User profiles for C. Tokheim
Collin TokheimResearch Fellow, Dana-Farber Cancer Institute Verified email at mail.dfci.harvard.edu Cited by 5339 |
[PDF][PDF] Comprehensive characterization of cancer driver genes and mutations
Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced
algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on …
algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on …
Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA
… 2b,c. The RIMA pipeline is useful for large-scale data processing and transcriptomic
characterization of the TME, thus offering insights into cancer genomics and immuno-oncology. …
characterization of the TME, thus offering insights into cancer genomics and immuno-oncology. …
Integrated informatics analysis of cancer-related variants
PURPOSE The modern researcher is confronted with hundreds of published methods to
interpret genetic variants. There are databases of genes and variants, phenotype-genotype …
interpret genetic variants. There are databases of genes and variants, phenotype-genotype …
The genomic landscape of response to EGFR blockade in colorectal cancer
…, B Lupo, M Sausen, J Phallen, CA Hruban, C Tokheim… - Nature, 2015 - nature.com
… We define eight exhaustive and disjoint sequence-based dinucleotide contexts: C in CpG,
G in CpG, C in TpC, G in GpA, and all other A, G, C, T. We represent the occurrences of each …
G in CpG, C in TpC, G in GpA, and all other A, G, C, T. We represent the occurrences of each …
[PDF][PDF] Perspective on oncogenic processes at the end of the beginning of cancer genomics
The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse
genomic alterations underlying human cancers. At this historic junction marking the completion …
genomic alterations underlying human cancers. At this historic junction marking the completion …
Evaluating the evaluation of cancer driver genes
CJ Tokheim, N Papadopoulos… - Proceedings of the …, 2016 - National Acad Sciences
… (C) Number of predicted driver genes. Driver gene is defined as having Benjamini–Hochberg
adjusted … 2 B and C, p was set to 0.107, which is the fraction of inactivating mutations in our …
adjusted … 2 B and C, p was set to 0.107, which is the fraction of inactivating mutations in our …
[PDF][PDF] Systematic functional annotation of somatic mutations in cancer
The functional impact of the vast majority of cancer somatic mutations remains unknown,
representing a critical knowledge gap for implementing precision oncology. Here, we report the …
representing a critical knowledge gap for implementing precision oncology. Here, we report the …
Minimal functional driver gene heterogeneity among untreated metastases
… (C) Relative occurrence of variants in driver genes along MetTrunk in individual COSMIC
samples was 0.32% compared with 0.0016% along MetBranch (two-sided Wilcoxon rank-sum …
samples was 0.32% compared with 0.0016% along MetBranch (two-sided Wilcoxon rank-sum …
[HTML][HTML] Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing
Background To determine genomic alterations in head and neck squamous cell carcinoma (HNSCC)
using formalin-fixed, paraffin-embedded (FFPE) tumors obtained through routine …
using formalin-fixed, paraffin-embedded (FFPE) tumors obtained through routine …
Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade
MHC-I loss or downregulation in cancer cells is a major mechanism of resistance to T cell–based
immunotherapies. Our study reveals that birinapant may be used for patients with low …
immunotherapies. Our study reveals that birinapant may be used for patients with low …