User profiles for I. H. Holmes

Ian Holmes

Professor, Computational Biology and Bioengineering, UC Berkeley
Verified email at berkeley.edu
Cited by 15030

Virus particles in epithelial cells of duodenal mucosa from children with acute non-bacterial gastroenteritis

RF Bishop, GP Davidson, IH Holmes, BJ Ruck - The Lancet, 1973 - Elsevier
Electron microscopy of duodenal mucosa from nine children with acute non-bacterial
gastroenteritis revealed virus particles in epithelial cells from six patients. The morphology of the …

JBrowse: a next-generation genome browser

…, AV Uzilov, LD Stein, CJ Mungall, IH Holmes - Genome …, 2009 - genome.cshlp.org
We describe an open source, portable, JavaScript-based genome browser, JBrowse, that can
be used to navigate genome annotations over the web. JBrowse helps preserve the user's …

[HTML][HTML] JBrowse: a dynamic web platform for genome visualization and analysis

…, CG Elsik, SE Lewis, L Stein, IH Holmes - Genome biology, 2016 - Springer
Background JBrowse is a fast and full-featured genome browser built with JavaScript and
HTML5. It is easily embedded into websites or apps but can also be served as a standalone …

Detection of a new virus by electron microscopy of faecal extracts from children with acute gastroenteritis

RF Bishop, GP Davidson, IH Holmes, BJ Ruck - The Lancet, 1974 - Elsevier
Electron microscopy of negatively stained fęcal extracts revealed particles resembling
orbiviruses in 11 of 14 children with acute non-bacterial gastroenteritis. No such particles were …

[HTML][HTML] Web Apollo: a web-based genomic annotation editing platform

…, CP Childers, RM Buels, L Stein, IH Holmes… - Genome biology, 2013 - Springer
Web Apollo is the first instantaneous, collaborative genomic annotation editor available on
the web. One of the natural consequences following from current advances in sequencing …

[HTML][HTML] JBrowse 2: a modular genome browser with views of synteny and structural variation

…, R Haw, S Cain, RM Buels, LD Stein, IH Holmes - Genome biology, 2023 - Springer
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced
visualization of complex structural variation and evolutionary relationships. It retains core …

Haloalkane Dehalogenases:  Structure of a Rhodococcus Enzyme,

…, L Kan, PE Swanson, JA Affholter, IH Holmes… - Biochemistry, 1999 - ACS Publications
The hydrolytic haloalkane dehalogenases are promising bioremediation and biocatalytic
agents. Two general classes of dehalogenases have been reported from Xanthobacter and …

Importance of a new virus in acute sporadic enteritis in children

GP Davidson, RF Bishop, RRW Townley, IH Holmes… - The Lancet, 1975 - Elsevier
In a year-long survey of children admitted with acute enteritis to hospital in Melbourne, Australia,
an ętiological agent was found in approximately 75% of patients. During most months …

Location of the major antigenic sites involved in rotavirus serotype-specific neutralization.

…, I Lazdins, GW Tregear, IH Holmes - Proceedings of the …, 1986 - National Acad Sciences
Antigenic sites on the rotavirus major outershell glycoprotein were identified by using mutant
viruses selected for resistance to neutralizing (serotype-specific) monoclonal antibodies. …

[HTML][HTML] Apollo: democratizing genome annotation

…, NL Harris, E Yao, H Rasche, IH Holmes… - PLoS computational …, 2019 - journals.plos.org
Genome annotation is the process of identifying the location and function of a genome's
encoded features. Improving the biological accuracy of annotation is a complex and iterative …