P Baldi

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Complex-valued autoencoders
    Pierre Baldi
    Department of Computer Science, UCI, Irvine, CA 92697 3435, USA
    Neural Netw 33:136-47. 2012
  2. pmc MotifMap: integrative genome-wide maps of regulatory motif sites for model species
    Kenneth Daily
    Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA
    BMC Bioinformatics 12:495. 2011
  3. pmc SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs
    Arlo Randall
    School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA
    BMC Struct Biol 8:52. 2008
  4. pmc Improved residue contact prediction using support vector machines and a large feature set
    Jianlin Cheng
    School of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816 2362, USA
    BMC Bioinformatics 8:113. 2007
  5. pmc Data structures and compression algorithms for high-throughput sequencing technologies
    Kenny Daily
    Department of Computer Science, University of California Irvine, Irvine, CA 92697 USA
    BMC Bioinformatics 11:514. 2010
  6. ncbi request reprint On the convergence of a clustering algorithm for protein-coding regions in microbial genomes
    P Baldi
    Department of Information and Computer Science, University of California, Irvine, CA 92697 3425, USA
    Bioinformatics 16:367-71. 2000
  7. doi request reprint Speeding up chemical database searches using a proximity filter based on the logical exclusive or
    Pierre 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
  8. pmc Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrieval
    Pierre 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
  9. ncbi request reprint On the relationship between deterministic and probabilistic directed Graphical models: from Bayesian networks to recursive neural networks
    Pierre Baldi
    School of Information and Computer Sciences, University of California, Irvine, CA 92697 3425, USA
    Neural Netw 18:1080-6. 2005
  10. ncbi request reprint Chemoinformatics, drug design, and systems biology
    Pierre 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

Collaborators

Detail Information

Publications81

  1. pmc Complex-valued autoencoders
    Pierre Baldi
    Department of Computer Science, UCI, Irvine, CA 92697 3435, USA
    Neural Netw 33:136-47. 2012
    ....
  2. pmc MotifMap: integrative genome-wide maps of regulatory motif sites for model species
    Kenneth 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...
  3. pmc SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs
    Arlo 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...
  4. pmc Improved residue contact prediction using support vector machines and a large feature set
    Jianlin 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...
  5. pmc Data structures and compression algorithms for high-throughput sequencing technologies
    Kenny 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...
  6. ncbi request reprint On the convergence of a clustering algorithm for protein-coding regions in microbial genomes
    P Baldi
    Department of Information and Computer Science, University of California, Irvine, CA 92697 3425, USA
    Bioinformatics 16:367-71. 2000
    ..The partition corresponds to three kinds of regions: (1) coding on the direct strand, (2) coding on the complementary strand, (3) non-coding...
  7. doi request reprint Speeding up chemical database searches using a proximity filter based on the logical exclusive or
    Pierre 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...
  8. pmc Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrieval
    Pierre 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...
  9. ncbi request reprint On the relationship between deterministic and probabilistic directed Graphical models: from Bayesian networks to recursive neural networks
    Pierre 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...
  10. ncbi request reprint Chemoinformatics, drug design, and systems biology
    Pierre 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
  11. pmc An intersection inequality sharper than the tanimoto triangle inequality for efficiently searching large databases
    Pierre 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...
  12. pmc Of bits and wows: A Bayesian theory of surprise with applications to attention
    Pierre 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...
  13. pmc BLASTing small molecules--statistics and extreme statistics of chemical similarity scores
    Pierre 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...
  14. ncbi request reprint Assessing the accuracy of prediction algorithms for classification: an overview
    P 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...
  15. ncbi request reprint Matching protein beta-sheet partners by feedforward and recurrent neural networks
    P 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...
  16. ncbi request reprint A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes
    P Baldi
    Department of Information and Computer Science, University of California at Irvine, Irvine, CA 92697 3425, USA
    Bioinformatics 17:509-19. 2001
    ..Current methods are unsatisfactory due to the lack of a systematic framework that can accommodate noise, variability, and low replication often typical of microarray data...
  17. ncbi request reprint Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths
    P Baldi
    Department of Information and Computer Science, College of Medicine, University of California, Irvine, CA 92697 3425, USA
    Bioinformatics 16:865-89. 2000
    ....
  18. ncbi request reprint ChemDB: a public database of small molecules and related chemoinformatics resources
    Jonathan Chen
    Institute for Genomics and Bioinformatics, University of California, Irvine, USA
    Bioinformatics 21:4133-9. 2005
    ..They can be used as combinatorial building blocks for chemical synthesis, as molecular probes in chemical genomics and systems biology, and for the screening and discovery of new drugs and other useful compounds...
  19. ncbi request reprint A machine learning information retrieval approach to protein fold recognition
    Jianlin Cheng
    Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, CA, USA
    Bioinformatics 22:1456-63. 2006
    ....
  20. ncbi request reprint Flexibility of the genetic code with respect to DNA structure
    P F Baisnée
    Department of Information and Computer Science, University of California, Irvine, CA 92697 3425, USA
    Bioinformatics 17:237-48. 2001
    ..the acceptable amino acid substitution patterns allow for the superimposition of DNA structural signals to protein coding sequences? Second, is the origin or evolution of the genetic code likely to have been constrained by DNA structure?..
  21. ncbi request reprint Statistical detection of chromosomal homology using shared-gene density alone
    S E Hampson
    School of Information and Computer Science, University of California, Irvine, Irvine, CA 92697, USA
    Bioinformatics 21:1339-48. 2005
    ..Existing algorithms that attempt to detect homology are based on shared-gene density and colinearity and possibly also strand information...
  22. ncbi request reprint ICBS: a database of interactions between protein chains mediated by beta-sheet formation
    Yimeng Dou
    School of Information and Computer Science, University of California, Irvine, CA 92697, USA
    Bioinformatics 20:2767-77. 2004
    ..These interactions play a central role in many biological processes and in diseases ranging from AIDS and cancer to anthrax and Alzheimer's...
  23. ncbi request reprint Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms
    Jianlin Cheng
    Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, CA 92697, USA
    Bioinformatics 21:i75-84. 2005
    ..Previous approaches for predicting beta-sheet topological features, such as beta-strand alignments, in general have not exploited the global covariation and constraints characteristic of beta-sheet architectures...
  24. ncbi request reprint Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
    G 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
    ..Because contact maps provide a translation and rotation invariant topological representation of a protein, they can be used as a fundamental intermediary step in protein structure prediction...
  25. pmc Hashing algorithms and data structures for rapid searches of fingerprint vectors
    Ramzi 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...
  26. ncbi request reprint Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity
    S Joshua Swamidass
    Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, CA, USA
    Bioinformatics 21:i359-68. 2005
    ....
  27. ncbi request reprint Graph kernels for chemical informatics
    Liva 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...
  28. pmc COBEpro: a novel system for predicting continuous B-cell epitopes
    Michael 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...
  29. pmc Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability
    DORA 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...
  30. ncbi request reprint ChemDB update--full-text search and virtual chemical space
    Jonathan 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...
  31. pmc An enhanced MITOMAP with a global mtDNA mutational phylogeny
    Eduardo 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...
  32. doi request reprint MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences
    Marty 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...
  33. ncbi request reprint From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis
    Suman 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...
  34. ncbi request reprint Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA
    Kirsty 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...
  35. pmc SCRATCH: a protein structure and structural feature prediction server
    J 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...
  36. ncbi request reprint Improved prediction of the number of residue contacts in proteins by recurrent neural networks
    G 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/...
  37. ncbi request reprint Mathematical correction for fingerprint similarity measures to improve chemical retrieval
    S 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...
  38. ncbi request reprint 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
    ..It also lacks a characterization of this symmetry and a convincing explanation or clarification of its origin...
  39. doi request reprint SOLpro: accurate sequence-based prediction of protein solubility
    Christophe N Magnan
    Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA
    Bioinformatics 25:2200-7. 2009
    ....
  40. pmc A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi
    Alan 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...
  41. pmc Influence relevance voting: an accurate and interpretable virtual high throughput screening method
    S 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...
  42. ncbi request reprint 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...
  43. doi request reprint Learning to play Go using recursive neural networks
    Lin 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...
  44. ncbi request reprint Differential analysis of DNA microarray gene expression data
    G 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...
  45. pmc MotifMap: a human genome-wide map of candidate regulatory motif sites
    Xiaohui Xie
    Department of Computer Sciences, University of California, Irvine, CA 92697, USA
    Bioinformatics 25:167-74. 2009
    ..Such efforts, however, have been significantly hindered by the overwhelming size of non-coding DNA regions and the statistical variability and complex spatial organizations of mammalian regulatory elements...
  46. ncbi request reprint Structural proteomics of the poxvirus family
    Arlo 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...
  47. ncbi request reprint The fixed-size Luria-Delbruck model with a nonzero death rate
    Natalia 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...
  48. pmc A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens
    Philip 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
    ....
  49. pmc Global landscape of recent inferred Darwinian selection for Homo sapiens
    Eric 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...
  50. pmc Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants
    Samuel 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)...
  51. pmc MITOMAP: a human mitochondrial genome database--2004 update
    Marty 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...
  52. pmc Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarrays
    Douglas 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...
  53. pmc Ty3 capsid mutations reveal early and late functions of the amino-terminal domain
    Liza 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...
  54. ncbi request reprint Distribution patterns of over-represented k-mers in non-coding yeast DNA
    Steven 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
    ..More importantly, we investigate the context and spatial distribution of over-represented k-mers in yeast USRs...
  55. pmc The TY3 Gag3 spacer controls intracellular condensation and uncoating
    Kristina 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...
  56. ncbi request reprint Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12
    A 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...
  57. ncbi request reprint Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    Gianluca 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/...
  58. pmc Data structures and compression algorithms for genomic sequence data
    Marty 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...
  59. ncbi request reprint Prediction of coordination number and relative solvent accessibility in proteins
    Gianluca 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/...
  60. pmc Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens
    Li 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...
  61. doi request reprint Discovery of power-laws in chemical space
    Ryan 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...
  62. pmc LineUp: statistical detection of chromosomal homology with application to plant comparative genomics
    Steve 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...
  63. ncbi request reprint Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
    Suman Sundaresh
    School of Information and Computer Sciences, University of California, Irvine, CA, USA
    Bioinformatics 22:1760-6. 2006
    ..These signals are a measure of antibody-antigen binding activity and provide a basis for understanding humoral immune responses to various infectious agents and supporting vaccine and diagnostic development...
  64. ncbi request reprint Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching
    Jianlin 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...
  65. ncbi request reprint TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins
    Arlo 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...
  66. pmc Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time
    S 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...
  67. pmc Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis
    Ting 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
    ....
  68. ncbi request reprint Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein
    She 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...
  69. ncbi request reprint Prediction of protein stability changes for single-site mutations using support vector machines
    Jianlin 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...
  70. pmc Retroviruses and yeast retrotransposons use overlapping sets of host genes
    Becky 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...
  71. doi request reprint PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure
    Michael 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...
  72. pmc When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values
    Pierre 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...
  73. ncbi request reprint One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties
    Chloé 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...
  74. ncbi request reprint Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling
    Michael 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...
  75. pmc Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery
    D 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...
  76. ncbi request reprint The absence of favorable aromatic interactions between beta-sheet peptides
    De 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
    ....
  77. pmc No electron left behind: a rule-based expert system to predict chemical reactions and reaction mechanisms
    Jonathan 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...
  78. ncbi request reprint Modular DAG-RNN architectures for assembling coarse protein structures
    Gianluca 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/...
  79. ncbi request reprint Assessment of predictions submitted for the CASP7 domain prediction category
    Michael 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...
  80. ncbi request reprint Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR
    Kirsty 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...
  81. ncbi request reprint Immunodominant Francisella tularensis antigens identified using proteome microarray
    Jim 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...