PubRank

Michael B Eisen

Author PubWeight™ 193.36‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007 18.01
2 Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007 11.66
3 In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006 10.60
4 Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 2002 8.56
5 Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A 2008 6.35
6 Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 2008 6.30
7 A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell 2008 5.63
8 Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 2009 5.23
9 Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol 2005 4.42
10 Noise minimization in eukaryotic gene expression. PLoS Biol 2004 4.36
11 Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 2002 4.24
12 Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol 2006 4.01
13 Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004 4.00
14 Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol 2004 3.36
15 Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol 2006 3.22
16 MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol 2004 3.15
17 Why PLoS became a publisher. PLoS Biol 2003 3.09
18 Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A 2005 3.04
19 Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet 2006 3.01
20 Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol 2004 2.81
21 Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res 2006 2.75
22 Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma 2007 2.73
23 The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol 2011 2.68
24 Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet 2008 2.67
25 Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol 2003 2.67
26 Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet 2011 2.65
27 Impact of chromatin structures on DNA processing for genomic analyses. PLoS One 2009 2.63
28 Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol 2011 2.43
29 Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol 2010 2.32
30 Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell 2011 2.00
31 Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A 2004 1.96
32 Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol 2004 1.96
33 Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLoS Genet 2011 1.95
34 Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet 2010 1.92
35 The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) 2011 1.86
36 Identification of regulatory elements using a feature selection method. Bioinformatics 2002 1.80
37 Aging and gene expression in the primate brain. PLoS Biol 2005 1.76
38 GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics 2005 1.66
39 Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc Natl Acad Sci U S A 2005 1.66
40 A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome. Genes Dev 2009 1.64
41 Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell 2009 1.52
42 A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res 2012 1.48
43 Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol 2007 1.47
44 Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus. PLoS One 2009 1.47
45 Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics 2006 1.44
46 Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol 2003 1.40
47 DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A 2012 1.39
48 Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proc Natl Acad Sci U S A 2008 1.25
49 Design of a combinatorial DNA microarray for protein-DNA interaction studies. BMC Bioinformatics 2006 1.20
50 A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genet 2011 1.17
51 Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PLoS Genet 2013 1.17
52 Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol 2005 1.16
53 Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 2013 1.09
54 Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts. PLoS Genet 2008 1.08
55 Mice infected with low-virulence strains of Toxoplasma gondii lose their innate aversion to cat urine, even after extensive parasite clearance. PLoS One 2013 1.05
56 Big genomes facilitate the comparative identification of regulatory elements. PLoS One 2009 1.04
57 Dual functions of TAF7L in adipocyte differentiation. Elife 2013 1.03
58 Integrating data clustering and visualization for the analysis of 3D gene expression data. IEEE/ACM Trans Comput Biol Bioinform 2010 1.03
59 Identification of direct T-box target genes in the developing zebrafish mesoderm. Development 2009 1.02
60 An essential role for zygotic expression in the pre-cellular Drosophila embryo. PLoS Genet 2013 1.00
61 Identifying cis-regulatory sequences by word profile similarity. PLoS One 2009 0.99
62 The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts. PLoS Genet 2010 0.98
63 Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. PLoS One 2013 0.98
64 Flexible promoter architecture requirements for coactivator recruitment. BMC Mol Biol 2006 0.96
65 Primate-specific evolution of an LDLR enhancer. Genome Biol 2006 0.94
66 Public-access group supports PubMed Central. Nature 2002 0.94
67 Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biol 2004 0.90
68 A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids. PLoS Genet 2008 0.90
69 Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain. PLoS Genet 2012 0.86
70 Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast. Pac Symp Biocomput 2008 0.86
71 Improving transcriptome assembly through error correction of high-throughput sequence reads. PeerJ 2013 0.84
72 Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS One 2007 0.83
73 Supervised detection of regulatory motifs in DNA sequences. Stat Appl Genet Mol Biol 2003 0.82
74 The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer. G3 (Bethesda) 2012 0.81
75 Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data. Procedia Comput Sci 2010 0.78
76 Spatial promoter recognition signatures may enhance transcription factor specificity in yeast. PLoS One 2013 0.77
77 Exploring the genetic basis of variation in gene predictions with a synthetic association study. PLoS One 2010 0.75
78 Estimating motifs under order restrictions. Stat Appl Genet Mol Biol 2005 0.75
79 PLoS Computational Biology: a new community journal. PLoS Comput Biol 2005 0.75