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View article: Pro-endometriosis macrophage release of IL-33 is key for endometriosis pain and lesion formation
Pro-endometriosis macrophage release of IL-33 is key for endometriosis pain and lesion formation Open
Endometriosis is a painful gynecological inflammatory disease affecting up to 10% of females. When released by sensory neurons, calcitonin gene-related peptide (CGRP) shapes immunity, a process known as neuroimmune communication. We previo…
View article: M2 Macrophages are Major Mediators of Germline Risk of Endometriosis and Explain Pleiotropy With Comorbid Traits
M2 Macrophages are Major Mediators of Germline Risk of Endometriosis and Explain Pleiotropy With Comorbid Traits Open
Endometriosis is a common gynecologic condition that causes chronic, life‐altering symptoms including pain and infertility. There is an urgent need for new non‐hormonal targeted therapeutics to treat endometriosis, but until very recently,…
View article: Methods for multi-omic data integration in cancer research
Methods for multi-omic data integration in cancer research Open
Multi-omics data integration is a term that refers to the process of combining and analyzing data from different omic experimental sources, such as genomics, transcriptomics, methylation assays, and microRNA sequencing, among others. Such …
View article: Functional impact of multi-omic interactions in lung cancer
Functional impact of multi-omic interactions in lung cancer Open
Lung tumors are a leading cause of cancer-related death worldwide. Lung cancers are highly heterogeneous on their phenotypes, both at the cellular and molecular levels. Efforts to better understand the biological origins and outcomes of lu…
View article: A systematic review and meta-analysis reveals a consensus transcriptional signature highlighting neutrophil degranulation as a preserved and critical biological process in atrial fibrillation
A systematic review and meta-analysis reveals a consensus transcriptional signature highlighting neutrophil degranulation as a preserved and critical biological process in atrial fibrillation Open
Background Atrial fibrillation (AF) is the most frequent persistent arrhythmia, and is associated with a high burden of disease, especially when co-occurring with other cardiovascular pathologies. Despite significant advances in the unders…
View article: Molecular mechanisms of multi-omic regulation in breast cancer
Molecular mechanisms of multi-omic regulation in breast cancer Open
Breast cancer is a complex disease that is influenced by the concurrent influence of multiple genetic and environmental factors. Recent advances in genomics and other high throughput biomolecular techniques (-omics) have provided numerous …
View article: Functional impact of multi-omic interactions in breast cancer subtypes
Functional impact of multi-omic interactions in breast cancer subtypes Open
Multi-omic approaches are expected to deliver a broader molecular view of cancer. However, the promised mechanistic explanations have not quite settled yet. Here, we propose a theoretical and computational analysis framework to semi-automa…
View article: An Information Theoretical Multilayer Network Approach to Breast Cancer Transcriptional Regulation
An Information Theoretical Multilayer Network Approach to Breast Cancer Transcriptional Regulation Open
Breast cancer is a complex, highly heterogeneous disease at multiple levels ranging from its genetic origins and molecular processes to clinical manifestations. This heterogeneity has given rise to the so-called intrinsic or molecular brea…
View article: Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes
Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes Open
Breast cancer is a disease that exhibits heterogeneity that goes from the genomic to the clinical levels. This heterogeneity is thought to be captured (at least partially) by the so-called breast cancer molecular subtypes. These molecular …
View article: The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook
The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook Open
Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene re…
View article: Co-mutation and exclusion analysis in human tumors, a means for cancer biology studies and treatment design
Co-mutation and exclusion analysis in human tumors, a means for cancer biology studies and treatment design Open
Background Malignant tumors originate from genomic and epigenomic alterations, which lead to loss of control of the cellular circuitry. These alterations relate with each other in patterns of mutual exclusion and co-occurrence that affect …
View article: Additional file 3: Table S1. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts
Additional file 3: Table S1. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts Open
YGOB data set analysis, including dN/dS data, likelihood-ratio tests' results, and S. cerevisiae protein properties and functions for 535 orthogroups. (XLSX 242Â kb)
View article: Additional file 4: Table S2. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts
Additional file 4: Table S2. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts Open
FOR data set analysis, including dN/dS data, likelihood-ratio tests' results for 462 orthogroups. (XLSX 57Â kb)