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Projects

Explore some of our key projects in low-resource NLP, explainable AI, efficient deep learning, and human-AI collaboration. All our projects are open-source and aim to make AI more accessible and impactful.

low-resource nlp explainable ai efficient deep learning human-ai collaboration

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Cool Tutorial

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Cool Web Server

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research/index.md

title: Research nav: order: 1 tooltip: Published works —

Research

Discover our latest research publications in the fields of natural language processing, explainable AI, efficient deep learning, and human-AI collaboration. We aim to advance the state-of-the-art while making AI more transparent and accessible.

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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 Sosinski, Faisal S Alquaddoomi, …, Vince 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

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Manuscript Source

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