PubRank

Pierre Baldi

Author PubWeight™ 153.56‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002 5.29
2 An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res 2006 4.51
3 Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci U S A 2005 3.77
4 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. Mol Cell Proteomics 2006 3.62
5 Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc Natl Acad Sci U S A 2005 3.59
6 MITOMAP: a human mitochondrial genome database--2004 update. Nucleic Acids Res 2005 3.35
7 Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 2006 3.00
8 A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proc Natl Acad Sci U S A 2010 2.90
9 Prediction of coordination number and relative solvent accessibility in proteins. Proteins 2002 2.66
10 Profiling humoral immune responses to P. falciparum infection with protein microarrays. Proteomics 2008 2.43
11 Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. J Biol Chem 2003 2.32
12 Coordination of the transcriptome and metabolome by the circadian clock. Proc Natl Acad Sci U S A 2012 2.22
13 ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics 2005 2.16
14 A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi. Infect Immun 2008 2.15
15 A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proc Natl Acad Sci U S A 2009 2.10
16 Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007 2.03
17 Data structures and compression algorithms for genomic sequence data. Bioinformatics 2009 1.96
18 Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time. J Chem Inf Model 2007 1.86
19 Bayesian surprise attracts human attention. Vision Res 2008 1.86
20 Graph kernels for chemical informatics. Neural Netw 2005 1.86
21 Immunodominant Francisella tularensis antigens identified using proteome microarray. Proteomics 2007 1.85
22 ChemDB update--full-text search and virtual chemical space. Bioinformatics 2007 1.83
23 PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 2008 1.78
24 A machine learning information retrieval approach to protein fold recognition. Bioinformatics 2006 1.75
25 MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics 2008 1.73
26 Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem 2005 1.73
27 Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. J Biol Chem 2002 1.69
28 From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Bioinformatics 2007 1.68
29 Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics 2006 1.65
30 Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol Cell Proteomics 2010 1.61
31 Cyber-T web server: differential analysis of high-throughput data. Nucleic Acids Res 2012 1.58
32 COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 2008 1.54
33 Sterile protective immunity to malaria is associated with a panel of novel P. falciparum antigens. Mol Cell Proteomics 2011 1.53
34 Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics 2005 1.47
35 Deep architectures for protein contact map prediction. Bioinformatics 2012 1.44
36 Differential analysis of DNA microarray gene expression data. Mol Microbiol 2003 1.43
37 Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2006 1.42
38 Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins 2006 1.41
39 Assessment of predictions submitted for the CASP7 domain prediction category. Proteins 2007 1.39
40 Retroviruses and yeast retrotransposons use overlapping sets of host genes. Genome Res 2005 1.38
41 The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. Nat Neurosci 2013 1.36
42 Leptin engages a hypothalamic neurocircuitry to permit survival in the absence of insulin. Cell Metab 2013 1.32
43 Data structures and compression algorithms for high-throughput sequencing technologies. BMC Bioinformatics 2010 1.31
44 Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics 2002 1.25
45 The stability and complexity of antibody responses to the major surface antigen of Plasmodium falciparum are associated with age in a malaria endemic area. Mol Cell Proteomics 2011 1.24
46 Why are complementary DNA strands symmetric? Bioinformatics 2002 1.23
47 A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics 2010 1.20
48 Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 2005 1.16
49 SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics 2009 1.14
50 CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics. Nat Methods 2012 1.14
51 LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Res 2003 1.14
52 Discovery of power-laws in chemical space. J Chem Inf Model 2008 1.11
53 Genome-wide identification of Bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling. PLoS One 2011 1.11
54 Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc Natl Acad Sci U S A 2013 1.11
55 Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling. Mol Cell Proteomics 2012 1.10
56 MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum Mutat 2009 1.10
57 MotifMap: integrative genome-wide maps of regulatory motif sites for model species. BMC Bioinformatics 2011 1.10
58 Small-molecule 3D structure prediction using open crystallography data. J Chem Inf Model 2013 1.10
59 One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties. J Chem Inf Model 2007 1.09
60 Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens. PLoS Negl Trop Dis 2010 1.08
61 TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Bioinformatics 2007 1.07
62 Circadian clock regulates the host response to Salmonella. Proc Natl Acad Sci U S A 2013 1.07
63 SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. BMC Struct Biol 2008 1.07
64 Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules. J Chem Inf Model 2013 1.07
65 Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors. PLoS Comput Biol 2010 1.06
66 Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarrays. Vaccine 2009 1.05
67 Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. J Virol 2007 1.03
68 Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. J Chem Inf Model 2011 1.02
69 ICBS: a database of interactions between protein chains mediated by beta-sheet formation. Bioinformatics 2004 1.02
70 The fixed-size Luria-Delbruck model with a nonzero death rate. Math Biosci 2007 1.01
71 Influence relevance voting: an accurate and interpretable virtual high throughput screening method. J Chem Inf Model 2009 1.00
72 A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs. Mol Cell Biol 2012 1.00
73 GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program. PLoS Genet 2012 0.99
74 Mitochondrial mutations and polymorphisms in psychiatric disorders. Front Genet 2012 0.98
75 Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy. Mol Cell Proteomics 2012 0.98
76 High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics 2010 0.97
77 Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during candidemia. PLoS Pathog 2010 0.96
78 Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat Struct Mol Biol 2013 0.96
79 Modular DAG-RNN architectures for assembling coarse protein structures. J Comput Biol 2006 0.93
80 Mathematical correction for fingerprint similarity measures to improve chemical retrieval. J Chem Inf Model 2007 0.93
81 Learning to predict chemical reactions. J Chem Inf Model 2011 0.92
82 Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability. Proc Natl Acad Sci U S A 2010 0.91
83 Identification of immunodominant antigens by probing a whole Chlamydia trachomatis open reading frame proteome microarray using sera from immunized mice. Infect Immun 2010 0.90
84 Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants. IEEE/ACM Trans Comput Biol Bioinform 2006 0.90
85 The absence of favorable aromatic interactions between beta-sheet peptides. J Am Chem Soc 2005 0.90
86 Retrotransposon profiling of RNA polymerase III initiation sites. Genome Res 2012 0.90
87 A bottom-up model of spatial attention predicts human error patterns in rapid scene recognition. J Vis 2007 0.89
88 Circadian control of fatty acid elongation by SIRT1 protein-mediated deacetylation of acetyl-coenzyme A synthetase 1. J Biol Chem 2014 0.89
89 ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning. J Chem Inf Model 2012 0.86
90 No electron left behind: a rule-based expert system to predict chemical reactions and reaction mechanisms. J Chem Inf Model 2009 0.85
91 Biomimetic Design of Protein Nanomaterials for Hydrophobic Molecular Transport. Adv Funct Mater 2012 0.85
92 Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre. J Chem Inf Model 2011 0.84
93 Hashing algorithms and data structures for rapid searches of fingerprint vectors. J Chem Inf Model 2010 0.82
94 SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations. Proteins 2011 0.82
95 Modeling of mitochondria bioenergetics using a composable chemiosmotic energy transduction rate law: theory and experimental validation. PLoS One 2011 0.82
96 Rationally selected single-site mutants of the Thermoascus aurantiacus endoglucanase increase hydrolytic activity on cellulosic substrates. Biotechnol Bioeng 2012 0.81
97 A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins. PLoS One 2013 0.80
98 Speeding up chemical searches using the inverted index: the convergence of chemoinformatics and text search methods. J Chem Inf Model 2012 0.80
99 The TY3 Gag3 spacer controls intracellular condensation and uncoating. J Virol 2011 0.79
100 ReactionMap: an efficient atom-mapping algorithm for chemical reactions. J Chem Inf Model 2013 0.79
101 Learning to play Go using recursive neural networks. Neural Netw 2008 0.78
102 Structural proteomics of the poxvirus family. Artif Intell Med 2004 0.78
103 Machine learning methods for protein structure prediction. IEEE Rev Biomed Eng 2008 0.78
104 Detecting Cardiovascular Disease from Mammograms with Deep Learning. IEEE Trans Med Imaging 2017 0.78
105 Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate. Cell Signal 2013 0.77
106 Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. Bioinformatics 2007 0.77
107 A Genomic Analysis Pipeline and Its Application to Pediatric Cancers. IEEE/ACM Trans Comput Biol Bioinform 2015 0.76
108 How noisy and replicable are DNA microarry data? Int J Bioinform Res Appl 2005 0.76
109 A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions. Bioinformatics 2013 0.75
110 A scalable and integrative system for pathway bioinformatics and systems biology. Adv Exp Med Biol 2010 0.75
111 COBRA: a computational brewing application for predicting the molecular composition of organic aerosols. Environ Sci Technol 2012 0.75
112 What time is it? Deep learning approaches for circadian rhythms. Bioinformatics 2016 0.75
113 Editorial: Charting Chemical Space: Challenges and Opportunities for Artificial Intelligence and Machine Learning. Mol Inform 2011 0.75
114 Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction. J Chem Inf Model 2016 0.75