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Abstract

References (101)

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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Fast and accurate short read alignment with Burrows–Wheeler transform

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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

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Gene Ontology: tool for the unification of biology

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KEGG: Kyoto Encyclopedia of Genes and Genomes

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

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ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

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Image processing with ImageJ

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A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

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A map of human genome variation from population-scale sequencing

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Table S2: Trans-factors and trinucleotide repeat instability Trans-factor

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Alternative isoform regulation in human tissue transcriptomes

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Cytoscape 2.8: new features for data integration and network visualization

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NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

2006 • 4,425 citations

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

2005 • 4,037 citations

Correlation between Protein and mRNA Abundance in Yeast

1999 • 3,800 citations

Human MicroRNA Targets

2004 • 3,702 citations

Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

2007 • 3,068 citations

SOAP: short oligonucleotide alignment program

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Java Treeview—extensible visualization of microarray data

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Hudson et al.

1977 • 2,560 citations

Integration of biological networks and gene expression data using Cytoscape

2007 • 2,402 citations

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

2011 • 2,399 citations

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

2009 • 1,977 citations

Antibodies to von Willebrand Factor–Cleaving Protease in Acute Thrombotic Thrombocytopenic Purpura

1998 • 1,749 citations

Mutations in a member of the ADAMTS gene family cause thrombotic thrombocytopenic purpura

2001 • 1,715 citations

Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome

2002 • 1,644 citations

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

2011 • 1,556 citations

Reactome: a database of reactions, pathways and biological processes

2010 • 1,553 citations

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

2009 • 1,447 citations

Inflammation and Activated Innate Immunity in the Pathogenesis of Type 2 Diabetes

2004 • 1,361 citations

Reactome: a knowledgebase of biological pathways

2004 • 1,258 citations

Mapping copy number variation by population-scale genome sequencing

2011 • 1,100 citations

Reactome knowledgebase of human biological pathways and processes

2008 • 875 citations

Cytoscape 2.8: new features for data integration and network

2011 • 823 citations

Transcriptome analysis by strand-specific sequencing of complementary DNA

2009 • 779 citations

NCBI Reference Sequences: current status, policy and new initiatives

2008 • 739 citations

Mutations inTERT,the Gene for Telomerase Reverse Transcriptase, in Aplastic Anemia

2005 • 706 citations

The International Protein Index: An integrated database for proteomics experiments

2004 • 697 citations

Bayesian Logical Data Analysis for the Physical Sciences: A Comparative Approach with Mathematica® Support

2005 • 683 citations

Bayesian Logical Data Analysis for the Physical Sciences

2005 • 679 citations

Clinical assessment incorporating a personal genome

2010 • 675 citations

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

2011 • 652 citations

Reactome: a knowledge base of biologic pathways and processes

2007 • 639 citations

Variation in Transcription Factor Binding Among Humans

2010 • 568 citations

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

2009 • 516 citations

Performance comparison of exome DNA sequencing technologies

2011 • 495 citations

Distribution of the Serial Correlation Coefficient

1942 • 456 citations

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

2011 • 441 citations

Mutations and common polymorphisms in ADAMTS13 gene responsible for von Willebrand factor-cleaving protease activity

2002 • 407 citations

Studies in astronomical time series analysis. III - Fourier transforms, autocorrelation functions, and cross-correlation functions of unevenly spaced data

1989 • 335 citations

AlleleSeq: analysis of allele‐specific expression and binding in a network framework

2011 • 328 citations

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

2011 • 314 citations

High-throughput telomere length quantification by FISH and its application to human population studies

2007 • 307 citations

Congenital Deficiency of a Factor in Normal Plasma That Reverses Microangiopathic Hemolysis and Thrombocytopenia

1978 • 277 citations

Identification of molecular subtypes of glioblastoma by gene expression profiling

2003 • 275 citations

Missense mutations in the pancreatic islet beta cell inwardly rectifying K + channel gene (KIR6.2/BIR ): a meta-analysis suggests a role in the polygenic basis of Type II diabetes mellitus in Caucasians

1998 • 271 citations

Building the sequence map of the human pan-genome

2009 • 256 citations

Detecting periodic patterns in unevenly spaced gene expression time series using Lomb–Scargle periodograms

2005 • 255 citations

Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays

2007 • 251 citations

Viral infections as potential triggers of type 1 diabetes

2006 • 227 citations

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

2011 • 206 citations

Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs

2010 • 205 citations

Mass spectrometry‐based holistic analytical approaches for metabolite profiling in systems biology studies

2011 • 193 citations

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

2009 • 190 citations

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

2010 • 189 citations

Evolutionarily conserved human targets of adenosine to inosine RNA editing

2005 • 187 citations

The Common P446L Polymorphism in GCKR Inversely Modulates Fasting Glucose and Triglyceride Levels and Reduces Type 2 Diabetes Risk in the DESIR Prospective General French Population

2008 • 175 citations

Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

2011 • 149 citations

Telomere length abnormalities in mammalian radiosensitive cells.

2001 • 143 citations

Personal genome sequencing: current approaches and challenges

2010 • 134 citations

A Procedure of Multiple Period Searching in Unequally Spaced Time-Series with the Lomb–Scargle Method

1999 • 121 citations

Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer

2010 • 118 citations

Gap filling and noise reduction of unevenly sampled data by means of the Lomb-Scargle periodogram

2009 • 78 citations

Relationship between serum concentrations of saturated fatty acids and unsaturated fatty acids and the homeostasis model insulin resistance index in Japanese patients with type 2 diabetes mellitus

2007 • 76 citations

Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes

2011 • 58 citations

Human BLCAP transcript: new editing events in normal and cancerous tissues

2010 • 57 citations

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data

2007 • 55 citations

ProCAT: a data analysis approach for protein microarrays.

2006 • 50 citations

Screening of human SNP database identifies recoding sites of A-to-I RNA editing

2008 • 45 citations

Emphasizing Difficulties in the Detection of Rhythms with Lomb-Scargle Periodograms

2001 • 44 citations

High expression level of EDIL3 in HCC predicts poor prognosis of HCC patients

2010 • 43 citations

Evidence for association of the TCF7 locus with type I diabetes

2009 • 31 citations

Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study

2008 • 23 citations

LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data

2011 • 21 citations

An Introduction to the Reactome Knowledgebase of Human Biological Pathways and Processes

2007 • 12 citations

Deleted Work

1955 • 0 citations

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Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes (2012) – Cell | Metascience Observatory Explorer