be instrumental in a wide area of biological research. The database is available at hive.biochemistry.gwu.edu/review/codon.
doi:10.1186/s12859-017-1793-7 pmid:28865429 pmcid:PMC5581930 fatcat:wlveqvoqr5byhfloqqxzorqyx4

Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX

Aikaterini Alexaki, Jacob Kames, Gaya K. Hettiarachchi, John C. Athey, Upendra K. Katneni, Ryan C. Hunt, Nobuko Hamasaki-Katagiri, David D. Holcomb, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
2020 F1000Research  
's system: Python 2.7 (Python Software Foundation, Wilmington, DE, USA), GFF Utilities (Johns Hopkins University, Baltimore, MD, USA), Bowtie (Johns Hopkins University, Baltimore, MD, USA), TopHat (Johns  ... 
doi:10.12688/f1000research.22400.1 pmid:33014344 pmcid:PMC7509596 fatcat:ruav275njjfffcz3lkolpyh524

Spectroscopic Confirmation of a Large Population of Active Galactic Nuclei in Clusters of Galaxies

Paul Martini, Daniel D. Kelson, Eunhyeuk Kim, John S. Mulchaey, Alex A. Athey
2006 Astrophysical Journal  
We have completed a spectroscopic survey of X-ray point sources in eight low-redshift clusters of galaxies (0.0510^41) 5 stress that additional, lower-luminosity AGN are expected to be present in the M_R < -20 mag cluster members. Our data unambiguously demonstrate that cluster galaxies host AGN more frequently than previously expected. Only four of these galaxies have obvious visible-wavelength AGN signatures, even though their X-ray luminosities are too high for their X-ray emission to be due
more » ... to populations of low-mass X-ray binaries or hot, gaseous halos. We attribute the significant difference in visible and X-ray AGN identification to dilution of low-luminosity AGN spectral signatures by host galaxy starlight and/or obscuration of accretion onto the central, supermassive black hole.
doi:10.1086/503521 fatcat:y4wz56nacvc65g4lnp5xnanrua

Translational and transcriptional responses in human primary hepatocytes under hypoxia

Gaya K Hettiarachchi, Upendra K Katneni, Ryan C Hunt, Jacob M Kames, John C Athey, Haim Bar, Zuben E Sauna, Joseph R McGill, Juan C Ibla, Chava Kimchi-Sarfaty
2019 American Journal of Physiology - Gastrointestinal and Liver Physiology  
The liver is the primary source of a large number of plasma proteins and plays a critical role in multiple biological processes. Inadequate oxygen supply characterizing various clinical settings such as liver transplantation exposes the liver to hypoxic conditions. Studies assessing hypoxia-induced global translational changes in liver are lacking. Here, we employed a recently developed ribosome-profiling technique to assess global translational responses of human primary hepatocytes exposed to
more » ... acute hypoxic stress (1% O2) for the short term. In parallel, transcriptome profiling was performed to assess mRNA expression changes. We found that translational responses appeared earlier and were predominant over transcriptional responses. A significant decrease in translational efficiency of several ribosome genes indicated translational inhibition of new ribosome protein synthesis in hypoxia. Pathway enrichment analysis highlighted altered translational regulation of MAPK signaling, drug metabolism, oxidative phosphorylation, and nonalcoholic fatty liver disease pathways. Gene Ontology enrichment analysis revealed terms related to translation, metabolism, angiogenesis, apoptosis, and response to stress. Transcriptional induction of genes encoding heat shock proteins was observed within 30 min of hypoxia. Induction of genes encoding stress response mediators, metabolism regulators, and proangiogenic proteins was observed at 240 min. Despite the liver being the primary source of coagulation proteins and the implicated role of hypoxia in thrombosis, limited differences were observed in genes encoding coagulation-associated proteins. Overall, our study demonstrates the predominance of translational regulation over transcription and highlights differentially regulated pathways or biological processes in short-term hypoxic stress responses of human primary hepatocytes. NEW & NOTEWORTHY The novelty of this study lies in applying parallel ribosome- and transcriptome-profiling analyses to human primary hepatocytes in hypoxia. To our knowledge, this is the first study to assess global translational responses using ribosome profiling in hypoxic hepatocytes. Our results demonstrate the predominance of translational responses over transcriptional responses in early hepatic hypoxic stress responses. Furthermore, our study reveals multiple pathways and specific genes showing altered regulation in hypoxic hepatocytes.
doi:10.1152/ajpgi.00331.2018 pmid:30920299 pmcid:PMC6620582 fatcat:4fkwchj4hnfttones35p7zk75e

Complete Genome Sequence of Spiroplasma kunkelii Strain CR2-3x, Causal Agent of Corn Stunt Disease in Zea mays L

Robert E. Davis, Jonathan Shao, Ellen L. Dally, Yan Zhao, Gail E. Gasparich, Brady J. Gaynor, John C. Athey, Nigel A. Harrison, Nicole Donofrio
2015 Genome Announcements  
Spiroplasma kunkelii causes corn stunt disease of Zea mays L. in the Americas. Here, we report the nucleotide sequence of the 1,463,926-bp circular chromosome and four plasmids of strain CR2-3x. This information will facilitate studies of Spiroplasma pathogenicity and evolutionary adaptations to transkingdom parasitism in plants and insect vectors.
doi:10.1128/genomea.01216-15 pmid:26494665 pmcid:PMC4616174 fatcat:ivmbvs56hjglbcazbddw4cs7h4

CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis

Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-Hui Huang, John Beverley, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S Omenn (+2 others)
2020 Scientific Data  
the Coronavirus Infectious Disease Ontology (CIDO) is a community-based ontology that supports coronavirus disease knowledge and data standardization, integration, sharing, and analysis.
doi:10.1038/s41597-020-0523-6 pmid:32533075 pmcid:PMC7293349 fatcat:mhnibrv3yvff3ida4wi5nu6rse

3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification [article]

Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Syed S. Husain, Jeffrey R. de Wet, Gerald A. Higgins, Gen Zheng, Amy Creekmore, John W. Wiley (+6 others)
2018 bioRxiv   pre-print
DK089503, P30 AG053760, T32 GM070449, UL1TR002240; the Department of Computational Medicine and Bioinformatics Research Account, University of Michigan; the James Buchanan Brady Urological Institute, John  ... 
doi:10.1101/313411 fatcat:hrifz7az2vcivfeg4trwnsimpu

A 7 Tesla Amygdalar-Hippocampal Shape Analysis of Lithium Response in Bipolar Disorder

Thomas L. Athey, Can Ceritoglu, Daniel J. Tward, Kwame S. Kutten, J. Raymond DePaulo, Kara Glazer, Fernando S. Goes, John R. Kelsoe, Francis Mondimore, Caroline M. Nievergelt, Kelly Rootes-Murdy, Peter P. Zandi (+2 others)
2021 Frontiers in Psychiatry  
ETHICS STATEMENT The studies involving human participants were reviewed and approved by Johns Hopkins Institutional Review Board.  ...  MATERIALS AND METHODS Participants Participants with BD were recruited at the Johns Hopkins site of the Pharmacogenomics of Bipolar Disorder Study (PGBD), an eleven site prospective trial of lithium  ...  Copyright © 2021 Athey, Ceritoglu, Tward, Kutten, DePaulo, Glazer, Goes, Kelsoe, Mondimore, Nievergelt, Rootes-Murdy, Zandi, Ratnanather and Mahon.  ... 
doi:10.3389/fpsyt.2021.614010 pmid:33664682 pmcid:PMC7920967 fatcat:d45hfd2uhvcehb6dqttggb5jau

3D Cell Nuclear Morphology: Microscopy Imaging Dataset and Voxel-Based Morphometry Classification Results [article]

Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Jeffrey R. de Wet, Gerald A. Higgins, Gen Zheng, Amy Creekmore, John W. Wiley, James E. Verdone (+5 others)
2017 bioRxiv   pre-print
Cell deformation is regulated by complex underlying biological mechanisms associated with spatial and temporal morphological changes in the nucleus that are related to cell differentiation, development, proliferation, and disease. Thus, quantitative analysis of changes in size and shape of nuclear structures in 3D microscopic images is important not only for investigating nuclear organization, but also for detecting and treating pathological conditions such as cancer. While many efforts have
more » ... n made to develop cell and nuclear shape characteristics in 2D or pseudo-3D, several studies have suggested that 3D morphometric measures provide better results for nuclear shape description and discrimination. A few methods have been proposed to classify cell and nuclear morphological phenotypes in 3D, however, there is a lack of publicly available 3D data for the evaluation and comparison of such algorithms. This limitation becomes of great importance when the ability to evaluate different approaches on benchmark data is needed for better dissemination of the current state of the art methods for bioimage analysis. To address this problem, we present a dataset containing two different cell collections, including original 3D microscopic images of cell nuclei and nucleoli. In addition, we perform a baseline evaluation of a number of popular classification algorithms using 2D and 3D voxel-based morphometric measures. To account for batch effects, while enabling calculations of AUROC and AUPR performance metrics, we propose a specific cross-validation scheme that we compare with commonly used k-fold cross-validation. Original and derived imaging data are made publicly available on the project web-page: http://www.socr.umich.edu/projects/3d-cell-morphometry/data.html.
doi:10.1101/208207 fatcat:pv6c5yygn5axvkylhmoshtg6mi

3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification

Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Syed S. Husain, Jeffrey R. de Wett, Gerald A. Higgins, Gen Zheng, Amy Creekmore, John W. Wiley (+6 others)
2018 Scientific Reports  
DK089503, P30 AG053760, T32 GM070449, UL1TR002240; the Department of Computational Medicine and Bioinformatics Research Account, University of Michigan; the James Buchanan Brady Urological Institute, John  ... 
doi:10.1038/s41598-018-31924-2 pmid:30209281 pmcid:PMC6135819 fatcat:kqrmkyfhdvffzcskzkjwenve5q
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