Deciphering cell–cell interactions and communication from gene expression

E Armingol, A Officer, O Harismendy… - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages …

Network pharmacology of cancer: From understanding of complex interactomes to the design of multi-target specific therapeutics from nature

P Poornima, JD Kumar, Q Zhao, M Blunder… - Pharmacological …, 2016 - Elsevier
Despite massive investments in drug research and development, the significant decline in
the number of new drugs approved or translated to clinical use raises the question, whether …

Gene co-expression analysis for functional classification and gene–disease predictions

S Van Dam, U Vosa, A van der Graaf… - Briefings in …, 2018 - academic.oup.com
Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

A mechanically active heterotypic E-cadherin/N-cadherin adhesion enables fibroblasts to drive cancer cell invasion

A Labernadie, T Kato, A Brugués, X Serra-Picamal… - Nature cell …, 2017 - nature.com
Cancer-associated fibroblasts (CAFs) promote tumour invasion and metastasis. We show
that CAFs exert a physical force on cancer cells that enables their collective invasion. Force …

Stromal integrin α11 regulates PDGFRβ signaling and promotes breast cancer progression

I Primac, E Maquoi, S Blacher… - The Journal of …, 2019 - Am Soc Clin Investig
Cancer-associated fibroblasts (CAFs) are key actors in modulating the progression of many
solid tumors, such as breast cancer (BC). Herein, we identify an integrin α11/PDGFRβ …

Integrative analysis of histopathological images and genomic data predicts clear cell renal cell carcinoma prognosis

J Cheng, J Zhang, Y Han, X Wang, X Ye, Y Meng… - Cancer research, 2017 - AACR
In cancer, both histopathologic images and genomic signatures are used for diagnosis,
prognosis, and subtyping. However, combining histopathologic images with genomic data …

Upregulation of lipid metabolism genes in the breast prior to cancer diagnosis

N Marino, R German, X Rao, E Simpson, S Liu… - NPJ Breast …, 2020 - nature.com
Histologically normal tissue adjacent to the tumor can provide insight of the
microenvironmental alterations surrounding the cancerous lesion and affecting the …

Extracellular vesicles in brain tumor progression

E D'Asti, S Chennakrishnaiah, TH Lee… - Cellular and molecular …, 2016 - Springer
Brain tumors can be viewed as multicellular 'ecosystems' with increasingly recognized
cellular complexity and systemic impact. While the emerging diversity of malignant disease …

(Differential) co-expression analysis of gene expression: a survey of best practices

HA Chowdhury, DK Bhattacharyya… - IEEE/ACM transactions …, 2019 - ieeexplore.ieee.org
Analysis of gene expression data is widely used in transcriptomic studies to understand
functions of molecules inside a cell and interactions among molecules. Differential co …

Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer

HR Ali, A Dariush, E Provenzano, H Bardwell… - Breast Cancer …, 2016 - Springer
Background There is a need to improve prediction of response to chemotherapy in breast
cancer in order to improve clinical management and this may be achieved by harnessing …