multinomial goodness-of-fit (2009)
fast and numerically robust method for exact
Refining motif finders with E-value calculations (2008)
Niranjan Nagarajan, Patrick Ng, Uri Keich
Motif finders are an important tool for searching for regulatory elements in DNA. Popular existing programs optimize the entropy score to efficiently search for motifs. While E-values are commonly...
A Faster Reliable Algorithm to Estimate the p-Value of the Multinomial llr Statistic (2008)
Abstract. The subject of estimating the p-value of the log-likelihood ratio statistic for multinomial distribution has been studied extensively in the statistical literature. Nevertheless,...
Refining motif finders with E-value calculations (2008)
Niranjan Nagarajan, Patrick Ng, Uri Keich
Motif finders are an important tool for searching for regulatory elements in DNA. Popular existing programs optimize the entropy score to efficiently search for motifs. While E-values are commonly...
Nagarajan, Niranjan, Keich, Uri
Summary: As was shown in Nagarajan et al. (2005), commonly used approximations for assessing the significance of multiple alignments can be be very inaccurate. To address this, we present here the...
Scaffolding and validation of bacterial genome assemblies using optical restriction maps (2008)
Nagarajan, Niranjan, Read, Timothy D., Pop, Mihai
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of...
A fast and numerically robust method for exact multinomial goodness-of-fit test (2006)
Evaluating the significance of goodness-of-fits tests for multinomial data in general, and estimating the p value of the log-likelihood ratio statistic G 2 in particular, have been studied...
Patrick Ng, Niranjan Nagarajan, Neil Jones, Uri Keich
doi:10.1093/bioinformatics/btl245
Ng, Patrick, Nagarajan, Niranjan, Jones, Neil, Keich, Uri
Motivation: Effective algorithms for finding relatively weak motifs are an important practical necessity while scanning long DNA sequences for regulatory elements. The success of such an algorithm...
Computing the P-value of the information content from an alignment of multiple sequences (2005)
Nagarajan, Niranjan, Jones, Neil, Keich, Uri
Motivation: The efficient and accurate computation of P-values is an essential requirement for motif-finding and alignment tools. We show that the approximation algorithms used in two popular...
Nagarajan, Niranjan, Yona, Golan
Motivation: We describe a novel method for detecting the domain structure protein from sequence information alone. The method is based on analyzing multiple sequence alignments that are derived from...
Nagarajan, Niranjan, Yona, Golan
Motivation: We describe a novel method for detecting the domain structure of a protein from sequence information alone. The method is based on analyzing multiple sequence alignments that are derived...
Nagarajan, Niranjan, Yona, Golan
Motivation: We describe a novel method for detecting the domain structure protein from sequence information alone. The method is based on analyzing multiple sequence alignments that are derived from...
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
Nagarajan, Niranjan, Read, Timothy D., Pop, Mihai
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of...
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
White, James Robert, Nagarajan, Niranjan, Pop, Mihai
Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more...
Reliability and efficiency of algorithms for computing the significance of the Mann–Whitney test
Numerical error, Exact computation, FFT,