Information Fusion and Intelligent System Laboratory (IFIS)

Research

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Highlighted

Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128
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Manubot
Manuscript Source
Website
open-science collaboration

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2025

Scalable data harmonization for single-cell image-based profiling with CytoTable
Scalable data harmonization for single-cell image-based profiling with CytoTable
Dave Bunten, Jenna Tomkinson, Erik Serrano, Michael J. Lippincott, Kenneth I. Brewer, Vince Rubinetti, Faisal Alquaddoomi, Gregory P. Way
Cold Spring Harbor Laboratory  ·  25 Jun 2025  ·  doi:10.1101/2025.06.19.660613

2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species
Tim E Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P Rubinetti, Faisal S Alquaddoomi, …, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel, Monica C Munoz-Torres
Nucleic Acids Research  ·  24 Nov 2023  ·  doi:10.1093/nar/gkad1082
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman
Cold Spring Harbor Laboratory  ·  11 Oct 2023  ·  doi:10.1101/2023.10.11.560955
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
Nucleic Acids Research  ·  18 Apr 2023  ·  doi:10.1093/nar/gkad289
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, …, David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene
Cold Spring Harbor Laboratory  ·  07 Jan 2023  ·  doi:10.1101/2023.01.05.522941

2022

Hetnet connectivity search provides rapid insights into how biomedical entities are related
Hetnet connectivity search provides rapid insights into how biomedical entities are related
Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, …, David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene
GigaScience  ·  28 Dec 2022  ·  doi:10.1093/gigascience/giad047
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
Jacob D Krol, Joseph T Burke, Samuel Z Chen, Lo M Sosinski, Faisal S Alquaddoomi, …, Vincent P Rubinetti, Shaddai Amolitos, Kellen M Reason, John B Johnston, Janani Ravi
Cold Spring Harbor Laboratory  ·  22 Feb 2022  ·  doi:10.1101/2022.02.18.461833

2020

Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
Manubot
Manuscript Source
Website
open-science collaboration
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Genome Biology  ·  11 May 2020  ·  doi:10.1186/s13059-020-02021-3
Constructing knowledge graphs and their biomedical applications
Constructing knowledge graphs and their biomedical applications
David N. Nicholson, Casey S. Greene
Computational and Structural Biotechnology Journal  ·  01 Jan 2020  ·  doi:10.1016/j.csbj.2020.05.017

2019

Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Cold Spring Harbor Laboratory  ·  11 Mar 2019  ·  doi:10.1101/573782

2018

Sci-Hub provides access to nearly all scholarly literature
Sci-Hub provides access to nearly all scholarly literature
Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
eLife  ·  01 Mar 2018  ·  doi:10.7554/eLife.32822