Aviv Regev

Author PubWeight™ 406.17‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011 53.86
2 Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009 35.48
3 Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 2009 20.66
4 Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 2010 18.44
5 An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet 2008 17.67
6 Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011 16.77
7 Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003 14.56
8 A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010 12.27
9 lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011 11.31
10 Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 2010 9.09
11 A module map showing conditional activity of expression modules in cancer. Nat Genet 2004 8.57
12 SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet 2009 7.48
13 Natural history and evolutionary principles of gene duplication in fungi. Nature 2007 7.26
14 Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 2011 7.03
15 Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 2013 6.50
16 A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 2012 6.34
17 Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 2009 6.07
18 Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A 2009 6.01
19 Comparative functional genomics of the fission yeasts. Science 2011 6.00
20 Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010 5.79
21 A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 2009 4.98
22 Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1. Nature 2013 4.74
23 Induction and molecular signature of pathogenic TH17 cells. Nat Immunol 2012 4.43
24 From signatures to models: understanding cancer using microarrays. Nat Genet 2005 4.29
25 Dynamic single-cell imaging of direct reprogramming reveals an early specifying event. Nat Biotechnol 2010 3.98
26 Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 2011 3.81
27 Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 2011 3.81
28 Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A 2005 3.58
29 High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 2011 3.53
30 Proto-genes and de novo gene birth. Nature 2012 3.43
31 Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 2011 3.20
32 Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol 2010 3.09
33 Dynamic regulatory network controlling TH17 cell differentiation. Nature 2013 3.07
34 A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell 2012 3.04
35 Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci U S A 2004 2.99
36 The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell 2012 2.78
37 Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science 2014 2.77
38 Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat Methods 2013 2.71
39 Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet 2008 2.67
40 Chromatin signature of embryonic pluripotency is established during genome activation. Nature 2010 2.64
41 Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science 2014 2.63
42 Transcriptional regulatory circuits: predicting numbers from alphabets. Science 2009 2.61
43 The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 2010 2.53
44 Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 2007 2.52
45 High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 2013 2.35
46 Dissecting timing variability in yeast meiosis. Cell 2007 2.35
47 Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods 2009 2.26
48 Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc Natl Acad Sci U S A 2013 1.94
49 Digital transcriptome profiling from attomole-level RNA samples. Genome Res 2010 1.83
50 Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell 2011 1.83
51 Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat Biotechnol 2008 1.82
52 Impulse control: temporal dynamics in gene transcription. Cell 2011 1.79
53 Identification of transcriptional regulators in the mouse immune system. Nat Immunol 2013 1.79
54 A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation. Dev Cell 2012 1.72
55 The transcriptional landscape of αβ T cell differentiation. Nat Immunol 2013 1.61
56 Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development 2013 1.54
57 Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nat Genet 2013 1.52
58 Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol 2012 1.44
59 Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res 2011 1.37
60 Gene duplication and the evolution of ribosomal protein gene regulation in yeast. Proc Natl Acad Sci U S A 2010 1.33
61 Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clin Cancer Res 2012 1.33
62 Minreg: inferring an active regulator set. Bioinformatics 2002 1.33
63 Revealing targeted therapy for human cancer by gene module maps. Cancer Res 2008 1.29
64 Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports 2013 1.19
65 Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol 2012 1.18
66 Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. Curr Biol 2010 1.15
67 Strategies to discover regulatory circuits of the mammalian immune system. Nat Rev Immunol 2011 1.10
68 Revisiting the Saccharomyces cerevisiae predicted ORFeome. Genome Res 2008 1.07
69 Evolutionary principles of modular gene regulation in yeasts. Elife 2013 1.05
70 Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. BMC Genomics 2012 1.05
71 Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nat Biotechnol 2013 1.03
72 Convergent Evolution of Calcineurin Pathway Roles in Thermotolerance and Virulence in Candida glabrata. G3 (Bethesda) 2012 1.02
73 From elements to modules: regulatory evolution in Ascomycota fungi. Curr Opin Genet Dev 2009 1.02
74 Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia. Nano Lett 2012 1.01
75 A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. Mol Syst Biol 2012 0.99
76 Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing. Curr Protoc Mol Biol 2014 0.99
77 Mouse ooplasm confers context-specific reprogramming capacity. Nat Genet 2012 0.98
78 Molecular analysis of transitional cell carcinoma using cDNA microarray. Oncogene 2003 0.96
79 Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules. Genome Res 2013 0.94
80 Physical Module Networks: an integrative approach for reconstructing transcription regulation. Bioinformatics 2011 0.92
81 Fungal regulatory evolution: cis and trans in the balance. FEBS Lett 2009 0.91
82 MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis. Genome Biol 2012 0.90
83 Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution. Annu Rev Cell Dev Biol 2015 0.88
84 Correction: Evolutionary principles of modular gene regulation in yeasts. Elife 2013 0.85
85 BRNI: Modular analysis of transcriptional regulatory programs. BMC Bioinformatics 2009 0.82
86 Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters. PLoS One 2012 0.81
87 Semiconductor-based DNA sequencing of histone modification states. Nat Commun 2013 0.78
88 In vivo profiles in malaria are consistent with a novel physiological state. Proc Natl Acad Sci U S A 2009 0.77
89 Reconstructing gene histories in Ascomycota fungi. Methods Enzymol 2010 0.75
90 The Human Cell Atlas: from vision to reality. Nature 2017 0.75
91 142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis. Neurosurgery 2016 0.75
92 ISMB 2003 BioPathways SIG and 5th BioPathways Meeting. Comp Funct Genomics 2003 0.75