A5014688170- Reliability and Maintenance Optimization
- Risk and Safety Analysis
- RNA Research and Splicing
- Software Reliability and Analysis Research
- Statistical Distribution Estimation and Applications
- Probabilistic and Robust Engineering Design
- Molecular Biology Techniques and Applications
- Gene expression and cancer classification
- Data Management and Algorithms
- Genomics and Phylogenetic Studies
- Electronic Packaging and Soldering Technologies
- Nuclear and radioactivity studies
- Distributed and Parallel Computing Systems
- Power System Reliability and Maintenance
- Cloud Computing and Resource Management
- Complex Network Analysis Techniques
- Genomics and Chromatin Dynamics
- Parallel Computing and Optimization Techniques
- Integrated Circuits and Semiconductor Failure Analysis
- Neural Networks and Applications
- Legume Nitrogen Fixing Symbiosis
- Advanced Optical Network Technologies
- Statistical Methods in Clinical Trials
- Nuclear Engineering Thermal-Hydraulics
- Transportation Systems and Safety
Princeton University
2013-2020
Heidelberg University
2010-2020
Cornell University
2020
Georgetown University
2009-2019
Sandia National Laboratories
1999-2018
Sandia National Laboratories California
2001-2018
Center for Systems Biology
2012
Harvard University
1989-2012
National Technical Information Service
2000-2011
Office of Scientific and Technical Information
2000-2011
"Open government" used to carry a hard political edge: it referred politically sensitive disclosures of government information. The phrase was first in the 1950s, debates leading up passage Freedom Information Act. But over last few years, that traditional meaning has blurred, and shifted toward technology.
A recent normative turn in computer science has brought concerns about fairness, bias, and accountability to the core of field. Yet scholarship warned that much this technical work treats problematic features status quo as fixed, fails address deeper patterns injustice inequality. While acknowledging these critiques, we posit computational research valuable roles play addressing social problems -- whose value can be recognized even from a perspective aspires toward fundamental change. In...
Background Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes two pink-pigmented facultative methylotrophic bacteria Alpha-proteobacterial genus Methylobacterium, reference species Methylobacterium extorquens strain AM1 and dichloromethane-degrading DM4, were compared. Methodology/Principal Findings 6.88 Mb genome comprises a 5.51 chromosome, 1.26 megaplasmid three plasmids, while 6.12 DM4 features 5.94 chromosome...
Abstract High-throughput quantitative DNA sequencing enables the parallel phenotyping of pools thousands mutants. However, appropriate analytical methods and experimental design that maximize efficiency these while maintaining statistical power are currently unknown. Here, we have used Bar-seq analysis Saccharomyces cerevisiae yeast deletion library to systematically test effect parameters sequence read depth on results. We present computational efficiently accurately estimate sizes their...
Abstract Motivation: Next-generation sequencing experiments, such as RNA-Seq, play an increasingly important role in biological research. One complication is that the power and accuracy of experiments depend substantially on number reads sequenced, so it challenging to determine optimal read depth for experiment or verify whether one has adequate existing experiment. Results: By randomly sampling lower depths from a determining where saturation occurs, can what most useful should be future...
The false discovery rate (FDR) measures the proportion of discoveries among a set hypothesis tests called significant. This quantity is typically estimated based on p-values or test statistics. In some scenarios, there additional information available that may be used to more accurately estimate FDR. We develop new framework for formulating and estimating FDRs q-values when an piece information, which we call "informative variable", available. For given test, informative variable provides...
Insertion sequences (ISs) are simple transposable elements present in most bacterial and archaeal genomes play an important role genomic evolution. The recent expansion of sequenced offers the opportunity to study ISs comprehensively, but this requires efficient accurate tools for IS annotation. We have developed open-source program called OASIS, or Optimized Annotation System Sequences, which automatically annotates within genomes. OASIS annotations 1737 offered unprecedented examine At a...
Understanding the differences between microarray and RNA-Seq technologies for measuring gene expression is necessary informed design of experiments choice data analysis methods. Previous comparisons have come to sometimes contradictory conclusions, which we suggest result from a lack attention intensity-dependent nature variation generated by technologies. To examine this trend, carried out parallel nested experiment performed simultaneously on two that systematically split into four stages...
In response to a wound, fibroblasts are activated migrate toward the proliferate and contribute wound healing process. We hypothesize that changes in pre-mRNA processing occurring as enter proliferative cell cycle also important for promoting their migration. RNA sequencing of induced into quiescence by contact inhibition reveals downregulation genes involved mRNA processing, including splicing cleavage polyadenylation factors. These show differential exon use, especially increased intron...
This paper proposes a new nonparametric reliability growth model for the analysis of failure rate system that is undergoing development test. The only restrictions on actual, unknown distribution each stage testing it be continuous, have one parameter θ, and an associated unimodal likelihood function. No assumptions regarding parametric form process are made, there no decay in during design changes. parameters assumed to ordered from test next such θ <sub...
Interphase nuclear architecture is disrupted and rapidly reformed with each cell division cycle. Successive generations exhibit a "memory" of this architecture, as well for gene expression. Furthermore, many features mitotic chromosome structure are recognizably species tissue specific. We wish to know what properties the underlying chromatin may determine these conserved architecture. Employing particular mouse autoimmune anti-nucleosome monoclonal antibody (PL2-6), combined deconvolution...
As part counts in high performance computing systems are projected to increase faster than reliabilities, there is increasing interest enabling jobs continue execute the presence of failures. Process replication has been shown be a viable method accomplish this, but previous studies have focussed on full levels (dual, triple, etc). In this work, we present model for studying job interrupt times arbitrary degree, and node failure distribution. We show agreement with previously developed...
The authors propose a nonparametric reliability-growth model based on Bayes analysis techniques. By using the unique properties of assumed prior distributions, moments posterior distribution failure rate at various stages during development test can be found. proposed is compared with US Army Material Systems Analysis Activity (AMSAA) relative and mean-square prediction errors. In all but one circumstance, performed better than either AMSAA or models. exception appears to when no information...
Understanding the changes in diverse molecular pathways underlying development of breast tumors is critical for improving diagnosis, treatment, and drug development. Here, we used RNA-profiling canine mammary (CMTs) coupled with a robust analysis framework to model human cancer. Our study leveraged key advantage model, frequent presence multiple naturally occurring at thus providing samples spanning normal tissue benign malignant from each patient. We showed cancer signals, both expression...
Quiescence, reversible exit from the cell division cycle, is characterized by large-scale changes in steady-state gene expression, yet mechanisms controlling these are need of further elucidation. In order to characterize effects post-transcriptional control on quiescent transcriptome human fibroblasts, we determined mRNA decay rates for over 10,000 genes using a transcription shut-off time-course.We found that ~500 monitored exhibited significant rate upon quiescence induction. Genes...
Understanding the differences between microarray and RNA-Seq technologies for measuring gene expression is necessary informed design of experiments choice data analysis methods. Previous comparisons have come to sometimes contradictory conclusions, which we suggest result from a lack attention intensity-dependent nature variation generated by technologies. To examine this trend, carried out parallel nested experiment performed simultaneously on two that systematically split into four stages...
The authors address the issue of optimal redundancy allocation, viz, improving reliability a system by adding cold-standby spares, through an algorithmic approach that uses unique characteristics assumed underlying failure distribution. Although applies to systems with mixed parallel and series configurations, discussion is limited components. lifetime distributions individual parts are phase type. This class probability chosen for its ease numerical implementation. formulation enhancement...
Abstract RNA-Seq studies require a sufficient read depth to detect biologically important genes. Sequencing below this threshold will reduce statistical power while sequencing above provide only marginal improvements in and incur unnecessary costs. Although existing methodologies can help assess whether there is depth, they are unable guide how many additional reads should be sequenced reach threshold. We new method called superSeq that models the relationship between depth. apply framework...