{{ page.title }}{% if page.external-url %} - {% endif %}
- - {% if page.img %}{% for tag in page.tags %}#{{tag}} {% endfor %}
-diff --git a/_posts/lit/2020-10-14-AXL-ABL2-TAZ-LUAD.markdown b/_posts/lit/2020-10-14-AXL-ABL2-TAZ-LUAD.markdown deleted file mode 100644 index 36bb594f..00000000 --- a/_posts/lit/2020-10-14-AXL-ABL2-TAZ-LUAD.markdown +++ /dev/null @@ -1,13 +0,0 @@ ---- -layout: post -title: A TAZ-AXL-ABL2 Feed-Forward Signaling Axis Promotes Lung Adenocarcinoma Brain Metastasis -date: 2019-12-10 00:00:01 -categories: literature -external-url: https://doi.org/10.1016/j.celrep.2019.11.018 -tags: -- Cancer Signaling -- AXL -- RTKs -- Metastasis ---- -Really relevant work on how the axis AXL-ABL2-TAZ engage in an autocrine positive feedback loop to promote brain metastasis in lung adenocarcinoma. These results suggest that the combination treatment of the AXL inhibitor R428 and the ABL allosteric inhibitor asciminib could be a novel route to block disease progression in AXL-driven lung cancers. \ No newline at end of file diff --git a/_posts/lit/2020-10-14-INKA-phosphoclustering.markdown b/_posts/lit/2020-10-14-INKA-phosphoclustering.markdown deleted file mode 100644 index f01b7973..00000000 --- a/_posts/lit/2020-10-14-INKA-phosphoclustering.markdown +++ /dev/null @@ -1,13 +0,0 @@ ---- -layout: post -title: INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases -date: 2019-04-12 00:00:01 -categories: literature -external-url: https://www.embopress.org/doi/full/10.15252/msb.20188250 -tags: -- Cellular Signal Transduction -- Cancer Systems Biology -- Phosphoproteomics -- Kinase Specificity ---- -Very interesting approach to disentangle signaling networks using global phosphoproteomic measurements. This novel method infers kinase activity by integrating the scores of two kinase-centric components; overall kinase phosphorylation levels and activation loop phosphorylation, and two substrate-centric components; quantification of experimentally reported kinase-substrate relationships shown in PhosphoSitePlus and levels of kinase substrates predicted by an algorithm–NetworKIN–that performs motif-based predictions to pinpoint kinases responsible for specific phosphorylation events. diff --git a/_posts/lit/2020-10-15-Chromatin-MediatedState-Sharma.md b/_posts/lit/2020-10-15-Chromatin-MediatedState-Sharma.md deleted file mode 100644 index 5bb4377a..00000000 --- a/_posts/lit/2020-10-15-Chromatin-MediatedState-Sharma.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: post -title: A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations -date: 2010-04-2 00:00:01 -categories: literature -external-url: https://doi.org/10.1016/j.cell.2010.02.027 -tags: -- Heterogeneity -- Reversible Drug Tolerance ---- -This paper is an exemplary study of phenotypic heterogeneity in drug response as a source of resistance. They observe that individual PC9 lung cancer cells transiently assume a reversibly drug-tolerant state to protect the population from eradication by potential lethal exposures. diff --git a/_posts/lit/2020-10-15-Perelson_multivalent_binding.markdown b/_posts/lit/2020-10-15-Perelson_multivalent_binding.markdown deleted file mode 100644 index 29d258b3..00000000 --- a/_posts/lit/2020-10-15-Perelson_multivalent_binding.markdown +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: post -title: Receptor Clustering on a Cell Surface -date: 1980-05-16 00:00:01 -categories: literature -external-url: https://doi.org/10.1016/0025-5564(81)90036-5 -tags: -- Computational method -- systems biology ---- -Our lab has developed a multi-ligand, multi-receptor, multi-valent binding model. It has been utilized to model the [antibody Fc-FcγR interactions](https://doi.org/10.1016/j.cels.2018.05.018) as well as to improve drug selective cell population binding. This classical biophysics work is the original wisdom that inspires our model. \ No newline at end of file diff --git a/_posts/lit/2020-10-15-StochasticStateTransit-PhenotypicHeterogeneity.md b/_posts/lit/2020-10-15-StochasticStateTransit-PhenotypicHeterogeneity.md deleted file mode 100644 index 48b237dc..00000000 --- a/_posts/lit/2020-10-15-StochasticStateTransit-PhenotypicHeterogeneity.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -layout: post -title: Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells -date: 2011-07-19 00:00:01 -categories: literature -external-url: https://doi.org/10.1016/j.cell.2011.07.026 -tags: -- Heterogeneity -- Cancer Cell States -- Markov Model -- State Transition ---- -A study that investigates the dynamics of phenotypic proportions in human breast cancer cell lines. They observe that subpopulations of purified phenotype return to their equilibrium and they find transition probabilities of this stochastic behavior by a Markov model. Their findings contribute to our understanding of cancer heterogeneity and reveal how stochasticity in single-cell behaviors promotes phenotypic equilibrium in populations of cancer cells. diff --git a/_posts/lit/2020-10-15-tensor-decomposition.markdown b/_posts/lit/2020-10-15-tensor-decomposition.markdown deleted file mode 100644 index 5c429b59..00000000 --- a/_posts/lit/2020-10-15-tensor-decomposition.markdown +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: post -title: Tensor Decompositions and Applications -date: 2019-08-05 00:00:01 -categories: literature -external-url: https://doi.org/10.1137/07070111X -tags: -- Computational method -- Tensor decomposition ---- -Tensor decomposition techniques have been used extensively in many projects in our lab, such as mapping model-predicted common gamma chain cytokine responses, reasoning antigen-specific systems serology data, and improving cancer cell line drug response predictions. To understand tensor decomposition methods, this paper is a good place to start. \ No newline at end of file diff --git a/_posts/news/2015-07-11-postdoc-listing.markdown b/_posts/news/2015-07-11-postdoc-listing.markdown deleted file mode 100755 index d0bad3f1..00000000 --- a/_posts/news/2015-07-11-postdoc-listing.markdown +++ /dev/null @@ -1,10 +0,0 @@ ---- -layout: post -title: Postdoctoral position available -date: 2015-09-09 00:00:00 -categories: archive ---- - -The Meyer lab is looking to hire a postdoctoral associate, to develop and implement new strategies evaluating immune-tumor cell communication and targeted therapy resistance. Will help design and implement quantitative biochemical and phenotypic assays, analyze data, and interpret biological significance. Responsibilities will include communicating results to the scientific community through publications and presentations. - -*Requirements:* A Ph.D. in biological sciences, computer science, engineering, physics, math, or related field. Must have experience in the following technical areas: computational methods and tools for analysis, and statistics; and biological experience in one of the following: molecular biology, immunology, or cancer biology. Strong analytical and problem-solving skills are highly valued. Seek a highly motivated, independent individual with excellent documentation skills; strong interpersonal skills; and the ability to contribute in a multidisciplinary team setting, prioritize and perform multiple tasks in a dynamic environment, and execute detailed technical protocols meticulously. \ No newline at end of file diff --git a/_posts/news/2017-08-29-postdoc-listing.markdown b/_posts/news/2017-08-29-postdoc-listing.markdown deleted file mode 100644 index 765b8bc0..00000000 --- a/_posts/news/2017-08-29-postdoc-listing.markdown +++ /dev/null @@ -1,18 +0,0 @@ ---- -layout: post -title: Postdoctoral position available -date: 2017-10-29 00:00:00 -categories: news ---- - -A postdoctoral associate position is available in the Department of Bioengineering at the University of California, Los Angeles (UCLA) to work in the laboratory of Dr. Aaron Meyer. The Meyer lab is an interdisciplinary academic research team that utilizes combined computational and experimental approaches to better understand cancer cell resistance and innate immune signaling. Multiple projects are available within the scope of the lab’s overall focus. A central goal of the lab is to help its members successfully become independent investigators by providing trainees with a supportive environment, close mentorship, and ample resources. - -Applicants should hold a Ph.D. degree in Bioengineering, Chemical Engineering, Computational Biology, or related quantitative biological sciences field. Must have experience in the following technical areas: computational methods and tools for analysis, and statistics; and biological experience in one of the following: molecular biology, immunology, or cancer biology. Applicants with exceptionally strong quantitative backgrounds but relatively less experience in biological sciences will be considered. Strong analytical and problem-solving skills are highly valued. Seek a highly motivated, independent individual with excellent documentation skills; strong interpersonal skills; and the ability to contribute in a multidisciplinary team setting, prioritize and perform multiple tasks in a dynamic environment, and execute detailed technical protocols meticulously. - -Interested applicants should submit a short cover letter and CV to Dr. Meyer (apply@asmlab.org). This should include a short description of the previous project that they are most proud of (science or non-science) and how it reflects the qualities above. - - - - - - diff --git a/_posts/news/2018-05-15-Ali-Rose-Hill.md b/_posts/news/2018-05-15-Ali-Rose-Hill.md deleted file mode 100644 index 187be608..00000000 --- a/_posts/news/2018-05-15-Ali-Rose-Hill.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Rose Hills Foundation Fellowship -date: 2018-05-15 00:00:01 -categories: news ---- -Congratulations to Ali Farhat on winning a Rose Hills Foundation Fellowship! diff --git a/_posts/news/2019-05-15-CSBC-west-coast.md b/_posts/news/2019-05-15-CSBC-west-coast.md deleted file mode 100644 index c4063f33..00000000 --- a/_posts/news/2019-05-15-CSBC-west-coast.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: CSBC West Coast Talk -date: 2019-05-15 00:00:01 -categories: news ---- -Drs. Meyer and Bae will present at the CSBC's Inaugural West Coast Symposium. diff --git a/_posts/news/2019-06-28-FCDA.md b/_posts/news/2019-06-28-FCDA.md deleted file mode 100644 index d42d01eb..00000000 --- a/_posts/news/2019-06-28-FCDA.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Faculty Career Development Award -date: 2019-06-28 00:00:01 -categories: news ---- -Dr. Meyer has received a UCLA Faculty Career Development Award! diff --git a/_posts/news/2020-10-07-Vanderbilt-talk.md b/_posts/news/2020-10-07-Vanderbilt-talk.md deleted file mode 100644 index 94fd5a54..00000000 --- a/_posts/news/2020-10-07-Vanderbilt-talk.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Vanderbilt Seminar -date: 2020-10-07 00:00:01 -categories: news ---- -Dr. Meyer will talk about the lab’s efforts for modeling tumor cell heterogeneity and AXL-driven drug resistance at [Vanderbilt's CSBC program](https://csbconsortium.org/research-centers/the-csbc-u54-research-center-vanderbilt/). diff --git a/_posts/news/2022-08-30-Marc-JCCC-fellowship.md b/_posts/news/2022-08-30-Marc-JCCC-fellowship.md deleted file mode 100644 index d5bb5b9c..00000000 --- a/_posts/news/2022-08-30-Marc-JCCC-fellowship.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Marc JCCC fellowship -date: 2022-08-30 12:00:00 -categories: news ---- -Congratulations to Marc Creixell for winning a Jonsson Comprehensive Cancer Center predoctoral fellowship! This award will partially support his studies during his final year of studies. \ No newline at end of file diff --git a/_posts/news/2023-07-01-tenure.md b/_posts/news/2023-07-01-tenure.md deleted file mode 100644 index 81c77016..00000000 --- a/_posts/news/2023-07-01-tenure.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Tenure -date: 2023-07-01 12:00:00 -categories: news ---- -Dr. Meyer was promoted to Associate Professor with tenure. \ No newline at end of file diff --git a/_posts/news/2024-08-16-Retreat.md b/_posts/news/2024-08-16-Retreat.md deleted file mode 100644 index c08eb378..00000000 --- a/_posts/news/2024-08-16-Retreat.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Lab retreat -date: 2024-08-16 12:00:00 -categories: news ---- -The lab headed to Big Bear Lake for a weekend retreat. In addition to fun, they discussed goals for the coming year. \ No newline at end of file diff --git a/public/css/_gfont.scss b/assets/css/_gfont.scss similarity index 100% rename from public/css/_gfont.scss rename to assets/css/_gfont.scss diff --git a/public/css/_responsive12col.scss b/assets/css/_responsive12col.scss similarity index 100% rename from public/css/_responsive12col.scss rename to assets/css/_responsive12col.scss diff --git a/public/css/_syntax.scss b/assets/css/_syntax.scss similarity index 100% rename from public/css/_syntax.scss rename to assets/css/_syntax.scss diff --git a/public/css/main.scss b/assets/css/main.scss old mode 100755 new mode 100644 similarity index 90% rename from public/css/main.scss rename to assets/css/main.scss index ea3d08b4..061d10d9 --- a/public/css/main.scss +++ b/assets/css/main.scss @@ -1,10 +1,6 @@ ---- ---- - -@use "sass:color"; -@use "syntax"; -@use "responsive12col"; -@use "gfont"; +@import "syntax"; +@import "responsive12col"; +@import "gfont"; $site-background-color: #fbfbfb; $contrast-color: #333; @@ -45,7 +41,7 @@ hr, blockquote { padding: 0 30px; - border-left: 2px solid color.adjust($site-background-color, $lightness: -15%, $space: hsl); + border-left: 2px solid darken($site-background-color, 15%); } ul, ol { @@ -88,7 +84,7 @@ table { } thead { - background-color: color.adjust($site-background-color, $lightness: -10%, $space: hsl); + background-color: darken($site-background-color, 10%); } } @@ -118,7 +114,7 @@ footer { } /*============================================================================*/ -.azul { a { color: color.adjust($azul-accent-color, $lightness: -22%, $space: hsl); +.azul { a { color: darken($azul-accent-color, 22%); &:hover { color: $azul-accent-color; }}} @@ -167,7 +163,7 @@ footer { margin-top: -5px; text-transform: uppercase; border-radius: 0 0 5px 5px; - border-bottom: 1px solid color.adjust($contrast-color, $lightness: 10%, $space: hsl); + border-bottom: 1px solid lighten($contrast-color, 10%); text-decoration: none; transition: all ease-in-out .3s; @@ -199,12 +195,12 @@ footer { } .single time { - color: #999; + color: darken(#999, 30%); font-size: .9rem; } .bundle { - border-top: 1px solid color.adjust($contrast-color, $lightness: 50%, $space: hsl); + border-top: 1px solid lighten($contrast-color, 50%); padding-top: 10px; margin-bottom: 10px; } diff --git a/content/_index.md b/content/_index.md new file mode 100644 index 00000000..2aa623ff --- /dev/null +++ b/content/_index.md @@ -0,0 +1,3 @@ +--- +title: / +--- diff --git a/contact/index.html b/content/contact/index.html similarity index 96% rename from contact/index.html rename to content/contact/index.html index 8f286593..434574a7 100644 --- a/contact/index.html +++ b/content/contact/index.html @@ -1,10 +1,7 @@ --- -layout: default title: Contact/Operations --- -Last week our lab reviewed what’s sure to be a seminal systems pharmacology paper from the Quaranta lab, Meyer et al. “Quantifying Drug Combination Synergy along Potency and Efficacy Axes”, in @CellSystemsCP. Thread 👇 pic.twitter.com/bSBgBDV8eg
— Aaron Meyer (@aarmey) April 22, 2019
+
-Our lab provides advanced multivalent binding modeling services to optimize the design of multi-specific immunotherapeutic agents. Using a flexible framework (detailed in [relevant publications](binding.html)), we accurately model complex agent-target cell interactions, quantitatively characterize receptor engagement dynamics, and predict therapeutic windows. We analyze key design parameters to understand their impact on therapeutic activity and potential toxicity. Our services range from data fitting and analysis of _in vitro_ assays to modeling immune cell interactions _in vivo_. We can deliver comprehensive reports on parameter contributions and provide custom software for analysis reproduction. Working closely with clients from startups to large pharmaceutical organizations, either via grants or work-for-hire, we provide actionable insights to accelerate drug development and improve candidate selection.
+Our lab provides advanced multivalent binding modeling services to optimize the design of multi-specific immunotherapeutic agents. Using a flexible framework (detailed in [relevant publications](../binding/)), we accurately model complex agent-target cell interactions, quantitatively characterize receptor engagement dynamics, and predict therapeutic windows. We analyze key design parameters to understand their impact on therapeutic activity and potential toxicity. Our services range from data fitting and analysis of _in vitro_ assays to modeling immune cell interactions _in vivo_. We can deliver comprehensive reports on parameter contributions and provide custom software for analysis reproduction. Working closely with clients from startups to large pharmaceutical organizations, either via grants or work-for-hire, we provide actionable insights to accelerate drug development and improve candidate selection.
### Tensor Modeling and Big Data Exploration
-
+
Our lab specializes in applying innovative tensor-based approaches to analyze complex, multidimensional biological datasets where traditional matrix methods fall short. By leveraging tensor decomposition, we help researchers extract meaningful patterns, preserving the inherent data structure and relationships often lost in simpler models. These techniques offer increased statistical power, uncover higher-order interactions, and provide interpretable dimensionality reduction, all while robustly handling the sparse, noisy, or incomplete data common in biological studies. We work collaboratively with clients, providing accessible software tools, comprehensive documentation, and expert consultation.
-[Relevant Publications](tensors.html)
+[Relevant Publications](../tensors/)
diff --git a/research/tensors.md b/content/research/tensors.md
similarity index 84%
rename from research/tensors.md
rename to content/research/tensors.md
index 55513297..8a9a603d 100644
--- a/research/tensors.md
+++ b/content/research/tensors.md
@@ -5,9 +5,4 @@ title: Tensor Learning Publications
Traditional data analysis methods organize data into matrix form—a two-dimensional (2D) grid of numbers wherein each column is a measurement and each row is an observation (e.g., genes by subjects). However, this approach overlooks how measurements are often systematically collected in biology. For example, measurements to understand the molecular response of cells to therapy might be collected over concentrations of drug, time, different sources of cells, and molecular features. In these cases, the data can be organized into a multidimensional (e.g., 4D) form. Generalization of statistical tools into these multidimensional/tensor forms exist, but their use has only begun to catch on in studies of biology and medicine because there is a lack of (1) knowledge about their benefits, (2) practical and useful implementations, and (3) algorithms for specific challenges that arise with biological data. By applying these techniques, developing new algorithms, and providing accessible implementations, we are [making these tools available in biomedical research](https://tensorly.org/stable/index.html).
-{% assign tensor_refs = site.data.pubs.references | where_exp: "ref", "ref.keyword contains 'tensor'" | sort: "issued" | reverse %}
-