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citations.yaml
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# DO NOT EDIT, GENERATED AUTOMATICALLY
- id: doi:10.1093/nar/gkad1082
title: "The Monarch Initiative in 2024: an analytic platform integrating phenotypes,\
\ genes\_and diseases across species"
authors:
- Tim E Putman
- Kevin Schaper
- Nicolas Matentzoglu
- "Vincent\_P Rubinetti"
- "Faisal\_S Alquaddoomi"
- Corey Cox
- J Harry Caufield
- Glass Elsarboukh
- Sarah Gehrke
- Harshad Hegde
- "Justin\_T Reese"
- Ian Braun
- "Richard\_M Bruskiewich"
- Luca Cappelletti
- Seth Carbon
- "Anita\_R Caron"
- "Lauren\_E Chan"
- "Christopher\_G Chute"
- "Katherina\_G Cortes"
- "Vin\xEDcius De\_Souza"
- Tommaso Fontana
- "Nomi\_L Harris"
- "Emily\_L Hartley"
- Eric Hurwitz
- "Julius\_O B Jacobsen"
- Madan Krishnamurthy
- "Bryan\_J Laraway"
- "James\_A McLaughlin"
- "Julie\_A McMurry"
- "Sierra\_A T Moxon"
- "Kathleen\_R Mullen"
- "Shawn\_T O\u2019Neil"
- "Kent\_A Shefchek"
- Ray Stefancsik
- Sabrina Toro
- "Nicole\_A Vasilevsky"
- "Ramona\_L Walls"
- "Patricia\_L Whetzel"
- David Osumi-Sutherland
- Damian Smedley
- "Peter\_N Robinson"
- "Christopher\_J Mungall"
- "Melissa\_A Haendel"
- "Monica\_C Munoz-Torres"
publisher: Nucleic Acids Research
date: '2023-11-24'
link: https://doi.org/gs6kmr
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1101/2023.10.11.560955
title: Integration of 168,000 samples reveals global patterns of the human gut microbiome
authors:
- Richard J. Abdill
- Samantha P. Graham
- Vincent Rubinetti
- Frank W. Albert
- Casey S. Greene
- Sean Davis
- Ran Blekhman
publisher: Cold Spring Harbor Laboratory
date: '2023-10-11'
link: https://doi.org/gsvf5z
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1093/nar/gkad289
title: 'MyGeneset.info: an interactive and programmatic platform for community-curated
and user-created collections of genes'
authors:
- Ricardo Avila
- Vincent Rubinetti
- Xinghua Zhou
- Dongbo Hu
- Zhongchao Qian
- Marco Alvarado Cano
- Everaldo Rodolpho
- Ginger Tsueng
- Casey Greene
- Chunlei Wu
publisher: Nucleic Acids Research
date: '2023-04-18'
link: https://doi.org/gr5hb5
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1101/2023.01.05.522941
title: Hetnet connectivity search provides rapid insights into how two biomedical
entities are related
authors:
- Daniel S. Himmelstein
- Michael Zietz
- Vincent Rubinetti
- Kyle Kloster
- Benjamin J. Heil
- Faisal Alquaddoomi
- Dongbo Hu
- David N. Nicholson
- Yun Hao
- Blair D. Sullivan
- Michael W. Nagle
- Casey S. Greene
publisher: Cold Spring Harbor Laboratory
date: '2023-01-07'
link: https://doi.org/grmcb9
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1093/gigascience/giad047
title: Hetnet connectivity search provides rapid insights into how biomedical entities
are related
authors:
- Daniel S Himmelstein
- Michael Zietz
- Vincent Rubinetti
- Kyle Kloster
- Benjamin J Heil
- Faisal Alquaddoomi
- Dongbo Hu
- David N Nicholson
- Yun Hao
- Blair D Sullivan
- Michael W Nagle
- Casey S Greene
publisher: GigaScience
date: '2022-12-28'
link: https://doi.org/gsd85n
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1101/2022.02.18.461833
title: 'MolEvolvR: A web-app for characterizing proteins using molecular evolution
and phylogeny'
authors:
- Jacob D Krol
- Joseph T Burke
- Samuel Z Chen
- Lo M Sosinski
- Faisal S Alquaddoomi
- Evan P Brenner
- Ethan P Wolfe
- Vincent P Rubinetti
- Shaddai Amolitos
- Kellen M Reason
- John B Johnston
- Janani Ravi
publisher: Cold Spring Harbor Laboratory
date: '2022-02-22'
link: https://doi.org/gstx7j
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1186/s13059-020-02021-3
title: Compressing gene expression data using multiple latent space dimensionalities
learns complementary biological representations
authors:
- Gregory P. Way
- Michael Zietz
- Vincent Rubinetti
- Daniel S. Himmelstein
- Casey S. Greene
publisher: Genome Biology
date: '2020-05-11'
link: https://doi.org/gg2mjh
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1371/journal.pcbi.1007128
title: Open collaborative writing with Manubot
authors:
- Daniel S. Himmelstein
- Vincent Rubinetti
- David R. Slochower
- Dongbo Hu
- Venkat S. Malladi
- Casey S. Greene
- Anthony Gitter
publisher: PLOS Computational Biology
date: '2020-12-04'
link: https://doi.org/c7np
orcid: 0000-0002-4655-3773
plugin: sources.py
file: sources.yaml
type: paper
description: Lorem ipsum _dolor_ **sit amet**, consectetur adipiscing elit, sed
do eiusmod tempor incididunt ut labore et dolore magna aliqua.
image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2
buttons:
- type: manubot
link: https://greenelab.github.io/meta-review/
- type: source
text: Manuscript Source
link: https://github.com/greenelab/meta-review
- type: website
link: http://manubot.org/
tags:
- open science
- collaboration
repo: greenelab/meta-review
- id: doi:10.1101/573782
title: Sequential compression of gene expression across dimensionalities and methods
reveals no single best method or dimensionality
authors:
- Gregory P. Way
- Michael Zietz
- Vincent Rubinetti
- Daniel S. Himmelstein
- Casey S. Greene
publisher: Cold Spring Harbor Laboratory
date: '2019-03-11'
link: https://doi.org/gfxjxf
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1016/j.csbj.2020.05.017
title: Constructing knowledge graphs and their biomedical applications
authors:
- David N. Nicholson
- Casey S. Greene
publisher: Computational and Structural Biotechnology Journal
date: '2020-01-01'
link: https://doi.org/gg7m48
image: https://ars.els-cdn.com/content/image/1-s2.0-S2001037020302804-gr1.jpg
plugin: sources.py
file: sources.yaml
- id: doi:10.7554/eLife.32822
title: Sci-Hub provides access to nearly all scholarly literature
authors:
- Daniel S Himmelstein
- Ariel Rodriguez Romero
- Jacob G Levernier
- Thomas Anthony Munro
- Stephen Reid McLaughlin
- Bastian Greshake Tzovaras
- Casey S Greene
publisher: eLife
date: '2018-03-01'
link: https://doi.org/ckcj
image: https://iiif.elifesciences.org/lax:32822%2Felife-32822-fig8-v3.tif/full/863,/0/default.webp
plugin: sources.py
file: sources.yaml