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David J. States
University of Michigan
112Publications
32H-index
6,653Citations
Publications 112
Newest
Published on Jan 1, 2014in Journal of Biomedical Semantics 1.60
Sirarat Sarntivijai8
Estimated H-index: 8
(University of Michigan),
Yu Lin10
Estimated H-index: 10
(University of Michigan)
+ 22 AuthorsHelen Parkinson33
Estimated H-index: 33
(European Bioinformatics Institute)
Background Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions.
31 Citations Source Cite
Published on May 15, 2012in Bioinformatics 5.48
Maureen A. Sartor40
Estimated H-index: 40
(University of Texas Health Science Center at Houston),
Alexander S. Ade6
Estimated H-index: 6
(University of Texas Health Science Center at Houston)
+ 4 AuthorsAlla Karnovsky15
Estimated H-index: 15
(University of Texas Health Science Center at Houston)
Summary: Progress in high-throughput genomic technologies has led to the development of a variety of resources that link genes to functional information contained in the biomedical literature. However, tools attempting to link small molecules to normal and diseased physiology and published data relevant to biologists and clinical investigators, are still lacking. With metabolomics rapidly emerging as a new omics field, the task of annotating small molecule metabolites becomes highly relevant. Ou...
21 Citations Source Cite
Published on Dec 15, 2010in Bioinformatics 5.48
Gang Su4
Estimated H-index: 4
(University of Texas Health Science Center at Houston),
Allan Kuchinsky16
Estimated H-index: 16
(University of Texas Health Science Center at Houston)
+ 2 AuthorsFan Meng1
Estimated H-index: 1
(University of Texas Health Science Center at Houston)
Summary: GLay provides Cytoscape users an assorted collection of versatile community structure algorithms and graph layout functions for network clustering and structured visualization. High performance is achieved by dynamically linking highly optimized C functions to the Cytoscape JAVA program, which makes GLay especially suitable for decomposition, display and exploratory analysis of large biological networks. Availability: http://brainarray.mbni.med.umich.edu/glay/ Contact: ude.hcimu@gnagus
83 Citations Source Cite
Arvind Rao10
Estimated H-index: 10
,
David J. States32
Estimated H-index: 32
(University of Michigan)
+ 1 AuthorsJames Douglas Engel68
Estimated H-index: 68
(University of Michigan)
Gene regulation in eukaryotes involves a complex interplay between the proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive precise spatio-temporal gene expression. The experimental localization and characterization of gene regulatory elements is a very complex and resource-intensive process. The computational identification of regulatory regions that confer spatiotemporally specific tissue-restricted expression of a gene is thus an important challenge...
1 Citations Source Cite
Published on Dec 1, 2010in BMC Medical Genomics 3.32
Junguk Hur19
Estimated H-index: 19
(University of Michigan),
Kelli A. Sullivan24
Estimated H-index: 24
(University of Michigan)
+ 5 AuthorsEva L. Feldman5
Estimated H-index: 5
(University of Michigan)
Background Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the genes associated with ROS.
23 Citations Source Cite
Published on Jan 1, 2009in Cancer Research 9.13
Rajasree Menon19
Estimated H-index: 19
(University of Michigan),
Qing Zhang30
Estimated H-index: 30
(Fred Hutchinson Cancer Research Center)
+ 7 AuthorsDavid J. States32
Estimated H-index: 32
(University of Michigan)
To assess the potential of tumor-associated, alternatively spliced gene products as a source of biomarkers in biological fluids, we have analyzed a large data set of mass spectra derived from the plasma proteome of a mouse model of human pancreatic ductal adenocarcinoma. MS/MS spectra were interrogated for novel splice isoforms using a nonredundant database containing an exhaustive three-frame translation of Ensembl transcripts and gene models from ECgene. This integrated analysis identified 420...
65 Citations Source Cite
Published on Jan 1, 2009in Nucleic Acids Research 11.56
V. Glenn Tarcea5
Estimated H-index: 5
(University of Michigan),
Terry E. Weymouth19
Estimated H-index: 19
(University of Michigan)
+ 15 AuthorsArzucan Özgür15
Estimated H-index: 15
(University of Michigan)
Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases, and deep merged this information while keeping track of provenance. Based on the feedback received from users, MiMI has been completely redesigned. ...
91 Citations Source Cite
Published on Mar 15, 2009in Bioinformatics 5.48
Junguk Hur19
Estimated H-index: 19
(University of Michigan),
Adam D. Schuyler13
Estimated H-index: 13
(University of Michigan)
+ 1 AuthorsEva L. Feldman81
Estimated H-index: 81
(University of Michigan)
Summary:SciMiner is a web-based literature mining and functional analysis tool that identifies genes and proteins using a context specific analysis of MEDLINE abstracts and full texts. SciMiner accepts a free text query (PubMed Entrez search) or a list of PubMed identifiers as input. SciMiner uses both regular expression patterns and dictionaries of gene symbols and names compiled from multiple sources. Ambiguous acronyms are resolved by a scoring scheme based on the co-occurrence of acronyms an...
87 Citations Source Cite
Published on Jan 1, 2009in Bioinformatics 5.48
Jing Gao5
Estimated H-index: 5
(University of Michigan),
Alexander S. Ade6
Estimated H-index: 6
(University of Michigan)
+ 4 AuthorsDavid J. States32
Estimated H-index: 32
(University of Michigan)
Summary: The MiMI molecular interaction repository integrates data from multiple sources, resolves interactions to standard gene names and symbols, links to annotation data from GO, MeSH and PubMed and normalizes the descriptions of interaction type. Here, we describe a Cytoscape plugin that retrieves interaction and annotation data from MiMI and links out to multiple data sources and tools. Community annotation of the interactome is supported. Availability: MiMI plugin v3.0.1 can be installed f...
107 Citations Source Cite
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