DeanLab

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

All

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
Phase I study of a novel glioblastoma radiation therapy schedule exploiting cell-state plasticity
Phase I study of a novel glioblastoma radiation therapy schedule exploiting cell-state plasticity
Jamie A Dean, Shyam K Tanguturi, Daniel Cagney, Kee-Young Shin, Gilbert Youssef, ..., Patrick Y Wen, Paul Catalano, Daphne Haas-Kogan, Brian M Alexander, Franziska Michor
Neuro-Oncology   ·   19 Nov 2022   ·   doi:10.1093/neuonc/noac253
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

2021

Computational modelling of perivascular-niche dynamics for the optimization of treatment schedules for glioblastoma
Computational modelling of perivascular-niche dynamics for the optimization of treatment schedules for glioblastoma
Amanda Randles, Hans-Georg Wirsching, Jamie A. Dean, Yu-Kang Cheng, Samuel Emerson, Siobhan S. Pattwell, Eric C. Holland, Franziska Michor
Nature Biomedical Engineering   ·   16 Apr 2021   ·   doi:10.1038/s41551-021-00710-3

2020

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
Evaluation of erectile potency and radiation dose to the penile bulb using image guided radiotherapy in the CHHiP trial
Evaluation of erectile potency and radiation dose to the penile bulb using image guided radiotherapy in the CHHiP trial
Julia Murray, Sarah Gulliford, Clare Griffin, Anna Wilkins, Isabel Syndikus, ..., Olivia Naismith, Helen Mossop, Clare Cruickshank, Emma Hall, David Dearnaley
Clinical and Translational Radiation Oncology   ·   01 Mar 2020   ·   doi:10.1016/j.ctro.2019.12.006
A randomised assessment of image guided radiotherapy within a phase 3 trial of conventional or hypofractionated high dose intensity modulated radiotherapy for prostate cancer
A randomised assessment of image guided radiotherapy within a phase 3 trial of conventional or hypofractionated high dose intensity modulated radiotherapy for prostate cancer
Julia Murray, Clare Griffin, Sarah Gulliford, Isabel Syndikus, John Staffurth, ..., Angela Baker, Helen Mossop, Clare Cruickshank, Emma Hall, David Dearnaley
Radiotherapy and Oncology   ·   01 Jan 2020   ·   doi:10.1016/j.radonc.2019.10.017

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

Incorporating spatial dose metrics in machine learning-based normal tissue complication probability (NTCP) models of severe acute dysphagia resulting from head and neck radiotherapy
Incorporating spatial dose metrics in machine learning-based normal tissue complication probability (NTCP) models of severe acute dysphagia resulting from head and neck radiotherapy
Jamie Dean, Kee Wong, Hiram Gay, Liam Welsh, Ann-Britt Jones, ..., Shreerang Bhide, Kevin Harrington, Joseph Deasy, Christopher Nutting, Sarah Gulliford
Clinical and Translational Radiation Oncology   ·   01 Jan 2018   ·   doi:10.1016/j.ctro.2017.11.009

2017

Normal Tissue Complication Probability (NTCP) Modelling of Severe Acute Mucositis using a Novel Oral Mucosal Surface Organ at Risk
Normal Tissue Complication Probability (NTCP) Modelling of Severe Acute Mucositis using a Novel Oral Mucosal Surface Organ at Risk
J.A. Dean, L.C. Welsh, K.H. Wong, A. Aleksic, E. Dunne, ..., K.L. Newbold, S.A. Bhide, K.J. Harrington, C.M. Nutting, S.L. Gulliford
Clinical Oncology   ·   01 Apr 2017   ·   doi:10.1016/j.clon.2016.12.001

2016

Functional Data Analysis Applied to Modeling of Severe Acute Mucositis and Dysphagia Resulting From Head and Neck Radiation Therapy
Functional Data Analysis Applied to Modeling of Severe Acute Mucositis and Dysphagia Resulting From Head and Neck Radiation Therapy
Jamie A. Dean, Kee H. Wong, Hiram Gay, Liam C. Welsh, Ann-Britt Jones, ..., Shreerang A. Bhide, Kevin J. Harrington, Joseph O. Deasy, Christopher M. Nutting, Sarah L. Gulliford
International Journal of Radiation Oncology*Biology*Physics   ·   01 Nov 2016   ·   doi:10.1016/j.ijrobp.2016.08.013
Normal tissue complication probability (NTCP) modelling using spatial dose metrics and machine learning methods for severe acute oral mucositis resulting from head and neck radiotherapy
Normal tissue complication probability (NTCP) modelling using spatial dose metrics and machine learning methods for severe acute oral mucositis resulting from head and neck radiotherapy
Jamie A. Dean, Kee H. Wong, Liam C. Welsh, Ann-Britt Jones, Ulrike Schick, Kate L. Newbold, Shreerang A. Bhide, Kevin J. Harrington, Christopher M. Nutting, Sarah L. Gulliford
Radiotherapy and Oncology   ·   01 Jul 2016   ·   doi:10.1016/j.radonc.2016.05.015
Assessment of fully-automated atlas-based segmentation of novel oral mucosal surface organ-at-risk
Assessment of fully-automated atlas-based segmentation of novel oral mucosal surface organ-at-risk
Jamie A. Dean, Liam C. Welsh, Dualta McQuaid, Kee H. Wong, Aleksandar Aleksic, ..., Kate L. Newbold, Shreerang A. Bhide, Kevin J. Harrington, Sarah L. Gulliford, Christopher M. Nutting
Radiotherapy and Oncology   ·   01 Apr 2016   ·   doi:10.1016/j.radonc.2016.02.022

2015

Quality assurance in MRI breast screening: comparing signal-to-noise ratio in dynamic contrast-enhanced imaging protocols
Quality assurance in MRI breast screening: comparing signal-to-noise ratio in dynamic contrast-enhanced imaging protocols
Evanthia Kousi, Marco Borri, Jamie Dean, Rafal Panek, Erica Scurr, Martin O Leach, Maria A Schmidt
Physics in Medicine and Biology   ·   25 Nov 2015   ·   doi:10.1088/0031-9155/61/1/37
Prospective, longitudinal, multi-modal functional imaging for radical chemo-IMRT treatment of locally advanced head and neck cancer: the INSIGHT study
Prospective, longitudinal, multi-modal functional imaging for radical chemo-IMRT treatment of locally advanced head and neck cancer: the INSIGHT study
Liam Welsh, Rafal Panek, Dualta McQuaid, Alex Dunlop, Maria Schmidt, ..., Shreerang Bhide, Martin O. Leach, Christopher Nutting, Kevin Harrington, Kate Newbold
Radiation Oncology   ·   15 May 2015   ·   doi:10.1186/s13014-015-0415-7
A novel method for delineation of oral mucosa for radiotherapy dose–response studies
A novel method for delineation of oral mucosa for radiotherapy dose–response studies
Jamie A. Dean, Liam C. Welsh, Sarah L. Gulliford, Kevin J. Harrington, Christopher M. Nutting
Radiotherapy and Oncology   ·   01 Apr 2015   ·   doi:10.1016/j.radonc.2015.02.020
Brain-Sparing Methods for IMRT of Head and Neck Cancer
Brain-Sparing Methods for IMRT of Head and Neck Cancer
Alex Dunlop, Liam Welsh, Dualta McQuaid, Jamie Dean, Sarah Gulliford, Vibeke Hansen, Shreerang Bhide, Chris Nutting, Kevin Harrington, Kate Newbold
PLOS ONE   ·   17 Mar 2015   ·   doi:10.1371/journal.pone.0120141

2014

Neurocognitive Function After (Chemo)-Radiotherapy for Head and Neck Cancer
Neurocognitive Function After (Chemo)-Radiotherapy for Head and Neck Cancer
L.C. Welsh, A.W. Dunlop, T. McGovern, D. McQuaid, J.A. Dean, S.L. Gulliford, S.A. Bhide, K.J. Harrington, C.M. Nutting, K.L. Newbold
Clinical Oncology   ·   01 Dec 2014   ·   doi:10.1016/j.clon.2014.06.014