Category: Publications
-
Studying Isoform-Specific mRNA Recruitment to Polyribosomes with Frac-seq.
Abstract: Gene expression profiling is widely used as a measure of the protein output of cells. However, it is becoming more evident that there are multiple layers of post-transcriptional gene regulation that greatly impact protein output (Battle et al., Science 347:664-667, 2014; Khan et al., Science 342:1100-1104, 2013; Vogel et al., Mol Syst Biol 6:400,…
-
Pilot: A Framework that Understands How to Do Performance Benchmarks The Right Way
Carrying out even the simplest performance benchmark requires considerable knowledge of statistics and computer systems, and painstakingly following many error-prone steps, which are distinct skill sets yet essential for getting statistically valid results. As a result, many performance measurements in peer-reviewed publications are flawed. Among many problems, they fall short in one or more of…
-
RESAR: Reliable Storage at Exabyte Scale
Stored data needs to be protected against device failure and irrecoverable sector read errors, yet doing so at exabyte scale can be challenging given the large number of failures that must be handled. We have developed RESAR (Robust, Efficient, Scalable, Autonomous, Reliable) storage, an approach to storage system redundancy that only uses XOR-based parity and…
-
The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)
Abstract: The complete 16,515 bp nucleotide sequence of the mitochondrial genome was determined for the black surfperch, Embiotoca jacksoni (Perciformes: Embiotocidae). The black surfperch mitochondrial genome contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the non-coding control region (D-loop), the gene order of which is identical to that observed in…
-
High-throughput Phenotyping of Lung Cancer Somatic Mutations
Abstract: Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood. Here we characterize 194 somatic mutations identified in primary lung adenocarcinomas. We present an expression-based variant-impact phenotyping (eVIP) method that uses gene expression changes to distinguish impactful from neutral somatic mutations. eVIP…
-
A federated ecosystem for sharing genomic, clinical data
Early data-sharing efforts have led to improved variant interpretation and development of treatments for rare diseases and some cancer types (1–3). However, such benefits will only be available to the general population if researchers and clinicians can access and make comparisons across data from millions of individuals. Read the full article here.
-
Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska
Abstract: Relict woolly mammoth (Mammuthus primigenius) populations survived on several small Beringian islands for thousands of years after mainland populations went extinct. Here we present multiproxy paleoenvironmental records to investigate the timing, causes, and consequences of mammoth disappearance from St. Paul Island, Alaska. Five independent indicators of extinction show that mammoths survived on St. Paul…
-
IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC.
Abstract: Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) expression correlates with malignancy, but its role(s) in pathogenesis remains enigmatic. We interrogated the IGF2BP3-RNA interaction network in pancreatic ductal adenocarcinoma (PDAC) cells. Using a combination of genome-wide approaches, we have identified 164 direct mRNA targets of IGF2BP3. These transcripts encode proteins enriched for functions…
-
Effects of Prolonged Media Usage and Long-term Planning on Archival Systems
Abstract: In archival systems, storage media are often replaced much earlier than their expected service life in exchange for other benefits of new media, such as higher capacity, bandwidth, and input/output operations per second, or lower costs. In an era of decreasing media density growth rates, retiring media early by considering only short-term benefits while…
-
Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
Abstract: To compare lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SqCC) and to identify new drivers of lung carcinogenesis, we examined the exome sequences and copy number profiles of 660 lung ADC and 484 lung SqCC tumor-normal pairs. Recurrent alterations in lung SqCCs were more similar to those of other squamous carcinomas than to…