PubRank

Ziv Bar-Joseph

Author PubWeight™ 122.68‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002 43.52
2 STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 2006 5.21
3 A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 2008 4.78
4 The sirtuin SIRT6 regulates lifespan in male mice. Nature 2012 4.07
5 Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 2006 3.78
6 Clustering short time series gene expression data. Bioinformatics 2005 3.48
7 Reconstructing dynamic regulatory maps. Mol Syst Biol 2007 2.36
8 Random forest similarity for protein-protein interaction prediction from multiple sources. Pac Symp Biocomput 2005 2.25
9 A probabilistic generative model for GO enrichment analysis. Nucleic Acids Res 2008 2.01
10 Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res 2010 1.84
11 Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways. Am J Respir Crit Care Med 2014 1.69
12 Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife 2013 1.64
13 A biological solution to a fundamental distributed computing problem. Science 2011 1.62
14 Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst Biol 2008 1.61
15 Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report. Am J Respir Crit Care Med 2014 1.54
16 Cross species analysis of microarray expression data. Bioinformatics 2009 1.47
17 A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol 2008 1.40
18 Discovering pathways by orienting edges in protein interaction networks. Nucleic Acids Res 2010 1.32
19 Protein complex identification by supervised graph local clustering. Bioinformatics 2008 1.32
20 Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol 2009 1.27
21 A mixture of feature experts approach for protein-protein interaction prediction. BMC Bioinformatics 2007 1.24
22 Alignment and classification of time series gene expression in clinical studies. Bioinformatics 2008 1.22
23 Biological interaction networks are conserved at the module level. BMC Syst Biol 2011 1.16
24 Extracting dynamics from static cancer expression data. IEEE/ACM Trans Comput Biol Bioinform 2008 1.14
25 Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res 2012 1.14
26 DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst Biol 2012 1.11
27 Combined analysis reveals a core set of cycling genes. Genome Biol 2007 1.10
28 Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat Biotechnol 2005 1.09
29 Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Mol Biol Cell 2009 1.09
30 Retracted Comparative expression profile of miRNA and mRNA in primary peripheral blood mononuclear cells infected with human immunodeficiency virus (HIV-1). PLoS One 2011 1.09
31 Probabilistic error correction for RNA sequencing. Nucleic Acids Res 2013 1.08
32 Reconstructing dynamic microRNA-regulated interaction networks. Proc Natl Acad Sci U S A 2013 1.01
33 MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts. BMC Infect Dis 2013 1.00
34 A patient-gene model for temporal expression profiles in clinical studies. J Comput Biol 2007 0.98
35 DECOD: fast and accurate discriminative DNA motif finding. Bioinformatics 2011 0.98
36 Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. Bioinformatics 2013 0.97
37 Identifying cycling genes by combining sequence homology and expression data. Bioinformatics 2006 0.97
38 Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 2010 0.97
39 Algorithms in nature: the convergence of systems biology and computational thinking. Mol Syst Biol 2011 0.96
40 ExpressionBlast: mining large, unstructured expression databases. Nat Methods 2013 0.96
41 Inferring pairwise regulatory relationships from multiple time series datasets. Bioinformatics 2007 0.92
42 Identifying proteins controlling key disease signaling pathways. Bioinformatics 2013 0.90
43 A high-throughput framework to detect synapses in electron microscopy images. Bioinformatics 2013 0.90
44 A network-based approach for predicting missing pathway interactions. PLoS Comput Biol 2012 0.90
45 Systematic prediction of human membrane receptor interactions. Proteomics 2009 0.90
46 Cross-species queries of large gene expression databases. Bioinformatics 2010 0.89
47 Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells. BMC Syst Biol 2013 0.87
48 Discriminative motif finding for predicting protein subcellular localization. IEEE/ACM Trans Comput Biol Bioinform 2011 0.86
49 A combined expression-interaction model for inferring the temporal activity of transcription factors. J Comput Biol 2009 0.86
50 Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes. BMC Genomics 2010 0.86
51 Continuous hidden process model for time series expression experiments. Bioinformatics 2007 0.84
52 Computational methods for analyzing dynamic regulatory networks. Methods Mol Biol 2010 0.82
53 IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability. PLoS One 2009 0.79
54 Matching experiments across species using expression values and textual information. Bioinformatics 2012 0.79
55 cDREM: inferring dynamic combinatorial gene regulation. J Comput Biol 2015 0.78
56 Cross species expression analysis of innate immune response. J Comput Biol 2010 0.77
57 Learning cellular sorting pathways using protein interactions and sequence motifs. J Comput Biol 2011 0.77
58 Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men. AIDS 2017 0.75
59 Topological properties of robust biological and computational networks. J R Soc Interface 2014 0.75
60 Preface: RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 special issue. J Comput Biol 2011 0.75
61 The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression. Methods Mol Biol 2016 0.75