| Rank |
Title |
Journal |
Year |
PubWeight™‹?› |
|
1
|
Initial sequencing and comparative analysis of the mouse genome.
|
Nature
|
2002
|
96.15
|
|
2
|
A method and server for predicting damaging missense mutations.
|
Nat Methods
|
2010
|
78.53
|
|
3
|
Human non-synonymous SNPs: server and survey.
|
Nucleic Acids Res
|
2002
|
50.45
|
|
4
|
Functional organization of the yeast proteome by systematic analysis of protein complexes.
|
Nature
|
2002
|
45.19
|
|
5
|
A human gut microbial gene catalogue established by metagenomic sequencing.
|
Nature
|
2010
|
43.63
|
|
6
|
Comparative metagenomics of microbial communities.
|
Science
|
2005
|
25.88
|
|
7
|
InterPro: the integrative protein signature database.
|
Nucleic Acids Res
|
2008
|
25.07
|
|
8
|
Recent improvements to the SMART domain-based sequence annotation resource.
|
Nucleic Acids Res
|
2002
|
25.06
|
|
9
|
The InterPro Database, 2003 brings increased coverage and new features.
|
Nucleic Acids Res
|
2003
|
24.72
|
|
10
|
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
|
Nature
|
2004
|
24.40
|
|
11
|
Enterotypes of the human gut microbiome.
|
Nature
|
2011
|
24.36
|
|
12
|
Comparative assessment of large-scale data sets of protein-protein interactions.
|
Nature
|
2002
|
24.25
|
|
13
|
Proteome survey reveals modularity of the yeast cell machinery.
|
Nature
|
2006
|
20.77
|
|
14
|
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
|
Nucleic Acids Res
|
2008
|
20.62
|
|
15
|
The genome sequence of the malaria mosquito Anopheles gambiae.
|
Science
|
2002
|
20.36
|
|
16
|
SMART 4.0: towards genomic data integration.
|
Nucleic Acids Res
|
2004
|
19.37
|
|
17
|
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
|
Nucleic Acids Res
|
2010
|
18.73
|
|
18
|
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
|
Nucleic Acids Res
|
2012
|
18.26
|
|
19
|
InterPro, progress and status in 2005.
|
Nucleic Acids Res
|
2005
|
17.53
|
|
20
|
SMART 5: domains in the context of genomes and networks.
|
Nucleic Acids Res
|
2006
|
17.13
|
|
21
|
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
|
Nat Biotechnol
|
2004
|
16.08
|
|
22
|
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
|
Bioinformatics
|
2006
|
14.96
|
|
23
|
Toward automatic reconstruction of a highly resolved tree of life.
|
Science
|
2006
|
14.96
|
|
24
|
InterPro in 2011: new developments in the family and domain prediction database.
|
Nucleic Acids Res
|
2011
|
13.45
|
|
25
|
New developments in the InterPro database.
|
Nucleic Acids Res
|
2007
|
12.49
|
|
26
|
STRING 7--recent developments in the integration and prediction of protein interactions.
|
Nucleic Acids Res
|
2006
|
12.16
|
|
27
|
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.
|
Nucleic Acids Res
|
2011
|
10.82
|
|
28
|
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
|
Nucleic Acids Res
|
2005
|
10.44
|
|
29
|
SMART 6: recent updates and new developments.
|
Nucleic Acids Res
|
2008
|
9.80
|
|
30
|
STRING: a database of predicted functional associations between proteins.
|
Nucleic Acids Res
|
2003
|
9.45
|
|
31
|
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.
|
Science
|
2002
|
9.43
|
|
32
|
Drug target identification using side-effect similarity.
|
Science
|
2008
|
9.24
|
|
33
|
SMART 7: recent updates to the protein domain annotation resource.
|
Nucleic Acids Res
|
2011
|
9.15
|
|
34
|
Bioinformatics in the post-sequence era.
|
Nat Genet
|
2003
|
8.83
|
|
35
|
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.
|
Genes Dev
|
2006
|
8.78
|
|
36
|
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
|
Nucleic Acids Res
|
2006
|
8.36
|
|
37
|
Literature mining for the biologist: from information retrieval to biological discovery.
|
Nat Rev Genet
|
2006
|
8.23
|
|
38
|
Protein disorder prediction: implications for structural proteomics.
|
Structure
|
2003
|
7.93
|
|
39
|
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
|
Nat Biotechnol
|
2011
|
7.53
|
|
40
|
Alternative splicing and genome complexity.
|
Nat Genet
|
2001
|
7.30
|
|
41
|
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
|
Proc Natl Acad Sci U S A
|
2002
|
7.21
|
|
42
|
Systematic discovery of in vivo phosphorylation networks.
|
Cell
|
2007
|
6.94
|
|
43
|
Richness of human gut microbiome correlates with metabolic markers.
|
Nature
|
2013
|
6.93
|
|
44
|
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
|
Nucleic Acids Res
|
2003
|
6.86
|
|
45
|
A side effect resource to capture phenotypic effects of drugs.
|
Mol Syst Biol
|
2010
|
6.75
|
|
46
|
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
|
Nature
|
2008
|
6.69
|
|
47
|
The ecoresponsive genome of Daphnia pulex.
|
Science
|
2011
|
6.55
|
|
48
|
The genome of the model beetle and pest Tribolium castaneum.
|
Nature
|
2008
|
6.50
|
|
49
|
Association of genes to genetically inherited diseases using data mining.
|
Nat Genet
|
2002
|
5.78
|
|
50
|
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.
|
Science
|
2010
|
5.56
|
|
51
|
Immunity-related genes and gene families in Anopheles gambiae.
|
Science
|
2002
|
5.47
|
|
52
|
Dynamic complex formation during the yeast cell cycle.
|
Science
|
2005
|
5.11
|
|
53
|
STITCH: interaction networks of chemicals and proteins.
|
Nucleic Acids Res
|
2007
|
4.88
|
|
54
|
Genomes in flux: the evolution of archaeal and proteobacterial gene content.
|
Genome Res
|
2002
|
4.85
|
|
55
|
eggNOG: automated construction and annotation of orthologous groups of genes.
|
Nucleic Acids Res
|
2007
|
4.84
|
|
56
|
Transcriptome complexity in a genome-reduced bacterium.
|
Science
|
2009
|
4.64
|
|
57
|
Update on XplorMed: A web server for exploring scientific literature.
|
Nucleic Acids Res
|
2003
|
4.42
|
|
58
|
Genomic variation landscape of the human gut microbiome.
|
Nature
|
2012
|
4.38
|
|
59
|
Genome-wide experimental determination of barriers to horizontal gene transfer.
|
Science
|
2007
|
4.37
|
|
60
|
A genome-wide survey of human pseudogenes.
|
Genome Res
|
2003
|
4.34
|
|
61
|
KEGG Atlas mapping for global analysis of metabolic pathways.
|
Nucleic Acids Res
|
2008
|
4.14
|
|
62
|
iPath: interactive exploration of biochemical pathways and networks.
|
Trends Biochem Sci
|
2008
|
4.03
|
|
63
|
Proteome organization in a genome-reduced bacterium.
|
Science
|
2009
|
3.97
|
|
64
|
Molecular eco-systems biology: towards an understanding of community function.
|
Nat Rev Microbiol
|
2008
|
3.95
|
|
65
|
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
|
Nucleic Acids Res
|
2011
|
3.94
|
|
66
|
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.
|
Genes Dev
|
2007
|
3.92
|
|
67
|
SuperTarget and Matador: resources for exploring drug-target relationships.
|
Nucleic Acids Res
|
2007
|
3.82
|
|
68
|
eggNOG v4.0: nested orthology inference across 3686 organisms.
|
Nucleic Acids Res
|
2013
|
3.77
|
|
69
|
Linear motif atlas for phosphorylation-dependent signaling.
|
Sci Signal
|
2008
|
3.77
|
|
70
|
Medusa: a simple tool for interaction graph analysis.
|
Bioinformatics
|
2005
|
3.74
|
|
71
|
Prediction of effective genome size in metagenomic samples.
|
Genome Biol
|
2007
|
3.73
|
|
72
|
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways.
|
EMBO J
|
2003
|
3.68
|
|
73
|
Systematic identification of novel protein domain families associated with nuclear functions.
|
Genome Res
|
2002
|
3.50
|
|
74
|
SmashCommunity: a metagenomic annotation and analysis tool.
|
Bioinformatics
|
2010
|
3.48
|
|
75
|
Function prediction and protein networks.
|
Curr Opin Cell Biol
|
2003
|
3.46
|
|
76
|
Impact of genome reduction on bacterial metabolism and its regulation.
|
Science
|
2009
|
3.45
|
|
77
|
Extraction of regulatory gene/protein networks from Medline.
|
Bioinformatics
|
2005
|
3.43
|
|
78
|
A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development.
|
Dev Cell
|
2006
|
3.29
|
|
79
|
Co-evolution of transcriptional and post-translational cell-cycle regulation.
|
Nature
|
2006
|
3.28
|
|
80
|
The DNA sequence of human chromosome 7.
|
Nature
|
2003
|
3.18
|
|
81
|
Get the most out of your metagenome: computational analysis of environmental sequence data.
|
Curr Opin Microbiol
|
2007
|
3.15
|
|
82
|
Accurate and universal delineation of prokaryotic species.
|
Nat Methods
|
2013
|
3.14
|
|
83
|
STITCH 2: an interaction network database for small molecules and proteins.
|
Nucleic Acids Res
|
2009
|
3.06
|
|
84
|
Environments shape the nucleotide composition of genomes.
|
EMBO Rep
|
2005
|
2.96
|
|
85
|
Structure-based assembly of protein complexes in yeast.
|
Science
|
2004
|
2.89
|
|
86
|
Quantifying environmental adaptation of metabolic pathways in metagenomics.
|
Proc Natl Acad Sci U S A
|
2009
|
2.89
|
|
87
|
Comparison of computational methods for the identification of cell cycle-regulated genes.
|
Bioinformatics
|
2004
|
2.83
|
|
88
|
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
|
Nat Biotechnol
|
2004
|
2.83
|
|
89
|
SHOT: a web server for the construction of genome phylogenies.
|
Trends Genet
|
2002
|
2.79
|
|
90
|
ASTD: The Alternative Splicing and Transcript Diversity database.
|
Genomics
|
2008
|
2.72
|
|
91
|
A holistic approach to marine eco-systems biology.
|
PLoS Biol
|
2011
|
2.71
|
|
92
|
The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia.
|
Genomics
|
2003
|
2.69
|
|
93
|
NetworKIN: a resource for exploring cellular phosphorylation networks.
|
Nucleic Acids Res
|
2007
|
2.69
|
|
94
|
InterPro: an integrated documentation resource for protein families, domains and functional sites.
|
Brief Bioinform
|
2002
|
2.66
|
|
95
|
Information extraction from full text scientific articles: where are the keywords?
|
BMC Bioinformatics
|
2003
|
2.64
|
|
96
|
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.
|
RNA
|
2005
|
2.59
|
|
97
|
The identification of functional modules from the genomic association of genes.
|
Proc Natl Acad Sci U S A
|
2002
|
2.59
|
|
98
|
Increase of functional diversity by alternative splicing.
|
Trends Genet
|
2003
|
2.59
|
|
99
|
Metagenomic species profiling using universal phylogenetic marker genes.
|
Nat Methods
|
2013
|
2.51
|
|
100
|
iPath2.0: interactive pathway explorer.
|
Nucleic Acids Res
|
2011
|
2.50
|
|
101
|
Common exon duplication in animals and its role in alternative splicing.
|
Hum Mol Genet
|
2002
|
2.47
|
|
102
|
Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile.
|
Cell
|
2011
|
2.46
|
|
103
|
4DXpress: a database for cross-species expression pattern comparisons.
|
Nucleic Acids Res
|
2007
|
2.38
|
|
104
|
Ancient animal microRNAs and the evolution of tissue identity.
|
Nature
|
2010
|
2.35
|
|
105
|
STITCH 4: integration of protein-chemical interactions with user data.
|
Nucleic Acids Res
|
2013
|
2.32
|
|
106
|
Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii.
|
Science
|
2005
|
2.31
|
|
107
|
Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
|
Nature
|
2005
|
2.27
|
|
108
|
SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia.
|
Nat Genet
|
2002
|
2.27
|
|
109
|
Systematic association of genes to phenotypes by genome and literature mining.
|
PLoS Biol
|
2005
|
2.25
|
|
110
|
Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes.
|
Oncogene
|
2003
|
2.21
|
|
111
|
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
|
Genome Res
|
2004
|
2.17
|
|
112
|
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
|
Mol Syst Biol
|
2008
|
2.12
|
|
113
|
The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold.
|
Trends Biochem Sci
|
2003
|
2.11
|
|
114
|
Quantification of insect genome divergence.
|
Trends Genet
|
2006
|
2.10
|
|
115
|
Evolution of biomolecular networks: lessons from metabolic and protein interactions.
|
Nat Rev Mol Cell Biol
|
2009
|
2.09
|
|
116
|
Genome evolution reveals biochemical networks and functional modules.
|
Proc Natl Acad Sci U S A
|
2003
|
2.08
|
|
117
|
STITCH 3: zooming in on protein-chemical interactions.
|
Nucleic Acids Res
|
2011
|
2.05
|
|
118
|
Predicting protein cellular localization using a domain projection method.
|
Genome Res
|
2002
|
1.98
|
|
119
|
The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations.
|
EMBO Rep
|
2002
|
1.94
|
|
120
|
Country-specific antibiotic use practices impact the human gut resistome.
|
Genome Res
|
2013
|
1.94
|
|
121
|
Deciphering a global network of functionally associated post-translational modifications.
|
Mol Syst Biol
|
2012
|
1.86
|
|
122
|
Human gut microbes impact host serum metabolome and insulin sensitivity.
|
Nature
|
2016
|
1.85
|
|
123
|
G2D: a tool for mining genes associated with disease.
|
BMC Genet
|
2005
|
1.85
|
|
124
|
The microbiome explored: recent insights and future challenges.
|
Nat Rev Microbiol
|
2013
|
1.82
|
|
125
|
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.
|
ISME J
|
2012
|
1.81
|
|
126
|
Computing fuzzy associations for the analysis of biological literature.
|
Biotechniques
|
2002
|
1.76
|
|
127
|
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
|
Genome Biol
|
2002
|
1.72
|
|
128
|
Alternative splicing and evolution.
|
Bioessays
|
2003
|
1.69
|
|
129
|
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.
|
Proc Natl Acad Sci U S A
|
2008
|
1.68
|
|
130
|
Protein domain analysis in the era of complete genomes.
|
FEBS Lett
|
2002
|
1.67
|
|
131
|
Drug-induced regulation of target expression.
|
PLoS Comput Biol
|
2010
|
1.65
|
|
132
|
Extraction of transcript diversity from scientific literature.
|
PLoS Comput Biol
|
2005
|
1.64
|
|
133
|
MOCAT: a metagenomics assembly and gene prediction toolkit.
|
PLoS One
|
2012
|
1.64
|
|
134
|
Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.
|
Mol Syst Biol
|
2013
|
1.63
|
|
135
|
Complex genomic rearrangements lead to novel primate gene function.
|
Genome Res
|
2005
|
1.62
|
|
136
|
Ontologies in quantitative biology: a basis for comparison, integration, and discovery.
|
PLoS Biol
|
2010
|
1.62
|
|
137
|
Assessment of metagenomic assembly using simulated next generation sequencing data.
|
PLoS One
|
2012
|
1.57
|
|
138
|
Large-scale prediction of drug-target relationships.
|
FEBS Lett
|
2008
|
1.56
|
|
139
|
Orthology prediction methods: a quality assessment using curated protein families.
|
Bioessays
|
2011
|
1.56
|
|
140
|
OGEE: an online gene essentiality database.
|
Nucleic Acids Res
|
2011
|
1.54
|
|
141
|
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
|
Mol Syst Biol
|
2007
|
1.53
|
|
142
|
Predicting biological networks from genomic data.
|
FEBS Lett
|
2008
|
1.51
|
|
143
|
Prediction of drug combinations by integrating molecular and pharmacological data.
|
PLoS Comput Biol
|
2011
|
1.51
|
|
144
|
High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
|
Genome Biol
|
2010
|
1.51
|
|
145
|
Metabolites: a helping hand for pathway evolution?
|
Trends Biochem Sci
|
2003
|
1.50
|
|
146
|
Identification and analysis of evolutionarily cohesive functional modules in protein networks.
|
Genome Res
|
2006
|
1.48
|
|
147
|
Gene annotation from scientific literature using mappings between keyword systems.
|
Bioinformatics
|
2004
|
1.47
|
|
148
|
Similar gene expression profiles do not imply similar tissue functions.
|
Trends Genet
|
2006
|
1.46
|
|
149
|
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
|
Mol Syst Biol
|
2011
|
1.45
|
|
150
|
A computational screen for type I polyketide synthases in metagenomics shotgun data.
|
PLoS One
|
2008
|
1.44
|
|
151
|
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.
|
Mol Syst Biol
|
2012
|
1.44
|
|
152
|
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.
|
Mol Syst Biol
|
2010
|
1.43
|
|
153
|
Update of the G2D tool for prioritization of gene candidates to inherited diseases.
|
Nucleic Acids Res
|
2007
|
1.42
|
|
154
|
Systematic discovery of analogous enzymes in thiamin biosynthesis.
|
Nat Biotechnol
|
2003
|
1.41
|
|
155
|
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome.
|
Dev Biol
|
2006
|
1.40
|
|
156
|
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
|
Nucleic Acids Res
|
2004
|
1.39
|
|
157
|
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
|
Nucleic Acids Res
|
2012
|
1.39
|
|
158
|
Role for urea in nitrification by polar marine Archaea.
|
Proc Natl Acad Sci U S A
|
2012
|
1.38
|
|
159
|
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
|
Environ Microbiol
|
2013
|
1.35
|
|
160
|
Assessing systems properties of yeast mitochondria through an interaction map of the organelle.
|
PLoS Genet
|
2006
|
1.31
|
|
161
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