Tumor microenvironment: barrier or opportunity towards effective cancer therapy
Tumor microenvironment (TME) is a specialized ecosystem of host components, designed
by tumor cells for successful development and metastasis of tumor. With the advent of 3D …
by tumor cells for successful development and metastasis of tumor. With the advent of 3D …
Quantifying tumor-infiltrating immune cells from transcriptomics data
F Finotello, Z Trajanoski - Cancer Immunology, Immunotherapy, 2018 - Springer
By exerting pro-and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly
influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the …
influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the …
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data
Immune cells infiltrating tumors can have important impact on tumor progression and
response to therapy. We present an efficient algorithm to simultaneously estimate the …
response to therapy. We present an efficient algorithm to simultaneously estimate the …
Cancer transcriptome profiling at the juncture of clinical translation
M Cieślik, AM Chinnaiyan - Nature Reviews Genetics, 2018 - nature.com
Methodological breakthroughs over the past four decades have repeatedly revolutionized
transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to …
transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to …
Computational deconvolution of transcriptomics data from mixed cell populations
Gene expression analyses of bulk tissues often ignore cell type composition as an important
confounding factor, resulting in a loss of signal from lowly abundant cell types. In this review …
confounding factor, resulting in a loss of signal from lowly abundant cell types. In this review …
Optimization and expansion of non-negative matrix factorization
X Lin, PC Boutros - BMC bioinformatics, 2020 - Springer
Background Non-negative matrix factorization (NMF) is a technique widely used in various
fields, including artificial intelligence (AI), signal processing and bioinformatics. However …
fields, including artificial intelligence (AI), signal processing and bioinformatics. However …
[HTML][HTML] Histone deacetylase-mediated tumor microenvironment characteristics and synergistic immunotherapy in gastric cancer
Y Lin, X Jing, Z Chen, X Pan, D Xu, X Yu, F Zhong… - Theranostics, 2023 - ncbi.nlm.nih.gov
Background: Studies have shown that the expression of histone deacetylases (HDACs) is
significantly related to the tumor microenvironment (TME) in gastric cancer. However, the …
significantly related to the tumor microenvironment (TME) in gastric cancer. However, the …
Systematic assessment of tumor purity and its clinical implications
PURPOSE The tumor microenvironment is complex, comprising heterogeneous cellular
populations. As molecular profiles are frequently generated using bulk tissue sections, they …
populations. As molecular profiles are frequently generated using bulk tissue sections, they …
[HTML][HTML] Immunological landscape of consensus clusters in colorectal cancer
P Karpinski, J Rossowska, MM Sasiadek - Oncotarget, 2017 - ncbi.nlm.nih.gov
Recent, large-scale expression–based subtyping has advanced our understanding of the
genomic landscape of colorectal cancer (CRC) and resulted in a consensus molecular …
genomic landscape of colorectal cancer (CRC) and resulted in a consensus molecular …
Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases
JCF Ng, J Quist, A Grigoriadis, MH Malim… - Nucleic acids …, 2019 - academic.oup.com
APOBEC3 cytidine deaminases are largely known for their innate immune protection from
viral infections. Recently, members of the family have been associated with a distinct …
viral infections. Recently, members of the family have been associated with a distinct …