PubRank

Ewan Birney

Author PubWeight™ 1129.31‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008 151.16
2 Initial sequencing and comparative analysis of the mouse genome. Nature 2002 96.15
3 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 75.09
4 The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002 58.63
5 The Pfam protein families database. Nucleic Acids Res 2002 51.34
6 Patterns of somatic mutation in human cancer genomes. Nature 2007 38.41
7 Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005 24.54
8 Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004 24.40
9 A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008 21.72
10 The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002 20.36
11 International network of cancer genome projects. Nature 2010 20.35
12 A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 2009 18.39
13 EnsMart: a generic system for fast and flexible access to biological data. Genome Res 2004 17.64
14 Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007 16.21
15 Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2008 15.69
16 The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 2009 14.90
17 Ensembl 2011. Nucleic Acids Res 2010 14.68
18 The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004 14.67
19 Ensembl 2012. Nucleic Acids Res 2011 14.55
20 Reactome: a knowledge base of biologic pathways and processes. Genome Biol 2007 13.36
21 EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 2008 12.72
22 Ensembl 2014. Nucleic Acids Res 2013 12.62
23 Prepublication data sharing. Nature 2009 12.24
24 Ensembl 2013. Nucleic Acids Res 2012 11.70
25 Optimized design and assessment of whole genome tiling arrays. Bioinformatics 2007 11.38
26 Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2010 11.23
27 Ensembl's 10th year. Nucleic Acids Res 2009 10.82
28 Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 2011 10.66
29 Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012 9.68
30 Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 2002 9.43
31 Genome sequence of Aedes aegypti, a major arbovirus vector. Science 2007 9.19
32 The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010 9.19
33 A high-resolution map of human evolutionary constraint using 29 mammals. Nature 2011 8.67
34 The Reactome pathway knowledgebase. Nucleic Acids Res 2013 8.56
35 Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res 2008 7.35
36 The Ensembl core software libraries. Genome Res 2004 7.30
37 The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res 2007 7.29
38 EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol 2006 7.06
39 Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 2007 7.05
40 Integrating biological data--the Distributed Annotation System. BMC Bioinformatics 2008 6.56
41 The European Nucleotide Archive. Nucleic Acids Res 2010 6.48
42 Challenges and standards in integrating surveys of structural variation. Nat Genet 2007 6.05
43 Heritable individual-specific and allele-specific chromatin signatures in humans. Science 2010 5.94
44 Genome analysis of the platypus reveals unique signatures of evolution. Nature 2008 5.74
45 The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res 2007 5.67
46 Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res 2011 5.60
47 Immunity-related genes and gene families in Anopheles gambiae. Science 2002 5.47
48 Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res 2008 5.21
49 The genomic basis of adaptive evolution in threespine sticklebacks. Nature 2012 5.20
50 Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res 2008 5.12
51 Improvements to services at the European Nucleotide Archive. Nucleic Acids Res 2009 5.00
52 A physical map of the mouse genome. Nature 2002 4.97
53 An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 2008 4.84
54 Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 2012 4.80
55 High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res 2010 4.69
56 A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics 2010 4.68
57 Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS One 2009 4.60
58 Sense from sequence reads: methods for alignment and assembly. Nat Methods 2009 4.44
59 Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 2011 4.43
60 Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med 2010 4.19
61 The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A 2007 3.93
62 Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res 2007 3.84
63 Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res 2012 3.80
64 Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc 2009 3.77
65 VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res 2008 3.73
66 Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol 2012 3.61
67 Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet 2003 3.45
68 Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A 2014 3.35
69 The European Bioinformatics Institute's data resources. Nucleic Acids Res 2003 3.34
70 Ensembl variation resources. BMC Genomics 2010 3.17
71 TranscriptSNPView: a genome-wide catalog of mouse coding variation. Nat Genet 2006 3.10
72 SNP and haplotype mapping for genetic analysis in the rat. Nat Genet 2008 2.96
73 VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res 2006 2.94
74 Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res 2011 2.87
75 Modeling gene expression using chromatin features in various cellular contexts. Genome Biol 2012 2.76
76 Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res 2012 2.66
77 Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. Genome Res 2004 2.58
78 Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 2013 2.56
79 The EBI RDF platform: linked open data for the life sciences. Bioinformatics 2014 2.55
80 Arabidopsis reactome: a foundation knowledgebase for plant systems biology. Plant Cell 2008 2.50
81 Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics 2008 2.46
82 Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res 2012 2.32
83 The Anopheles gambiae genome: an update. Trends Parasitol 2004 2.10
84 A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell 2012 2.02
85 Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat Methods 2007 2.01
86 Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol 2012 1.97
87 What everybody should know about the rat genome and its online resources. Nat Genet 2008 1.94
88 A survey of homozygous deletions in human cancer genomes. Proc Natl Acad Sci U S A 2005 1.94
89 Major submissions tool developments at the European Nucleotide Archive. Nucleic Acids Res 2011 1.94
90 Genome browsing with Ensembl: a practical overview. Brief Funct Genomic Proteomic 2007 1.93
91 Genomic information infrastructure after the deluge. Genome Biol 2010 1.89
92 The future of DNA sequence archiving. Gigascience 2012 1.85
93 Sockeye: a 3D environment for comparative genomics. Genome Res 2004 1.80
94 EMMA--mouse mutant resources for the international scientific community. Nucleic Acids Res 2009 1.75
95 RNAcentral: A vision for an international database of RNA sequences. RNA 2011 1.73
96 Genome annotation techniques: new approaches and challenges. Drug Discov Today 2002 1.65
97 The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol 2005 1.58
98 Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res 2011 1.53
99 Identification of novel peptide hormones in the human proteome by hidden Markov model screening. Genome Res 2007 1.50
100 The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res 2010 1.45
101 Update of the Anopheles gambiae PEST genome assembly. Genome Biol 2007 1.44
102 Confounding between recombination and selection, and the Ped/Pop method for detecting selection. Genome Res 2008 1.42
103 Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Res 2004 1.38
104 Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria. Mol Cell Proteomics 2010 1.38
105 Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. Nat Rev Genet 2008 1.35
106 A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res 2010 1.22
107 Gene finding in the chicken genome. BMC Bioinformatics 2005 1.20
108 The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res 2013 1.17
109 ENFIN--A European network for integrative systems biology. C R Biol 2009 1.17
110 Policy challenges of clinical genome sequencing. BMJ 2013 1.14
111 The systematic annotation of the three main GPCR families in Reactome. Database (Oxford) 2010 1.09
112 Genome information resources - developments at Ensembl. Trends Genet 2004 1.09
113 Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database (Oxford) 2010 1.08
114 A SNP map of the rat genome generated from cDNA sequences. Science 2004 1.06
115 MAPU 2.0: high-accuracy proteomes mapped to genomes. Nucleic Acids Res 2008 1.06
116 Estimating the neutral rate of nucleotide substitution using introns. Mol Biol Evol 2006 1.00
117 In vivo validation of a computationally predicted conserved Ath5 target gene set. PLoS Genet 2007 1.00
118 Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish. G3 (Bethesda) 2014 1.00
119 Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. Nucleic Acids Res 2013 0.94
120 Discovering novel cis-regulatory motifs using functional networks. Genome Res 2003 0.92
121 An effective model for natural selection in promoters. Genome Res 2010 0.90
122 Dry work in a wet world: computation in systems biology. Mol Syst Biol 2006 0.90
123 ENFIN a network to enhance integrative systems biology. Ann N Y Acad Sci 2007 0.87
124 Journey to the genetic interior. Interview by Stephen S Hall. Sci Am 2012 0.87
125 The consequence of natural selection on genetic variation in the mouse. Genomics 2010 0.82
126 Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. Genome Biol 2011 0.81
127 Picking pyknons out of the human genome. Cell 2006 0.80
128 Evolutionary genomics: come fly with us. Nature 2007 0.79
129 Advanced genomic data mining. PLoS Comput Biol 2008 0.76
130 Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A 2014 0.76
131 Unrestricted free access works and must continue. Nature 2003 0.75
132 Double Dutch for duplications. Nat Genet 2007 0.75
133 Levers and fulcrums: progress in cis-regulatory motif models. Nat Methods 2008 0.75
134 Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLoS Genet 2015 0.75
135 Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004. Syst Biol (Stevenage) 2005 0.75
136 Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nat Genet 2017 0.75
137 Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 2017 0.75