Microbiome profiles in periodontitis in relation to host and disease characteristics.

Periodontitis is an inflammatory condition that affects the supporting tissues surrounding teeth. The occurrence of periodontitis is associated with shifts in the structure of the communities that inhabit the gingival sulcus. Although great inter-subject variability in the subgingival microbiome has been observed in subjects with periodontitis, it is unclear whether distinct community types exist and if differences in microbial signatures correlate with host characteristics or with the variable clinical presentations of periodontitis.

Transplantation-associated long-term immunosuppression promotes oral colonization by potentially opportunistic pathogens without impacting other members of the salivary bacteriome.

Solid-organ transplant recipients rely on pharmacological immunosuppression to prevent allograft rejection. The effect of such chronic immunosuppression on the microflora at mucosal surfaces is not known. We evaluated the salivary bacterial microbiome of 20 transplant recipients and 19 nonimmunosuppressed controls via 454 pyrosequencing of 16S rRNA gene amplicons.

Determining significance of pairwise co-occurrences of events in bursty sequences.

Background: Event sequences where different types of events often occur close together arise, e.g., when studying potential transcription factor binding sites (TFBS, events) of certain transcription factors (TF, types) in a DNA sequence.

Comparing segmentations by applying randomization techniques.

Background: There exist many segmentation techniques for genomic sequences, and the segmentations can also be based on many different biological features. We show how to evaluate and compare the quality of segmentations obtained by different techniques and alternative biological features.

Results: We apply randomization techniques for evaluating the quality of a given segmentation.