Volume 17,
Number 1,
January 2001
Ditorial
Original Papers
- Ekaterina Myasnikova, Anastassia Samsonova, Konstantin Kozlov, Maria Samsonova, John Reinitz:
Registration of the expression patterns of Drosophila segmentation genes by two independent methods.
3-12 BibTeX
- Andrey A. Mironov, Pavel S. Novichkov, Mikhail S. Gelfand:
Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors.
13-15 BibTeX
- Prasith Baccam, Robert J. Thompson, Olivier Fedrigo, Susan Carpenter, James L. Cornette:
PAQ: Partition Analysis of Quasispecies.
16-22 BibTeX
- Gill Bejerano, Golan Yona:
Variations on probabilistic suffix trees: statistical modeling and prediction of protein families.
23-43 BibTeX
- Dmitrij Frishman, Kaj Albermann, Jean Hani, Klaus Heumann, Agnes Metanomski, Alfred Zollner, Hans-Werner Mewes:
Functional and structural genomics using PEDANT.
44-57 BibTeX
- Salvatore Lanzavecchia, Francesca Cantele, Pier Luigi Bellon:
Alignment of 3D structures of macromolecular assemblies.
58-62 BibTeX
- Liam J. McGuffin, Kevin Bryson, David T. Jones:
What are the baselines for protein fold recognition?
63-72 BibTeX
- Catherine Letondal:
A Web interface generator for molecular biology programs in Unix.
73-82 BibTeX
- Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral:
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources.
83-94 BibTeX
Discovery Notes
Applications Notes
- Günter Raddatz, Michaela Dehio, Thomas F. Meyer, Christoph Dehio:
PrimeArray: genome-scale primer design for DNA-microarray construction.
98-99 BibTeX
- William C. Ray, Charles J. Daniels:
The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysis.
100-104 BibTeX
- J. N. Selley, J. Swift, Terri K. Attwood:
EASY-an Expert Analysis SYstem for interpreting database search outputs.
105-106 BibTeX
- Christoph Helma, Ross D. King, Stefan Kramer, Ashwin Srinivasan:
The Predictive Toxicology Challenge 2000-2001.
107-108 BibTeX
Volume 17,
Numer 2,
February
Editorial
Reviews
Original Papers
- Javier Herrero, Alfonso Valencia, Joaquín Dopazo:
A hierarchical unsupervised growing neural network for clustering gene expression patterns.
126-136 BibTeX
- Bruce A. Shapiro, Jin Chu Wu, David Bengali, Mark J. Potts:
The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation.
137-148 BibTeX
- Ming Li, Jonathan H. Badger, Xin Chen, Sam Kwong, Paul E. Kearney, Haoyong Zhang:
An information-based sequence distance and its application to whole mitochondrial genome phylogeny.
149-154 BibTeX
- Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, Toshihisa Takagi:
Automated extraction of information on protein-protein interactions from the biological literature.
155-161 BibTeX
- Raja Mazumder, Ashok S. Kolaskar, Donald Seto:
GeneOrder: comparing the order of genes in small genomes.
162-166 BibTeX
- Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai:
ORI-GENE: gene classification based on the evolutionary tree.
167-173 BibTeX
- Frédéric Tores, Emmanuel Barillot:
The art of pedigree drawing: algorithmic aspects.
174-179 BibTeX
- Robert Stevens, Carole A. Goble, Patricia G. Baker, Andy Brass:
A classification of tasks in bioinformatics.
180-188 BibTeX
Discovery Notes
- Hiromi Nishida:
Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomes.
189-191 BibTeX
Applications Notes
- Matej Lexa, J. Horak, B. Brzobohaty:
Virtual PCR.
192-193 BibTeX
- Kevin P. Micallef, Mark Cooper, Dean W. Podlich:
Using clusters of computers for large QU-GENE simulation experiments.
194-195 BibTeX
- Cécile André, Pierre Vincens, Jean-François Boisvieux, Serge A. Hazout:
MOSAIC: segmenting multiple aligned DNA sequences.
196-197 BibTeX
- P. M. Stothard:
COMBOSA3D: combining sequence alignments with three-dimensional structures.
198-199 BibTeX
- Asim S. Siddiqui, Uwe Dengler, Geoffrey J. Barton:
3Dee: a database of protein structural domains.
200-201 BibTeX
- Piero Fariselli, Rita Casadio:
RCNPRED: prediction of the residue co-ordination numbers in proteins.
202-204 BibTeX
Volume 17,
Number 3,
March 2001
Original Papers
- David Hall, Suchendra M. Bhandarkar, Jonathan Arnold, Tongzhang Jiang:
Physical mapping with automatic capture of hybridization data.
205-213 BibTeX
- Thomas Kämpke, Markus Kieninger, Michael Mecklenburg:
Efficient primer design algorithms.
214-225 BibTeX
- Siu-wai Leung, Chris Mellish, Dave Robertson:
Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences.
226-236 BibTeX
- Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen:
Flexibility of the genetic code with respect to DNA structure.
237-248 BibTeX
- Kevin A. T. Silverstein, Elizabeth Shoop, James E. Johnson, Ernest F. Retzel:
MetaFam: a unified classification of protein families. I. Overview and statistics.
249-261 BibTeX
- Elizabeth Shoop, Kevin A. T. Silverstein, James E. Johnson, Ernest F. Retzel:
MetaFam: a unified classification of protein families. II. Schema and query capabilities.
262-271 BibTeX
- Andreas Heger, Liisa Holm:
Picasso: generating a covering set of protein family profiles.
272-279 BibTeX
Applications Notes
- T. Andrew Ronneberg, Stephen J. Freeland, Laura F. Landweber:
Genview and Gencode: a pair of programs to test theories of genetic code evolution.
280-281 BibTeX
- Weizhong Li, Lukasz Jaroszewski, Adam Godzik:
Clustering of highly homologous sequences to reduce the size of large protein databases.
282-283 BibTeX
- Kurt S. Thorn, Andrew A. Bogan:
ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions.
284-285 BibTeX
- Neema Jamshidi, Jeremy S. Edwards, Tom Fahland, George M. Church, Bernhard O. Palsson:
Dynamic simulation of the human red blood cell metabolic network.
286-287 BibTeX
- Pedro Mendes, Douglas B. Kell:
MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems.
288-289 BibTeX
Volume 17,
Number 4,
April 2001
Editorial
Original Papers
- Christian J. Stoeckert Jr., Angel Pizarro, Elisabetta Manduchi, M. Gibson, Brian P. Brunk, Jonathan Crabtree, Jonathan Schug, Shai Shen-Orr, G. Christian Overton:
A relational schema for both array-based and SAGE gene expression experiments.
300-308 BibTeX
- Ka Yee Yeung, David R. Haynor, Walter L. Ruzzo:
Validating clustering for gene expression data.
309-318 BibTeX
- Daniel R. Masys, John B. Welsh, J. Lynn Fink, Michael Gribskov, Igor Klacansky, Jacques Corbeil:
Use of keyword hierarchies to interpret gene expression patterns.
319-326 BibTeX
- Abdullah N. Arslan, Ömer Egecioglu, Pavel A. Pevzner:
A new approach to sequence comparison: normalized sequence alignment.
327-337 BibTeX
- Rainer Spang, Martin Vingron:
Limits of homology detection by pairwise sequence comparison.
338-342 BibTeX
- Christian E. V. Storm, Erik L. L. Sonnhammer:
NIFAS: visual analysis of domain evolution in proteins.
343-348 BibTeX
- Chris H. Q. Ding, Inna Dubchak:
Multi-class protein fold recognition using support vector machines and neural networks.
349-358 BibTeX
- Edward M. Marcotte, Ioannis Xenarios, David Eisenberg:
Mining literature for protein-protein interactions.
359-363 BibTeX
- Hubert Hug, Rainer Schuler:
Strategies for the development of a peptide computer.
364-368 BibTeX
Applications Notes
- B. Dysvik, Inge Jonassen:
J-Express: exploring gene expression data using Java.
369-370 BibTeX
- J. L. Lessem, Stacey S. Cherny:
DeFries-Fulker multiple regression analysis of sibship QTL data: a SAS®macro.
371-372 BibTeX
- Cédric Notredame:
Mocca: semi-automatic method for domain hunting.
373-374 BibTeX
- S. Sujatha, S. Balaji, Narayanaswamy Srinivasan:
PALI: a database of alignments and phylogeny of homologous protein structures.
375-376 BibTeX
- Christoph Gille, Cornelius Frömmel:
STRAP: editor for STRuctural Alignments of Proteins.
377-378 BibTeX
- Kim Lan Sim, Tomoyuki Uchida, Satoru Miyano:
ProDDO: a database of disordered proteins from the Protein Data Bank (PDB).
379-380 BibTeX
- Eran Eyal, Rafael Najmanovich, Vladimir Sobolev, Marvin Edelman:
MutaProt: a web interface for structural analysis of point mutations.
381-382 BibTeX
- Christian M. Zmasek, Sean R. Eddy:
ATV: display and manipulation of annotated phylogenetic.
383-384 BibTeX
- Fiona S. L. Brinkman, Ivan Wan, Robert E. W. Hancock, Ann M. Rose, Steven J. Jones:
PhyloBLAST: facilitating phylogenetic analysis of BLAST results.
385-387 BibTeX
Volume 17,
Number 5,
May 2001
Editorial
Reviews
- Webb Miller:
Comparison of genomic DNA sequences: solved and unsolved problems.
391-397 BibTeX
Original Papers
- Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, M. Jaroszewski, Wojciech T. Markiewicz:
Construction of DNA restriction maps based on a simplified experiment.
398-404 BibTeX
- Alexander V. Lukashin, Rainer Fuchs:
Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters.
405-414 BibTeX
- Brian Gaschen, Carla Kuiken, Bette Korber, Brian T. Foley:
Retrieval and on-the-fly alignment of sequence fragments from the HIV database.
415-418 BibTeX
- Jeremy Buhler:
Efficient large-scale sequence comparison by locality-sensitive hashing.
419-428 BibTeX
- Jonas S. Almeida, João A. Carriço, António Maretzek, Peter A. Noble, Madilyn Fletcher:
Analysis of genomic sequences by Chaos Game Representation.
429-437 BibTeX
- Tony Y. T. Chan:
Unsupervised classification of noisy chromosomes.
438-444 BibTeX
- Ross D. King, Andreas Karwath, Amanda Clare, Luc Dehaspe:
The utility of different representations of protein sequence for predicting functional class.
445-454 BibTeX
- Joel R. Bock, David A. Gough:
Predicting protein-protein interactions from primary structure.
455-460 BibTeX
- Moritz Y. Becker, Isabel Rojas:
A graph layout algorithm for drawing metabolic pathways.
461-467 BibTeX
- Yury V. Bukhman, Jeffrey Skolnick:
BioMolQuest: integrated database-based retrieval of protein structural and functional information.
468-478 BibTeX
Applications Notes
Volume 17,
Number 6,
June 2001
Editorial
- Win Hide:
ExScript: An `EX'-Centric Approach to the Description of Transcript Diversity.
485-486 BibTeX
Original Papers
- Eric Harley, Anthony J. Bonner, Nathan Goodman:
Uniform integration of genome mapping data using intersection graphs.
487-494 BibTeX
- John Aach, George M. Church:
Aligning gene expression time series with time warping algorithms.
495-508 BibTeX
- Pierre Baldi, Anthony D. Long:
A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes.
509-519 BibTeX
- Olga G. Troyanskaya, Michael Cantor, Gavin Sherlock, Patrick O. Brown, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman:
Missing value estimation methods for DNA microarrays.
520-525 BibTeX
- Peter D. Karp, Suzanne M. Paley, Jingchun Zhu:
Database verification studies of SWISS-PROT and GenBank.
526-532 BibTeX
- Rolf Apweiler, Paul Kersey, Vivien Junker, Amos Bairoch:
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al.
533-534 BibTeX
- Ingrid B. Jakobsen, Jennifer A. Saleeba, Michael Poidinger, Timothy G. Littlejohn:
TreeGeneBrowser: phylogenetic data mining of gene sequences from public databases.
535-540 BibTeX
- Charlotte M. Deane, Quentin Kaas, Tom L. Blundell:
SCORE: predicting the core of protein models.
541-550 BibTeX
- Robert Garian:
Prediction of quaternary structure from primary structure.
551-556 BibTeX
Discovery Notes
Applications Notes
- Pierre R. Bushel, Hisham Hamadeh, Lee Bennett, Stella Sieber, Karla Martin, Emile F. Nuwaysir, Kate Johnson, Kelli Reynolds, Richard S. Paules, Cynthia A. Afshari:
MAPS: a microarray project system for gene expression experiment information and data validation.
564-565 BibTeX
- Michael E. Wall, Patricia A. Dyck, Thomas S. Brettin:
SVDMAN-singular value decomposition analysis of microarray data.
566-568 BibTeX
- Xuhua Xia, Zheng Xie:
AMADA: analysis of microarray data.
569-570 BibTeX
- Birgitta Geier, Gabi Kastenmüller, Matthias Fellenberg, Hans-Werner Mewes, Burkhard Morgenstern:
The HIB database of annotated UniGene clusters.
571-572 BibTeX
- Ari Löytynoja, Michel C. Milinkovitch:
SOAP, cleaning multiple alignments from unstable blocks.
573-574 BibTeX
- Nicolas Le Novère, Thomas Simon Shimizu:
STOCHSIM: modelling of stochastic biomolecular processes.
575-576 BibTeX
- Malay Kumar Basu:
SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services.
577-578 BibTeX
Volume 17,
Supplement,
June 2001
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, July 21-25, 2001, Copenhagen, Denmark.
2001
Contents BibTeX
Volume 17,
Number 7,
July 2001
Editorial
Original Papers
- Xiayi Ke, William Tapper, Andrew Collins:
LDB2000: sequence-based integrated maps of the human genome.
581-586 BibTeX
- Barbara A. Eckman, Anthony Kosky, Leonardo A. Laroco Jr.:
Extending traditional query-based integration approaches for functional characterization of post-genomic data.
587-601 BibTeX
- Jack E. Tabaska, Ramana V. Davuluri, Michael Q. Zhang:
Identifying the 3'-terminal exon in human DNA.
602-607 BibTeX
- Debraj Guha Thakurta, Gary D. Stormo:
Identifying target sites for cooperatively binding factors.
608-621 BibTeX
- Rongxiang Liu, Thomas W. Blackwell, David J. States:
Conformational model for binding site recognition by the E.coli MetJ transcription factor.
622-633 BibTeX
- Matthias Steinfath, Wasco Wruck, Henrik Seidel, Hans Lehrach, Uwe Radelof, John O'Brien:
Automated image analysis for array hybridization experiments.
634-641 BibTeX
- Jan Gorodkin, Christian Zwieb, Bjarne Knudsen:
Semi-automated update and cleanup of structural RNA alignment databases.
642-645 BibTeX
- Steffen Möller, Michael D. R. Croning, Rolf Apweiler:
Evaluation of methods for the prediction of membrane spanning regions.
646-653 BibTeX
Applications Notes
- Jochen Hampe, Andreas Wollstein, Timothy Lu, Hans-Jürgen Frevel, Marcus Will, Carl Manaster, Stefan Schreiber:
An integrated system for high throughput TaqManTM based SNP genotyping.
654-655 BibTeX
- Raf M. Podowski, Erik L. L. Sonnhammer:
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
656-657 BibTeX
- Rob M. Ewing, J. Michael Cherry:
Visualization of expression clusters using Sammon's non-linear mapping.
658-659 BibTeX
- Yoshiyuki Suzuki, Takashi Gojobori, Masatoshi Nei:
ADAPTSITE: detecting natural selection at single amino acid sites.
660-661 BibTeX
- Alexei Drummond, Korbinian Strimmer:
PAL: an object-oriented programming library for molecular evolution and phylogenetics.
662-663 BibTeX
- Vladimir Makarenkov:
T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks.
664-668 BibTeX
- Ralf Mrowka:
A Java applet for visualizing protein-protein interaction.
669-671 BibTeX
Volume 17,
Number 8,
August 2001
Original Papers
- Meena K. Sakharkar, Tin Wee Tan, Sandro J. de Souza:
Generation of a database containing discordant intron positions in eukaryotic genes (MIDB).
671-675 BibTeX
- Avril Coghlan, Dónall A. Mac Dónaill, Nigel H. Buttimore:
Representation of amino acids as five-bit or three-bit patterns for filtering protein databases.
676-685 BibTeX
- Zsuzsanna Dosztányi, Andrew E. Torda:
Amino acid similarity matrices based on force fields.
686-699 BibTeX
- Jimin Pei, Nick V. Grishin:
AL2CO: calculation of positional conservation in a protein sequence alignment.
700-712 BibTeX
- Kevin Karplus, Birong Hu:
Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set.
713-720 BibTeX
- Sujun Hua, Zhirong Sun:
Support vector machine approach for protein subcellular localization prediction.
721-728 BibTeX
- W. R. Pitt, M. A. Williams, M. Steven, B. Sweeney, Alan J. Bleasby, David S. Moss:
The Bioinformatics Template Library-generic components for biocomputing.
729-737 BibTeX
Applications Notes
- David G. Cox, Federico Canzian:
Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis.
738-739 BibTeX
- Yang He, Xiangming Xu, Kenneth R. Tobutt, Martin S. Ridout:
Polylink: to support two-point linkage analysis in autotetraploids.
740-741 BibTeX
- Gonçalo R. Abecasis, Stacey S. Cherny, W. O. C. Cookson, Lon R. Cardon:
GRR: graphical representation of relationship errors.
742-743 BibTeX
- Liqun Xing, Volker Brendel:
Multi-query sequence BLAST output examination with MuSeqBox.
744-745 BibTeX
- Marc A. Martí-Renom, Valentin A. Ilyin, Andrej Sali:
DBAli: a database of protein structure alignments.
746-747 BibTeX
- Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, J. Shi, Hiroki Shirai, Tom L. Blundell:
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.
748-749 BibTeX
- Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski:
Structure prediction meta server.
750-751 BibTeX
- Dominique Douguet, Gilles Labesse:
Easier threading through web-based comparisons and cross-validations.
752-753 BibTeX
- John P. Huelsenbeck, Fredrik Ronquist:
MRBAYES: Bayesian inference of phylogenetic trees.
754-755 BibTeX
- Chenna Ramu:
SIR: a simple indexing and retrieval system for biological flat file databases.
756-758 BibTeX
Volume 17,
Number 9,
September 2001
Editorial
Original Papers
Applications Notes
- Xiayi Ke, Andrew Collins, Shu Ye:
PIRA PCR designer for restriction analysis of single nucleotide polymorphisms.
838-839 BibTeX
- Jacques Colinge, Georg Feger:
Detecting the impact of sequencing errors on SAGE data.
840-842 BibTeX
- Izabela Makalowska, Joseph F. Ryan, Andreas D. Baxevanis:
GeneMachine: gene prediction and sequence annotation.
843-844 BibTeX
- Leo Goodstadt, Chris P. Ponting:
CHROMA: consensus-based colouring of multiple alignments for publication.
845-846 BibTeX
- Evgeni M. Zdobnov, Rolf Apweiler:
InterProScan - an integration platform for the signature-recognition methods in InterPro.
847-848 BibTeX
- Gábor E. Tusnády, István Simon:
The HMMTOP transmembrane topology prediction server.
849-850 BibTeX
- John J. Salama, Howard J. Feldman, Christopher W. V. Hogue:
VISTRAJ: exploring protein conformational space.
851-852 BibTeX
- Anton J. Enright, Christos A. Ouzounis:
BioLayout-an automatic graph layout algorithm for similarity visualization.
853-854 BibTeX
- Pentti Riikonen, Jorma Boberg, Tapio Salakoski, Mauno Vihinen:
BioWAP, mobile Internet service for bioinformatics.
855-856 BibTeX
- Kimberly F. Johnson, Simon M. Lin:
Critical Assessment of Microarray Data Analysis: the 2001 challenge.
857-858 BibTeX
Volume 17,
Number 10,
October 2001
Editorial
- Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin:
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA).
859-861 BibTeX
Original Papers
- Vinhthuy T. Phan, Steven Skiena:
Dealing with errors in interactive sequencing by hybridization.
862-870 BibTeX
- Samuel Levy, Sridhar Hannenhalli, Christopher T. Workman:
Enrichment of regulatory signals in conserved non-coding genomic sequence.
871-877 BibTeX
- Martin C. Frith, Ulla Hansen, Zhiping Weng:
Detection of cis -element clusters in higher eukaryotic DNA.
878-889 BibTeX
- Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, Luciano Milanesi:
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a `weak' context of the start codon.
890-900 BibTeX
- Eileen Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, Jonathan Arnold:
An analysis of gene-finding programs for Neurospora crassa.
901-912 BibTeX
- Artemis G. Hatzigeorgiou, Petko Fiziev, Martin Reczko:
DIANA-EST: a statistical analysis.
913-919 BibTeX
- Ernst Kretschmann, Wolfgang Fleischmann, Rolf Apweiler:
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT.
920-926 BibTeX
- Gill Bejerano, Yevgeny Seldin, Hanah Margalit, Naftali Tishby:
Markovian domain fingerprinting: statistical segmentation of protein sequences.
927-934 BibTeX
- Eva Bolten, Alexander Schliep, Sebastian Schneckener, Dietmar Schomburg, Rainer Schrader:
Clustering protein sequences-structure prediction by transitive homology.
935-941 BibTeX
- R. R. Mallios:
Predicting class II MHC/peptide multi-level binding with an iterative stepwise discriminant analysis meta-algorithm.
942-948 BibTeX
- Jerry Tsai, Neil Voss, Mark Gerstein:
Determining the minimum number of types necessary to represent the sizes of protein atoms.
949-956 BibTeX
- Piero Fariselli, Rita Casadio:
Prediction of disulfide connectivity in proteins.
957-964 BibTeX
- I. King Jordan, G. Reid Bishop, Daniel S. Gonzalez:
Sequence and structural aspects of functional diversification in class I-mannosidase evolution.
965-976 BibTeX
- Ka Yee Yeung, Chris Fraley, A. Murua, Adrian E. Raftery, Walter L. Ruzzo:
Model-based clustering and data transformations for gene expression data.
977-987 BibTeX
- Andrey Rzhetsky, Shawn M. Gomez:
Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome.
988-996 BibTeX
Volume 17,
Number 11,
November 2001
Editorial
BGRS Papers
- Victor G. Levitsky, Olga A. Podkolodnaya, Nikolay A. Kolchanov, Nikolay L. Podkolodny:
Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis.
998-1010 BibTeX
- Pavel S. Novichkov, Mikhail S. Gelfand, Andrey A. Mironov:
Gene recognition in eukaryotic DNA by comparison of genomic sequences.
1011-1018 BibTeX
- Szymon M. Kielbasa, Jan O. Korbel, Dieter Beule, Johannes Schuchhardt, Hanspeter Herzel:
Combining frequency and positional information to predict transcription factor binding sites.
1019-1026 BibTeX
- Ponraj Prabakaran, Jianghong An, M. Michael Gromiha, Samuel Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai:
Thermodynamic database for protein-nucleic acid interactions (ProNIT).
1027-1034 BibTeX
- Dmitry A. Afonnikov, Dmitry Yu. Oshchepkov, Nikolay A. Kolchanov:
Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions.
1035-1046 BibTeX
- Eugenia Migliavacca, Alexei A. Adzhubei, Manuel C. Peitsch:
MDB: a database system utilizing automatic construction of modules and STAR-derived universal language.
1047-1052 BibTeX
- Frank Schacherer, Claudia Choi, Ulrike Götze, Mathias Krull, Susanne Pistor, Edgar Wingender:
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks.
1053-1057 BibTeX
- Rosel Kretschmer-Kazemi Far, Wolfgang Nedbal, Georg Sczakiel:
Concepts to automate the theoretical design of effective antisense oligonucleotides.
1058-1061 BibTeX
Discovery Notes
Applications Notes
Original Papers
- Fugen Li, Gary D. Stormo:
Selection of optimal DNA oligos for gene expression arrays.
1067-1076 BibTeX
- Man-Suen Chan, Martin C. J. Maiden, Brian G. Spratt:
Database-driven Multi Locus Sequence Typing (MLST) of bacterial pathogens.
1077-1083 BibTeX
- P. S. Umesh Adiga, A. Bhomra, M. G. Turri, A. Nicod, S. R. Datta, Peter Jeavons, Richard Mott, Jonathan Flint:
Automatic analysis of agarose gel images.
1084-1089 BibTeX
Volume 17,
Number 12,
December 2001
Editorial
Original Papers
- Hui-Hsien Chou, Michael H. Holmes:
DNA sequence quality trimming and vector removal.
1093-1104 BibTeX
- William C. Ray, Robert S. Munson Jr., Charles J. Daniels:
Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features.
1105-1112 BibTeX
- Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau:
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.
1113-1122 BibTeX
- Baris E. Suzek, Maria D. Ermolaeva, Mark Schreiber, Steven Salzberg:
A probabilistic method for identifying start codons in bacterial genomes.
1123-1130 BibTeX
- Leping Li, Clarice R. Weinberg, Thomas A. Darden, Lee G. Pedersen:
Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method.
1131-1142 BibTeX
- Katsuhisa Horimoto, Hiroyuki Toh:
Statistical estimation of cluster boundaries in gene expression profile data.
1143-1151 BibTeX
- Stefania Bortoluzzi, F. d'Alessi, Chiara Romualdi, Gian Antonio Danieli:
Differential expression of genes coding for ribosomal proteins in different human tissues.
1152-1157 BibTeX
- Caleb Webber, Geoffrey J. Barton:
Estimation of P-values for global alignments of protein sequences.
1158-1167 BibTeX
- Georg Fuellen, Johann-Wolfgang Wägele, Robert Giegerich:
Minimum conflict: a divide-and-conquer approach to phylogeny estimation.
1168-1178 BibTeX
- Michael Wildpaner, Georg Schneider, Alexander Schleiffer, Frank Eisenhaber:
Taxonomy workbench.
1179-1182 BibTeX
- Andreas Wagner:
How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps.
1183-1197 BibTeX
- Frank Kose, Wolfram Weckwerth, Thomas Linke, Oliver Fiehn:
Visualizing plant metabolomic correlation networks using clique-metabolite matrices.
1198-1208 BibTeX
- Mark Hoebeke, Hélène Chiapello, Philippe Noirot, Philippe Bessières:
SPiD: a subtilis protein interaction database.
1209-1212 BibTeX
- Michael V. Boland, Robert F. Murphy:
A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells.
1213-1223 BibTeX
Discovery Notes
- Hiromi Nishida:
Evolution of amino acid biosynthesis and enzymes with broad substrate specificity.
1224-1225 BibTeX
Applications Notes
- Nicolas Le Novère:
MELTING, computing the melting temperature of nucleic acid duplex.
1226-1227 BibTeX
- Michael Baudis, Michael L. Cleary:
Progenetix.net: an online repository for molecular cytogenetic aberration data.
1228-1229 BibTeX
- Keith A. Jolley, E. J. Feil, Man-Suen Chan, Martin C. J. Maiden:
Sequence type analysis and recombinational tests (START).
1230-1231 BibTeX
- Theresa Zhang, Michael Q. Zhang:
Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes.
1232-1233 BibTeX
- Thomas Junier, Marco Pagni, Philipp Bucher:
mmsearch: a motif arrangement language and search program.
1234-1235 BibTeX
- Harpreet Singh, G. P. S. Raghava:
ProPred: prediction of HLA-DR binding sites.
1236-1237 BibTeX
- Roberto C. Togawa, John F. Antoniw, Jonathan G. L. Mullins:
TMCompare: transmembrane region sequence and structure.
1238-1239 BibTeX
- Leszek Rychlewski:
ToolShop: prerelease inspections for protein structure prediction servers.
1240-1241 BibTeX
- Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost:
EVA: continuous automatic evaluation of protein structure prediction servers.
1242-1243 BibTeX
- Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, Masatoshi Nei:
MEGA2: molecular evolutionary genetics analysis software.
1244-1245 BibTeX
- Hidetoshi Shimodaira, Masami Hasegawa:
CONSEL: for assessing the confidence of phylogenetic tree selection.
1246-1247 BibTeX
Copyright © Sat May 16 23:51:27 2009
by Michael Ley (ley@uni-trier.de)
