Posttranscriptional processing of mRNA is an integral component of the gene expression
program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA,
after thermal inactivation of a temperature-sensitive RNA polymerase II. The half-lives varied …

Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive assessment of
cancer burden, but existing ctDNA detection methods have insufficient sensitivity or patient
coverage for broad clinical applicability. Here we introduce cancer personalized profiling by …

In S. cerevisiae, histone variant H2A. Z is deposited in euchromatin at the flanks of silent
heterochromatin to prevent its ectopic spread. We show that H2A. Z nucleosomes are found
at promoter regions of nearly all genes in euchromatin. They generally occur as two …

We have analyzed the translational status of each mRNA in rapidly growing Saccharomyces
cerevisiae. mRNAs were separated by velocity sedimentation on a sucrose gradient, and 14
fractions across the gradient were analyzed by quantitative microarray analysis, providing a …

Inhibitory receptors on immune cells are pivotal regulators of immune escape in cancer.
Among these inhibitory receptors, CTLA-4 (targeted clinically by ipilimumab) serves as a
dominant off-switch while other receptors such as PD-1 and LAG-3 seem to serve more …

Covalent modification of histone proteins plays a role in virtually every process on eukaryotic
DNA, from transcription to DNA repair. Many different residues can be covalently modified,
and it has been suggested that these modifications occur in a great number of independent …

The innate immune response is crucial for defense against microbial pathogens. To
investigate the molecular choreography of this response, we carried out a systematic
examination of the gene expression program in human peripheral blood mononuclear cells …

Molecular profiles of tumors and tumor-associated cells hold great promise as biomarkers of
clinical outcomes. However, existing data sets are fragmented and difficult to analyze
systematically. Here we present a pan-cancer resource and meta-analysis of expression …

Although eukaryotic genomes are generally thought to be entirely chromatin-associated, the
activated PHO5 promoter in yeast is largely devoid of nucleosomes. We systematically
evaluated nucleosome occupancy in yeast promoters by immunoprecipitating nucleosomal …

We introduce CIBERSORT, a method for characterizing cell composition of complex tissues
from their gene expression profiles. When applied to enumeration of hematopoietic subsets
in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT …