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Deciphering citation statistics.: Nature neuroscience, Vol. 11, No. 6. (June 2008)

Source: Nature neuroscience, Vol. 11, No. 6. (June 2008)
BioDownloader: Bioinformatics downloads and updates in a few clicks.: Bioinformatics (5 May 2007)SUMMARY: There are many ftp or http servers storing data required for biological research. While some download applications are available, there is no user-friendly download application with a graphical interface specifically designed and adapted to meet the requirements of bioinformatics . BioDownloader is a program for downloading and updating files from ftp and http servers. It is optimized to work robustly with large numbers of files. It allows the selective retrieval of only the required files (batch downloads, multiple file masks, ls-lR file parsing, recursive search, recent updates, etc). BioDownloader has a built-in repository containing the settings for common bioinformatics file-synchroni zation needs, including the PDB and NCBI databases. It can post-process downloaded files, including archive extraction and file conversions. AVAILABILITY: The program can be installed from http://dunbrac k.fccc.edu/Bio Downloader. The software is freely available for both non-commercial and commercial users under the BSD license.

Source: Bioinformatics (5 May 2007)
Neuronal morphology in the human cochlear nucleus.: Archives of otolaryngology --head & neck surgery, Vol. 112, No. 12. (December 1986), pp. 1253-1261.Neur onal morphology in the human cochlear nucleus was studied with a Golgi method to better understand the organization of the nucleus. In ventral portions of the nucleus, three principal cell types and two small cell types previously seen in animals were found. In the dorsal portions of the nucleus, predominant cell types found in animals appear to be absent, indicating that cellular organization here is quite different from that in animals. On the other hand, cell morphology in the ventral nucleus suggests that signal processing here is fundamentally similar to that in animals. A review of the organization of these cells in animals is presented to provide a context of present results. The findings have great relevance in light of efforts to implant electrical prostheses in the nucleus.

Source: Archives of otolaryngology--head & neck surgery, Vol. 112, No. 12. (December 1986), pp. 1253-1261.
Benchmarks for shop scheduling problems: European Journal of Operational Research, Vol. 109, No. 1. (16 August 1998), pp. 137-141.In this paper we present extensive sets of randomly generated test problems for the problems of minimizing makespan (Cmax) and maximum lateness (Lmax) in flow shops and job shops. The 600 problems include three different types of routings, four different due date configurations and a variety of problem sizes. The problems, as well as the best existing solution and a lower bound on the optimal value are available on the world-wide web.

Source: European Journal of Operational Research, Vol. 109, No. 1. (16 August 1998), pp. 137-141.
In silico sequence evolution with site-specific interactions along phylogenetic trees: Bioinformatics , Vol. 22, No. 6. (15 March 2006), pp. 716-722.

Source: Bioinformatics, Vol. 22, No. 6. (15 March 2006), pp. 716-722.
LIBSVM: a Library for Support Vector Machines: (2001)LIBSVM is a library for support vector machines (SVM). Its goal is to help users can easily use SVM as a tool. In this document, we present all its implementation details.

Source: (2001)
MULTIPROSPECTO R: an algorithm for the prediction of protein-protei n interactions by multimeric threading.: Proteins, Vol. 49, No. 3. (15 November 2002), pp. 350-364.In this postgenomic era, the ability to identify protein-protei n interactions on a genomic scale is very important to assist in the assignment of physiological function. Because of the increasing number of solved structures involving protein complexes, the time is ripe to extend threading to the prediction of quaternary structure. In this spirit, a multimeric threading approach has been developed. The approach is comprised of two phases. In the first phase, traditional threading on a single chain is applied to generate a set of potential structures for the query sequences. In particular, we use our recently developed threading algorithm, PROSPECTOR. Then, for those proteins whose template structures are part of a known complex, we rethread on both partners in the complex and now include a protein-protei n interfacial energy. To perform this analysis, a database of multimeric protein structures has been constructed, the necessary interfacial pairwise potentials have been derived, and a set of empirical indicators to identify true multimers based on the threading Z-score and the magnitude of the interfacial energy have been established. The algorithm has been tested on a benchmark set comprised of 40 homodimers, 15 heterodimers, and 69 monomers that were scanned against a protein library of 2478 structures that comprise a representative set of structures in the Protein Data Bank. Of these, the method correctly recognized and assigned 36 homodimers, 15 heterodimers, and 65 monomers. This protocol was applied to identify partners and assign quaternary structures of proteins found in the yeast database of interacting proteins. Our multimeric threading algorithm correctly predicts 144 interacting proteins, compared to the 56 (26) cases assigned by PSI-BLAST using a (less) permissive E-value of 1 (0.01). Next, all possible pairs of yeast proteins have been examined. Predictions (n = 2865) of protein-protei n interactions are made; 1138 of these 2865 interactions have counterparts in the Database of Interacting Proteins. In contrast, PSI-BLAST made 1781 predictions, and 1215 have counterparts in DIP. An estimation of the false-negative rate for yeast-predicte d interactions has also been provided. Thus, a promising approach to help assist in the assignment of protein-protei n interactions on a genomic scale has been developed.

Source: Proteins, Vol. 49, No. 3. (15 November 2002), pp. 350-364.
PAML: a program package for phylogenetic analysis by maximum likelihood.: Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.

Source: Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.
PDBML: the representation of archival macromolecular structure data in XML: Bioinformatics , Vol. 21, No. 7. (01 April 2005), pp. 988-992.

Source: Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 988-992.
Pise: software for building bioinformatics webs.: Brief Bioinform, Vol. 3, No. 4. (December 2002), pp. 405-409.Pise is interface construction software for bioinformatics applications that run by command-line operations. It creates common, easy-to-use interfaces to these applications for the Web, or other uses. It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web services.

Source: Brief Bioinform, Vol. 3, No. 4. (December 2002), pp. 405-409.

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