Published in BMC Bioinformatics on February 06, 2007
A high-coverage genome sequence from an archaic Denisovan individual. Science (2012) 7.89
A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol (2007) 3.71
The genomic landscape of Neanderthal ancestry in present-day humans. Nature (2014) 2.59
Targeted investigation of the Neandertal genome by array-based sequence capture. Science (2010) 2.49
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res (2008) 2.46
Temperature stress mediates decanalization and dominance of gene expression in Drosophila melanogaster. PLoS Genet (2015) 2.14
The draft genome of the parasitic nematode Trichinella spiralis. Nat Genet (2011) 2.03
Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol (2010) 1.92
Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A (2009) 1.78
Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One (2009) 1.53
Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science (2016) 1.41
Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. Mol Biol Evol (2010) 1.38
Human and chimpanzee gene expression differences replicated in mice fed different diets. PLoS One (2008) 1.35
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol (2010) 1.33
Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci U S A (2009) 1.31
Patterns of coding variation in the complete exomes of three Neandertals. Proc Natl Acad Sci U S A (2014) 1.29
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinformatics (2012) 1.27
Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors. Am J Hum Genet (2016) 1.23
Genome of the human hookworm Necator americanus. Nat Genet (2014) 1.18
Single sample expression-anchored mechanisms predict survival in head and neck cancer. PLoS Comput Biol (2012) 1.16
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution. J Biomed Semantics (2011) 1.15
Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome. Mol Biol Evol (2012) 1.13
Evaluation of research in biomedical ontologies. Brief Bioinform (2012) 1.12
Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species. PLoS One (2011) 1.08
RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. BMC Bioinformatics (2011) 1.08
The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans. Curr Biol (2016) 1.05
Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles. Genome Med (2012) 1.01
Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance. Proc Natl Acad Sci U S A (2014) 0.98
Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. Plant Physiol (2013) 0.95
Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon. PLoS Pathog (2013) 0.95
A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet (2016) 0.94
Novel venom gene discovery in the platypus. Genome Biol (2010) 0.94
Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation. BMC Genomics (2010) 0.93
Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum. PLoS Negl Trop Dis (2014) 0.93
Transcription factors are targeted by differentially expressed miRNAs in primates. Genome Biol Evol (2012) 0.93
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. Nucleic Acids Res (2014) 0.91
An effective model for natural selection in promoters. Genome Res (2010) 0.90
Transcription profiling reveals stage- and function-dependent expression patterns in the filarial nematode Brugia malayi. BMC Genomics (2012) 0.88
Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments. Mol Cell Proteomics (2015) 0.88
Functional transcriptomics of a migrating cell in Caenorhabditis elegans. Proc Natl Acad Sci U S A (2012) 0.87
Identification of putative target genes of the transcription factor RUNX2. PLoS One (2013) 0.86
Evolution of neuronal and endothelial transcriptomes in primates. Genome Biol Evol (2010) 0.85
Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction. BMC Genomics (2013) 0.84
Analyzing gene expression data in mice with the Neuro Behavior Ontology. Mamm Genome (2013) 0.84
Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes. Nat Commun (2014) 0.82
Linking tissues to phenotypes using gene expression profiles. Database (Oxford) (2014) 0.82
The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. Nat Genet (2015) 0.81
Systems biology studies of adult paragonimus lung flukes facilitate the identification of immunodominant parasite antigens. PLoS Negl Trop Dis (2014) 0.81
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology. PLoS One (2015) 0.81
Effects of doxycycline on gene expression in Wolbachia and Brugia malayi adult female worms in vivo. J Biomed Sci (2012) 0.80
Visual annotation display (VLAD): a tool for finding functional themes in lists of genes. Mamm Genome (2015) 0.79
Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. BMC Evol Biol (2012) 0.78
Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biol (2015) 0.78
Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock. Biotechnol Adv (2015) 0.78
Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues. Mol Genet Genomics (2013) 0.78
Differentially expressed genes in hypothalamus in relation to genomic regions under selection in two chicken lines resulting from divergent selection for high or low body weight. Neurogenetics (2011) 0.78
Gene expression analysis in Musa acuminata during compatible interactions with Meloidogyne incognita. Ann Bot (2017) 0.77
An evidence-based approach to identify aging-related genes in Caenorhabditis elegans. BMC Bioinformatics (2015) 0.77
The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi. Vet Parasitol (2009) 0.77
Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals. Front Plant Sci (2016) 0.77
A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe. Front Genet (2016) 0.77
Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont. Nat Microbiol (2016) 0.77
Human adaptation and population differentiation in the light of ancient genomes. Nat Commun (2016) 0.76
Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res (2017) 0.76
Genetic Evidence of Human Adaptation to a Cooked Diet. Genome Biol Evol (2016) 0.76
Trichinella spiralis: Adaptation and parasitism. Vet Parasitol (2016) 0.75
ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain. Bioinformatics (2016) 0.75
Identification of candidate genes and physiological pathways involved in gonad deformation in whitefish (Coregonus spp.) from Lake Thun, Switzerland. Int J Environ Res Public Health (2011) 0.75
Human Lineage-Specific Transcriptional Regulation through GA-Binding Protein Transcription Factor Alpha (GABPa). Mol Biol Evol (2016) 0.75
Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini. Parasit Vectors (2016) 0.75
Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans. BMC Evol Biol (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Serial analysis of gene expression. Science (1995) 60.15
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
Adaptive protein evolution at the Adh locus in Drosophila. Nature (1991) 31.65
GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics (2004) 30.14
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (2004) 26.64
Initial sequence of the chimpanzee genome and comparison with the human genome. Nature (2005) 25.67
GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63
Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics (2003) 16.60
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics (2005) 14.02
Global functional profiling of gene expression. Genomics (2003) 12.05
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33
GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics (2004) 11.23
GeneMerge--post-genomic analysis, data mining, and hypothesis testing. Bioinformatics (2003) 9.27
Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A (2005) 8.75
eVOC: a controlled vocabulary for unifying gene expression data. Genome Res (2003) 5.41
Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics (2005) 4.27
GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. Nucleic Acids Res (2004) 4.10
Comparing functional annotation analyses with Catmap. BMC Bioinformatics (2004) 2.92
Comparison of methods for estimating the number of true null hypotheses in multiplicity testing. J Biopharm Stat (2003) 2.83
OntologyTraverser: an R package for GO analysis. Bioinformatics (2004) 2.56
Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression. Bioinformatics (2004) 2.47
Human specific loss of olfactory receptor genes. Proc Natl Acad Sci U S A (2003) 2.23
Genomics, prior probability, and statistical tests of multiple hypotheses. Genome Res (2004) 1.96
Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics (2004) 1.95
Statistical concerns about the GSEA procedure. Nat Genet (2004) 1.91
Sequence divergence, functional constraint, and selection in protein evolution. Annu Rev Genomics Hum Genet (2003) 1.84
GOAL: automated Gene Ontology analysis of expression profiles. Nucleic Acids Res (2004) 1.79
Handling multiple testing while interpreting microarrays with the Gene Ontology Database. BMC Bioinformatics (2004) 1.19
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet (2007) 20.22
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature (2010) 8.99
Sequencing and analysis of Neanderthal genomic DNA. Science (2006) 8.06
Intra- and interspecific variation in primate gene expression patterns. Science (2002) 7.92
A high-coverage genome sequence from an archaic Denisovan individual. Science (2012) 7.89
The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell (2008) 6.98
Analysis of one million base pairs of Neanderthal DNA. Nature (2006) 6.17
Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A (2007) 6.12
Molecular evolution of FOXP2, a gene involved in speech and language. Nature (2002) 5.89
Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet (2002) 5.80
Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science (2009) 5.79
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science (2005) 5.68
A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature (2005) 5.51
Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48
Fine-scale recombination patterns differ between chimpanzees and humans. Nat Genet (2005) 5.00
Evidence for gradients of human genetic diversity within and among continents. Genome Res (2004) 4.70
Early allelic selection in maize as revealed by ancient DNA. Science (2003) 4.38
From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res (2007) 4.26
Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24
The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature (2010) 3.90
Accelerated evolution of conserved noncoding sequences in humans. Science (2006) 3.87
Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics (2009) 3.87
Regional patterns of gene expression in human and chimpanzee brains. Genome Res (2004) 3.84
No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol (2004) 3.81
Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature (2005) 3.74
A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice. Cell (2009) 3.63
A neutral explanation for the correlation of diversity with recombination rates in humans. Am J Hum Genet (2003) 3.57
Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet (2011) 3.53
A neutral model of transcriptome evolution. PLoS Biol (2004) 3.44
Genomic sequencing of Pleistocene cave bears. Science (2005) 3.40
The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol (2007) 3.39
Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One (2010) 3.35
Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol (2008) 3.21
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res (2009) 3.09
A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol (2009) 3.09
Evolution of primate gene expression. Nat Rev Genet (2006) 3.04
Aspm specifically maintains symmetric proliferative divisions of neuroepithelial cells. Proc Natl Acad Sci U S A (2006) 3.03
Great ape genetic diversity and population history. Nature (2013) 2.95
Autosomal recessive primary microcephaly (MCPH): a review of clinical, molecular, and evolutionary findings. Am J Hum Genet (2005) 2.86
PatMaN: rapid alignment of short sequences to large databases. Bioinformatics (2008) 2.77
Neanderthals in central Asia and Siberia. Nature (2007) 2.64
Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS One (2012) 2.60
Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin Chem (2009) 2.57
Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biol (2004) 2.56
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc Natl Acad Sci U S A (2012) 2.54
The bonobo genome compared with the chimpanzee and human genomes. Nature (2012) 2.49
Targeted investigation of the Neandertal genome by array-based sequence capture. Science (2010) 2.49
Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res (2003) 2.48
The Neandertal genome and ancient DNA authenticity. EMBO J (2009) 2.46
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci U S A (2013) 2.45
Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am J Hum Genet (2003) 2.44
MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res (2010) 2.44
The date of interbreeding between Neandertals and modern humans. PLoS Genet (2012) 2.35
Why do human diversity levels vary at a megabase scale? Genome Res (2005) 2.33
DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci U S A (2013) 2.31
Impaired synaptic plasticity and motor learning in mice with a point mutation implicated in human speech deficits. Curr Biol (2008) 2.27
Human specific loss of olfactory receptor genes. Proc Natl Acad Sci U S A (2003) 2.23
Histone demethylase UTX-1 regulates C. elegans life span by targeting the insulin/IGF-1 signaling pathway. Cell Metab (2011) 2.22
Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol (2004) 2.22
The Neandertal type site revisited: interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. Proc Natl Acad Sci U S A (2002) 1.98
Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea. Am J Hum Genet (2002) 1.86
Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol (2005) 1.82
COnto-Diff: generation of complex evolution mappings for life science ontologies. J Biomed Inform (2012) 1.80
Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A (2009) 1.78
Mutations in mouse Aspm (abnormal spindle-like microcephaly associated) cause not only microcephaly but also major defects in the germline. Proc Natl Acad Sci U S A (2010) 1.76
Aging and gene expression in the primate brain. PLoS Biol (2005) 1.76
Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics (2009) 1.76
Recent origin and cultural reversion of a hunter-gatherer group. PLoS Biol (2005) 1.75
Mitochondrial DNA of an Iberian Neandertal suggests a population affinity with other European Neandertals. Curr Biol (2006) 1.69