Ian Holmes - Publications, H-index & Citations

Ian Holmes

California State University System

57H指数

256论文数

2.1W被引数

收录论文 30

发表时间

Proteins in the Genome Browser: integration of phylogenies, alignments, and structures with nucleotide-level evidence in JBrowse 2

Journal of Molecular Biology

IF4.5

2026-01-19

PREAI

Colin Diesh; Garrett Stevens; Caroline Bridge; Gregory Hogue; Robert Buels; Scott Cain; Lincoln Stein; Ian Holmes

Setting up JBrowse 2 for Visualizing Genome Synteny 配置JBrowse 2以可视化基因组共线性

CURRENT PROTOCOLS

IF2.2

2025-12-01

OAAI

Diesh, Colin; Stevens, Garrett; Cain, Scott; Stein, Lincoln; Holmes, Ian

Chemical Cross-Linking Ligand Shell Influence on the Mechanical Properties of TiO2-Polymer Composites 化学交联配体壳对TiO2-聚合物复合材料力学性能的影响

ACS APPLIED ENGINEERING MATERIALS

IF3.5

2025-12-01

PREAI

Holmes, Ian; Ishihara, Kristi M.; Kasem, Keith; Rios, Javier; Tian, Fangyuan; Kalman, Joseph

Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications

MOLECULAR BIOLOGY AND EVOLUTION

IF5.3

2024-08-22

OAAI

Redelings, Benjamin D.; Holmes, Ian; Lunter, Gerton; Pupko, Tal; Anisimova, Maria

Randomized trial of gastric and colorectal endoscopic submucosal dissection defect closure comparing a novel through-the-scope suturing system with an over-the-scope suturing system (with video)

GASTROINTESTINAL ENDOSCOPY

IF7.5

2024-02-01

PREAI

Agnihotri, Abhishek; Mitsuhashi, Shuji; Holmes, Ian; Kamal, Faisal; Chiang, Austin; Loren, David E.; Kowalski, Thomas E.; Schlachterman, Alexander; Kumar, Anand R.

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

GENOME BIOLOGY

IF9.4

2023-04-17

OAAI

Diesh, Colin; Stevens, Garrett J.; Xie, Peter; Martinez, Teresa De Jesus; Hershberg, Elliot A.; Leung, Angel; Guo, Emma; Dider, Shihab; Zhang, Junjun; Bridge, Caroline; Hogue, Gregory; Duncan, Andrew; Morgan, Matthew; Flores, Tia; Bimber, Benjamin N.; Haw, Robin; Cain, Scott; Buels, Robert M.; Stein, Lincoln D.; Holmes, Ian H.

GrainGenes: a data-rich repository for small grains genetics and genomics

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION

IF3.6

2022-05-25

OAAI

Yao, Eric; Blake, Victoria C.; Cooper, Laurel; Wight, Charlene P.; Michel, Steve; Cagirici, H. Busra; Lazo, Gerard R.; Birkett, Clay L.; Waring, David J.; Jannink, Jean-Luc; Holmes, Ian; Waters, Amanda J.; Eickholt, David P.; Sen, Taner Z.

Manufacturing a TiO2-Based Semiconductor Film with Nanofluid Pool Boiling and Sintering Processes toward Solar-Cell Applications

NANOMATERIALS

IF4.3

2022-03-31

OAAI

Vafaei, Saeid; Holmes, Ian; Errion, Benjamin; Thukka, Zigmey; Narita, Ryoki; Sugiura, Takashi; Manseki, Kazuhiro

CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing CNVpytor: 全基因组测序中从读取深度和等位基因失衡进行拷贝数变异检测和分析的工具

GIGASCIENCE

IF3.9

2021-11-18

OAAI

Suvakov, Milovan; Panda, Arijit; Diesh, Colin; Holmes, Ian; Abyzov, Alexej

Evidence of stock connectivity, hybridization, and misidentification in white anglerfish supports the need of a genetics-informed fisheries management framework

EVOLUTIONARY APPLICATIONS

IF3.2

2021-08-04

OAAI

Aguirre-Sarabia, Imanol; Diaz-Arce, Natalia; Pereda-Agirre, Iker; Mendibil, Inaki; Urtizberea, Agurtzane; Gerritsen, Hans D.; Burns, Finlay; Holmes, Ian; Landa, Jorge; Coscia, Ilaria; Quinconces, Inaki; Santurtun, Marina; Zanzi, Antonella; Martinsohn, Jann T.; Rodriguez-Ezpeleta, Naiara

Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing

GENOME BIOLOGY

IF9.4

2021-01-19

OAAI

Silvestre-Ryan, Jordi; Holmes, Ian

Prophylactic intranasal administration of a TLR2/6 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model

EBIOMEDICINE

IF10.8

2021-01-01

OAAI

Proud, Pamela C.; Tsitoura, Daphne; Watson, Robert J.; Chua, Brendon Y.; Aram, Marilyn J.; Bewley, Kevin R.; Cavell, Breeze E.; Cobb, Rebecca; Dowall, Stuart; Fotheringham, Susan A.; Ho, Catherine M. K.; Lucas, Vanessa; Ngabo, Didier; Rayner, Emma; Ryan, Kathryn A.; Slack, Gillian S.; Thomas, Stephen; Wand, Nadina, I; Yeates, Paul; Demaison, Christophe; Zeng, Weiguang; Holmes, Ian; Jackson, David C.; Bartlett, Nathan W.; Mercuri, Francesca; Carroll, Miles W.

A Model of Indel Evolution by Finite-State, Continuous-Time Machines

GENETICS

IF5.1

2020-12-01

OAAI

Holmes, Ian

Avulsion for the treatment of visible residual neoplasia during EMR of colorectal polyps: Is heat required? Response

GASTROINTESTINAL ENDOSCOPY

IF7.5

2017-07-01

OAAI

Holmes, Ian; Kim, Hyun Gun; Yang, Dong-Hoon; Friedland, Shai

Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process

PROCEEDINGS OF THE IEEE

IF25.9

2017-03-01

OAAI

Harris, Keith; Parsons, Todd L.; Ijaz, Umer Z.; Lahti, Leo; Holmes, Ian; Quince, Christopher

JBrowse: a dynamic web platform for genome visualization and analysis JBrowse: 用于基因组可视化和分析的动态web平台

GENOME BIOLOGY

IF9.4

2016-04-12

572

OAAI

Buels, Robert; Yao, Eric; Diesh, Colin M.; Hayes, Richard D.; Munoz-Torres, Monica; Helt, Gregg; Goodstein, David M.; Elsik, Christine G.; Lewis, Suzanna E.; Stein, Lincoln; Holmes, Ian H.

AAV Ancestral Reconstruction Library Enables Selection of Broadly Infectious Viral Variants

MOLECULAR THERAPY

IF12

2015-05-01

OAAI

Ojala, David S.; Santiago-Ortiz, Jorge; Westesson, Oscar; Weinstein, John R.; Wong, Sophie Y.; Steinsapir, Andrew; Kumar, Sanjay; Holmes, Ian; Schaffer, David

Web Apollo: a web-based genomic annotation editing platform

GENOME BIOLOGY

IF9.4

2013-08-30

290

OAAI

Lee, Eduardo; Helt, Gregg A.; Reese, Justin T.; Munoz-Torres, Monica C.; Childers, Chris P.; Buels, Robert M.; Stein, Lincoln; Holmes, Ian H.; Elsik, Christine G.; Lewis, Suzanna E.

Estimating Empirical Codon Hidden Markov Models 估计经验密码子隐马尔可夫模型

MOLECULAR BIOLOGY AND EVOLUTION

IF5.3

2012-11-27

OAAI

De Maio, Nicola; Holmes, Ian; Schloetterer, Christian; Kosiol, Carolin

Visualizing next-generation sequencing data with JBrowse 使用JBrowse可视化下一代测序数据

BRIEFINGS IN BIOINFORMATICS

IF7.7

2012-03-12

OAAI

Westesson, Oscar; Skinner, Mitchell; Holmes, Ian

研究方向