Journal: Bioinformatics

Volume 7, Issue 4

447 -- 456Webb Miller, J. Barr, Kenneth E. Rudd. Improved algorithms for searching restriction maps
457 -- 460C. J. Gartmann, U. Grob. A menu-shell for the GCG programs
461 -- 469R. J. Brammer, T. N. Bryant, J. H. May. Investigation of an expert systems approach to bacterial identification
471 -- 477Seán I. O Donoghue. Structural interpretation of fluorescence resonance-energy transfer measurements
479 -- 484M. P. Berger, Peter J. Munson. A novel randomized iterative strategy for aligning multiple protein sequences
485 -- 487Istvan Ladunga, F. Czako, I. Csabai, T. Geszti. Improving signal peptide prediction accuracy by simulated neural network
495 -- 500P. Taylor, P. Rosenberg, Maria Samsonova. A new method for finding long consensus patterns in nucleic acid sequences
501 -- 507P. R. Smith, Alexander Ropelewski, D. A. Balog, S. Gottesman, David W. Deerfield II. A simple approach for the distribution of computationally intense tasks in an heterogeneous environment: distribution of the MDPP image-processing package
509 -- 513A. Danckaert, Colombe Chappey, Serge A. Hazout. Size leap algorithm: an efficient extraction of the longest common motifs from a molecular sequence set. Application to the DNA sequence reconstruction
515 -- 524J. Saldanha, J. Eccles. The application of SSADM to modelling the logical structure of proteins
525 -- 529K. Lucas, M. Busch, S. Mossinger, J. A. Thompson. An improved microcomputer program for finding gene- or gene family-specific oligonucleotides suitable as primers for polymerase chain reactions or as probes
531 -- 532A. Bekker, S. Von Hagen, J. Yarmush. A Macintosh Hypercard stack to simulate the pharmacokinetics of infusion of intravenous anesthetic drugs (NarSim)
533 -- 534P. J. O Hara, D. Venezia. PRIMEGEN, a tool for designing primers from multiple alignments
535 -- 536Peter R. Sibbald, H. Sommerfeldt, P. Argos. Automated protein sequence pattern handling and PROSITE searching

Volume 7, Issue 3

287 -- 293Ruth Nussinov. Compositional variations in DNA sequences
295 -- 299Ruth Nussinov. Signals in DNA sequences and their potential properties
301 -- 308Peter D. Karp. Artificial intelligence methods for theory representation and hypothesis formation
309 -- 315Roderic Guigó, A. Johansson, Temple F. Smith. Automatic evaluation of protein sequence functional patterns
317 -- 319M. Grabner, R. Hofbauer. A computer program for molecular weight determination of DNA fragments (HOWBIG)
321 -- 326Julio Collado-Vides. The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars
327 -- 336M. Farza, A. Cheruy. CAMBIO: software for modelling and simulation of bioprocesses
337 -- 340P. Reiner, M. Brenowitz. Quantitative densitometry of autoradiograms: digital images representative of optical density
341 -- 346R. Schnobel. Integrated displays of aligned amino acid sequences and protein structures
347 -- 352D. K. Chiu, T. Kolodziejczak. Inferring consensus structure from nucleic acid sequences
353 -- 357P. Arrigo, F. Giuliano, F. Scalia, A. Rapallo, G. Damiani. Identification of a new motif on nucleic acid sequence data using Kohonen s self-organizing map
365 -- 371G. Mancini, A. Valbonesi. MCS/SEL/BAS program - an overlapping clustering method with examples from mating type interactions of ciliated protozoa
373 -- 378R. S. Carmenes. LSTSQ: a module for reliable constrained and unconstrained nonlinear regression
379 -- 381U. Grob, C. J. Gartmann. COOL - a VAX program for finding COmmon OLigomers in nucleic acid sequences. Thyroid hormone receptor sequences used as an example
391 -- 393J. W. Brown. Phylogenetic comparative analysis of RNA structure on Macintosh computers
395 -- 396Antonio Facchiano, Francesco Facchiano, R. Ragone, Giovanni Colonna. Converter: a program to convert crystallographic coordinates among different molecular graphics standards on PC-IBM platforms
397 -- 0J. W. Brown. Materials methods: a Macintosh hypercard stack for laboratory protocols
398 -- 0T. J. Gleeson, Rodger Staden. An X windows and UNIX implementation of our sequence analysis package
399 -- 401József Baranyi, Tibor Illeni. A back-step algorithm for simulation of Monod-type models

Volume 7, Issue 2

133 -- 142Jean Garnier, J. M. Levin. The protein structure code: what is its present status?
143 -- 154E. A. Cheever, G. Christian Overton, David B. Searls. Fast Fourier transform-based correlation of DNA sequences using complex plane encoding
155 -- 160P. Blaise, C. Gessler. Geobase: a simple geographical information system on a personal computer
161 -- 167H. E. Dayringer, S. A. Sammons. POLLUX: a program for simulated cloning, mutagenesis and database searching of DNA constructs
169 -- 174R. Hernandez, J. A. Esteban, M. Garcia, F. Moran. PASHEMOS: a versatile program written in Pascal to simulate patterns on the shells of molluscs, according to the Meinhardt model
175 -- 187Sheldon S. Ball, Vei H. Mah, Perry L. Miller. SENEX: a computer-based representation of cellular signal transduction processes in the central nervous system
189 -- 193T. N. Bryant. Software for the development and evaluation of probabilistic identification matrices
195 -- 202Colombe Chappey, A. Danckaert, Philippe Dessen, Serge A. Hazout. MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences
203 -- 206D. S. Prestridge. SIGNAL SCAN: a computer program that scans DNA sequences for eukaryotic transcriptional elements
207 -- 215D. H. Fitch, M. Goodman. Phylogenetic scanning: a computer-assisted algorithm for mapping gene conversions and other recombinational events
217 -- 224G. M. Studnicka. ELISA assay optimization using hyperbolic regression
225 -- 232Alain Jacot-Descombes, Krassimir Todorov, Denis F. Hochstrasser, Christian Pellegrini, Thierry Pun. LaboImage: a workstation environment for research in image processing and analysis
233 -- 235D. J. Parry-Smith, Terri K. Attwood. SOMAP: a novel interactive approach to multiple protein sequences alignment
237 -- 247A. S. Deshpande, D. S. Richards, William R. Pearson. A platform for biological sequence comparison on parallel computers
249 -- 256K. Y. Jiang, J. Zheng, S. B. Higgins. A generic algorithm for finding restriction sites within DNA sequences
257 -- 260Michael J. E. Sternberg. PROMOT: a FORTRAN program to scan protein sequences against a library of known motifs
261 -- 263G. H. Dibdin. Precise charge-coupling calculations for finite difference diffusion problems using a modification of the add-on algorithm Q-COUPLE
265 -- 266P. J. Russell, J. M. Doenias, S. J. Russell. GELYMAC: a Macintosh application for calculating DNA fragment size from gel electrophoresis migration data
268 -- 0Amos Bairoch. SEQANALREF: a sequence analysis bibliographic reference databank
269 -- 0S. Barron, M. Witten, R. Harkness, J. Driver. A bibliography on computational algorithms in molecular biology and genetics

Volume 7, Issue 1

1 -- 7John L. Spouge. Fast optimal alignment
9 -- 19Douglas L. Brutlag, A. R. Galper, D. H. Millis. Knowledge-based simulation of DNA metabolism: prediction of enzyme action
21 -- 26S. Morante, Valerio Parisi. Building structural models of peptides: a semi-automatic software
27 -- 29Federico M. Stefanini, A. Camussi. An APL procedure to estimate genotype by environment interaction when two environments are considered
31 -- 38E. Ollivier, Henry Soldano, Alain Viari. Multifrequency location and clustering of sequence patterns from proteins
39 -- 49C. G. Kozhukhin, Pavel A. Pevzner. Genome inhomogeneity is determined mainly by WW and SS dinucleotides
51 -- 55Shu-Yun Le, Jih-H. Chen, Jacob V. Maizel. Detection of unusual RNA folding regions in HIV and SIV sequences
57 -- 60A. Zaritsky, E. Forester. A simulation program to display specific digestion products of predicted RNA foldings
61 -- 62M. Hauer-Jensen. Statistical analysis in dBASE-compatible databases
63 -- 69A. Colosimo, E. Rota, P. Omodeo. A Hypercard program for the identification of biological specimens [published erratum appears in Comput Appl Biosci 1991 Apr;7(2): 285]
71 -- 78Perry L. Miller, Prakash M. Nadkarni, N. M. Carriero. Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm
79 -- 83J. A. Bradshaw, K. J. Carden, D. Riordan. Ecological applications using a novel expert system shell
85 -- 88Geoffrey J. Barton. Scanning protein sequence databanks using a distributed processing workstation network
89 -- 93A. Cornish-Bowden, J. H. Hofmeyr. MetaModel: a program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles
95 -- 98C. G. Moore. A didactic computer simulation of the environmental impact of a pollution discharge
99 -- 101M. Cheminant, R. Labia. The Michaelis-Menten equation: computing substrate concentration as a function of time without restrictions on the initial conditions
103 -- 104K. P. Fung, J. Lee. BASIC program for polynomial regression and smoothing
105 -- 106Rainer Fuchs. MacPattern: protein pattern searching on the Apple Macintosh
107 -- 108D. Shalloway, C. Royer. SMGWS 2: improved microcomputer-based three-dimensional stereoscopic macromolecular graphics display
109 -- 110N. R. Deering, D. Shalloway. GelMetric: semi-automated electrophoretic mobility analysis
111 -- 112R. H. Smith, S. Gottesman, B. Hobbs, E. Lear, D. Kristofferson, D. Benton, P. R. Smith. A mechanism for maintaining an up-to-date GenBank database via Usenet
113 -- 115Jean-Michel Claverie, C. Daulmerie. Smoothing profiles with sliding windows: better to wear a hat!