Research Topics
| P BaldiSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Complex-valued autoencodersPierre Baldi
Department of Computer Science, UCI, Irvine, CA 92697 3435, USA
Neural Netw 33:136-47. 2012....- MotifMap: integrative genome-wide maps of regulatory motif sites for model speciesKenneth Daily
Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA
BMC Bioinformatics 12:495. 2011..Genome-wide catalogs of regulatory elements for all model species simply do not yet exist... - SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERsArlo Randall
School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA
BMC Struct Biol 8:52. 2008..The purpose of this work was to develop a structure-based model selection method based on predicted structural features that could be applied successfully to any set of models... - Improved residue contact prediction using support vector machines and a large feature setJianlin Cheng
School of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816 2362, USA
BMC Bioinformatics 8:113. 2007..It is useful for ab initio structure prediction and understanding protein folding. In spite of steady progress over the past decade, contact prediction remains still largely unsolved... - Data structures and compression algorithms for high-throughput sequencing technologiesKenny Daily
Department of Computer Science, University of California Irvine, Irvine, CA 92697 USA
BMC Bioinformatics 11:514. 2010..As experiments scale up, HTS technologies create new bioinformatics challenges for the storage and sharing of HTS data... 
On the convergence of a clustering algorithm for protein-coding regions in microbial genomesP Baldi
Department of Information and Computer Science, University of California, Irvine, CA 92697 3425, USA
Bioinformatics 16:367-71. 2000..We also provide a partial justification for the uniqueness of the partition based on identifiability. Other possible variations and improvements are briefly discussed...
Speeding up chemical database searches using a proximity filter based on the logical exclusive orPierre Baldi
Department of Computer Science, Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, California 92697 3435, USA
J Chem Inf Model 48:1367-78. 2008..For a Tanimoto threshold of 0.5 (respectively 0.9), this approach requires searching less than 50% (respectively 10%) of the database, leading to typical search speedups of 2 to 3 times over the previous state-of-the-art...- Statistical detection of chromosomal homology using shared-gene density aloneS E Hampson
School of Information and Computer Science, University of California, Irvine, Irvine, CA 92697, USA
Bioinformatics 21:1339-48. 2005..AVAILABILITY: CloseUp and supplementary information are available at http://www.igb.uci.edu/servers/cgss.html CONTACT: ... - Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrievalPierre Baldi
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, Irvine, CA 92697 3435, USA
J Chem Inf Model 47:2098-109. 2007..g., Tanimoto) between molecules can be computed exactly from their compressed representations, leading to significant improvements in retrival performance, as shown on six benchmark data sets of druglike molecules... - On the relationship between deterministic and probabilistic directed Graphical models: from Bayesian networks to recursive neural networksPierre Baldi
School of Information and Computer Sciences, University of California, Irvine, CA 92697 3425, USA
Neural Netw 18:1080-6. 2005..Implications for the design of mixed architectures and the corresponding inference algorithms are briefly discussed... - Chemoinformatics, drug design, and systems biologyPierre Baldi
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, 92697-3425, USA
Genome Inform 16:281-5. 2005 - An intersection inequality sharper than the tanimoto triangle inequality for efficiently searching large databasesPierre Baldi
School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA 92697 3435, USA
J Chem Inf Model 49:1866-70. 2009..We show how the intersection inequality can be generalized immediately to these integer representations and used to search large databases of binary fingerprint vectors efficiently... - Of bits and wows: A Bayesian theory of surprise with applications to attentionPierre Baldi
Department of Computer Science, UCI, Irvine, CA 92697 3435, USA
Neural Netw 23:649-66. 2010..6 for simpler intensity contrast-based predictor, and 0.5 for chance). The resulting theory of surprise is applicable across different spatio-temporal scales, modalities, and levels of abstraction... - Assessing the accuracy of prediction algorithms for classification: an overviewP Baldi
Department of Information and Computer Science, University of California, Irvine, CA 92697, USA
Bioinformatics 16:412-24. 2000..While the principles are general, we illustrate the applicability on specific problems such as protein secondary structure and signal peptide prediction... - BLASTing small molecules--statistics and extreme statistics of chemical similarity scoresPierre Baldi
Department of Computer Science, University of California, Irvine, CA 92697 3435, USA
Bioinformatics 24:i357-65. 2008..In order to develop a BLAST-like tool for small molecules, one must first understand the statistical behavior of molecular similarity scores... - Matching protein beta-sheet partners by feedforward and recurrent neural networksP Baldi
Department of Information and Computer Science, University of California, Irvine 92697 3425, USA
Proc Int Conf Intell Syst Mol Biol 8:25-36. 2000..Prediction on both coupled and non-coupled residues currently approaches 84% accuracy, better than any previously reported method... - A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changesP Baldi
Department of Information and Computer Science, University of California at Irvine, Irvine, CA 92697 3425, USA
Bioinformatics 17:509-19. 2001..Simulations show that these point estimates, combined with a t -test, provide a systematic inference approach that compares favorably with simple t -test or fold methods, and partly compensate for the lack of replication... - Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengthsP Baldi
Department of Information and Computer Science, College of Medicine, University of California, Irvine, CA 92697 3425, USA
Bioinformatics 16:865-89. 2000..Tandem repeats are likely to result from a variety of different mechanisms, a fraction of which is likely to depend on profiles characterized by extreme structural features... - ChemDB: a public database of small molecules and related chemoinformatics resourcesJonathan Chen
Institute for Genomics and Bioinformatics, University of California, Irvine, USA
Bioinformatics 21:4133-9. 2005..2 million counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities. AVAILABILITY: Database and datasets are available on http://cdb.ics.uci.edu... - A machine learning information retrieval approach to protein fold recognitionJianlin Cheng
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, CA, USA
Bioinformatics 22:1456-63. 2006..Using predictions of the top-ranked template, the sensitivity is approximately 85, 56, and 27% at the family, superfamily and fold levels respectively. Using the 5 top-ranked templates, the sensitivity increases to 90, 70, and 48%... - Flexibility of the genetic code with respect to DNA structureP F Baisnée
Department of Information and Computer Science, University of California, Irvine, CA 92697 3425, USA
Bioinformatics 17:237-48. 2001..This result is consistent with the view that DNA structure is not likely to have played a significant role in the origin and evolution of the genetic code... - ICBS: a database of interactions between protein chains mediated by beta-sheet formationYimeng Dou
School of Information and Computer Science, University of California, Irvine, CA 92697, USA
Bioinformatics 20:2767-77. 2004..AVAILABILITY: The database is available at: http://www.igb.uci.edu/servers/icbs/.. - Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithmsJianlin Cheng
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, CA 92697, USA
Bioinformatics 21:i75-84. 2005..The approach is evaluated using cross-validation methods on a large non-homologous dataset and yields significant improvements over previous methods. AVAILABILITY: http://www.igb.uci.edu/servers/psss.html... - Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal cornersG Pollastri
Institute for Genomics and Bioinformatics, Department of Information and Computer Science, University of California, Irvine, Irvine, CA 92697 3425, USA
Bioinformatics 18:S62-70. 2002..While several extensions and improvements are in progress, the current version can accurately predict 60.5% of contacts at a distance cutoff of 8 A and 45% of distant contacts at 10 A, for proteins of length up to 300... - Hashing algorithms and data structures for rapid searches of fingerprint vectorsRamzi Nasr
School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697 3435, USA
J Chem Inf Model 50:1358-68. 2010..All theoretical results and predictions are corroborated by large-scale simulations using molecules from the ChemDB. Several possible algorithmic extensions are discussed... - Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activityS Joshua Swamidass
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, CA, USA
Bioinformatics 21:i359-68. 2005..The results derived using cross-validation methods are state-of-the-art. Tradeoffs between various kernels are briefly discussed. AVAILABILITY: Datasets available from http://www.igb.uci.edu/servers/servers.html.. - Graph kernels for chemical informaticsLiva Ralaivola
School of Information and Computer Sciences, University of California, Irvine, CA 92697 3425, USA
Neural Netw 18:1093-110. 2005..Properties and tradeoffs of these kernels, as well as other proposed kernels that leverage 1D or 3D representations of molecules, are briefly discussed... - COBEpro: a novel system for predicting continuous B-cell epitopesMichael J Sweredoski
Department of Computer Science, University of California, Irvine, 92697 3435, USA
Protein Eng Des Sel 22:113-20. 2009..829 on the fragment epitopic propensity scoring task and an AUC up to 0.628 on the residue epitopic propensity scoring task. COBEpro is incorporated into the SCRATCH prediction suite at http://scratch.proteomics.ics.uci.edu... - Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stabilityDORA L GUZMAN
Department of Chemistry, University of California, Irvine, CA 92697 2025, USA
Proc Natl Acad Sci U S A 107:1989-94. 2010..Our study reveals that shielding water accessibility to the load-bearing strands is a critical molecular determinant for enhancing the mechanical stability of proteins... - ChemDB update--full-text search and virtual chemical spaceJonathan H Chen
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, USA
Bioinformatics 23:2348-51. 2007..AVAILABILITY: ChemDB and Supplementary Materials are available at http://cdb.ics.uci.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online... - An enhanced MITOMAP with a global mtDNA mutational phylogenyEduardo Ruiz Pesini
Center for Molecular and Mitochondrial Medicine and Genetics MAMMAG and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of California, Irvine, CA 92697 3900, USA
Nucleic Acids Res 35:D823-8. 2007..These additions position MITOMAP for the implementation of our automated mtDNA sequence analysis system, Mitomaster... - MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequencesMarty C Brandon
Department of Information and Computer Science, University of California, Irvine, Irvine, California 92697 3940, USA
Hum Mutat 30:1-6. 2009..This system should be beneficial for mtDNA analyses of biomedical physicians and investigators, population biologists and forensic scientists. MITOMASTER can be accessed at http://mammag.web.uci.edu/twiki/bin/view/Mitomaster... - From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensisSuman Sundaresh
School of Information and Computer Sciences, University of California, Irvine, CA, USA
Bioinformatics 23:i508-18. 2007..The findings from this study have direct relevance to rapid, broad-based diagnostic and vaccine development... - Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcAKirsty A Salmon
Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095 1489, USA
J Biol Chem 280:15084-96. 2005..The strict statistical analyses that we have performed on our data allow us to predict that 1139 genes in the E. coli genome are regulated either directly or indirectly by the ArcA protein with a 99% confidence level... - SCRATCH: a protein structure and structural feature prediction serverJ Cheng
Institute for Genomics and Bioinformatics, University of California Irvine, CA, USA
Nucleic Acids Res 33:W72-6. 2005..The user simply provides an amino acid sequence and selects the desired predictions, then submits to the server. Results are emailed to the user. The server is available at http://www.igb.uci.edu/servers/psss.html... - Improved prediction of the number of residue contacts in proteins by recurrent neural networksG Pollastri
Department of Information and Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697-3425, USA
Bioinformatics 17:S234-42. 2001..Combination of different radius predictors further improves the performance. SERVER: http://promoter.ics.uci.edu/BRNN-PRED/... - Mathematical correction for fingerprint similarity measures to improve chemical retrievalS Joshua Swamidass
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697 3435, USA
J Chem Inf Model 47:952-64. 2007..Experiments on various data sets and fingerprint sizes demonstrate how, with a negligible computational overhead, the correction noticeably improves the sensitivity and specificity of chemical retrieval... - Why are complementary DNA strands symmetric?Pierre François Baisnée
Department of Information and Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine 92697 3425, USA
Bioinformatics 18:1021-33. 2002.... - SOLpro: accurate sequence-based prediction of protein solubilityChristophe N Magnan
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA
Bioinformatics 25:2200-7. 2009.... - A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferiAlan G Barbour
Pacific Southwest Center for Research on Emerging Infections, University of California Irvine, 3012 Hewitt, Irvine, CA 92697 4028, USA
Infect Immun 76:3374-89. 2008..These results indicate that the majority of deduced proteins of B. burgdorferi do not elicit antibody responses during infection and that the limited sets of immunogens are similar for two different host species... - Influence relevance voting: an accurate and interpretable virtual high throughput screening methodS Joshua Swamidass
School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697 3435, USA
J Chem Inf Model 49:756-66. 2009..Combined with its performance, these qualities make the IRV particularly well suited for vHTS... - How noisy and replicable are DNA microarry data?Suman Sundaresh
Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
Int J Bioinform Res Appl 1:31-50. 2005..Replicability is assessed quantitatively using correlation analysis as a global measure and differential expression analysis and ANOVA at the level of individual genes... - Learning to play Go using recursive neural networksLin Wu
School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA 92697, USA
Neural Netw 21:1392-400. 2008..A system trained using only 9 x 9 amateur game data performs surprisingly well on a test set derived from 19 x 19 professional game data. Possible directions for further improvements are briefly discussed... - Differential analysis of DNA microarray gene expression dataG Wesley Hatfield
Department of Microbiology, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
Mol Microbiol 47:871-7. 2003..This method provides a probability of differential expression for each gene based on experiment-wide false-positive and -negative levels driven by experimental error and biological variance... - MotifMap: a human genome-wide map of candidate regulatory motif sitesXiaohui Xie
Department of Computer Sciences, University of California, Irvine, CA 92697, USA
Bioinformatics 25:167-74. 2009..The initial map provides a systematic view of gene regulation in the genome, which will be refined as additional motifs become available... - Structural proteomics of the poxvirus familyArlo Z Randall
Department of Information and Computer Science, University of California, Irvine, CA 92697 3425, USA
Artif Intell Med 31:105-15. 2004..Inclusion of additional poxvirus genomes in the PPDB is in progress. The PPDB has an upward scalable informatics infrastructure that can readily be applied to viral, bacterial, as well as eukaryotic genomes... - The fixed-size Luria-Delbruck model with a nonzero death rateNatalia L Komarova
Department of Mathematics, University of California, Irvine, CA 92697, United States
Math Biosci 210:253-90. 2007..Finally, we investigate the applicability of the traditional, 'fixed-time' approach and find that it approximates the 'fixed-size' problem whenever stochastic effects are negligible... - A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigensPhilip L Felgner
Department of Medicine, Division of Infectious Diseases, University of California, Irvine, CA 92697, USA
Proc Natl Acad Sci U S A 106:13499-504. 2009.... - Global landscape of recent inferred Darwinian selection for Homo sapiensEric T Wang
Department of Biological Chemistry, College of Medicine, Donald Bren School of Information and Computer Sciences, and Institute of Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
Proc Natl Acad Sci U S A 103:135-40. 2006..Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host-pathogen interactions, reproduction, DNA metabolism/cell cycle, protein metabolism, and neuronal function... - Functional census of mutation sequence spaces: the example of p53 cancer rescue mutantsSamuel A Danziger
University of California, Irvine, CA 92697 3435, USA
IEEE/ACM Trans Comput Biol Bioinform 3:114-25. 2006..92 afterward. Useful mutants were chosen early (overall r = 0.80). Code and data are freely available (http://www.igb.uci.edu/research/research.html, corresponding authors: R.H.L. for computation and R.K.B. for biology)... - MITOMAP: a human mitochondrial genome database--2004 updateMarty C Brandon
Department of Information and Computer Science, University of California, Irvine, CA 92697, USA
Nucleic Acids Res 33:D611-3. 2005..System administrative changes have been made to improve security and efficiency, and to make MITOMAP compatible with a new automatic mtDNA sequence analyzer known as Mitomaster... - Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarraysDouglas M Molina
ImmPORT Therapeutics, 1 Technology Drive, Suite E309, Irvine, CA 92618, USA
Vaccine 28:3014-24. 2010..In conclusion, using a high throughput protein microarray we have identified a set of novel proteins that can be tested for their ability to protect against a chlamydial infection... - Ty3 capsid mutations reveal early and late functions of the amino-terminal domainLiza S Z Larsen
Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, USA
J Virol 81:6957-72. 2007..Particle formation was generally resistant to localized substitutions, possibly indicating that multiple domains are involved... - Distribution patterns of over-represented k-mers in non-coding yeast DNASteven Hampson
Department of Information and Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697 3425, USA
Bioinformatics 18:513-28. 2002.... - The TY3 Gag3 spacer controls intracellular condensation and uncoatingKristina Clemens
Department of Biological Chemistry, University of California, Irvine, Irvine CA 92697, USA
J Virol 85:3055-66. 2011..These interactions promote CA domain multimerization. In the third phase, a negatively charged SP domain destabilizes the remaining CA-SP shell for cDNA release... - Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12A D Long
Department of Ecology, School of Biological Sciences, University of California, Irvine, California 92697, USA
J Biol Chem 276:19937-44. 2001..All the described tests are implemented in a simple-to-use web interface called Cyber-T that is located on the University of California at Irvine genomics web site... - Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profilesGianluca Pollastri
Department of Information and Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697-3425, USA
Proteins 47:228-35. 2002..SSpro and SSpro8 are implemented as web servers, available together with other structural feature predictors at: http://promoter.ics.uci.edu/BRNN-PRED/... - Data structures and compression algorithms for genomic sequence dataMarty C Brandon
Department of Computer Science, UCI, Irvine, CA 92697, USA
Bioinformatics 25:1731-8. 2009..Here, we develop data structures and algorithms for the efficient storage of genomic and other sequence data that may also facilitate querying and protecting the data... - Prediction of coordination number and relative solvent accessibility in proteinsGianluca Pollastri
Department of Information and Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697-3425, USA
Proteins 47:142-53. 2002..The prediction programs are implemented in the form of two web servers, CONpro and ACCpro, available at http://promoter.ics.uci.edu/BRNN-PRED/... - Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigensLi Liang
Division of Infectious Diseases, Department of Medicine, University of California Irvine, Irvine, California, USA
PLoS Negl Trop Dis 4:e673. 2010..These data demonstrate that an experimentally infected natural reservoir host produces a fundamentally different immune response than a naturally infected accidental human host... - Discovery of power-laws in chemical spaceRyan W Benz
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697 3435, USA
J Chem Inf Model 48:1138-51. 2008..More importantly, we also show how the power-laws can be leveraged to efficiently compress chemical fingerprints in a lossless manner, useful for the improved storage and retrieval of molecules in large chemical databases... - LineUp: statistical detection of chromosomal homology with application to plant comparative genomicsSteve Hampson
Institute for Genomics and Bioinformatics, Department of Information and Computer Science and Department of Ecology and Evolutionary Biology, and Department of Biological Chemistry, University of California at Irvine, Irvine, California 92697, USA
Genome Res 13:999-1010. 2003..The variation among maps has important implications for evolutionary inference from genetic map data... - Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniquesSuman Sundaresh
School of Information and Computer Sciences, University of California, Irvine, CA, USA
Bioinformatics 22:1760-6. 2006..AVAILABILITY: All software programs (in R) used for the analysis described in this paper are freely available for academic purposes at www.igb.uci.edu/servers/servers.html... - Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matchingJianlin Cheng
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine 92697, USA
Proteins 62:617-29. 2006..The disulphide bridge prediction server (DIpro), software, and datasets are available through www.igb.uci.edu/servers/psss.html... - TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteinsArlo Randall
School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA
Bioinformatics 24:513-20. 2008..Yet, because TMB structures conform to specific construction rules that restrict the conformational space drastically, it should be possible for methods that do not depend on target-template homology to be applied successfully... - Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear timeS Joshua Swamidass
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, Irvine, CA 92697 3435, USA
J Chem Inf Model 47:302-17. 2007..6) for the top K hits in current large databases. This pruning approach yields subsecond search times across the 5 million compounds in the ChemDB database, without any loss of accuracy... - Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosisTing Wan Lin
Department of Molecular Biology and Biochemistry, University of California, Irvine, 92697, USA
Proc Natl Acad Sci U S A 103:3072-7. 2006.... - Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory proteinShe pin Hung
Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
J Biol Chem 277:40309-23. 2002..This allows the experimenter to compute posterior probabilities of differential expression for each individual differential gene expression measurement... - Prediction of protein stability changes for single-site mutations using support vector machinesJianlin Cheng
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, California 92697-3425, USA
Proteins 62:1125-32. 2006..The web server for predictions of protein stability changes upon mutations (MUpro), software, and datasets are available at http://www.igb.uci.edu/servers/servers.html... - Retroviruses and yeast retrotransposons use overlapping sets of host genesBecky Irwin
Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
Genome Res 15:641-54. 2005..Host factors, such as these, shared by distantly related Ty retroelements and retroviruses are novel candidates for antiviral targets... - PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposureMichael J Sweredoski
Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 3435, USA
Bioinformatics 24:1459-60. 2008..Up to 90% of B-cell epitopes are discontinuous in nature, yet most predictors focus on linear epitopes. Even when the tertiary structure of the antigen is available, the accurate prediction of B-cell epitopes remains challenging... - When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme valuesPierre Baldi
School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697 3435, USA
J Chem Inf Model 50:1205-22. 2010..Numerous and diverse experiments that have been performed, in part with large sets of molecules from the ChemDB, show remarkable agreement between theory and empirical results... - One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological propertiesChloé Agathe Azencott
School of Information and Computer Sciences, University of California Irvine, Irvine, California 92697 3435, USA
J Chem Inf Model 47:965-74. 2007..Kernel predictors for aqueous solubility (kSOL), LogP (kLOGP), and melting point (kMELT) are available over the Web through: http://cdb.ics.uci.edu... - Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labelingMichael J Sweredoski
Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, USA
Bioinformatics 23:2829-35. 2007..The labeling schedules, which are derived by the optimization of a cost function, are tailored to a specific protein and NMR experiment... - Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discoveryD Huw Davies
Center for Virus Research, University of California, Irvine, CA 92697, USA
Proc Natl Acad Sci U S A 102:547-52. 2005..These results verify this platform as a rapid way to comprehensively scan humoral immunity from vaccinated or infected humans and animals... - The absence of favorable aromatic interactions between beta-sheet peptidesDe Michael Chung
Department of Chemistry, and the Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697-2025, USA
J Am Chem Soc 127:9998-9. 2005.... - No electron left behind: a rule-based expert system to predict chemical reactions and reaction mechanismsJonathan H Chen
Institute for Genomics and Bioinformatics and Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697 3435, USA
J Chem Inf Model 49:2034-43. 2009..Select applications are available via http://cdb.ics.uci.edu... - Modular DAG-RNN architectures for assembling coarse protein structuresGianluca Pollastri
School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland
J Comput Biol 13:631-50. 2006..The fully integrated rod-shaped protein builder (predictor of contact maps + reconstruction algorithm) can be accessed at http://distill.ucd.ie/... - Assessment of predictions submitted for the CASP7 domain prediction categoryMichael Tress
Structural and Biological Computation Programme, Spanish National Cancer Research Centre, Madrid, Spain
Proteins 69:137-51. 2007..Two thirds of the targets submitted were single domains and hence regarded as easy to predict. Even those targets defined as having multiple domains always had at least one domain with a similar template structure... - Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNRKirsty Salmon
Department of Microbiology, Immunology, and Molecular Genetics and The Molecular Biology Institute, UCLA, Los Angeles, Cal ifornia, 90095 1489, USA
J Biol Chem 278:29837-55. 2003..In particular, we describe an approach for identifying gene expression patterns (clusters) obtained from multiple perturbation experiments based on a subset of genes that exhibit high probability for differential expression values... - Immunodominant Francisella tularensis antigens identified using proteome microarrayJim E Eyles
Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
Proteomics 7:2172-83. 2007..These data give insight into the protective immune response and have potentially important implications for the rational design of non-living vaccines for tularemia and other intracellular pathogens...