Published in BMC Genomics on May 10, 2005
Sequencing technologies and genome sequencing. J Appl Genet (2011) 2.52
SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genet (2008) 1.92
A high utility integrated map of the pig genome. Genome Biol (2007) 1.88
Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet (2012) 1.63
Discovery of porcine microRNAs and profiling from skeletal muscle tissues during development. PLoS One (2008) 1.55
Cloning, characterization and expression analysis of porcine microRNAs. BMC Genomics (2009) 1.49
Advances in QTL mapping in pigs. Int J Biol Sci (2007) 1.42
Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A. BMC Biotechnol (2006) 1.41
MicroRNAome of porcine pre- and postnatal development. PLoS One (2010) 1.40
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol (2007) 1.39
Deciphering the porcine intestinal microRNA transcriptome. BMC Genomics (2010) 1.30
Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci (2007) 1.29
The uncoupling protein 1 gene (UCP1) is disrupted in the pig lineage: a genetic explanation for poor thermoregulation in piglets. PLoS Genet (2006) 1.26
Identification of a single killer immunoglobulin-like receptor (KIR) gene in the porcine leukocyte receptor complex on chromosome 6q. Immunogenetics (2006) 1.26
LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs. Genome Biol (2007) 1.25
MicroRNA: biological and computational perspective. Genomics Proteomics Bioinformatics (2005) 1.23
Discovery of porcine microRNAs in multiple tissues by a Solexa deep sequencing approach. PLoS One (2011) 1.22
Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response. BMC Genomics (2010) 1.19
A gene expression atlas of the domestic pig. BMC Biol (2012) 1.18
Structural and functional annotation of the porcine immunome. BMC Genomics (2013) 1.16
Completion of the swine genome will simplify the production of swine as a large animal biomedical model. BMC Med Genomics (2012) 1.14
What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). BMC Genomics (2009) 1.12
Optimizing culture conditions of a porcine epithelial cell line IPEC-J2 through a histological and physiological characterization. Cytotechnology (2011) 1.10
Genome sequences of wild and domestic bactrian camels. Nat Commun (2012) 1.07
Genetically modified pigs for biomedical research. J Inherit Metab Dis (2012) 1.05
Mining for single nucleotide polymorphisms in pig genome sequence data. BMC Genomics (2009) 1.02
Identification and characterization of new microRNAs from pig. Mamm Genome (2008) 1.00
Design and development of exome capture sequencing for the domestic pig (Sus scrofa). BMC Genomics (2014) 0.98
Gene expression profiles in testis of pigs with extreme high and low levels of androstenone. BMC Genomics (2007) 0.98
Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae. BMC Genomics (2012) 0.96
Genome-wide association analyses for fatty acid composition in porcine muscle and abdominal fat tissues. PLoS One (2013) 0.93
Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology. BMC Genomics (2011) 0.93
Structured RNAs and synteny regions in the pig genome. BMC Genomics (2014) 0.92
Gene expression profiles in liver of pigs with extreme high and low levels of androstenone. BMC Vet Res (2008) 0.91
Farm animal genomics and informatics: an update. Nucleic Acids Res (2005) 0.90
Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery. DNA Res (2011) 0.89
A robust linkage map of the porcine autosomes based on gene-associated SNPs. BMC Genomics (2009) 0.89
Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs. BMC Genomics (2015) 0.88
The adult boar testicular and epididymal transcriptomes. BMC Genomics (2009) 0.88
A comprehensive expression profile of microRNAs in porcine pituitary. PLoS One (2011) 0.88
Mapping and expression studies of the mir17-92 cluster on pig chromosome 11. Mamm Genome (2005) 0.88
PigGIS: Pig Genomic Informatics System. Nucleic Acids Res (2006) 0.87
Detection of RNA structures in porcine EST data and related mammals. BMC Genomics (2007) 0.86
Pig genomics for biomedicine. Nat Biotechnol (2013) 0.86
Microglia processes associate with diffusely injured axons following mild traumatic brain injury in the micro pig. J Neuroinflammation (2015) 0.84
Realistic artificial DNA sequences as negative controls for computational genomics. Nucleic Acids Res (2014) 0.83
Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary. BMC Genomics (2014) 0.82
Advanced technologies for genomic analysis in farm animals and its application for QTL mapping. Genetica (2008) 0.82
Functional characterization of the ER stress induced X-box-binding protein-1 (Xbp-1) in the porcine system. BMC Mol Biol (2011) 0.82
Molecular characterization and exclusion of porcine GUSB as a candidate gene for congenital hernia inguinalis/scrotalis. BMC Vet Res (2006) 0.81
Early-life stress origins of gastrointestinal disease: animal models, intestinal pathophysiology, and translational implications. Am J Physiol Gastrointest Liver Physiol (2015) 0.81
Displacement and strain estimation for evaluation of arterial wall stiffness using a familial hypercholesterolemia swine model of atherosclerosis. Med Phys (2012) 0.81
A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China. Philos Trans R Soc Lond B Biol Sci (2007) 0.81
Identification and analysis of pig chimeric mRNAs using RNA sequencing data. BMC Genomics (2012) 0.80
Comparative analysis of a BAC contig of porcine chromosome 13q31-q32 and human chromosome 3q21-q22. BMC Genomics (2005) 0.80
Investigation of TXNIP (thioredoxin-interacting protein) and TRX (thioredoxin) genes for growth-related traits in pigs. Mamm Genome (2007) 0.80
Genome survey sequencing provides clues into glucosinolate biosynthesis and flowering pathway evolution in allotetrapolyploid Brassica juncea. BMC Genomics (2014) 0.80
Identification and characterization of the porcine (Sus scrofa) survival motor neuron (SMN1) gene: an animal model for therapeutic studies. Dev Dyn (2008) 0.79
Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian muntjac (Muntiacus muntjak vaginalis). Chromosoma (2006) 0.79
EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues. BMC Genomics (2007) 0.79
From QTL to QTN: candidate gene set approach and a case study in porcine IGF1-FoxO pathway. PLoS One (2013) 0.78
Dissecting the role of milk components on gut microbiota composition. Gut Microbes (2012) 0.78
Transcriptome profiling identifies differentially expressed genes in postnatal developing pituitary gland of miniature pig. DNA Res (2013) 0.78
Respiratory nanoparticle-based vaccines and challenges associated with animal models and translation. J Control Release (2015) 0.77
Neoplastic transformation of porcine mammary epithelial cells in vitro and tumor formation in vivo. BMC Cancer (2015) 0.77
A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits. BMC Genomics (2015) 0.77
Altered adipocyte structure and function in nutritionally programmed microswine offspring. J Dev Orig Health Dis (2012) 0.77
Age-Related 1H NMR Characterization of Cerebrospinal Fluid in Newborn and Young Healthy Piglets. PLoS One (2016) 0.77
Early Activation of MAPK p44/42 Is Partially Involved in DON-Induced Disruption of the Intestinal Barrier Function and Tight Junction Network. Toxins (Basel) (2016) 0.77
Quantitative proteomics and bioinformatic analysis provide new insight into the dynamic response of porcine intestine to Salmonella Typhimurium. Front Cell Infect Microbiol (2015) 0.76
Porcine models of muscular dystrophy. ILAR J (2015) 0.76
Expression Profiles and Biological Roles of miR-196a in Swine. Genes (Basel) (2016) 0.76
Laparoscopic Roux-en-Y gastric bypass in super obese Göttingen minipigs. Am J Transl Res (2013) 0.76
Meganucleases Revolutionize the Production of Genetically Engineered Pigs for the Study of Human Diseases. Toxicol Pathol (2015) 0.76
Early life adversity in piglets induces long-term upregulation of the enteric cholinergic nervous system and heightened, sex-specific secretomotor neuron responses. Neurogastroenterol Motil (2016) 0.76
Accelerated growth without prepubertal obesity in nutritionally programmed microswine offspring. J Dev Orig Health Dis (2012) 0.76
Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome. BMC Genomics (2015) 0.76
Phenotypic and genetic characterization of a novel phenotype in pigs characterized by juvenile hairlessness and age dependent emphysema. BMC Genomics (2008) 0.75
Measurements of wall shear stress and aortic pulse wave velocity in swine with familial hypercholesterolemia. J Magn Reson Imaging (2014) 0.75
Development of Accelerated Coronary Atherosclerosis Model Using Low Density Lipoprotein Receptor Knock-Out Swine with Balloon Injury. PLoS One (2016) 0.75
Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PLoS One (2015) 0.75
Absence of an intron splicing silencer in porcine Smn1 intron 7 confers immunity to the exon skipping mutation in human SMN2. PLoS One (2014) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
The human genome browser at UCSC. Genome Res (2002) 168.23
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
CAP3: A DNA sequence assembly program. Genome Res (1999) 50.04
A greedy algorithm for aligning DNA sequences. J Comput Biol (2000) 47.89
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol (1985) 47.78
PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07
Human-mouse alignments with BLASTZ. Genome Res (2003) 35.49
The microRNA Registry. Nucleic Acids Res (2004) 29.45
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
A uniform system for microRNA annotation. RNA (2003) 20.28
Ultraconserved elements in the human genome. Science (2004) 17.14
Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics (1999) 12.22
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics (2003) 12.00
Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci U S A (2003) 6.29
An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res (2004) 4.38
DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature (2004) 4.12
Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol (1995) 2.65
An examination of the generation-time effect on molecular evolution. Proc Natl Acad Sci U S A (1993) 1.57
Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. BMC Biol (2005) 1.51
The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol (2004) 1.28
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Enterotypes of the human gut microbiome. Nature (2011) 24.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
International network of cancer genome projects. Nature (2010) 20.35
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell (2005) 14.32
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
Prepublication data sharing. Nature (2009) 12.24
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet (2010) 8.75
The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A (2005) 8.60
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res (2008) 7.45
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09
Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia. Nat Genet (2010) 7.08
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res (2008) 6.73
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Aberrant excitatory neuronal activity and compensatory remodeling of inhibitory hippocampal circuits in mouse models of Alzheimer's disease. Neuron (2007) 6.60
iPS cells produce viable mice through tetraploid complementation. Nature (2009) 6.51
Clinical features of the initial cases of 2009 pandemic influenza A (H1N1) virus infection in China. N Engl J Med (2009) 6.45
Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses. Lancet (2013) 6.10
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell (2007) 5.99
Regulation of JAK-STAT signalling in the immune system. Nat Rev Immunol (2003) 5.77
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics (2009) 5.67
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Building the sequence map of the human pan-genome. Nat Biotechnol (2009) 5.53
Aryl hydrocarbon receptor antagonists promote the expansion of human hematopoietic stem cells. Science (2010) 5.50
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules. Mol Biol Cell (2002) 5.20
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
Bone marrow edema and its relation to progression of knee osteoarthritis. Ann Intern Med (2003) 4.98
Acute myeloid leukemia or myelodysplastic syndrome following use of granulocyte colony-stimulating factors during breast cancer adjuvant chemotherapy. J Natl Cancer Inst (2007) 4.97
Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res (2002) 4.92