Notes update 2024-09-02

Biology/Computational Biology MIT/Appendix/MLE vs. Bayesian Parameter Estimation.md

@@ -78,7 +78,7 @@ $$
 
 ### The prior
 
-The prior can be hard to define as a probability distribution. It is also argued that since different prior beliefs will lead to different posteriors, the Bayesian approach is not scientific enough. The counter argument says that many subject choices are already made in conducting an experiment.
+The prior can be hard to define as a probability distribution. It is also argued that since different prior beliefs will lead to different posteriors, the Bayesian approach is not scientific enough. The counter argument says that many subjective choices are already made in conducting an experiment.
 
 ### The constant of integration
 

Biology/Concepts/Binding Site Maps.md

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+# Binding Site Maps
+
+In the context of the [study](Single-cell%20ATAC%20and%20RNA%20sequencing%20reveal%20pre-existing%20and%20persistent%20cells%20associated%20with%20prostate%20cancer%20relapse.md) on enzalutamide (ENZ) resistance in prostate cancer, **binding site maps** refer to the genomic locations where specific transcription factors, such as MYC and AR (androgen receptor), bind to DNA. These maps are crucial for understanding how transcription factors regulate gene expression and contribute to cellular processes and disease states.
+
+## Key Points About Binding Site Maps
+
+1. **Purpose:**
+   - Binding site maps identify the specific DNA sequences where transcription factors bind, providing insights into the regulatory networks controlled by these factors.
+   - They help elucidate how changes in transcription factor binding contribute to cellular responses, such as drug resistance.
+
+2. **Techniques Used:**
+   - **ChIP-seq (Chromatin Immunoprecipitation Sequencing):** A common technique for mapping transcription factor binding sites. It involves crosslinking proteins to DNA, immunoprecipitating the DNA-protein complexes with specific antibodies, and sequencing the bound DNA fragments.
+   - **[FAIRE-seq](FAIRE-seq.md) (Formaldehyde-Assisted Isolation of Regulatory Elements Sequencing)**: Although primarily used to identify open chromatin regions, it can also provide information about regions where transcription factors are likely to bind, especially in combination with other data.
+
+## MYC and AR Binding Site Maps in the Study
+
+1. **MYC Binding Site Maps:**
+   - **Increased MYC Activity:** The study found that ENZ-resistant cells exhibit increased chromatin accessibility at MYC-binding sites, suggesting enhanced MYC activity.
+   - **Regulatory Regions:** MYC binding site maps help identify regulatory regions where MYC exerts its effects, promoting the transcription of genes involved in cell proliferation, metabolism, and survival.
+
+2. **AR Binding Site Maps:**
+   - **Altered AR Activity:** In the context of ENZ resistance, the study noted changes in chromatin accessibility at AR-binding sites, indicating altered AR activity.
+   - **Regulation of Target Genes:** AR binding site maps are essential for understanding how AR regulates target genes and how its activity changes under different conditions, such as drug treatment or resistance.
+
+## Findings from the Study
+
+1. **Chromatin Reprogramming:**
+   - The study highlights that ENZ resistance is associated with extensive chromatin reprogramming, leading to changes in the accessibility of binding sites for transcription factors like MYC and AR.
+   - **Open Chromatin Regions:** Increased open chromatin regions at MYC-binding sites suggest that MYC plays a significant role in the transcriptional reprogramming observed in ENZ-resistant cells.
+
+2. **Transcriptional Reprogramming:**
+   - The altered binding patterns of MYC and AR are linked to changes in the expression of their target genes, driving the resistance phenotype.
+   - **Compensatory Mechanisms:** The study suggests that in the absence of functional AR signaling due to ENZ treatment, prostate cancer cells may rely more on MYC signaling to sustain growth and survival.
+
+## Implications for Prostate Cancer Research
+
+1. **Understanding Resistance Mechanisms:**
+   - Binding site maps provide critical insights into the molecular mechanisms underlying drug resistance, helping to identify potential therapeutic targets.
+   - **Targeting MYC:** Given the increased MYC activity in ENZ-resistant cells, targeting MYC or its downstream pathways could be a potential strategy to overcome resistance.
+
+2. **Developing Combination Therapies:**
+   - Combining AR-targeted therapies like ENZ with inhibitors of MYC signaling might prevent or delay the development of resistance, offering more effective treatment options for prostate cancer patients.
+
+### Summary
+
+**Binding site maps** for transcription factors like MYC and AR are essential tools in understanding the regulatory networks that drive cellular responses and disease states. In the study on ENZ resistance, these maps revealed significant chromatin reprogramming and transcriptional changes associated with increased MYC activity and altered AR activity. These findings underscore the importance of MYC in compensating for inhibited AR signaling and highlight potential avenues for therapeutic intervention in resistant prostate cancer.

Biology/Concepts/Cell Cycle.md

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+# Cell Cycle
+
+## Phases
+
+The cell cycle consists of four main phases:
+
+1. **G1 Phase (Gap 1 phase)**: This is the first growth phase where the cell grows and carries out its normal functions. It prepares for DNA replication.
+
+2. **S Phase (Synthesis phase)**: During this phase, DNA synthesis or replication occurs. The cell duplicates its genetic material to prepare for division.
+
+3. **G2 Phase (Gap 2 phase)**: In this phase, the cell continues to grow and prepares for **mitosis** (cell division). It also synthesizes proteins and organelles needed for division.
+
+4. **M Phase (Mitotic phase)**: This is the phase where actual cell division occurs. It includes two main processes:
+   - **Mitosis**: The division of the cell nucleus into two identical nuclei, each with a full set of chromosomes.
+   - **Cytokinesis**: The division of the cytoplasm and other organelles to form two separate daughter cells.
+
+These phases ensure that the cell grows, replicates its DNA accurately, and divides properly into two daughter cells.
+
+## Cell Cycle Hetero

Biology/Concepts/Co-Accessible Peaks.md

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+# Co-accessible Peaks
+
+**Co-accessible peaks** in single-cell ATAC-seq ([scATAC-seq](scATAC-seq.md)) refer to regions of [Open Chromatin Regions](Open%20Chromatin%20Regions.md) that show coordinated accessibility across single cells. These peaks often correspond to [regulatory](Transcription%20Regulation.md) elements such as [Promoter](Promoter.md)s, [Enhancer](Enhancer.md)s, or other cis-regulatory elements that are functionally linked. The concept of co-accessibility suggests that the accessibility of one region of the genome is related to the accessibility of another, indicating a potential _regulatory interaction_ between these regions.
+
+## Importance of Co-accessible Peaks
+
+1. **Regulatory Interactions**: Co-accessible peaks can identify potential regulatory interactions between different genomic regions, such as enhancer-promoter interactions.
+2. **Chromatin Architecture**: They provide insights into the three-dimensional organization of the genome and how chromatin looping brings distant regulatory elements into proximity with their target genes.
+3. **Cell-type Specificity**: Identifying co-accessible peaks can help delineate cell-type-specific [Regulatory Network](Gene%20Regulatory%20Network.md)s and understand how gene regulation varies between different cell types or states.
+
+### Identification of Co-accessible Peaks
+
+Identifying co-accessible peaks involves several computational steps:
+
+1. **Peak Calling**:
+    - Initially, peaks of accessible chromatin are identified for each single cell or aggregated across cells using peak calling algorithms (e.g., MACS2).
+    - These peaks represent regions of the genome where the chromatin is accessible to the Tn5 transposase used in ATAC-seq.
+
+2. **Accessibility Matrix Construction**:
+    - An _accessibility matrix_ is constructed where rows represent individual peaks, columns represent individual cells, and the entries indicate the accessibility status of each peak in each cell.
+    - The matrix can be binary (accessible or not) or quantitative (degree of accessibility).
+
+3. **Correlation Analysis**:
+    - Correlation or other statistical measures are used to assess the co-accessibility between pairs of peaks across the single cells.
+    - Highly correlated peaks are considered co-accessible, suggesting a functional relationship.
+
+4. **Graph-based Methods**:
+    - Peaks can be represented as nodes in a graph, with edges connecting co-accessible peaks.
+    - Graph-based clustering algorithms can identify modules or clusters of co-accessible peaks, representing putative regulatory elements working together.
+
+5. **Latent Variable Models**:
+    - Methods such as latent semantic indexing (LSI) or topic modeling can be used to identify patterns of co-accessibility, capturing the underlying structure of chromatin accessibility data.
+
+6. **Integration with Other Data**:
+    - Co-accessibility analysis can be integrated with other genomic data, such as gene expression ([scRNA-seq](scRNA-seq.md)), to correlate co-accessible peaks with gene regulatory activity.
+    - Chromatin conformation data (e.g., Hi-C) can be used to validate and refine co-accessible peak predictions.
+
+## Tools for Identifying Co-accessible Peaks
+
+Several computational tools and frameworks have been developed for identifying co-accessible peaks in scATAC-seq data:
+
+1. **Cicero**:
+    - Part of the Monocle3 package, Cicero identifies co-accessible peaks by constructing co-accessibility maps using single-cell chromatin accessibility data.
+    - It uses a machine-learning approach to infer regulatory interactions and visualize chromatin structure.
+
+2. **ArchR**:
+    - ArchR is a comprehensive package for analyzing single-cell chromatin accessibility data.
+    - It includes functionality for identifying co-accessible peaks and integrating with other single-cell omics data.
+
+3. **Signac**:
+    - Part of the Seurat ecosystem, Signac is designed for the analysis of single-cell chromatin data.
+    - It provides tools for peak calling, dimensionality reduction, and identification of co-accessible peaks.
+
+## Biological Implications
+
+- **Gene Regulation**: Co-accessible peaks help in mapping the regulatory landscape of the genome, identifying potential enhancers and promoters that work together to control gene expression.
+- **Cell Identity**: They reveal cell-type-specific regulatory networks, contributing to our understanding of how different cell types establish and maintain their identity.
+- **Development and Differentiation**: Co-accessibility analysis provides insights into dynamic changes in chromatin structure during development and differentiation.
+- **Disease Mechanisms**: Understanding co-accessible peaks can uncover regulatory disruptions in diseases such as cancer, where chromatin accessibility patterns are often altered.
+
+Overall, identifying co-accessible peaks in scATAC-seq data is crucial for understanding the complex regulatory interactions and chromatin architecture that underlie gene regulation and cellular function.

Biology/Concepts/FAIRE-seq.md

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+# FAIRE-seq: Formaldehyde-Assisted Isolation of Regulatory Elements Sequencing
+
+**FAIRE-seq** is a genomic technique used to identify [Open Chromatin Regions](Open%20Chromatin%20Regions.md), which are often associated with active regulatory elements such as [Promoter](Promoter.md)s, [Enhancer](Enhancer.md)s, and other [Transcription Factor](Transcription%20Factor.md) binding sites. The method leverages the fact that open chromatin regions are more accessible and less tightly bound to nucleosomes compared to closed chromatin regions.
+
+## Steps
+
+1. **Crosslinking:**
+   - Cells are treated with formaldehyde, which crosslinks proteins to DNA, thereby preserving protein-DNA interactions in both open and closed chromatin regions.
+
+2. **Chromatin Fragmentation:**
+   - The crosslinked chromatin is then sheared into small fragments using sonication or other mechanical methods.
+
+3. **Phenol-Chloroform Extraction:**
+   - The fragmented chromatin is subjected to phenol-chloroform extraction, a method used to separate proteins from DNA. Open chromatin regions, which are less protein-bound, preferentially partition into the aqueous phase, whereas the protein-bound (closed) chromatin remains in the organic phase.
+
+4. **DNA Purification:**
+   - The DNA from the aqueous phase is purified. This DNA represents the regions of open chromatin.
+
+5. **Sequencing:**
+   - The purified DNA is then subjected to high-throughput sequencing. The sequencing reads are aligned to a reference genome to identify the genomic locations of open chromatin regions.
+
+## Applications of FAIRE-seq
+
+1. **Identification of Regulatory Elements:**
+   - FAIRE-seq is used to map active [regulatory elements](Transcription%20Regulation.md) such as promoters, enhancers, and insulators across the genome.
+
+2. **Comparison of Chromatin States:**
+   - By comparing FAIRE-seq profiles under different conditions or in different cell types, researchers can identify changes in chromatin accessibility associated with various biological processes or diseases.
+
+3. **Gene Regulation Studies:**
+   - FAIRE-seq helps in understanding the regulatory architecture of the genome and how changes in chromatin accessibility affect gene expression.
+
+4. **Cancer Research:**
+   - In cancer research, FAIRE-seq can be used to identify regulatory elements that are aberrantly activated or repressed in cancer cells, providing insights into mechanisms of oncogenesis and potential therapeutic targets.
+
+## Advantages of FAIRE-seq
+
+1. **High Resolution:**
+   - FAIRE-seq provides high-resolution maps of open chromatin regions, enabling precise identification of regulatory elements.
+
+2. **No Antibodies Required:**
+   - Unlike ChIP-seq (Chromatin Immunoprecipitation sequencing), which requires specific antibodies for the target proteins, FAIRE-seq does not rely on antibodies, making it more straightforward and less biased.
+
+3. **Applicability to Various Conditions:**
+   - FAIRE-seq can be applied to any cell type or condition, allowing for broad utility in different biological contexts.
+
+## Comparison with Other Techniques
+
+1. **DNase-seq:**
+   - DNase-seq uses DNase I to digest accessible chromatin regions and identifies them through sequencing. It also maps open chromatin but can have different biases compared to FAIRE-seq.
+
+2. **ATAC-seq:**
+   - [ATAC-seq](scATAC-seq.md) (Assay for Transposase-Accessible Chromatin using sequencing) uses a transposase enzyme to insert sequencing adapters into open chromatin regions. It is faster and requires fewer cells compared to FAIRE-seq and DNase-seq.
+
+## vs. ATAC-seq
+
+**FAIRE-seq** and **ATAC-seq** are both techniques used to map open chromatin regions in the genome. However, they differ in their methodologies, sensitivities, and specific applications.
+
+### FAIRE-seq
+
+**Methodology:**
+1. **Crosslinking:** Cells are treated with formaldehyde to crosslink proteins to DNA, preserving protein-DNA interactions.
+2. **Chromatin Fragmentation:** The chromatin is sheared into small fragments using sonication.
+3. **Phenol-Chloroform Extraction:** The fragmented chromatin is subjected to phenol-chloroform extraction to separate open chromatin regions into the aqueous phase.
+4. **DNA Purification:** The DNA from the aqueous phase is purified and sequenced.
+
+**Advantages:**
+1. **No Specific Antibodies Required:** Unlike ChIP-seq, FAIRE-seq does not require specific antibodies, reducing bias and simplifying the procedure.
+2. **Broad Applicability:** Can be applied to various cell types and conditions without needing specific reagents for each context.
+
+**Disadvantages:**
+1. **Lower Sensitivity:** FAIRE-seq may have lower sensitivity compared to ATAC-seq, especially for regions with moderate accessibility.
+2. **Formaldehyde Crosslinking:** The requirement for formaldehyde crosslinking can introduce variability and requires careful handling.
+
+### ATAC-seq
+
+**Methodology:**
+1. **Transposase Tagmentation:** A transposase enzyme inserts sequencing adapters into regions of open chromatin.
+2. **Fragmentation:** The transposase simultaneously fragments the DNA and adds adapters, targeting accessible regions.
+3. **Sequencing:** The tagmented DNA is purified and sequenced.
+
+**Advantages:**
+1. **High Sensitivity:** ATAC-seq is _highly sensitive_ and can detect regions with varying degrees of chromatin accessibility, including those that are less accessible.
+2. **Low Input Requirement:** Requires fewer cells and less starting material compared to FAIRE-seq.
+3. **Rapid Protocol:** The entire procedure is faster, often taking less than a day from cell preparation to library preparation.
+
+**Disadvantages:**
+1. **Transposase Bias:** The transposase enzyme may introduce some sequence bias, affecting the uniformity of chromatin accessibility detection. Meaning the transposase may prefer some open regions than others.
+2. **Cost:** ATAC-seq can be more expensive due to the specialized reagents and equipment required.
+
+### Applications and Suitability
+
+**FAIRE-seq:**
+- **Broad Mapping of Open Chromatin:** Suitable for general mapping of open chromatin regions, particularly in studies where antibody specificity is a concern.
+- **Historical Use:** Has been a standard method for many years and is well-established in the literature.
+- **Comparative Studies:** Can be used alongside other techniques to validate findings or to study chromatin accessibility under different conditions.
+
+**ATAC-seq:**
+- **High-Resolution and Sensitivity:** Ideal for high-resolution mapping of chromatin accessibility, including fine-scale variations.
+- **Single-Cell Applications:** ATAC-seq can be adapted for single-cell applications (scATAC-seq), enabling the study of chromatin accessibility at the single-cell level.
+- **Quick Turnaround:** Useful in time-sensitive studies due to its rapid protocol.
+
+### Summary
+
+Both FAIRE-seq and ATAC-seq are valuable for mapping open chromatin regions, but they have distinct advantages and limitations. FAIRE-seq is a robust, broadly applicable method with no need for specific antibodies, while ATAC-seq offers higher sensitivity, requires less input material, and can be adapted for single-cell analysis. The choice between the two techniques depends on the specific requirements of the study, including the desired sensitivity, resolution, and throughput.