#### Filter Results:

- Full text PDF available (21)

#### Publication Year

1996

2017

- This year (3)
- Last 5 years (12)
- Last 10 years (19)

#### Publication Type

#### Co-author

#### Journals and Conferences

#### Key Phrases

#### Method

Learn More

- Josephine F. Reyes, Andrew R. Francis, Mark M. Tanaka
- BMC Bioinformatics
- 2008

Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing such data is to construct graphs, including phylogenies. Inferences from graph representations of data assist in understanding the patterns of… (More)

- Andrew R. Francis, Mike A. Steel
- Systematic biology
- 2015

A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on "2-SAT") that efficiently determines whether or not any given network can be realized in this way. Moreover, the proof provides a polynomial-time algorithm for… (More)

- Attila Egri-Nagy, Volker Gebhardt, Mark M. Tanaka, Andrew R. Francis
- Journal of mathematical biology
- 2014

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent than longer, and those that move the terminus of replication are less probable than those that do not. Current methods… (More)

- Mark M. Tanaka, Andrew R. Francis, Fabio Luciani, Scott A. Sisson
- Genetics
- 2006

Tuberculosis can be studied at the population level by genotyping strains of Mycobacterium tuberculosis isolated from patients. We use an approximate Bayesian computational method in combination with a stochastic model of tuberculosis transmission and mutation of a molecular marker to estimate the net transmission rate, the doubling time, and the… (More)

- Fabio Luciani, Scott A. Sisson, Honglin Jiang, Andrew R. Francis, Mark M. Tanaka
- Proceedings of the National Academy of Sciences…
- 2009

The emergence of antibiotic resistance in Mycobacterium tuberculosis has raised the concern that pathogen strains that are virtually untreatable may become widespread. The acquisition of resistance to antibiotics results in a longer duration of infection in a host, but this resistance may come at a cost through a decreased transmission rate. This raises the… (More)

- Mark M. Tanaka, Andrew R. Francis
- Proceedings of the National Academy of Sciences…
- 2006

The W-Beijing strain of tuberculosis has been identified in many molecular epidemiological studies as being particularly prevalent. This identification has been made possible through the development of a number of genotyping technologies including spoligotyping. Highly prevalent genotypes associated with outbreaks, such as the W-Beijing strain, are… (More)

In this paper we prove the Dipper–James conjecture that the centre of the Iwahori–Hecke algebra of type A is the set of symmetric polynomials in the Jucys–Murphy operators. © 2006 Elsevier Inc. All rights reserved.

- Chaka Tang, Josephine F. Reyes, Fabio Luciani, Andrew R. Francis, Mark M. Tanaka
- Bioinformatics
- 2008

spolTools is a collection of online programs designed to manipulate and analyze spoligotype datasets of the Mycobacterium tuberculosis complex. These tools are integrated into a repository currently containing 1179 spoligotypes and 6278 isolates across 30 datasets. Users can search this database to export for external use or to pass on to the integrated… (More)

- Fabio Luciani, Andrew R. Francis, Mark M. Tanaka
- Infection, genetics and evolution : journal of…
- 2008

Molecular techniques such as IS6110-RFLP typing and spacer oligonucleotide typing (spoligotyping) have aided in understanding the transmission patterns of Mycobacterium tuberculosis. The degree of clustering of isolates on the basis of genotypes is informative of the extent of transmission in a given geographic area. We analyzed 130 published data sets of… (More)

- Andrew R. Francis, Mike A. Steel
- Mathematical biosciences
- 2015

Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any two extant species, reflecting the possible pathways that genetic material may have been passed down from a common… (More)