Filters








204 Hits in 1.7 sec

SBGN Activity Flow Update

Huaiyu Mi
2011 Nature Precedings  
doi:10.1038/npre.2011.5680.1 fatcat:mngyrzjktzbv5eno25isfdt74a

PharmGKB summary

Huaiyu Mi, Paul D. Thomas, Huijun Z. Ring, Ruhong Jiang, Katrin Sangkuhl, Teri E. Klein, Russ B. Altman
2011 Pharmacogenetics & Genomics  
doi:10.1097/fpc.0b013e32833ee605 pmid:20736885 pmcid:PMC3091980 fatcat:2px2vmzmfvb5rknoabp4j354rq

Induction of Astrocyte Differentiation by Endothelial Cells

Huaiyu Mi, Henry Haeberle, Ben A. Barres
2001 Journal of Neuroscience  
At E17, most of the astrocyte lineage cells within the nerve are APC s (Mi and Barres, 1999) .  ...  E17 or P1 optic nerves were enzymatically dissociated as described previously (Mi and Barres, 1999) .  ... 
doi:10.1523/jneurosci.21-05-01538.2001 pmid:11222644 fatcat:ugpmee3hdrewrgcp7nki7ybhcq

GOTaxon: Representing the evolution of biological functions in the Gene Ontology [article]

Haiming Tang, Christopher J Mungall, Huaiyu Mi, Paul D Thomas
2018 arXiv   pre-print
The Gene Ontology aims to define the universe of functions known for gene products, at the molecular, cellular and organism levels. While the ontology is designed to cover all aspects of biology in a "species independent manner", the fact remains that many if not most biological functions are restricted in their taxonomic range. This is simply because functions evolve, i.e. like other biological characteristics they are gained and lost over evolutionary time. Here we introduce a general method
more » ... f representing the evolutionary gain and loss of biological functions within the Gene Ontology. We then apply a variety of techniques, including manual curation, logical reasoning over the ontology structure, and previously published "taxon constraints" to assign evolutionary gain and loss events to the majority of terms in the GO. These gain and loss events now almost triple the number of terms with taxon constraints, and currently cover a total of 76% of GO terms, including 40% of molecular function terms, 78% of cellular component terms, and 89% of biological process terms. Database URL: GOTaxon is freely available at https://github.com/haimingt/GOTaxonConstraint
arXiv:1802.06004v1 fatcat:jwwelk7s6zfntcz267jjebf3m4

Systems Biology Graphical Notation: Process Description language Level 1

Stuart Moodie, Nicolas Le Novere, Emek Demir, Huaiyu Mi, Falk Schreiber
2011 Nature Precedings  
Mi.  ...  Level 1 Release 1.0 The specification of was written by Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Yukiko Matsuoka, Katja Wegner and Hiroaki  ... 
doi:10.1038/npre.2011.3721.3 fatcat:szir5ozfqrb77kylksoozxvohq

Systems Biology Graphical Notation: Process Description language Level 1

Stuart Moodie, Nicolas Le Novere, Anatoly Sorokin, Huaiyu Mi, Falk Schreiber
2009 Nature Precedings  
Mi.  ...  Level 1 Release 1.0 The specification of was written by Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Yukiko Matsuoka, Katja Wegner and Hiroaki  ... 
doi:10.1038/npre.2009.3721.1 fatcat:laqk6dvxl5dwbgjlkeyupesnga

Systems Biology Graphical Notation: Entity Relationship language Level 1

Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Falk Schreiber, Huaiyu Mi
2009 Nature Precedings  
doi:10.1038/npre.2009.3719.1 fatcat:fjpkoe22ezdgziprtjbe7pgh7a

Systems Biology Graphical Notation: Activity Flow language Level 1

Huaiyu Mi, Falk Schreiber, Nicolas Le Novére, Stuart Moodie, Anatoly Sorokin
2009 Nature Precedings  
Level 1 Release 1.0 The specification was written by Huaiyu Mi, Falk Schreiber, Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Michael Hucka, Emek Demir, Yukiko Matsuoka, Katja Wegner and Hiroaki Kitano  ...  For a general description of SBGN, one can read: Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I Aladjem, Sarala M Wimalaratne  ... 
doi:10.1038/npre.2009.3724.1 fatcat:m4at4zuupzffpbkbj3f6brwuzi

Systems Biology Graphical Notation: Process Description language Level 1

Stuart Moodie, Nicolas Le Novere, Emek Demir, Huaiyu Mi, Falk Schreiber
2010 Nature Precedings  
Mi.  ...  Level 1 Release 1.0 The specification of was written by Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Yukiko Matsuoka, Katja Wegner and Hiroaki  ... 
doi:10.1038/npre.2010.3721.2 fatcat:64ubulaowretpd747ybqkd6vbq

Systems Biology Graphical Notation: Process Description language Level 1

Stuart Moodie, Stuart Moodie, Nicolas Le Novere, Emek Demir, Huaiyu Mi, Alice Villeger
2011 Nature Precedings  
Mi.  ...  Level 1 Release 1.0 The specification of was written by Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Yukiko Matsuoka, Katja Wegner and Hiroaki  ... 
doi:10.1038/npre.2011.3721.4 fatcat:ty5fbdn6rrb6viuqt7yg6ghjru

Ontologies and Standards in Bioscience Research: For Machine or for Human

Huaiyu Mi, Paul D. Thomas
2011 Frontiers in Physiology  
Because of the wide acceptance of GO, PANTHER retired its PANTHER Index in 2009 and developed GO-slim for its annotation (Mi et al., 2010) .  ...  Copyright © 2011 Mi and Thomas.  ... 
doi:10.3389/fphys.2011.00005 pmid:21519400 pmcid:PMC3081276 fatcat:oe472gyzvrgwtdo2joqdn3koja

Systems Biology Graphical Notation: Process Description language Level 1

Stuart Moodie, Stuart Moodie, Nicolas Le Novere, Anatoly Sorokin, Huaiyu Mi, Falk Schreiber
2009 Nature Precedings  
Mi.  ...  Level 1 Release 1.0 The specification of was written by Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Yukiko Matsuoka, Katja Wegner and Hiroaki  ... 
doi:10.1038/npre.2009.3721 fatcat:h3oykumim5h4nmbcigb7p5hxeq

Systems Biology Graphical Notation: Entity Relationship language Level 1

Nicolas Le Novère, Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Falk Schreiber, Huaiyu Mi
2010 Nature Precedings  
doi:10.1038/npre.2010.3719.2 fatcat:2qdsyi2imjardjqzwn7q7sjxpa

Automation of gene function prediction through modeling human curators' decisions in GO phylogenetic annotation project [article]

Haiming Tang, Paul D Thomas, Huaiyu Mi
2018 arXiv   pre-print
Currently reference trees in PANTHER database are annotated by PAINT, which include protein-coding genes from all the 12 GO Reference Genomes, and 104 genomes covering all major taxa of species (Mi, et  ... 
arXiv:1802.07204v1 fatcat:q62otjeidbc5zoxlghkqlmlvi4

Intercellular signaling network underlies biological time across multiple temporal scales [article]

Joshua Millstein, Keith C Summa, Xia Yang, Jun Zhu, Huaiyu Mi, Martha H Vitaterna, Fred W Turek, Bing Zhang
2018 bioRxiv   pre-print
To further investigate molecular functions of genes in the consensus network, PANTHER overrepresentation tests were conducted with Bonferroni corrections using the GO Ontology database (Mi, et al., 2016  ... 
doi:10.1101/315788 fatcat:n4msjgdtrzc33b2onksf4rvgdi
« Previous Showing results 1 — 15 out of 204 results