|
|
CBMI Related Publications - Pierre Baldi Real-time PUB-MED lookup: 70 Results No electron left behind: a rule-based expert system to predict chemical reactions and reaction mechanisms.Chen JH, Baldi P J Chem Inf Model. 2009 Sep;49(9):2034-43 A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Felgner PL, Kayala MA, Vigil A, Burk C, Nakajima-Sasaki R, Pablo J, Molina DM, Hirst S, Chew JS, Wang D, Tan G, Duffield M, Yang R, Neel J, Chantratita N, Bancroft G, Lertmemongkolchai G, Davies DH, Baldi P, Peacock S, Titball RW Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13499-504 An intersection inequality sharper than the tanimoto triangle inequality for efficiently searching large databases. Baldi P, Hirschberg DS J Chem Inf Model. 2009 Aug;49(8):1866-70 SOLpro: accurate sequence-based prediction of protein solubility. Magnan CN, Randall A, Baldi P Bioinformatics. 2009 Sep 1;25(17):2200-7 Data structures and compression algorithms for genomic sequence data. Brandon MC, Wallace DC, Baldi P Bioinformatics. 2009 Jul 15;25(14):1731-8 Influence relevance voting: an accurate and interpretable virtual high throughput screening method. Swamidass SJ, Azencott CA, Lin TW, Gramajo H, Tsai SC, Baldi P J Chem Inf Model. 2009 Apr;49(4):756-66 COBEpro: a novel system for predicting continuous B-cell epitopes. Sweredoski MJ, Baldi P Protein Eng Des Sel. 2009 Mar;22(3):113-20 SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. Randall A, Baldi P BMC Struct Biol. 2008 Dec 3;8:52 MotifMap: a human genome-wide map of candidate regulatory motif sites. Xie X, Rigor P, Baldi P Bioinformatics. 2009 Jan 15;25(2):167-74 Profiling humoral immune responses to P. falciparum infection with protein microarrays. Doolan DL, Mu Y, Unal B, Sundaresh S, Hirst S, Valdez C, Randall A, Molina D, Liang X, Freilich DA, Oloo JA, Blair PL, Aguiar JC, Baldi P, Davies DH, Felgner PL Proteomics. 2008 Nov;8(22):4680-94 Bayesian surprise attracts human attention. Itti L, Baldi P Vision Res. 2009 May;49(10):1295-306 Speeding up chemical database searches using a proximity filter based on the logical exclusive or. Baldi P, Hirschberg DS, Nasr RJ J Chem Inf Model. 2008 Jul;48(7):1367-78 BLASTing small molecules--statistics and extreme statistics of chemical similarity scores. Baldi P, Benz RW Bioinformatics. 2008 Jul 1;24(13):i357-65 MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Brandon MC, Ruiz-Pesini E, Mishmar D, Procaccio V, Lott MT, Nguyen KC, Spolim S, Patil U, Baldi P, Wallace DC Hum Mutat. 2009 Jan;30(1):1-6 Discovery of power-laws in chemical space. Benz RW, Swamidass SJ, Baldi P J Chem Inf Model. 2008 Jun;48(6):1138-51 A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi. Barbour AG, Jasinskas A, Kayala MA, Davies DH, Steere AC, Baldi P, Felgner PL Infect Immun. 2008 Aug;76(8):3374-89 PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Sweredoski MJ, Baldi P Bioinformatics. 2008 Jun 15;24(12):1459-60 Learning to play Go using recursive neural networks. Wu L, Baldi P Neural Netw. 2008 Nov;21(9):1392-400 How noisy and replicable are DNA microarry data? Sundaresh S, Hung SP, Hatfield GW, Baldi P Int J Bioinform Res Appl. 2005;1(1):31-50 TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Randall A, Cheng J, Sweredoski M, Baldi P Bioinformatics. 2008 Feb 15;24(4):513-20 A bottom-up model of spatial attention predicts human error patterns in rapid scene recognition. Einhäuser W, Mundhenk TN, Baldi P, Koch C, Itti L J Vis. 2007 Jul 20;7(10):6.1-13 Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrieval. Baldi P, Benz RW, Hirschberg DS, Swamidass SJ J Chem Inf Model. 2007 Nov-Dec;47(6):2098-109 Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. Sweredoski MJ, Donovan KJ, Nguyen BD, Shaka AJ, Baldi P Bioinformatics. 2007 Nov 1;23(21):2829-35 Assessment of predictions submitted for the CASP7 domain prediction category. Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I Proteins. 2007;69 Suppl 8:137-51 From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Sundaresh S, Randall A, Unal B, Petersen JM, Belisle JT, Hartley MG, Duffield M, Titball RW, Davies DH, Felgner PL, Baldi P Bioinformatics. 2007 Jul 1;23(13):i508-18 ChemDB update--full-text search and virtual chemical space. Chen JH, Linstead E, Swamidass SJ, Wang D, Baldi P Bioinformatics. 2007 Sep 1;23(17):2348-51 The fixed-size Luria-Delbruck model with a nonzero death rate. Komarova NL, Wu L, Baldi P Math Biosci. 2007 Nov;210(1):253-90 Immunodominant Francisella tularensis antigens identified using proteome microarray. Crown Copyright 2007 Dstl. Eyles JE, Unal B, Hartley MG, Newstead SL, Flick-Smith H, Prior JL, Oyston PC, Randall A, Mu Y, Hirst S, Molina DM, Davies DH, Milne T, Griffin KF, Baldi P, Titball RW, Felgner PL Proteomics. 2007 Jun;7(13):2172-83 Mathematical correction for fingerprint similarity measures to improve chemical retrieval. Swamidass SJ, Baldi P J Chem Inf Model. 2007 May-Jun;47(3):952-64 Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. Larsen LS, Zhang M, Beliakova-Bethell N, Bilanchone V, Lamsa A, Nagashima K, Najdi R, Kosaka K, Kovacevic V, Cheng J, Baldi P, Hatfield GW, Sandmeyer S J Virol. 2007 Jul;81(13):6957-72 Improved residue contact prediction using support vector machines and a large feature set. Cheng J, Baldi P BMC Bioinformatics. 2007 Apr 2;8:113 One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties. Azencott CA, Ksikes A, Swamidass SJ, Chen JH, Ralaivola L, Baldi P J Chem Inf Model. 2007 May-Jun;47(3):965-74 Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time. Swamidass SJ, Baldi P J Chem Inf Model. 2007 Mar-Apr;47(2):302-17 Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae. Wang N, Baldi PF, Gaut BS Mol Phylogenet Evol. 2007 Jun;43(3):1066-75 An enhanced MITOMAP with a global mtDNA mutational phylogeny. Ruiz-Pesini E, Lott MT, Procaccio V, Poole JC, Brandon MC, Mishmar D, Yi C, Kreuziger J, Baldi P, Wallace DC Nucleic Acids Res. 2007 Jan;35(Database issue):D823-8 Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. Dou Y, Fox-Walsh KL, Baldi PF, Hertel KJ RNA. 2006 Dec;12(12):2047-56 Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants. Danziger SA, Swamidass SJ, Zeng J, Dearth LR, Lu Q, Chen JH, Cheng J, Hoang VP, Saigo H, Luo R, Baldi P, Brachmann RK, Lathrop RH IEEE/ACM Trans Comput Biol Bioinform. 2006 Apr-Jun;3(2):114-25 Chemoinformatics, drug design, and systems biology. Baldi P Genome Inform. 2005;16(2):281-5 Modular DAG-RNN architectures for assembling coarse protein structures. Pollastri G, Vullo A, Frasconi P, Baldi P J Comput Biol. 2006 Apr;13(3):631-50 Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Sundaresh S, Doolan DL, Hirst S, Mu Y, Unal B, Davies DH, Felgner PL, Baldi P Bioinformatics. 2006 Jul 15;22(14):1760-6 A machine learning information retrieval approach to protein fold recognition. Cheng J, Baldi P Bioinformatics. 2006 Jun 15;22(12):1456-63 Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Lin TW, Melgar MM, Kurth D, Swamidass SJ, Purdon J, Tseng T, Gago G, Baldi P, Gramajo H, Tsai SC Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3072-7 A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Tagwerker C, Flick K, Cui M, Guerrero C, Dou Y, Auer B, Baldi P, Huang L, Kaiser P Mol Cell Proteomics. 2006 Apr;5(4):737-48 Prediction of protein stability changes for single-site mutations using support vector machines. Cheng J, Randall A, Baldi P Proteins. 2006 Mar 1;62(4):1125-32 Global landscape of recent inferred Darwinian selection for Homo sapiens. Wang ET, Kodama G, Baldi P, Moyzis RK Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):135-40 Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Cheng J, Saigo H, Baldi P Proteins. 2006 Mar 15;62(3):617-29 The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16176-81 ChemDB: a public database of small molecules and related chemoinformatics resources. Chen J, Swamidass SJ, Dou Y, Bruand J, Baldi P Bioinformatics. 2005 Nov 15;21(22):4133-9 Graph kernels for chemical informatics. Ralaivola L, Swamidass SJ, Saigo H, Baldi P Neural Netw. 2005 Oct;18(8):1093-110 On the relationship between deterministic and probabilistic directed Graphical models: from Bayesian networks to recursive neural networks. Baldi P, Rosen-Zvi M Neural Netw. 2005 Oct;18(8):1080-6 The absence of favorable aromatic interactions between beta-sheet peptides. Chung DM, Dou Y, Baldi P, Nowick JS J Am Chem Soc. 2005 Jul 20;127(28):9998-9 Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Cheng J, Baldi P Bioinformatics. 2005 Jun;21 Suppl 1:i75-84 Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Swamidass SJ, Chen J, Bruand J, Phung P, Ralaivola L, Baldi P Bioinformatics. 2005 Jun;21 Suppl 1:i359-68 Retroviruses and yeast retrotransposons use overlapping sets of host genes. Irwin B, Aye M, Baldi P, Beliakova-Bethell N, Cheng H, Dou Y, Liou W, Sandmeyer S Genome Res. 2005 May;15(5):641-54 Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP J Biol Chem. 2005 Apr 15;280(15):15084-96 Polymodal sensory function of the Caenorhabditis elegans OCR-2 channel arises from distinct intrinsic determinants within the protein and is selectively conserved in mammalian TRPV proteins. Sokolchik I, Tanabe T, Baldi PF, Sze JY J Neurosci. 2005 Jan 26;25(4):1015-23 Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Davies DH, Liang X, Hernandez JE, Randall A, Hirst S, Mu Y, Romero KM, Nguyen TT, Kalantari-Dehaghi M, Crotty S, Baldi P, Villarreal LP, Felgner PL Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):547-52 MITOMAP: a human mitochondrial genome database--2004 update. Brandon MC, Lott MT, Nguyen KC, Spolim S, Navathe SB, Baldi P, Wallace DC Nucleic Acids Res. 2005 Jan 1;33(Database issue):D611-3 Structural proteomics of the poxvirus family. Randall AZ, Baldi P, Villarreal LP Artif Intell Med. 2004 Jun;31(2):105-15 ICBS: a database of interactions between protein chains mediated by beta-sheet formation. Dou Y, Baisnée PF, Pollastri G, Pécout Y, Nowick J, Baldi P Bioinformatics. 2004 Nov 1;20(16):2767-77 Extensive gene gain associated with adaptive evolution of poxviruses. McLysaght A, Baldi PF, Gaut BS Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15655-60 Comprehensive mutagenesis of the C-terminal domain of the M13 gene-3 minor coat protein: the requirements for assembly into the bacteriophage particle. Weiss GA, Roth TA, Baldi PF, Sidhu SS J Mol Biol. 2003 Sep 26;332(4):777-82 Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP J Biol Chem. 2003 Aug 8;278(32):29837-55 LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Hampson S, McLysaght A, Gaut B, Baldi P Genome Res. 2003 May;13(5):999-1010 Differential analysis of DNA microarray gene expression data. Hatfield GW, Hung SP, Baldi P Mol Microbiol. 2003 Feb;47(4):871-7 Why are complementary DNA strands symmetric? Baisnée PF, Hampson S, Baldi P Bioinformatics. 2002 Aug;18(8):1021-33 Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. Hung SP, Baldi P, Hatfield GW J Biol Chem. 2002 Oct 25;277(43):40309-23 Distribution patterns of over-represented k-mers in non-coding yeast DNA. Hampson S, Kibler D, Baldi P Bioinformatics. 2002 Apr;18(4):513-28 Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Pollastri G, Przybylski D, Rost B, Baldi P Proteins. 2002 May 1;47(2):228-35 Prediction of coordination number and relative solvent accessibility in proteins. Pollastri G, Baldi P, Fariselli P, Casadio R Proteins. 2002 May 1;47(2):142-53 |
|||||||||||||||||