Published in Bioinformatics on February 10, 2004
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
The human microbiome project. Nature (2007) 28.53
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics (2009) 16.52
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res (2007) 13.08
The regulated retrotransposon transcriptome of mammalian cells. Nat Genet (2009) 5.79
Genomic analysis of mouse retinal development. PLoS Biol (2004) 4.66
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res (2012) 3.80
Global analysis of X-chromosome dosage compensation. J Biol (2006) 3.78
seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res (2010) 3.74
Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res (2013) 3.61
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57
High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science (2011) 3.53
Iron regulation of the major virulence factors in the AIDS-associated pathogen Cryptococcus neoformans. PLoS Biol (2006) 3.43
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. BMC Bioinformatics (2011) 3.42
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res (2009) 3.36
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res (2005) 3.36
Statistical mixture modeling for cell subtype identification in flow cytometry. Cytometry A (2008) 3.06
Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature (2007) 3.04
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell (2008) 2.96
The draft genome of sweet orange (Citrus sinensis). Nat Genet (2012) 2.81
Comprehensive expression profiling of tumor cell lines identifies molecular signatures of melanoma progression. PLoS One (2007) 2.77
Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat Genet (2004) 2.75
Human umbilical cord plasma proteins revitalize hippocampal function in aged mice. Nature (2017) 2.71
Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol (2007) 2.69
Cyclic changes in metabolic state during the life of a yeast cell. Proc Natl Acad Sci U S A (2007) 2.65
Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol (2007) 2.60
Transcription analysis of arabidopsis membrane transporters and hormone pathways during developmental and induced leaf senescence. Plant Physiol (2006) 2.57
Information-based clustering. Proc Natl Acad Sci U S A (2005) 2.57
The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res (2012) 2.55
DMRT1 prevents female reprogramming in the postnatal mammalian testis. Nature (2011) 2.53
Genome-wide analysis of long noncoding RNA stability. Genome Res (2012) 2.49
Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol (2011) 2.43
Distinct brain transcriptome profiles in C9orf72-associated and sporadic ALS. Nat Neurosci (2015) 2.42
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet (2011) 2.41
Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat Genet (2014) 2.38
Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells. Sci Signal (2011) 2.33
Condition-adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf. Aging Cell (2009) 2.32
A core MYC gene expression signature is prominent in basal-like breast cancer but only partially overlaps the core serum response. PLoS One (2009) 2.29
Differential L1 regulation in pluripotent stem cells of humans and apes. Nature (2013) 2.29
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res (2013) 2.23
Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol (2004) 2.22
Rhinovirus-induced modulation of gene expression in bronchial epithelial cells from subjects with asthma. Mucosal Immunol (2009) 2.22
Mir193b-365 is essential for brown fat differentiation. Nat Cell Biol (2011) 2.20
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20
RNA editing in the human ENCODE RNA-seq data. Genome Res (2012) 2.18
Molecular mechanisms related to parturition-induced stress urinary incontinence. Eur Urol (2008) 2.17
An in-depth comparison of latent HIV-1 reactivation in multiple cell model systems and resting CD4+ T cells from aviremic patients. PLoS Pathog (2013) 2.16
Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proc Natl Acad Sci U S A (2008) 2.16
Mutant-specific gene programs in the zebrafish. Blood (2005) 2.15
Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J (2011) 2.10
m(6)A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature (2017) 2.07
Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res (2006) 2.04
Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae. Plant Cell (2009) 2.03
Regulatory T Cells in Skin Facilitate Epithelial Stem Cell Differentiation. Cell (2017) 2.03
Clustering cancer gene expression data: a comparative study. BMC Bioinformatics (2008) 2.00
Identification of glucose-regulated miRNAs from pancreatic {beta} cells reveals a role for miR-30d in insulin transcription. RNA (2008) 1.95
Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol (2008) 1.95
The metabolic footprint of aging in mice. Sci Rep (2011) 1.93
An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics (2011) 1.92
A simple array platform for microRNA analysis and its application in mouse tissues. RNA (2007) 1.91
Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol (2013) 1.88
DICER1 mutations in familial multinodular goiter with and without ovarian Sertoli-Leydig cell tumors. JAMA (2011) 1.85
Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature (2014) 1.81
Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis. Sci Transl Med (2013) 1.81
A common set of DNA regulatory elements shapes Drosophila appendages. Dev Cell (2013) 1.79
The Bacillus subtilis sigma(M) regulon and its contribution to cell envelope stress responses. Mol Microbiol (2008) 1.78
A global analysis of genetic interactions in Caenorhabditis elegans. J Biol (2007) 1.78
A gene regulatory network for root epidermis cell differentiation in Arabidopsis. PLoS Genet (2012) 1.75
GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics (2004) 1.75
Combined PI3K/mTOR and MEK inhibition provides broad antitumor activity in faithful murine cancer models. Clin Cancer Res (2012) 1.74
Human spontaneous labor without histologic chorioamnionitis is characterized by an acute inflammation gene expression signature. Am J Obstet Gynecol (2006) 1.73
3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res (2010) 1.71
Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci U S A (2010) 1.71
IL-1β production through the NLRP3 inflammasome by hepatic macrophages links hepatitis C virus infection with liver inflammation and disease. PLoS Pathog (2013) 1.67
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. Genome Res (2010) 1.67
Grading the severity of cervical neoplasia based on combined histopathology, cytopathology, and HPV genotype distribution among 1,700 women referred to colposcopy in Oklahoma. Int J Cancer (2009) 1.65
Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Mol Cell (2013) 1.62
A resource for analysis of microRNA expression and function in pancreatic ductal adenocarcinoma cells. Cancer Biol Ther (2009) 1.61
Identification of Arx transcriptional targets in the developing basal forebrain. Hum Mol Genet (2008) 1.58
Tolerance is established in polyclonal CD4(+) T cells by distinct mechanisms, according to self-peptide expression patterns. Nat Immunol (2016) 1.57
Vagus nerve stimulation mediates protection from kidney ischemia-reperfusion injury through α7nAChR+ splenocytes. J Clin Invest (2016) 1.56
ChemMine. A compound mining database for chemical genomics. Plant Physiol (2005) 1.56
Retracted Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics. PLoS One (2013) 1.55
Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments. Nucleic Acids Res (2006) 1.54
Synthesis of methylphosphonic acid by marine microbes: a source for methane in the aerobic ocean. Science (2012) 1.53
Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains. Genome Res (2012) 1.52
DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0. Chem Cent J (2008) 1.52
Large-scale profiling of Rab GTPase trafficking networks: the membrome. Mol Biol Cell (2005) 1.49
Il10 deficiency rebalances innate immunity to mitigate Alzheimer-like pathology. Neuron (2015) 1.49
Defining estrogenic mechanisms of bisphenol A analogs through high throughput microscopy-based contextual assays. Chem Biol (2014) 1.49
Role of p53 serine 46 in p53 target gene regulation. PLoS One (2011) 1.48
High-resolution analysis with novel cell-surface markers identifies routes to iPS cells. Nature (2013) 1.48
Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proc Natl Acad Sci U S A (2009) 1.48
Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. PLoS Med (2016) 1.48
S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics. Mol Cell Proteomics (2011) 1.48
Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. Proc Natl Acad Sci U S A (2010) 1.46
LGR5 Activates Noncanonical Wnt Signaling and Inhibits Aldosterone Production in the Human Adrenal. J Clin Endocrinol Metab (2015) 1.45
Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol (2013) 1.45
Multifactorial index of cardiac risk in noncardiac surgical procedures. N Engl J Med (1977) 8.24
Airway management in the emergency department. Br J Anaesth (2002) 4.80
Metabolic effects of troglitazone monotherapy in type 2 diabetes mellitus. A randomized, double-blind, placebo-controlled trial. Ann Intern Med (1998) 3.41
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac Symp Biocomput (1999) 3.27
Early clinical failure of the Birmingham metal-on-metal hip resurfacing is associated with metallosis and soft-tissue necrosis. J Bone Joint Surg Br (2009) 2.61
A defence of the NICE guidelines on intravenous fluids. Anaesthesia (2014) 2.55
ERC 2010 guidelines for adult and pediatric resuscitation: summary of major changes. Minerva Anestesiol (2011) 2.04
A three-year trial of atromid therapy in exudative diabetic retinopathy. Diabetes (1968) 1.95
Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. Pac Symp Biocomput (2004) 1.94
Eye injuries in organised sport in a rural area. Br J Ophthalmol (1983) 1.89
The Key Extended Entry Program (KEEP): a methadone treatment program for opiate-dependent inmates. Mt Sinai J Med (2001) 1.84
Exercise-induced left ventricular dysfunction in alcoholic and non-alcoholic cirrhosis. J Hepatol (1995) 1.84
Evaluation and comparison of guidelines for the management of people with type 2 diabetes from eight European countries. Diabetes Res Clin Pract (2009) 1.79
Finding optimal models for small gene networks. Pac Symp Biocomput (2004) 1.74
The relationship between QT intervals and mortality in ambulant patients with chronic heart failure. The united kingdom heart failure evaluation and assessment of risk trial (UK-HEART) Eur Heart J (1999) 1.68
Tidal volumes which are perceived to be adequate for resuscitation. Resuscitation (1996) 1.65
Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics (2000) 1.60
A randomised control trial to determine if use of the iResus© application on a smart phone improves the performance of an advanced life support provider in a simulated medical emergency. Anaesthesia (2011) 1.59
The biomechanical effect of postoperative hypolordosis in instrumented lumbar fusion on instrumented and adjacent spinal segments. Spine (Phila Pa 1976) (2000) 1.57
Spontaneous regression of hepatocellular carcinoma and review of literature. J Gastroenterol Hepatol (2000) 1.50
Recreational drug misuse: issues for the cardiologist. Heart (2000) 1.49
Recommendations for uniform reporting of data following major trauma--the Utstein Style. An International Trauma Anaesthesia and Critical Care Society (ITACCS) initiative. Eur J Emerg Med (1999) 1.40
Digoxin and mortality in chronic heart failure. UK Heart Investigation. Lancet (1999) 1.40
Lifetime occupational exercise and colon cancer. Am J Epidemiol (1985) 1.40
VFA production in the pig large intestine. J Anim Sci (1978) 1.39
MRI of early symptomatic metal-on-metal total hip arthroplasty: a retrospective review of radiological findings in 20 hips. Clin Radiol (2007) 1.39
A psychosocial group intervention for Japanese women with primary breast carcinoma. Cancer (2000) 1.39
A novel index for predicting intraocular pressure reduction following cataract surgery. Br J Ophthalmol (2005) 1.38
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. J Comput Biol (2000) 1.38
Nail gun injuries in residential carpentry: lessons from active injury surveillance. Inj Prev (2003) 1.38
Advanced life support resuscitation protocols. Br J Hosp Med (Lond) (2009) 1.38
Algorithms for inferring qualitative models of biological networks. Pac Symp Biocomput (2000) 1.37
Vitamin D absorption in healthy subjects and in patients with intestinal malabsorption syndromes. Am J Clin Nutr (1985) 1.30
European Resuscitation Council Guidelines 2000 for Adult Advanced Life Support. A statement from the Advanced Life Support Working Group(1) and approved by the Executive Committee of the European Resuscitation Council. Resuscitation (2001) 1.29
Enuresis: a descriptive analysis and a controlled trial. Dev Med Child Neurol (1972) 1.27
Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput (2000) 1.26
Statistical analysis of a small set of time-ordered gene expression data using linear splines. Bioinformatics (2002) 1.22
A cohort evaluation of the paediatric i-gel(™) airway during anaesthesia in 120 children. Anaesthesia (2011) 1.15
Fibrotic focus in invasive ductal carcinoma of the breast: a histopathological prognostic parameter for tumor recurrence and tumor death within three years after the initial operation. Jpn J Cancer Res (1997) 1.14
Factors correlated with fatigue in disease-free breast cancer patients: application of the Cancer Fatigue Scale. Support Care Cancer (2000) 1.12
The posttraining plans of international medical graduates and US medical graduates in New York State. JAMA (2000) 1.11
Novel recurrent mutations in the RAS-like GTP-binding gene RIT1 in myeloid malignancies. Leukemia (2013) 1.10
Cardiac risk factors and complications in non-cardiac surgery. Medicine (Baltimore) (1978) 1.10
Radial artery anomaly and its influence on transradial coronary procedural outcome. Heart (2008) 1.10
Heterocyclic mono-N-oxides with potential applications as bioreductive anti-tumour drugs: Part 1. 8-Alkylamino-substituted phenylimidazo [1,2-a] quinoxalines. Anticancer Drug Des (1993) 1.08
CT and MRI of hip arthroplasty. Clin Radiol (2007) 1.06
Malignant phyllodes tumour with a noninvasive ductal carcinoma component. Virchows Arch (1998) 1.05
Diet in the epidemiology of gastric cancer. Nutr Cancer (1990) 1.04
Myelofibrosis complicated by infection due to Candida albicans: emergence of resistance to antifungal agents during therapy. Clin Infect Dis (1997) 1.04
Potentiation of the anti-tumour effect of melphalan by the vasoactive agent, hydralazine. Br J Cancer (1988) 1.04
1998 European guidelines on resuscitation. Simplifications should make them easier to teach and implement. BMJ (1998) 1.02
Relationship of multiple forms of chromogranin. J Biol Chem (1985) 1.01
VFA metabolism in the pig. J Anim Sci (1978) 1.00
DUSP22/LMW-DSP2 regulates estrogen receptor-alpha-mediated signaling through dephosphorylation of Ser-118. Oncogene (2007) 0.99
A clinical experience of major multiple trauma in Maryland. Md State Med J (1976) 0.98
Mesenteric fibromatosis presenting as fever of unknown origin. Am J Gastroenterol (1992) 0.98
A comparative study of amino acid consumption by rat islet cells and the clonal beta-cell line BRIN-BD11 - the functional significance of L-alanine. J Endocrinol (2003) 0.98
Visual perceptions induced by intravitreous injections of therapeutic agents. Eye (Lond) (2011) 0.97
Ruthenium complex-catalyzed direct ortho arylation and alkenylation of 2-arylpyridines with organic halides. Org Lett (2001) 0.97
Late, intermittent obstruction of a mitral prosthesis by chordal remnants. Eur J Cardiothorac Surg (1997) 0.97
Predicting sudden death in patients with mild to moderate chronic heart failure. Heart (2004) 0.97
Double-blind, placebo-controlled analgesic study of ibuprofen or rofecoxib in combination with paracetamol for tonsillectomy in children. Br J Anaesth (2002) 0.96
Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution. Bioinformatics (2004) 0.95
Predictors of tumour involvement in remaining axillary lymph nodes of breast cancer patients with positive sentinel lymph node. Eur J Surg Oncol (2005) 0.95
Push, blow or both: is there a role for compression-only CPR? Anaesthesia (2010) 0.95
The medial approach for operative release of post-traumatic contracture of the elbow. J Bone Joint Surg Br (2000) 0.94
A two-year, double-blind comparison of estrogen-androgen and conjugated estrogens in surgically menopausal women. Effects on bone mineral density, symptoms and lipid profiles. J Reprod Med (1999) 0.94
Further applications of Archimedes' principle in the correction of asymmetrical breasts. Ann Plast Surg (1986) 0.94
Impact of objectively measured sedentary behaviour on changes in insulin resistance and secretion over 3 years in the RISC study: interaction with weight gain. Diabetes Metab (2013) 0.94
Microscopic distribution of misonidazole in mouse tissues. Br J Cancer (1989) 0.93
NAD(P)H nitroblue tetrazolium reductase levels in apparently normoxic tissues: a histochemical study correlating enzyme activity with binding of radiolabelled misonidazole. Br J Cancer (1990) 0.93
Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks. Pac Symp Biocomput (2004) 0.92
Biomedical and psychosocial determinants of psychiatric morbidity among postoperative ambulatory breast cancer patients. Breast Cancer Res Treat (2001) 0.92
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. Bioinformatics (2004) 0.92
Present status of clofibrate therapy in ophthalmology. Br J Ophthalmol (1969) 0.92
Implementation of a diagnostic and interventional transradial programme: resource and organisational implications. Heart (2003) 0.92
Observations and warning signs prior to cardiac arrest. Should a medical emergency team intervene earlier? Acta Anaesthesiol Scand (2005) 0.92
Intrasplicing--analysis of long intron sequences. Pac Symp Biocomput (2003) 0.91
Effects of bisphosphonate on the remodeling of rat sagittal suture after rapid expansion. Angle Orthod (2001) 0.91
Highly proliferative fibroblasts forming fibrotic focus govern metastasis of invasive ductal carcinoma of the breast. Mod Pathol (2001) 0.91
Fibrotic focus in invasive ductal carcinoma: an indicator of high tumor aggressiveness. Jpn J Cancer Res (1996) 0.91
Oral (po) dosing with RSU 1069 or RB 6145 maintains their potency as hypoxic cell radiosensitizers and cytotoxins but reduces systemic toxicity compared with parenteral (ip) administration in mice. Int J Radiat Oncol Biol Phys (1991) 0.90
The acute effects of cigarette smoke exposure on experimental skin flaps. Plast Reconstr Surg (1985) 0.90
Oxidative stress levels in myelodysplastic syndrome patients: their relationship to serum ferritin and haemoglobin values. J Int Med Res (2011) 0.90
A multicenter validation study of sentinel lymph node biopsy by the Japanese Breast Cancer Society. Breast Cancer Res Treat (2000) 0.90
Value of laparoscopic microwave coagulation therapy for hepatocellular carcinoma in relation to tumor size and location. Endoscopy (2000) 0.89
Inflammatory pseudotumor of the liver in a patient with chronic hepatitis C: difficulty in differentiating it from hepatocellular carcinoma. Pathol Int (1999) 0.89
Differing patterns of cardiac parasympathetic activity and their evolution in selected patients with a first myocardial infarction. J Am Coll Cardiol (1993) 0.89
Control group bias: a potential cause of over-estimating the benefit of videolaryngoscopy on laryngeal view. Br J Anaesth (2013) 0.89
Chromogranin, an integral membrane protein. J Biol Chem (1985) 0.88
Autonomic function in cirrhosis assessed by cardiovascular reflex tests and 24-hour heart rate variability. Am J Gastroenterol (1994) 0.88
Clinical aspects of unilateral aphakia. Trans Ophthalmol Soc U K (1974) 0.88
Advanced life support training. Resuscitation (2001) 0.88
Mechanisms of resistance to chemicals in arthropod parasites of veterinary importance. Vet Parasitol (1985) 0.87
Continuing professional education: identifying the characteristics of an effective system. J Adv Nurs (1995) 0.87