default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBMC Bioinformatics, Volume 5
Volume 5, 2004
- Andrew Butterfield, Vivek Vedagiri, Edward Lang, Cath Lawrence, Matthew J. Wakefield
, Alexander Isaev, Gavin A. Huttley:
PyEvolve: a toolkit for statistical modelling of molecular evolution. 1 - Vadim Alexandrov, Mark Gerstein:
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. 2 - Bin Li, Warren J. Gallin:
VKCDB: Voltage-gated potassium channel database. 3 - France Denoeud, Gilles Vergnaud:
Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource. 4 - Tomokazu Konishi:
Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. 5 - Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen:
Benchmarking tools for the alignment of functional noncoding DNA. 6 - Benjamin Schuster-Böckler, Jörg Schultz, Sven Rahmann:
HMM Logos for visualization of protein families. 7 - Estienne C. Swart, Winston A. Hide, Cathal Seoighe:
FRAGS: estimation of coding sequence substitution rates from fragmentary data. 8 - Romesh Stanislaus, Liu Hong Jiang, Martha Swartz, John M. Arthur, Jonas S. Almeida:
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. 9 - Radu Dobrin, Qasim K. Beg, Albert-László Barabási, Zoltán N. Oltvai:
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. 10 - Erich J. Baker, Leslie Galloway, Barbara Jackson, Denise Schmoyer, Jay Snoddy:
MuTrack: a genome analysis system for large-scale mutagenesis in the mouse. 11 - Andreas Petri, Jan Fleckner, Mads Wichmann Matthiessen:
Array-A-Lizer: A serial DNA microarray quality analyzer. 12 - Bryan Chi, Ronald J. deLeeuw, Bradley P. Coe, Calum MacAulay, Wan L. Lam:
SeeGH - A software tool for visualization of whole genome array comparative genomic hybridization data. 13 - Afshin Nadershahi, Scott C. Fahrenkrug, Lynda B. M. Ellis:
Comparison of computational methods for identifying translation initiation sites in EST data. 14 - Sara Light, Per Kraulis:
Network analysis of metabolic enzyme evolution in Escherichia coli. 15 - Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy:
GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. 16 - Zhenjun Hu, Joseph C. Mellor, Jie Wu, Charles DeLisi:
VisANT: an online visualization and analysis tool for biological interaction data. 17 - Dominic J. Allocco, Isaac S. Kohane, Atul J. Butte:
Quantifying the relationship between co-expression, co-regulation and gene function. 18 - Jules J. Berman, Milton W. Datta, André Alexander Kajdacsy-Balla, Jonathan Melamed, Jan Orenstein, Kevin Dobbin, Ashok Patel, Rajiv Dhir, Michael J. Becich:
The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. 19 - Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq, Stéphane Vialette:
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states. 20 - Kamesh Munagala, Robert Tibshirani, Patrick O. Brown:
Cancer characterization and feature set extraction by discriminative margin clustering. 21 - Rainer Merkl:
SIGI: score-based identification of genomic islands. 22 - Shaun Mahony, James O. McInerney, Terry J. Smith, Aaron Golden:
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. 23 - David Adalsteinsson, David R. McMillen, Timothy C. Elston:
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. 24 - Remko de Knikker, Youjun Guo, Jin-Long Li, Albert K. H. Kwan, Kevin Y. Yip, David W. Cheung, Kei-Hoi Cheung:
A web services choreography scenario for interoperating bioinformatics applications. 25 - Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.:
Computational protein biomarker prediction: a case study for prostate cancer. 26 - Henry R. Bigelow, Adam S. Wenick, Allan Wong, Oliver Hobert:
CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting. 27 - Shashi B. Pandit, Rana Bhadra, V. S. Gowri, S. Balaji, B. Anand, Narayanaswamy Srinivasan:
SUPFAM: A database of sequence superfamilies of protein domains. 28 - Pantelis G. Bagos, Theodore Liakopoulos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas:
A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. 29 - Jan C. Biro, Josephine M. K. Biro:
Frequent occurrence of recognition Site-like sequences in the restriction endonucleases. 30 - Feng Gao, Barrett C. Foat, Harmen J. Bussemaker:
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. 31 - Petri Törönen:
Selection of informative clusters from hierarchical cluster tree with gene classes. 32 - Alberto Riva, Isaac S. Kohane:
A SNP-centric database for the investigation of the human genome. 33 - Rainer Breitling, Anna Amtmann, Pawel Herzyk:
Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. 34 - Anirban Bhaduri, Ganesan Pugalenthi, Ramanathan Sowdhamini:
PASS2: an automated database of protein alignments organised as structural superfamilies. 35 - Ching Yu Austin Huang, Joel F. Studebaker, Anton Yuryev, Jianping Huang, Kathryn E. Scott, Jennifer Kuebler, Shobha Varde, Steven Alfisi, Craig A. Gelfand, Mark Pohl, Michael T. Boyce-Jacino:
Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks. 36 - Artem Cherkasov, Steven J. M. Jones:
Structural characterization of genomes by large scale sequence-structure threading. 37 - Lan V. Zhang, Sharyl L. Wong, Oliver D. King, Frederick P. Roth:
Predicting co-complexed protein pairs using genomic and proteomic data integration. 38 - Alexander V. Diemand, Holger Scheib:
MolTalk - a programming library for protein structures and structure analysis. 39 - Sohrab P. Shah, David Y. M. He, Jessica N. Sawkins, Jeffrey C. Druce, Gerald T. Quon, Drew Lett, Grace X. Y. Zheng, Tao Xu, B. F. Francis Ouellette:
Pegasys: software for executing and integrating analyses of biological sequences. 40 - Marc N. Offman, Ramil N. Nurtdinov, Mikhail S. Gelfand, Dmitrij Frishman:
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. 41 - Leah Barrera, Chris Benner, Yong-Chuan Tao, Elizabeth A. Winzeler, Yingyao Zhou:
Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays. 42 - J. Daniel Navarro, Naveen Talreja, Suraj Peri, B. M. Vrushabendra, B. P. Rashmi, N. Padma, Vineeth Surendranath, Chandra Kiran Jonnalagadda, P. S. Kousthub, Nandan Deshpande, K. Shanker, Akhilesh Pandey:
BioBuilder as a database development and functional annotation platform for proteins. 43 - Olga V. Matveeva, Brian T. Foley, Vladimir A. Nemtsov, Raymond F. Gesteland, Senya Matsufuji, John F. Atkins, Aleksey Y. Ogurtsov, Svetlana A. Shabalina:
Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. 44 - Timothy J. Harlow, J. Peter Gogarten, Mark A. Ragan:
A hybrid clustering approach to recognition of protein families in 114 microbial genomes. 45 - Guohui Zhou, Xinyu Wen, Hang Liu, Michael J. Schlicht, Martin J. Hessner, Peter J. Tonellato, Milton W. Datta:
B.E.A.R. GeneInfo: A tool for identifying gene-related biomedical publications through user modifiable queries. 46 - Jörg Rahnenführer, Daniel Bozinov:
Hybrid clustering for microarray image analysis combining intensity and shape features. 47 - Timothy Hughes, Young Hyun, David A. Liberles:
Visualising very large phylogenetic trees in three dimensional hyperbolic space. 48 - Christopher S. Coffey, Patricia R. Hebert, Marylyn D. Ritchie, Harlan M. Krumholz, J. Michael Gaziano, Paul M. Ridker, Nancy J. Brown, Douglas E. Vaughan, Jason H. Moore:
An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene Interactions on risk of myocardial infarction: The importance of model validation. 49 - Allegra Via, Manuela Helmer-Citterich:
A structural study for the optimisation of functional motifs encoded in protein sequences. 50 - Shandar Ahmad, M. Michael Gromiha, Hamed Fawareh, Akinori Sarai:
ASAView: Database and tool for solvent accessibility representation in proteins. 51 - Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck, Donald Seto:
GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes. 52 - Igor Dozmorov, Nicholas Knowlton, Yuhong Tang, Michael Centola:
Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays. 53 - Jeffrey P. Townsend:
Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. 54 - Vincent Nègre, Christoph Grunau:
eL-DASionator: an LDAS upload file generator. 55 - Lachlan James M. Coin, Alex Bateman, Richard Durbin:
Enhanced protein domain discovery using taxonomy. 56 - Davide Corà, Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo, Michele Caselle:
Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs. 57 - Laurent Fourrier, Cristina Benros, Alexandre G. de Brevern:
Use of a structural alphabet for analysis of short loops connecting repetitive structures. 58 - Ian Korf:
Gene finding in novel genomes. 59 - Kellie J. Archer, Catherine I. Dumur, Viswanathan Ramakrishnan:
Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals. 60 - Artem Cherkasov, Steven J. M. Jones:
An approach to large scale identification of non-obvious structural similarities between proteins. 61 - Gavin C. Conant, Andreas Wagner:
A fast algorithm for determining the best combination of local alignments to a query sequence. 62 - Tristan Mary-Huard, Jean-Jacques Daudin, Stéphane Robin, Frédérique Bitton, Eric Cabannes, Pierre Hilson:
Spotting effect in microarray experiments. 63 - Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé, Yves Van de Peer:
Feature selection for splice site prediction: A new method using EDA-based feature ranking. 64 - Gordana Pavlovic-Lazetic, Nenad S. Mitic, Milos V. Beljanski:
Bioinformatics analysis of SARS coronavirus genome polymorphism. 65 - Qinghua Cui, Tianzi Jiang, Bing Liu, Songde Ma:
Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms. 66 - Meena K. Sakharkar, Pandjassarame Kangueane:
Genome SEGE: A database for 'intronless' genes in eukaryotic genomes. 67 - Andrea Bisognin, Stefania Bortoluzzi, Gian Antonio Danieli:
Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma. 68 - Thomas Lütteke, Claus-Wilhelm von der Lieth:
pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files. 69 - Yingchun Liu, Markus Ringnér:
Multiclass discovery in array data. 70 - Robin D. Dowell, Sean R. Eddy:
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. 71 - Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom:
Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology. 72 - Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen:
Correction: Benchmarking tools for the alignment of functional noncodingDNA. 73 - Junbai Wang, Leonardo A. Meza-Zepeda, Stine H. Kresse, Ola Myklebost:
M-CGH: Analysing microarray-based CGH experiments. 74 - Drew Lett, Michael Hsing, Frederic Pio:
Interaction profile-based protein classification of death domain. 75 - Michelle L. Green, Peter D. Karp:
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. 76 - Helene H. Thygesen, Aeilko H. Zwinderman:
Comparing transformation methods for DNA microarray data. 77 - Kai Huang, Robert F. Murphy:
Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. 78 - Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J. Gibson:
Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins. 79 - Barry Zeeberg, Joseph Riss, David W. Kane, Kimberly J. Bussey, Edward Uchio, W. Marston Linehan, J. Carl Barrett, John N. Weinstein:
Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. 80 - Hongying Jiang, Youping Deng, Huann-Sheng Chen, Lin Tao, Qiuying Sha, Jun Chen, Chung-Jui Tsai, Shuanglin Zhang:
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. 81 - Tomokazu Konishi:
Correction: Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. 82 - Lisa C. Romero, Thanh Vinh Nguyen, Benoit Deville, Oluwasanmi Ogunjumo, Anthony A. James:
The MB2 gene family of Plasmodium species has a unique combination of S1 and GTP-binding domains. 83 - Eric H. Baehrecke, Niem Dang, Ketan Babaria, Ben Shneiderman:
Visualization and analysis of microarray and gene ontology data with treemaps. 84 - Hao Zhu, Peter Y. H. Pang, Yan Sun, Pawan Dhar:
Asynchronous adaptive time step in quantitative cellular automata modeling. 85 - Keith A. Jolley, Man-Suen Chan, Martin C. J. Maiden:
mlstdbNet - distributed multi-locus sequence typing (MLST) databases. 86 - R. Henrik Nilsson, Balaji Rajashekar, Karl-Henrik Larsson, Björn M. Ursing:
galaxieEST: addressing EST identity through automated phylogenetic analysis. 87 - Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan, Tamar Schlick:
RAG: RNA-As-Graphs web resource. 88 - Peisen Zhang, Huitao Sheng, Ryuhei Uehara:
A double classification tree search algorithm for index SNP selection. 89 - Oleg N. Reva, Burkhard Tümmler:
Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. 90 - Luis Sánchez-Pulido, Ana María Rojas, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia:
SPOC: A widely distributed domain associated with cancer, apoptosis and transcription. 91 - Matthias Wjst:
Target SNP selection in complex disease association studies. 92 - Matthew J. Cockerill:
Delayed impact: ISI's citation tracking choices are keeping scientists in the dark. 93 - Olivier Andrieu, Anna-Sophie Fiston, Dominique Anxolabéhère, Hadi Quesneville:
Detection of transposable elements by their compositional bias. 94 - Marie-Christine Brun, Carl Herrmann, Alain Guénoche:
Clustering proteins from interaction networks for the prediction of cellular functions. 95 - Ryan Brodie, Alex J. Smith, Rachel L. Roper, Vasily Tcherepanov, Chris Upton:
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments. 96 - Dankyu Yoon, Sung-Gon Yi, Ju-Han Kim, Taesung Park:
Two-stage normalization using background intensities in cDNA microarray data. 97 - Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik:
Integrated web service for improving alignment quality based on segments comparison. 98 - Bin Yao, Sanjay N. Rakhade, Qunfang Li, Sharlin Ahmed, Raul Krauss, Sorin Draghici, Jeffrey A. Loeb:
Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells. 99 - Rainer Breitling, Anna Amtmann, Pawel Herzyk:
Graph-based iterative Group Analysis enhances microarray interpretation. 100 - Artem Cherkasov, Shannan J. Ho Sui, Robert C. Brunham, Steven J. M. Jones:
Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics. 101 - Baozhen Qiao, Ronald M. Weigel:
A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequences. 102 - Chao Lu:
Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays. 103 - Jens Reeder, Robert Giegerich:
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. 104 - Kishore J. Doshi, Jamie J. Cannone, Christian W. Cobaugh, Robin Ray Gutell:
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. 105 - Ruslan Sadreyev, Nick V. Grishin:
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. 106 - Roberto H. Higa, Roberto C. Togawa, Arnaldo J. Montagner, Juliana F. Palandrani, Igor K. S. Okimoto, Paula R. Kuser, Michel E. B. Yamagishi, Adauto L. Mancini, Goran Neshich:
STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes. 107 - Bahrad A. Sokhansanj, J. Patrick Fitch, Judy N. Quong, Andrew A. Quong:
Linear fuzzy gene network models obtained from microarray data by exhaustive search. 108 - Shane C. Dillon, Alex Bateman:
The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. 109 - James Lyons-Weiler, Satish Patel, Michael J. Becich, Tony E. Godfrey:
Tests for finding complex patterns of differential expression in cancers: towards individualized medicine. 110 - Laurent Gautier, Morten Møller, Lennart Friis-Hansen, Steen Knudsen:
Alternative mapping of probes to genes for Affymetrix chips. 111 - Jibin Sun, An-Ping Zeng:
IdentiCS - Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. 112 - Robert C. Edgar:
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. 113 - Alexandre G. de Brevern, Serge A. Hazout, Alain Malpertuy:
Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering. 114 - Zhaoyang Feng, Christopher J. Cronin, John H. Wittig Jr., Paul W. Sternberg, William R. Schafer:
An imaging system for standardized quantitative analysis of C. elegans behavior. 115