The strongly connected reliability of complete digraphs
Given a digraph D, consider the model where each vertex is always operational, but the edges are independently operational with probability p. The strongly connected reliability of D, scRel(D, p), is the probability that the spanning subgraph of D consisting of the operational edges is strongly connected. One can view strongly connected reliability as the probability that any vertex can send information to any other vertex, given that edges fail independently. ∗Partially supported by a grant from NSERC. Communicating author.

title: The existence of uniquely -G colourable graphs
abstract: Given graphs F and G and a nonnegative integer k , a function π : V ( F ) → 1, …, k is a − G k-colouring of F if no induced copy of is monochromatic; F is − G k-chromatic if F has a − G k -colouring but no − G ( k − 1)-colouring. Further, we say F is uniquely − G k -colourable if F is − G k -chromatic and, up to a permutation of colours, it has only one − G k -colouring. Such notions are extensions of the well-known corresponding definitions from chromatic theory. It was conjectured that for all graphs G of order at least two and all positive integers k there exist uniquely − G k -colourable graphs. We prove the conjecture and show that, in fact, in all cases infinitely many such graphs exist.

title: Average independence polynomials
abstract: The independence polynomial of a graph G is the function i(G, x) = Σ k ≥ 0 ik xk, where ik is the number of independent sets of vertices in G of cardinality k. We investigate here the average independence polynomial, where the average is taken over all independence polynomials of (labeled) graphs of order n. We prove that while almost every independence polynomial has a nonreal root, the average independence polynomials always have all real, simple roots.

title: On chromatic roots with negative real part

title: A ramsey type problem concerning vertex colourings
abstract: Let H → k v G denote the fact that for every function π: V ( H ) → {1, …, k } there is an induced subgraph G ′ of H with G ′ ≅ G and V ( G ′) ⊆ π −1 ( i ) for some i . Folkman has shown that for all graphs G and for all positive integers k such a graph H exists. We examine here f ( G , k ), the minimum order of a graph H for which H → k v G . We show that for any fixed integer k ≥ 2 there are positive constants C 1 and C 2 such that C 1 n 2 ≤ max{ f ( G , k ): | V ( G )| = n } ≤ C 2 n 2 log 2 n .

title: The Complexity of Generalized Graph Colorings
abstract: Given a graph property P and positive integer k, a P k-coloring of a graph G is an assignment of one of k colors to each vertex of the graph so that the subgraphs induced by each color class have property P. This notion generalizes the standard definition of graph coloring, and has been investigated for many properties. We consider here the complexity of the decision problem. In particular, for the property —G, of not containing an induced subgraph isomorphic to G, we conjecture (and provide strong evidence) that —G k-colorability is NP-complete whenever G has order at least 3 and k ⩾ 2. The techniques rely on new NP-completeness results for hypergraph colorings.

title: A Macintosh Hypercard compilation of small subunit ribosomal RNA sequences
abstract: Molecular biologists, particularly those working with unicellular organisms, are becoming increasingly aware of the importance of understanding the phylogenetic (evolutionary) relationships between their model systems and other organisms. Currently, the best method for determining quantitatively the phylogenetic relationships in a group of organisms is the analysis of small subunit ribosomal RNA (ssu RNA) sequences (Woese, 1984). To assist in this type of analysis, the Ribosomal RNA Database Project (RDP) collects and distributes ssu rRNA sequences and software for phylogenetic analysis (Olsen et al., 1991). The ssu rRNA sequence stack is collection of almost 500 aligned ssu rRNA sequences taken from the first public release of the RDP sequence collection. The ssu rRNA sequence stack consists of a series of 'cards' each containing the ssu rRNA sequence of a single organism , from which the sequence can be copied (either with or without alignment information) or saved as a text file in GenBank format. Navigation in the stack is via a series of linked phylogenetic trees. Starting with a 'universal tree', clicking on the branch of interest takes the user to increasingly more specific and detailed trees. In the most specific trees, clicking on a branch either takes the user directly to the sequence card (if only one sequence is available representing that group) or presents the user with a pop-up menu of available sequences. Alternatively, the user can choose the desired sequence from a list containing the names of all of the available sequences, or choose to search the sequence names for a specific character string. The ssu rRNA sequence stack is written in Hypertalk v. 2.1, and requires v. 2.0 (or greater) of HyperCard, which in turn requires at least a Macintosh Plus, 1 Mbyte of RAM, the Macintosh operating system v 6.0.5 (or greater), and preferably a hard disk drive. The ssu rRNA sequence stack is available by anonymous FTP from ftp.bio.indiana.edu, by E-mail from the author at jwbrown@bio.indiana.edu or brownjw@iubacs.bitnet, or on floppy disk (enclose a single formatted high-density disk) free of charge on written request to the author.

title: The ribonuclease P database
abstract: The Ribonuclease P Sequence database is a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information. In its initial form, the database contains information on RNase P RNA in bacteria and archaea, and RNase P protein in bacteria. The sequences themselves are presented phylogenetically ordered and aligned. The database also contains secondary structures of bacterial and archaeal RNAs, including specially annotated 'reference' secondary structures of Escherichia coli and Bacillus subtilis RNase P RNAs, a minimum phylogenetic consensus structure, and coordinates for models of three-dimensional structure.

title: Theories of Causal Ordering
abstract: This paper is a response to Iwasaki and Simon  which criticizes de Kleer and Brown . We argue that many of their criticisms, particularly concerning causality, modeling and stability, originate from the difference of concerns between engineering and economics. Our notion of causality arises from considering the interconnections of components, not equations. When no feedback is present, the ordering produced by our qualitative physics is similar to theirs. However, when feedback is present, our qualitative physics determines a causal ordering around feedback loops as well. Causal ordering is a general technique not only applicable to qualitative reasoning. Therefore we also explore the relationship between causal ordering and propagation of constraints upon which the methods of qualitative physics are based.

title: Plant snoRNA database
abstract: The Plant snoRNA database (http://www.scri.sari.ac.uk/plant_snoRNA/) provides information on small nucleolar RNAs from Arabidopsis and eighteen other plant species. Information includes sequences, expression data, methylation and pseudouridylation target modification sites, initial gene organization (polycistronic, single gene and intronic) and the number of gene variants. The Arabidopsis information is divided into box C/D and box H/ACA snoRNAs, and within each of these groups, by target sites in rRNA, snRNA or unknown. Alignments of orthologous genes and gene variants from different plant species are available for many snoRNA genes. Plant snoRNA genes have been given a standard nomenclature, designed wherever possible, to provide a consistent identity with yeast and human orthologues.

title: The Social Life of Documents
abstract: Documents are evolving as means for structuring and navigating information space, and resources for constructing and negotiating social space