Refresh content for 2024 (#25)

* rename resources to software

* update text

* edit research and test add sources

* Generate citations

* add select pubs

* Generate citations

* minor modifications

---------

Co-authored-by: gwaybio <[email protected]>

_data/citations.yaml

@@ -1,20 +1,104 @@
 # GENERATED AUTOMATICALLY, DO NOT EDIT
 
-- id: 10.1101/2023.05.02.539137
-  title: High-content microscopy reveals a morphological signature of bortezomib resistance
+- id: 10.1016/j.slasd.2023.08.009
+  title: Evolution and impact of high content imaging
+  authors:
+  - Gregory P. Way
+  - Heba Sailem
+  - Steven Shave
+  - Richard Kasprowicz
+  - Neil O. Carragher
+  publisher: SLAS Discovery
+  date: '2023-10-01'
+  link: https://doi.org/gtcgfv
+  image: https://ars.els-cdn.com/content/image/1-s2.0-S2472555223000667-gr2.jpg
+  tags:
+  - review
+  - high-content imaging
+- id: 10.1101/2023.08.06.552164
+  title: A genome-wide atlas of human cell morphology
   authors:
-  - M.E. Kelley
-  - A.Y. Berman
-  - D.R. Stirling
-  - B.A. Cimini
-  - Y. Han
-  - S. Singh
-  - A.E. Carpenter
-  - T.M. Kapoor
-  - G.P. Way
+  - Meraj Ramezani
+  - Julia Bauman
+  - Avtar Singh
+  - Erin Weisbart
+  - John Yong
+  - Maria Lozada
+  - Gregory P. Way
+  - Sanam L. Kavari
+  - Celeste Diaz
+  - Marzieh Haghighi
+  - Thiago M. Batista
+  - "Joaqu\xEDn P\xE9rez-Schindler"
+  - Melina Claussnitzer
+  - Shantanu Singh
+  - Beth A. Cimini
+  - Paul C. Blainey
+  - Anne E. Carpenter
+  - Calvin H. Jan
+  - James T. Neal
   publisher: Cold Spring Harbor Laboratory
-  date: '2023-05-02'
-  link: https://doi.org/gsfpj4
+  date: '2023-08-07'
+  link: https://doi.org/gszn2s
+  image: https://www.ncbi.nlm.nih.gov/corecgi/tileshop/tileshop.fcgi?p=PMC3&id=704470&s=171&r=2&c=2
+  tags:
+  - cell painting
+  - cell morphology
+  - assay
+- id: https://arxiv.org/abs/2311.13417
+  title: Reproducible image-based profiling with Pycytominer
+  authors:
+  - Erik Serrano
+  - Srinivas Niranj Chandrasekaran
+  - Dave Bunten
+  - Kenneth I. Brewer
+  - Jenna Tomkinson
+  - Roshan Kern
+  - Michael Bornholdt
+  - Stephen Fleming
+  - Ruifan Pei
+  - John Arevalo
+  - Hillary Tsang
+  - Vincent Rubinetti
+  - Callum Tromans-Coia
+  - Tim Becker
+  - Erin Weisbart
+  - Charlotte Bunne
+  - Alexandr A. Kalinin
+  - Rebecca Senft
+  - Stephen J. Taylor
+  - Nasim Jamali
+  - Adeniyi Adeboye
+  - Hamdah Shafqat Abbasi
+  - Allen Goodman
+  - Juan C. Caicedo
+  - Anne E. Carpenter
+  - Beth A. Cimini
+  - Shantanu Singh
+  - Gregory P. Way
+  publisher: arXiv
+  date: '2023-11-22'
+  link: http://arxiv.org/abs/2311.13417
+  image: https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/just-icon.png
+  repo: https://github.com/cytomining/pycytominer
+  tags:
+  - software
+  - cell morphology
+- id: 10.7554/eLife.91362
+  title: High-content microscopy reveals a morphological signature of bortezomib resistance
+  authors:
+  - Megan E Kelley
+  - Adi Y Berman
+  - David R Stirling
+  - Beth A Cimini
+  - Yu Han
+  - Shantanu Singh
+  - Anne E Carpenter
+  - Tarun M Kapoor
+  - Gregory P Way
+  publisher: eLife
+  date: '2023-09-27'
+  link: https://doi.org/gtcgdd
   image: https://raw.githubusercontent.com/broadinstitute/profiling-resistance-mechanisms/master/3.resistance-signature/figures/bortezomib_roc_curve.png
   repo: https://github.com/broadinstitute/profiling-resistance-mechanisms
   tags:

_data/sources.yaml

@@ -1,4 +1,24 @@
-- id: 10.1101/2023.05.02.539137 
+- id: 10.1016/j.slasd.2023.08.009
+  image: https://ars.els-cdn.com/content/image/1-s2.0-S2472555223000667-gr2.jpg
+  tags:
+    - review
+    - high-content imaging
+
+- id: 10.1101/2023.08.06.552164
+  image: https://www.ncbi.nlm.nih.gov/corecgi/tileshop/tileshop.fcgi?p=PMC3&id=704470&s=171&r=2&c=2
+  tags:
+    - cell painting
+    - cell morphology
+    - assay
+
+- id: https://arxiv.org/abs/2311.13417
+  image: https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/just-icon.png
+  repo: https://github.com/cytomining/pycytominer
+  tags:
+    - software
+    - cell morphology
+
+- id: 10.7554/eLife.91362
   image: https://raw.githubusercontent.com/broadinstitute/profiling-resistance-mechanisms/master/3.resistance-signature/figures/bortezomib_roc_curve.png
   repo: https://github.com/broadinstitute/profiling-resistance-mechanisms
   tags:

_members/gregory-way.md

@@ -23,14 +23,12 @@ links:
 
 
 Greg is the Principal Investigator (PI) of the Way Lab.
-He is an Assistant Professor in the Department of [Biochemistry and Molecular Genetics](https://medschool.cuanschutz.edu/biochemistry) and a member of the [Center for Health AI](https://medschool.cuanschutz.edu/ai) in the [School of Medicine at University of Colorado Anschutz](https://medschool.cuanschutz.edu/).
+He is an Assistant Professor in the Department of [Biomedical Informatics](https://medschool.cuanschutz.edu/dbmi) and a member of the [Center for Health AI](https://medschool.cuanschutz.edu/ai) in the [School of Medicine at University of Colorado Anschutz](https://medschool.cuanschutz.edu/).
 He sets forward the lab's scientific path of inquiry, acquires funding, and establishes a lab environment where scientists of all backgrounds can flourish.
-He is currently interested in developing morphology as a systems biology readout of disease states to link molecular information with higher order phenotypes in order to improve treatment decisions.
+He is currently interested in developing morphology as a systems biology readout of disease states to link molecular information with higher order phenotypes in order to improve drug discovery and translational research.
 He is an optimist who believes that the next generation of biological discoveries will require lots of data, lots of compute, reproducible software, and a lot more diverse people with diverse ideas to forge an equitable and prosperous path forward for humanity.
 
-Before founding the Way Lab in 2021, Greg earned a B.S. in Biology and Environmental Studies from [The College of New Jersey](https://tcnj.edu/) in 2011, and an M.S. in Biology from [Saint Joseph's University](https://www.sju.edu/) in 2014.
-In 2018, he earned his Ph.D. in [Genomics and Computational Biology](https://www.med.upenn.edu/gcb/) from [The University of Pennsylvania](https://www.upenn.edu/) for his research studying applied machine learning to genomic and transcriptomic data.
-He later moved to the [Broad Institute of MIT and Harvard](https://www.broadinstitute.org/) where he worked as a postdoc in the [Imaging Platform](https://www.broadinstitute.org/imaging) from 2018-2021 studying image-based profiling, high-throughput assay development, software engineering, and drug discovery.
-Greg's overarching mission is to reduce human suffering through biomedical data science methods and applications.
-
-When not in the lab, he is probably either hanging out with family and friends, playing with his two cats, hiking in the woods, watching the Mets lose, or sipping an IPA.
+Before founding the Way Lab in 2021, Greg earned a B.S. in Biology and Environmental Studies from [The College of New Jersey](https://tcnj.edu/), an M.S. in Biology from [Saint Joseph's University](https://www.sju.edu/), and a Ph.D. [Genomics and Computational Biology](https://www.med.upenn.edu/gcb/) from [The University of Pennsylvania](https://www.upenn.edu/).
+His PhD research applied machine learning to genomic and transcriptomic data.
+He later moved to the [Broad Institute of MIT and Harvard](https://www.broadinstitute.org/) where he worked as a postdoc in the [Imaging Platform](https://www.broadinstitute.org/imaging) studying image-based profiling, high-throughput assay development, software engineering, and drug discovery.
+Greg's overarching mission is to reduce human suffering through biomedical data science methods and applications.

contact/index.md

@@ -13,13 +13,15 @@ Anschutz Health Sciences Building<br/>
 1890 N Revere Ct<br/>
 Aurora, CO 80045
 
+Email: [email protected]
+
 {%
   include figure.html
   image="images/contact_ahs.jpg"
   caption="Anschutz Health Sciences Building"
   width="400px"
 %}
-
+<!---
 {%
   include link.html
   type="email"
@@ -29,7 +31,7 @@ Aurora, CO 80045
   link="[email protected]"
   style="button"
 %}
-<!---
+
 {%
   include link.html
   type="phone"

index.md

@@ -2,11 +2,9 @@
 title: Home
 ---
 
-# Biomedical data science
-
 Welcome to the Way Lab at [The University of Colorado Anschutz](https://www.cuanschutz.edu/)!
 
-The mission of our lab is to reduce human suffering by integrating biomedical data science and software engineering into drug discovery.
+The mission of our lab is to reduce human suffering by integrating biomedical data science and software engineering into drug discovery and translational research.
 We develop new computational methods, innovative approaches, assays, and software for analyzing high-dimensional genomic, molecular, and microscopy data.
 We focus on pediatric diseases, including pediatric cancer and Neurofibromatosis Type 1 (NF1).
 
@@ -24,8 +22,8 @@ We also perform open science, making all of our work immediately open for anyone
 {%
   include link.html
   icon="fas fa-users"
-  text="Join the Team"
-  link="join/"
+  text="Contact us"
+  link="contact/"
   style="button"
 %}
 {:.center}
@@ -41,7 +39,7 @@ We also perform open science, making all of our work immediately open for anyone
 {% capture text %}
 We develop computational methods and innovative approaches to find better drugs for pediatric diseases.
 
-[See what we've published  →](research)
+[Research focus and publications  →](research)
 {:.center}
 {% endcapture %}
 
@@ -54,36 +52,36 @@ We develop computational methods and innovative approaches to find better drugs
 %}
 
 {% capture text %}
-We also release public data and open source software to enable reproducible computational biology analyses and workflows.
+We release public data and open source software to enable reproducible computational biology analyses and workflows.
 
-[See our resources  →](resources)
+[Software  →](software)
 {:.center}
 {% endcapture %}
 
 {%
   include feature.html
   image="images/network.png"
   link="resources"
-  headline="Software and data"
+  headline="Biomedical software"
   text=text
 %}
 
 {% capture text %}
-Our group is a welcoming, diverse, and inclusive team.
+Our lab is a welcoming, diverse, and inclusive team.
 We are collaborative, curious, and passionate about our work.
 
-[Meet our team  →](team)
+[Meet our lab  →](team)
 {:.center}
 {% endcapture %}
 
 {%
   include feature.html
   image="images/team.jpeg"
   link="team"
-  headline="Our lab team"
+  headline="Our lab"
   text=text
 %}
-
+<!---
 {%
   include link.html
   type="github"
@@ -93,3 +91,4 @@ We are collaborative, curious, and passionate about our work.
   style="button"
 %}
 {:.center}
+-->

research/index.md

@@ -7,27 +7,24 @@ nav:
 
 # <i class="fas fa-microscope"></i>Research
 
-We are building the next generation of data science methods for curing pediatric diseases.
+We are building the next generation of data science methods for curing disease.
 
-We are specifically focused on the following research:
+We are specifically focused on the following work:
 
-- **Reproducible software for processing high-dimensional microscopy readouts.** We are building infrastructure to support reproducible, large-scale microscopy data processing, and developing specific tools like [pycytominer](https://github.com/cytomining/pycytominer), [CytoTable](https://github.com/cytomining/cytotable), and [CytoSnake](https://github.com/WayScience/cytosnake) to process large-scale microscopy images. Our aim is to improve data processing pipelines, reproducibility, data provenance, and dataset interoperability for this emerging data type. 
-- **Microscopy representations of cell state.** We derive and benchmark different approaches to extracting biologically-meaningful and reproducible representations from microscopy images. We train artificial intelligence and machine learning (AI/ML) algorithms to predict cell phenotypes from these representations. These phenotypes include cell states including various cell health and death mechanisms. Our aim is to use these representations to annotate drug screening data with phenotype and mechanism.
 - **Drug screening for pediatric diseases.** We perform microscopy-based, in vitro drug screens to identify promising drug candidates. Our goal is to identify new therapeutic options for children with diseases like Neurofibromatosis Type 1 (NF1), neuroblastoma, and pediatric high grade glioma.
-- **New models of pediatric disease to aid drug screening.** We develop new assays and computational methods to support finding better drugs for pediatric diseases. This includes modeling NF1 and other pediatric diseases using patient-derived organoids, developing gene-network-based targets that take advantage of polypharmacology, developing CRISPRi approaches to simulate specific high-dimensional phenotypes, and more.
+- **Reproducible software for processing high-dimensional microscopy readouts.** We are building open source software to support reproducible image-based profiling. We develop [pycytominer](https://github.com/cytomining/pycytominer), [CytoTable](https://github.com/cytomining/cytotable), and [CytoSnake](https://github.com/WayScience/cytosnake) to process large-scale microscopy images. Our aim is to improve data processing pipelines, reproducibility, data provenance, and dataset interoperability. 
+- **Microscopy representations of cell state.** We analyze high-content information from microscopy images, extracting biologically-meaningful and reproducible representations which contain systems biology information. We train artificial intelligence and machine learning (AI/ML) algorithms to predict cell phenotypes from these representations. These phenotypes include  various cell health states and cell death mechanisms. Our aim is to use these representations to annotate drug screening data with phenotype and mechanism.
+- **Innovative method development for drug screening and translational research.** We develop new assays and computational methods to improve human health. This includes modeling NF1 and other pediatric diseases using patient-derived organoids, developing gene-network-based targets that take advantage of polypharmacology, developing CRISPRi approaches to simulate specific high-dimensional phenotypes, modeling cell resistance to cancer therapies, predicting heart failure subtypes, and more.
 
 ## How we do science
 
-How science is performed is as important as the research topic.
-Science hinges on reproducibility, and our procedure maximizes both biological and computational reproducibility.
-
-Biology is messy, but computational biology need not be!
-
-- **Open science and software.** We perform all of our work in the open and release all of our software as open source. We aim to maximize the impact and reproducibility of our research by making everything we do immediately available for others to build upon.
+- **Open science and software.** We perform all of our work in the open and release all of our software as open source. We aim to maximize the impact and reproducibility of our research by making everything we do immediately available for others to build upon. We host all of our code, data, and analysis at [https://github.com/WayScience](https://github.com/WayScience).
 - **Scientific publishing.** We submit preprints of our work and subsequently publish in peer-reviewed journals to disseminate knowledge more formally. We use pre-print review services (like [Review Commons](https://www.reviewcommons.org/)) whenever possible to improve the peer-review process. For each project, we also share project-specific github repositories (representing a lab notebook) to facilitate computational reproducibility.
 
 We strive for creativity, integrity, inclusivity, and rigor in everything that we do.
 
+See [here](https://scholar.google.com/citations?user=iDKZaA4AAAAJ&hl=en) for a full list of work.
+
 See below for a selection of our recent papers.
 
 {% include section.html %}

resources/index.md → software/index.md

@@ -1,11 +1,11 @@
 ---
-title: Resources
+title: Software
 nav:
   order: 2
   tooltip: Software and data
 ---
 
-# <i class="fas fa-tools"></i>Resources
+# <i class="fas fa-tools"></i>Software
 
 {% include search-info.html %}