Recent advances in DNA sequencing technologies have the potential to transform the field of clinical and public health microbiology, and in the last few years numerous case studies have demonstrated successful applications in this context. Among other considerations, a lack of user-friendly data analysis and interpretation tools has been frequently cited as a major barrier to routine use of the...

VERA P. KRYMSKAYA,1 RAYMOND B. PENN,2 MICHAEL J. ORSINI,2 PAMELA H. SCOTT,3 ROBIN J. PLEVIN,3 TREVOR R. WALKER,4 ANDREW J. ESZTERHAS,1 YASSINE AMRANI,1 EDWIN R. CHILVERS,4 AND REYNOLD A. PANETTIERI, JR.1 1Pulmonary and Critical Care Division, Department of Medicine, University of Pennsylvania Medical Center, Philadelphia 19104-4283; 2Department of Pharmacology, Jefferson Cancer Institute, Thoma...

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A complete sequence (an) is a strictly increasing sequence of positive integers such that every su ciently large positive integer is representable as the sum of one or more distinct terms from (an). In this paper, we consider the more general notion of an r-complete sequence where every su ciently large positive integer is now representable as the sum of r or more distinct terms from (an). In p...

Deciphering the interaction links between proteins has become one of the main tasks of experimental and bioinformatic methodologies. Reconstruction of complex networks of interactions in simple cellular systems by integrating predicted interaction networks with available experimental data is becoming one of the most demanding needs in the postgenomic era. On the basis of the study of correlated...

The technique of affine gaps allows calculations to perform alignment scoring without a strict linear score or gaps. Finding the best scoring alignment with this technique requires multiple arrays to be kept because the maximum score at any midpoint is not purely deterministic on the predecessors (which would require only one array) rather, multiple possible scores must be kept for each locatio...

Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological and biochemical functions. There is often significant structural diversity around the common scaffold of secondary structure elements of the f...

Protein structure classification hierarchically clusters domain structures based on structure and/or sequence similarities and plays important roles in the study of protein structure-function relationship and protein evolution. Among many classifications, SCOP and CATH are widely viewed as the gold standards. Fold classification is of special interest because this is the lowest level of classif...

UNLABELLED Lectins, a class of carbohydrate-binding proteins and widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes encompass different members that are diverse in their protein structures, carbohydrate affinities and specificities, their larger biological roles and potential applications. To attain an effectiv...