JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
JASPAR ( http://jaspar.genereg.net ) is the largest open-access database of matrix-based
nucleotide profiles describing the binding preference of transcription factors from multiple …
nucleotide profiles describing the binding preference of transcription factors from multiple …
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
JASPAR ( http://jaspar.genereg.net ) is an open-access database storing curated, non-redundant
transcription factor (TF) binding profiles representing transcription factor binding …
transcription factor (TF) binding profiles representing transcription factor binding …
Cancer stemness, intratumoral heterogeneity, and immune response across cancers
Regulatory programs that control the function of stem cells are active in cancer and confer
properties that promote progression and therapy resistance. However, the impact of a stem cell…
properties that promote progression and therapy resistance. However, the impact of a stem cell…
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
We performed phylogenetic analysis of high-grade serous ovarian cancers (68 samples from
seven patients), identifying constituent clones and quantifying their relative abundances at …
seven patients), identifying constituent clones and quantifying their relative abundances at …
[HTML][HTML] Ovarian cancer mutational processes drive site-specific immune evasion
High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability 1
, 2 , 3 – 4 patterned by distinct mutational processes 5 , 6 , tumour heterogeneity 7 , 8 – 9 …
, 2 , 3 – 4 patterned by distinct mutational processes 5 , 6 , tumour heterogeneity 7 , 8 – 9 …
[PDF][PDF] Interfaces of malignant and immunologic clonal dynamics in ovarian cancer
High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with
widespread but non-random patterns of disease dissemination. We investigated whether …
widespread but non-random patterns of disease dissemination. We investigated whether …
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling
AW Zhang, C O'Flanagan, EA Chavez, JLP Lim… - Nature …, 2019 - nature.com
Single-cell RNA sequencing has enabled the decomposition of complex tissues into
functionally distinct cell types. Often, investigators wish to assign cells to cell types through …
functionally distinct cell types. Often, investigators wish to assign cells to cell types through …
Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes
We studied the whole-genome point mutation and structural variation patterns of 133 tumors
(59 high-grade serous (HGSC), 35 clear cell (CCOC), 29 endometrioid (ENOC), and 10 …
(59 high-grade serous (HGSC), 35 clear cell (CCOC), 29 endometrioid (ENOC), and 10 …
[HTML][HTML] Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses
Background Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex
biological systems, such as tumor heterogeneity and tissue microenvironments. However, …
biological systems, such as tumor heterogeneity and tissue microenvironments. However, …
Clonal fitness inferred from time-series modelling of single-cell cancer genomes
…, J Biele, J Brimhall, D Gee, H Lee, J Ting, AW Zhang… - Nature, 2021 - nature.com
Progress in defining genomic fitness landscapes in cancer, especially those defined by copy
number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of …
number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of …