Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome.

PubWeight™: 0.78‹?›

🔗 View Article (PMC 3273931)

Published in Evol Bioinform Online on January 24, 2012

Authors

Felix Dreher1, Atanas Kamburov, Ralf Herwig

Author Affiliations

1: Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.

Articles by these authors

An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24

The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res (2012) 2.94

ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res (2010) 2.79

ConsensusPathDB--a database for integrating human functional interaction networks. Nucleic Acids Res (2008) 2.77

A gene expression map of human chromosome 21 orthologues in the mouse. Nature (2002) 2.76

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res (2010) 2.61

Transcript level alterations reflect gene dosage effects across multiple tissues in a mouse model of down syndrome. Genome Res (2004) 2.29

Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics (2011) 2.24

Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells. Stem Cells (2006) 2.18

A prospective evaluation of pain associated with stone passage, stents, and stent removal using a visual analog scale. Urology (2013) 2.05

Dynamic protein-protein interaction wiring of the human spliceosome. Mol Cell (2012) 2.04

Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells. Stem Cells (2005) 1.68

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. Genome Res (2003) 1.65

Kidney fusion anomalies revisited: clinical and radiological analysis of 209 cases of crossed fused ectopia and horseshoe kidney. BJU Int (2008) 1.61

Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics (2011) 1.46

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics (2013) 1.38

Proteomic and functional analysis of the mitotic Drosophila centrosome. EMBO J (2010) 1.27

Reverse engineering of gene regulatory networks: a comparative study. EURASIP J Bioinform Syst Biol (2009) 1.22

Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics (2010) 1.19

A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks. Genome Biol (2007) 1.19

Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays. BMC Genomics (2004) 1.16

Resources, standards and tools for systems biology. Brief Funct Genomic Proteomic (2007) 1.15

Renal tumour size measured radiologically before surgery is an unreliable variable for predicting histopathological features: benign tumours are not necessarily small. BJU Int (2007) 1.15

DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer. PLoS Genet (2013) 1.13

GeNGe: systematic generation of gene regulatory networks. Bioinformatics (2009) 1.11

Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters. Genome Res (2003) 1.11

In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. BMC Genomics (2009) 1.09

Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics (2008) 1.08

Matrix metalloproteinases of epithelial origin in facial sebum of patients with acne and their regulation by isotretinoin. J Invest Dermatol (2005) 1.05

Gene expression variation in Down's syndrome mice allows prioritization of candidate genes. Genome Biol (2007) 1.04

Nodal signaling activates differentiation genes during zebrafish gastrulation. Dev Biol (2007) 1.03

Human embryonic stem cell derived hepatocyte-like cells as a tool for in vitro hazard assessment of chemical carcinogenicity. Toxicol Sci (2011) 1.02

Age-specific hormonal decline is accompanied by transcriptional changes in human sebocytes in vitro. Aging Cell (2006) 1.01

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics (2005) 1.01

Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes. BMC Genomics (2011) 1.00

Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PLoS Comput Biol (2011) 0.99

Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression. Physiol Genomics (2007) 0.99

A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics (2006) 0.99

Dual coordination of post translational modifications in human protein networks. PLoS Comput Biol (2013) 0.99

RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene. Toxicol Sci (2012) 0.98

Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo. Genome Res (2004) 0.98

alpha-Blockers improve chronic ischaemia of the lower urinary tract in patients with lower urinary tract symptoms. BJU Int (2007) 0.97

ARH: predicting splice variants from genome-wide data with modified entropy. Bioinformatics (2009) 0.95

LGALS3BP regulates centriole biogenesis and centrosome hypertrophy in cancer cells. Nat Commun (2013) 0.94

DEFOG: a practical scheme for deciphering families of genes. Genomics (2002) 0.92

Correlation of leukocytospermia with clinical infection and the positive effect of antiinflammatory treatment on semen quality. Fertil Steril (2006) 0.89

IntScore: a web tool for confidence scoring of biological interactions. Nucleic Acids Res (2012) 0.88

Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis. BMC Bioinformatics (2002) 0.88

Dynamics of biological systems: role of systems biology in medical research. Expert Rev Mol Diagn (2006) 0.88

Transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models. Carcinogenesis (2013) 0.87

Cluster-based assessment of protein-protein interaction confidence. BMC Bioinformatics (2012) 0.87

The Post-Ureteroscopic Lesion Scale (PULS): a multicenter video-based evaluation of inter-rater reliability. World J Urol (2013) 0.86

Evaluation of database-derived pathway development for enabling biomarker discovery for hepatotoxicity. Biomark Med (2014) 0.86

Gene polymorphisms and prostate cancer: the evidence. BJU Int (2009) 0.86

Prediction in the face of uncertainty: a Monte Carlo-based approach for systems biology of cancer treatment. Mutat Res (2012) 0.85

Synchronous bilateral malignant mesothelioma of tunica vaginalis testis: early diagnosis. Urology (2004) 0.84

DIPSBC--data integration platform for systems biology collaborations. BMC Bioinformatics (2012) 0.84

Oxidative stress and epididymal sperm transport, motility and morphological defects. Eur J Obstet Gynecol Reprod Biol (2009) 0.83

Molecular characterization of cultured adult human liver progenitor cells. Tissue Eng Part C Methods (2010) 0.82

Urinary continence after radical prostatectomy: the patient perspective. Can J Urol (2011) 0.81

Case report: laparoscopic ureteropyelostomy and distal ureterectomy for management of duplication with ectopia. J Endourol (2007) 0.80

Development and application of a DNA microarray-based yeast two-hybrid system. Nucleic Acids Res (2012) 0.80

Circulating PSA-containing macrophages as a possible target for the detection of prostate cancer: a three-color/five-parameter flow cytometric study on peripheral blood samples. Am J Clin Pathol (2008) 0.80

Urinary acetonitrile concentrations correlate with recent smoking behaviour. BJU Int (2005) 0.80

Gene ontology analysis of the centrosome proteomes of Drosophila and human. Commun Integr Biol (2011) 0.79

Effects of local estrogen therapy on recurrent urinary tract infections in young females under oral contraceptives. Eur Urol (2005) 0.79

Elevated levels of carbonyl proteins in cerebrospinal fluid of patients with neurodegenerative diseases. Tohoku J Exp Med (2014) 0.78

Multiplexed hybridizations of positively charge-tagged peptide nucleic acids detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom (2004) 0.78

Glans reconstruction with the use of an inverted urethral flap after distal penile amputation for carcinoma. Arch Ital Urol Androl (2013) 0.78

Peyronie's Disease: Nonsurgical Therapy Options. Rev Urol (2011) 0.78

Power Doppler ultrasound imaging for quantification of urinary bladder neck blood flow changes. Ultrasound Med Biol (2004) 0.77

The enzymatic activity of the VEGFR2 receptor for the biosynthesis of dinucleoside polyphosphates. J Mol Med (Berl) (2013) 0.77

Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. BMC Genomics (2011) 0.77

The influence of left renal vein entrapment on outcome after surgical varicocele repair: a color Doppler sonographic demonstration. J Ultrasound Med (2004) 0.76

Pathway deregulation and expression QTLs in response to Actinobacillus pleuropneumoniae infection in swine. Mamm Genome (2014) 0.76

Treatment of severe bilateral nerve pain after Pfannenstiel incision. Urology (2006) 0.76

An integrative computational analysis provides evidence for FBN1-associated network deregulation in trisomy 21. Biol Open (2013) 0.75

Identification of QTL affecting resistance/susceptibility to acute Actinobacillus pleuropneumoniae infection in swine. Mamm Genome (2014) 0.75

Urethral support with PelviSoft after artificial urinary sphincter erosion at revision procedures. Wien Med Wochenschr (2007) 0.75

Matching anticancer compounds and tumor cell lines by neural networks with ranking loss. NAR Genom Bioinform (2022) 0.75

Method development and validation for the analysis of a new anti-cancer infusion solution via HPLC. J Sep Sci (2010) 0.75

Oligonucleotide fingerprinting of arrayed genomic DNA sequences using LNA-modified hybridization probes. Comb Chem High Throughput Screen (2007) 0.75

Complete recovery after the removal of an ectopic testicle in a case of primary reninism and retroperitoneal hemangioma. Asian J Androl (2006) 0.75

Giant seminal vesicle cyst. Wien Klin Wochenschr (2005) 0.75

High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell (2017) 0.75

Aging of human sebocytes in vitro induced by exposure to a defined hormone environment. Dermatology (2006) 0.75

"4D Biology for health and disease" workshop report. N Biotechnol (2010) 0.75