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PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas
2020 Nucleic Acids Research  
The evolutionary classification is based on a library of over 15,000 phylogenetic trees, and the functional classifications include Gene Ontology terms and pathways.  ...  The PANTHER Protein Class ontology has been completely refactored, and 6101 PANTHER families have been manually assigned to a Protein Class, providing a high level classification of protein families and  ...  ACKNOWLEDGEMENTS The authors want to thank the GO Phylogenetic Annotation curators for QA of the phylogenetic trees and family members: Marc Feuermann, Michael Kesling, Pascale Gaudet, Karen Christie,  ... 
doi:10.1093/nar/gkaa1106 pmid:33290554 pmcid:PMC7778891 fatcat:ud5tcejh2fgifjkxjwoz7rc6aq

Gene Ontology Consortium: going forward

2014 Nucleic Acids Research  
We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions.  ...  The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data.  ...  The AmiGO 2 set of tools also provides a JavaScript API for better access and integration with other tools, and both provides and consumes REST APIs to help better integrate resources, such as the PANTHER  ... 
doi:10.1093/nar/gku1179 pmid:25428369 pmcid:PMC4383973 fatcat:kvchjgs5zzchrbtuqof5bopmee

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari (+17 others)
2020 Nucleic Acids Research  
The current release, #63 (October 2020), hosts 93 reference genomes—over 3.9 million genes in 122 947 families with orthologous and paralogous classifications.  ...  Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species.  ...  that have helped us to improve the overall quality of Gramene as a community resource.  ... 
doi:10.1093/nar/gkaa979 pmid:33170273 fatcat:atundz637bfalivwtye3vb3twe

BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae [article]

Rafal Donczew, Steven Hahn
2021 bioRxiv   pre-print
Human bromodomain-containing BET family members are promising targets for therapy of cancer and immunoinflammatory diseases, but their mechanisms of action and functional redundancies are poorly understood  ...  Surprisingly, we discovered that hypersensitivity of genes to Bdf1/2 depletion results from combined defects in transcription initiation and processive elongation, a striking functional similarity to human  ...  PANTHER 903 version 16: a revised family classification, tree-based classification tool, enhancer regions and 904 extensive API.  ... 
doi:10.1101/2021.04.20.440672 fatcat:gsi3igdwzfb43ptk3ujqycyxee

Social Web and Knowledge Management [chapter]

Peter Dolog, Markus Krötzsch, Sebastian Schaffert, Denny Vrandečić
2009 Weaving Services and People on the World Wide Web  
Acknowledgements The authors acknowledge the financial support of the Italian Ministry of Education, University and Research (MIUR) within the FIRB project number RBIN04M8S8.  ...  Semantic Wikis, like Semantic MediaWiki [12] , IkeWiki [16] and many others 12 , further enhance Wikis to make the collaborative knowledge contributed by users more explicit and formal.  ...  We expand upon the definition and significance of these groups as needed in section 6. TOOLS DEVELOPED To process the sizable dataset, we created a set of small, robust, stream-based tools in C.  ... 
doi:10.1007/978-3-642-00570-1_11 dblp:conf/www/DologKSV08a fatcat:z6glljv7sfdxromng3d66jchne

The Retrospective on Atypical Brucella Species Leads to Novel Definitions

Alessandra Occhialini, Dirk Hofreuter, Christoph-Martin Ufermann, Sascha Al Dahouk, Stephan Köhler
2022 Microorganisms  
Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between  ...  , Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals.  ...  Acknowledgments: We thank Holger Brendebach (BfR, Berlin, Germany) for his assistance with the phylogenetic trees, and Daniela de Biase (Sapienza University, Rome, Italy) for helpful discussions on acid  ... 
doi:10.3390/microorganisms10040813 pmid:35456863 pmcid:PMC9025488 fatcat:bnxas4p3dngofodpegraet6xc4

Recommendations for Preventing the Spread of Vancomycin Resistance

Hospital Infection Control Practices Advisory Committee
1995 Emerging Infectious Diseases  
The field part of this study is supported by a regional grant of the Public Service of Wallonia. About the Authors Dr.  ...  About the Author We used CSI Phylogeny version 1.4 (https://cge.cbs. dtu.dk/services/CSIPhylogeny) for phylogenomic analysis on the basis of single-nucleotide polymorphisms (SNPs) and called among core  ...  JF957361 and JF957363; isolated in the United Kingdom) by using Sequence Demarcation Tool version 1.2 (31) .  ... 
doi:10.3201/eid0102.950210 fatcat:bndbkyzbzfhzbjmcvam3lqwwmi

Functional unknomics: closing the knowledge gap to accelerate biomedical research [article]

Joao Rocha, Satish Arcot Jayaram, Tim J Stevens, Nadine Muschalik, Rajen D Shah, Sahar Emran, Cristina Robles, Matthew Freeman, Sean Munro
2022 bioRxiv   pre-print
Scientific and social factors have resulted in a focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected.  ...  To address this, we have developed an "Unknome database" that ranks proteins based on how little is known about them.  ...  Funding was from the Medical Research Council, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation), file reference number MC_U105178783.  ... 
doi:10.1101/2022.06.28.497983 fatcat:vo5nja364rez5ab32hjhb6ocjy

Biological Sequence Indexing Using Persistent Java

Elzbieta Pustulka-Hunt
2001 Zenodo  
This methodology allowed us to develop a practical algorithm for the construction of suffix trees on disk up to any size supported by the available file and addressing space, which has hitherto not been  ...  The third contribution is a new experimental methodology for examining the usefulness of suffix indexes, and the use of this methodology in an empirical investigation of the indexing gain achieved by combining  ...  Acknowledgements I would like to thank my family for their support, and in particular my parents who volunteered to spend a long time in Glasgow in order to help me concentrate on research.  ... 
doi:10.5281/zenodo.1341577 fatcat:jeeostwznzdrtakbhhw4bepsy4

OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization [article]

Nathan H. Cho, Keith C. Cheveralls, Andreas-David Brunner, Kibeom Kim, Andre C. Michaelis, Preethi Raghavan, Hirofumi Kobayashi, Laura Savy, Jason Y. Li, Hera Canaj, James Y.S. Kim, Edna M. Setwart (+15 others)
2021 bioRxiv   pre-print
Our approach provides a data-driven description of the molecular and spatial networks that organize the human proteome.  ...  For this, we generated a library of 1,311 CRISPR-edited cell lines harboring fluorescent tags that also serve as handles for affinity capture, and applied a new machine learning framework to encode the  ...  PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res 49, gkaa1106-(2020). Nat Biotechnol 32, 223-226 (2014). 81.  ... 
doi:10.1101/2021.03.29.437450 fatcat:7g2pp24txjdjfjwddznieuhr7q

Development of Methodology to Investigate the Surface SMALPome of Mammalian Cells

Kerrie A. Morrison, Kate J. Heesom, Karen J. Edler, James Doutch, Gareth J. Price, Francoise Koumanov, Paul Whitley
2021 Frontiers in Molecular Biosciences  
SMA nanodiscs are compatible with analytical techniques, such as small-angle scattering, NMR spectroscopy, and DLS, and are therefore an attractive medium for membrane protein characterization.  ...  For this, cell surface proteins of 3T3L1 fibroblasts were biotinylated and extracted using either SMA or detergent.  ...  ., Muruganujan, A., Mills, C., Albou, L.-P., Mushayamaha, T., et al. (2021). PANTHER Version 16: a Revised Family Classification, Tree-Based Classification Tool, Enhancer Regions and Extensive API.  ... 
doi:10.3389/fmolb.2021.780033 pmid:34869600 pmcid:PMC8637157 fatcat:6bzqz6wc6zafdfg7pntfcman2m

Modeling autism-associated SHANK3 deficiency using human cortico-striatal organoids generated from single neural rosettes [article]

Yueqi Wang, Simone Chiola, Guang Yang, Chad Russell, Celeste J Armstrong, Yuanyuan Wu, Jay Spampanato, Paisley Tarboton, Amelia N Chang, David A Harmin, Elena Vezzoli, Dario Besusso (+4 others)
2021 bioRxiv   pre-print
We developed a new method for generating human cortico-striatal organoids from stem cell-derived single neural rosettes (SNRs) and used it to investigate cortico-striatal development and deficits caused  ...  Together, this study describes a new method for using SNRs to generate organoids, provides new insights into the cell lineages associated with human cortico-striatal development, and identifies specific  ...  PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 49, D394-D403.  ... 
doi:10.1101/2021.01.25.428022 fatcat:ogzrrpkgvzavjmcnfb5kj7a55y

Conservation biology for all

2010 ChoiceReviews  
Gómez-Pompa, A., Vázquez-Yanes, C., and Guevara, S. (1972). The tropical rainforest: a non-renewable resource. Science, 177, 762-765. Grifo, F. T. and Rosenthal, J., eds (1997).  ...  Thresholds for survival: criteria for maintenance of fitness and evolutionary potential. In M. E. Soulé, and B. A.  ...  Applying the formula, the region should have retained 84% of its species and so lost 16%. Now 16% of 160 species is 26 species and that is clearly not the right answer.  ... 
doi:10.5860/choice.48-2055 fatcat:qwhlin7vk5cqllgqrijinrsmka

International Conference on Emerging Infectious Diseases 2015 Poster and Oral Presentation Abstracts

2015 Emerging Infectious Diseases  
Acknowledgements: To Neil Vora and Yu Li from CDC Atlanta for supporting this.  ...  CIs can require extensive resources and record review; therefore, electronic health data can be a useful tool to improve the timeliness and accuracy of healthcare-associated CIs.  ...  We evaluated BCBS cases, defined as a Tennessee resident beneficiary with ≥3 primary or secondary International Classification of Diseases, Ninth Revision (ICD-9) codes for LD (088.81) recorded in their  ... 
doi:10.3201/eid2109.nn2109 fatcat:dlu3wgxsbngsdasrh3t5u6shpu

Guidance on the environmental risk assessment of plant pests

2011 EFSA Journal  
To ensure the consistency and transparency of the assessment, a rating system has also been developed based on a probabilistic approach with an evaluation of the degree of uncertainty.  ...  The guidance is primarily addressed to the EFSA PLH Panel and has been conceived as an enhancement of the relevant parts of the "Guidance on a harmonised framework for pest risk assessment and the identification  ...  This is a less detailed version of the EPPO and modified EPPO scheme mentioned under method 1 and method 2.  ... 
doi:10.2903/j.efsa.2011.2460 fatcat:4j6ik5u7c5btjcjt3pxitg2lse
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