Abstract Motivation: Nonlinear dose–response models are primary tools for estimating the potency [e.g. half-maximum inhibitory concentration (IC) known as IC50] of anti-cancer drugs. We present drexplorer software, which enables biologists to evaluate replicate reproducibility, detect outlier data points, fit different models, select the best model, estimate IC values at different percentiles and assess drug–drug interactions. drexplorer serves as a computation engine within the R environment and a graphical interface for users who do not have programming backgrounds. Availability and implementation: The drexplorer R package is freely available from GitHub at https://github.com/nickytong/drexplorer. A graphical user interface is shipped with the package. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

Power supply noise is very important in delay testing. Excessive noise can cause circuit delay increases that lead to test overkill. Test patterns that are too quiet can lead to test escapes. In this work, we introduce a realistic low cost delay test compaction flow that guardbands circuit delay during test using a sequence of estimation metrics. Significant reductions in CPU time are demonstrated over prior work.

Translating the overwhelming amount of data generated in high-throughput genomics experiments into biologically meaningful evidence, which may for example point to a series of biomarkers or hint at a relevant pathway, is a matter of great interest in bioinformatics these days. Genes showing similar experimental profiles, it is hypothesized, share biological mechanisms that if understood could provide clues to the molecular processes leading to pathological events. It is the topic of further study to learn if or how a priori information about the known genes may serve to explain coexpression. One popular method of knowledge discovery in high-throughput genomics experiments, enrichment analysis (EA), seeks to infer if an interesting collection of genes is 'enriched' for a Consortium particular set of a priori Gene Ontology Consortium (GO) classes. For the purposes of statistical testing, the conventional methods offered in EA software implicitly assume independence between the GO classes. Genes may be annotated for more than one biological classification, and therefore the resulting test statistics of enrichment between GO classes can be highly dependent if the overlapping gene sets are relatively large. There is a need to formally determine if conventional EA results are robust to the independence assumption. We derive the exact null distribution for testing enrichment of GO classes by relaxing the independence assumption using well-known statistical theory. In applications with publicly available data sets, our test results are similar to the conventional approach which assumes independence. We argue that the independence assumption is not detrimental.

Excessive power supply noise can affect path delay and cause overkill during delay test. This paper presents low-cost noise models for fast power supply noise analysis and timing analysis considering noise impact. Our prior work only considered array-bond chips. This work proposes a noise analysis methodology that can be applied to wire-bond chips as well as array-bond chips. Experiments were performed on an industrial design. Silicon results show as much as a 15% delay variation due to different don't care fill approaches. The power supply noise impact on delay must be taken into account when delay tests are applied

Excessive power supply noise can lead to overkill during delay test. A static test vector compaction solution is described to prevent such overkill. Low-cost power supply noise models are developed and used in compaction. An error analysis of these models is given. This paper improves on prior work in terms of models and algorithm to increase accuracy and performance. Experimental results are given on ISCAS89 circuits

Excessive power supply noise can lead to overkill during delay test. A static compaction algorithm is described in this paper that prevents such overkill. A power supply noise estimation tool has been built and integrated into the compaction process. Compaction results for KLPG delay tests for ISCAS89 circuits under different power grid environments are presented.

SUMMARY: We propose a beta-mixture model approach to solve a variety of problems related to correlations of gene-expression levels. For example, in meta-analyses of microarray gene-expression datasets, a threshold value of correlation coefficients for gene-expression levels is used to decide whether gene-expression levels are strongly correlated across studies. Ad hoc threshold values such as 0.5 are often used. In this paper, we use a beta-mixture model approach to divide the correlation coefficients into several populations so that the large correlation coefficients can be identified. Another important application of the proposed method is in finding co-expressed genes. Two examples are provided to illustrate both applications. Through our analysis, we also discover that the popular model selection criteria BIC and AIC are not suitable for the beta-mixture model. To determine the number of components in the mixture model, we suggest an alternative criterion, ICL-BIC, which is shown to perform better in selecting the correct mixture model. SUPPLEMENTARY INFORMATION: http://odin.mdacc.tmc.edu/~yuanj/highcorgeneanno.html.

To detect the smallest delay faults at a fault site, the longest path(s) through it must be tested at full speed. Existing test generation tools are inefficient in automatically identifying the longest testable paths due to the high computational complexity. In this work a test generation methodology for scan-based synchronous sequential circuits is presented, under two at-speed test strategies used in industry. The two strategies are compared and the test generation efficiency is evaluated on ISCAS89 benchmark circuits and industrial designs. Experiments show that testing transition faults through the longest paths can be done in reasonable test set size.

The path delay fault model is the most realistic model for delay faults. Testing all the paths in a circuit achieves 100% delay fault coverage according to traditional path delay fault coverage metrics. These metrics result in unrealistically low fault coverage if only a subset of paths is tested, and the real test quality is not reflected. For example, the traditional path delay fault coverage of any practical test for circuit c6288 is close to 0 because this circuit has an exponential number of paths. In this paper, a statistical and realistic path delay fault coverage metric is presented. Then the quality of several existing test sets (path selection methods) is evaluated in terms of local and global delay faults using this metric, in comparison with the transition fault and traditional path delay fault coverage metrics.

Abstract Motivation: A major focus of current cancer research is to identify genes that can be used as markers for prognosis and diagnosis, and as targets for therapy. Microarray technology has been applied extensively for this purpose, even though it has been reported that the agreement between microarray platforms is poor. A critical question is: how can we best combine the measurements of matched genes across microarray platforms to develop diagnostic and prognostic tools related to the underlying biology? Results: We introduce a statistical approach within a Bayesian framework to combine the microarray data on matched genes from three investigations of gene expression profiling of B-cell chronic lymphocytic leukemia (CLL) and normal B cells (NBC) using three different microarray platforms, oligonucleotide arrays, cDNA arrays printed on glass slides and cDNA arrays printed on nylon membranes. Using this approach, we identified a number of genes that were consistently differentially expressed between CLL and NBC samples. Availability: Glass slide cDNA array data are available through the public archives of Stanford University at http://cmgm.stanford.edu/pbrown/. Oligonucleotide array data are available in the supplemental material from Klein ηl. Nylon membrane cDNA microarray data are freely available at our website, http://bioinformatics.mdanderson.org/pubdata.html. Software to batch-process gene annotations (GeneLink) is available at http://bioinformatics.mdanderson.org/GeneLink.html. Image quantification software (ScanAlyze) is available at http://rana.lbl.gov/downloads/ScanAlyze.zip. Statistical software (S-Plus 2000) is available commercially from Insightful Corp., Seattle, WA. Software to determine the co-occurrence of terms in PubMed abstracts (PDQ_MED) is commercially available from Inpharmix Inc., Greenwood, IN.