The Buckley Lab website under construction (Fall 2024)

Research

Our research aims to understand the ongoing changes of the polar oceans by synthesizing information from remote sensing observations for a richer picture. We utilize high-resolution remote sensing measurements to study ocean and sea ice properties and processes at both large and small scales. Bespoke algorithms are required for processing new observations and ingenuity is necessary for synthesizing datasets in an ever-changing landscape of remote sensing instruments. As the Arctic warms and the sea ice continues to disintegrate and become less reliable and stable for in situ measurements, remote sensing will become increasingly important for monitoring the polar regions, a vital sign of the planet.

Ongoing Work

See the projects page for our current research focuses.

Publications

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

Classification of Sea Ice Summer Melt Features in High‐Resolution IceBridge Imagery
Classification of Sea Ice Summer Melt Features in High‐Resolution IceBridge Imagery
Ellen M. Buckley, Sinéad L. Farrell, Kyle Duncan, Laurence N. Connor, John M. Kuhn, RoseAnne T. Dominguez
Journal of Geophysical Research: Oceans  ·  04 Dec 2020  ·  doi:10.1029/2019JC015738
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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

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  ·  24 Jun 2019  ·  doi:10.1371/journal.pcbi.1007128
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