Ian Holmes

MedicineBiochemistry, Genetics and Molecular BiologyAgricultural and Biological Sciences

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 15 papers. Top paper: “JBrowse Jupyter: A Python interface to JBrowse 2”.

JBrowse Jupyter: A Python interface to JBrowse 2

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.11.491552

N/A

0.241DataRank · unranked

4 citations

Elliot A. Hershberg, Emma Guo, Garrett Stevens, Colin Diesh, Peter Xie +7 more

Setting Up the JBrowse 2 Genome Browser

Current Protocols(2024)10.1002/cpz1.1120

N/A

0.165DataRank · unranked

2 citations

Robert Buels, Garrett Stevens, Caroline Bridge, Scott Cain, Lincoln Stein +2 more

Machine Boss: rapid prototyping of bioinformatic automata

Bioinformatics(2020)10.1093/bioinformatics/btaa633

N/A

0DataRank · unranked

3 citations

Yujie Wang, Mehak Sharma, Stephen Lin, Yolanda Shen, Shihab Dider +2 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.25.956771

N/A

0DataRank · unranked

6 citations

Ian Holmes, Jordi Silvestre-Ryan

Machine Boss: Rapid Prototyping of Bioinformatic Automata

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.13.945071

N/A

0DataRank · unranked

1 citations

Y. Wang, Madhvi Sharma, Simon Lin, Yulin Shen, Shihab Dider +2 more

JBrowseR: an R interface to the JBrowse 2 genome browser

Bioinformatics(2021)10.1093/bioinformatics/btab459

N/A

0DataRank · unranked

26 citations

Garrett Stevens, Colin Diesh, Peter Xie, Teresa De Jesus Martinez, Robert Buels +3 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.28.501447

N/A

0DataRank · unranked

31 citations

Garrett Stevens, Peter Xie, Teresa De Jesus Martinez, Elliot A. Hershberg, Angel Leung +15 more

CellScape: Protein structure visualization with vector graphics cartoons

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.14.495869

N/A

0DataRank · unranked

3 citations

Daniel A. Fletcher, Ian Holmes, Jordi Silvestre-Ryan

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

Genome biology(2023)10.1186/s13059-023-02914-z

N/A

0DataRank · unranked

880 citations

Garrett Stevens, Peter Xie, Teresa De Jesus Martinez, Elliot A. Hershberg, Angel Leung +15 more

JBrowse Jupyter: a Python interface to JBrowse 2

Bioinformatics(2023)10.1093/bioinformatics/btad032

N/A

0DataRank · unranked

7 citations

Elliot A. Hershberg, Emma Guo, Garrett Stevens, Colin Diesh, Peter Xie +7 more

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

Molecular Biology and Evolution(2024)10.1093/molbev/msae177

N/A

0DataRank · unranked

31 citations

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

Selective State Space Models Outperform Transformers at Predicting RNA-Seq Read Coverage

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.13.638190

N/A

0DataRank · unranked

4 citations

Johannes Linder, David R. Kelley, Ian Holmes

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

Genetics(2020)10.1534/genetics.120.303630

N/A

0DataRank · unranked

15 citations

Ian Holmes

Setting up JBrowse 2 for Visualizing Genome Synteny

Current Protocols(2025)10.1002/cpz1.70236

N/A

0DataRank · unranked

0 citations

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

JBrowse Connect: A server API to connect JBrowse instances and users

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007261

N/A

0DataRank · unranked

4 citations

Robert Buels, Lincoln Stein, Taner Z. Sen, Ian Holmes, Eric Yao