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Article
Open AccessImpact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma
The relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803 patients with PDAC (42% with metastatic disease) at M...
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Article
Utility of Circulating Tumor DNA in Appendiceal Tumors
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Article
Open AccessSurvival improvement for patients with metastatic colorectal cancer over twenty years
Over the past two decades of successive clinical trials in metastatic colorectal cancer (CRC), the median overall survival of both control and experimental arms has steadily improved. However, the incremental ...
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Article
Open AccessEstimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression
Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of ...
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Article
Oncogene addiction to GNAS in GNASR201 mutant tumors
The GNASR201 gain-of-function mutation is the single most frequent cancer-causing mutation across all heterotrimeric G proteins, driving oncogenesis in various low-grade/benign gastrointestinal and pancreatic tum...
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Article
Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective
We have established considerable expertise in studying the role of platelets in cancer biology. From this expertise, we were keen to recognize the numerous venous-, arterial-, microvascular-, and macrovascular...
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Article
Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients
Cell-line screens create expansive datasets for learning predictive markers of drug response, but these models do not readily translate to the clinic with its diverse contexts and limited data. In the present ...
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Article
Open AccessLamotrigine-induced hemophagocytic lymphohistiocytosis with Takotsubo cardiomyopathy: a case report
Hemophagocytic lymphohistiocytosis is a rare hematological syndrome characterized by excessive and uncontrolled activation of the immune system. The often nonspecific nature of early symptoms and the potential...
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Protocol
Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate
Systematic measurements of genetic interactions have been used to classify gene functions and to categorize genes into protein complexes, functional pathways and biological processes. This protocol describes h...
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Article
Open AccessTy** tumors using pathways selected by somatic evolution
Many recent efforts to analyze cancer genomes involve aggregation of mutations within reference maps of molecular pathways and protein networks. Here, we find these pathway studies are impeded by molecular int...
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Article
A global transcriptional network connecting noncoding mutations to changes in tumor gene expression
Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcri...
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Article
Correcting CRISPR for copy number
The CRISPR–Cas9 system enables global screens of gene function with high sensitivity and specificity, but off-target effects have been reported for CRISPR guide RNAs targeting genes that are amplified at high ...
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Article
Combinatorial CRISPR–Cas9 screens for de novo map** of genetic interactions
A library of plasmids expressing two gRNAs allows for the map** of combinatorial genetic interactions with the CRISPR system. Results in cancer cells suggest that cellular context is an important factor for ...
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Article
Genetic interaction map** in mammalian cells using CRISPR interference
CRISPR interference screens with pairs of sgRNAs allow for quantitative characterization of genetic interactions.
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Chapter
Characterization of Value Locality in Java Programs
Recent works have reported significant repetition of instruction result values in RISC programs.This phenomenon was termed value locality. This chapter gains an initial understanding of value locality in the c...
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Article
A Buffer-Oriented Methodology for Microarchitecture Validation
We propose a methodology for validating microarchitecture specifications. We view microarchitecture features as specific operations on entries of various buffers in the processor. Our validation approach is to...
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Chapter and Conference Paper
Mispredicted Path Cache Effects
As superscalar pipelines become wider and deeper, the percentage of dynamic instructions fetched into the machine from the mispredicted path significantly increases. This paper discusses how a new cycle-accura...
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Article
Exploiting Value Locality to Exceed the Dataflow Limit
The serialization constraints imposed by true data dependences have always been regarded as an absolute dataflow limit on the parallel execution of serial programs. This paper describes value prediction, a new...
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Article
Post-pass partitioning of signal processing programs
Symmetric multiprocessor systems are increasingly common, not only as high-throughput servers, but as a vehicle for executing a single application in parallel in order to reduce its execution latency. This art...
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Chapter and Conference Paper
A realistic study on multithreaded superscalar processor design
Simultaneous multithreading is a recently proposed technique in which instructions from multiple threads are dispatched and/or issued concurrently in every clock cycle. This technique has been claimed to impro...
