The real cost of sequencing: higher than you think!

The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods (2012) 3.89

Big Data: Astronomical or Genomical? PLoS Biol (2015) 2.59

The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet (2013) 1.66

The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol (2016) 1.53

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. Brief Bioinform (2012) 1.50

Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. BMC Genomics (2012) 1.38

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Brief Bioinform (2012) 1.23

Evolving approaches to the ethical management of genomic data. Trends Genet (2013) 1.18

Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial. Front Genet (2014) 1.17

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Comput Biol (2013) 1.17

On the future of genetic risk assessment. J Community Genet (2012) 1.12

Protein interface classification by evolutionary analysis. BMC Bioinformatics (2012) 1.11

Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. Biomed Res Int (2014) 1.08

PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinb) (2014) 1.06

Quantification of private information leakage from phenotype-genotype data: linking attacks. Nat Methods (2016) 1.05

Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants. Genet Epidemiol (2013) 1.04

Haplotype-based methods for detecting uncommon causal variants with common SNPs. Genet Epidemiol (2012) 1.04

ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq. PLoS One (2013) 0.99

Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects. Eur J Hum Genet (2015) 0.97

Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol (2014) 0.97

SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics. BMC Bioinformatics (2013) 0.91

Exome Sequencing: Current and Future Perspectives. G3 (Bethesda) (2015) 0.91

The right drugs at the right time for the right patient: the MD Anderson precision oncology decision support platform. Drug Discov Today (2015) 0.90

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping. Genetics (2015) 0.89

Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment. PLoS One (2014) 0.89

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. BMC Genomics (2014) 0.89

Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology. BMC Bioinformatics (2014) 0.88

Compressive mapping for next-generation sequencing. Nat Biotechnol (2016) 0.88

A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing. Front Genet (2015) 0.88

Assessing the Costs and Cost-Effectiveness of Genomic Sequencing. J Pers Med (2015) 0.87

Rapid and inexpensive whole-genome genotyping-by-sequencing for crossover localization and fine-scale genetic mapping. G3 (Bethesda) (2015) 0.87

Updating RNA-Seq analyses after re-annotation. Bioinformatics (2013) 0.84

Scalable and cost-effective NGS genotyping in the cloud. BMC Med Genomics (2015) 0.84

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). Bioinformatics (2014) 0.83

Portraying the Expression Landscapes of B-CellLymphoma-Intuitive Detection of Outlier Samples and of Molecular Subtypes. Biology (Basel) (2013) 0.83

Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PLoS One (2015) 0.81

Human Transcriptome and Chromatin Modifications: An ENCODE Perspective. Genomics Inform (2013) 0.81

A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach. BMC Genomics (2014) 0.81

Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights. BMC Genomics (2015) 0.81

Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations. J Med Genet (2014) 0.80

Rare genetic variants in cellular transporters, metabolic enzymes, and nuclear receptors can be important determinants of interindividual differences in drug response. Genet Med (2016) 0.80

Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers. Pharmaceuticals (Basel) (2016) 0.80

The aggregate site frequency spectrum for comparative population genomic inference. Mol Ecol (2015) 0.79

High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology. Pathogens (2014) 0.78

GFVO: the Genomic Feature and Variation Ontology. PeerJ (2015) 0.78

Biological intuition in alignment-free methods: response to Posada. J Mol Evol (2013) 0.78

Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes. BMC Genomics (2015) 0.78

Development of HuMiChip for functional profiling of human microbiomes. PLoS One (2014) 0.78

Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes. PLoS One (2014) 0.77

Clinical and ethical considerations of massively parallel sequencing in transplantation science. World J Transplant (2013) 0.76

Advantages of Array-Based Technologies for Pre-Emptive Pharmacogenomics Testing. Microarrays (Basel) (2016) 0.76

Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. BMC Bioinformatics (2017) 0.75

Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. Oncotarget (2016) 0.75

Asymmetrical barcode adapter-assisted recovery of duplicate reads and error correction strategy to detect rare mutations in circulating tumor DNA. Sci Rep (2017) 0.75

Precision medicine driven by cancer systems biology. Cancer Metastasis Rev (2017) 0.75

ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time. PLoS Comput Biol (2017) 0.75

Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution. Ecol Evol (2014) 0.75

DMSO Increases Mutation Scanning Detection Sensitivity of High-Resolution Melting in Clinical Samples. Clin Chem (2015) 0.75

NEAT: a framework for building fully automated NGS pipelines and analyses. BMC Bioinformatics (2016) 0.75

Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma. PLoS One (2015) 0.75

De novo construction of a "Gene-space" for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources. BMC Res Notes (2016) 0.75

The cost and cost trajectory of whole-genome analysis guiding treatment of patients with advanced cancers. Mol Genet Genomic Med (2017) 0.75

The eBioKit, a stand-alone educational platform for bioinformatics. PLoS Comput Biol (2017) 0.75

The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

A map of human genome variation from population-scale sequencing. Nature (2010) 121.13

The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81

Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76

Sequencing technologies - the next generation. Nat Rev Genet (2009) 40.57

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99

Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78

The variant call format and VCFtools. Bioinformatics (2011) 25.88

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72

The impact of next-generation sequencing technology on genetics. Trends Genet (2008) 21.07

A draft sequence of the Neandertal genome. Science (2010) 19.55

Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (2008) 16.48

Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85

NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38

HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17

Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res (2010) 11.32

Searching for SNPs with cloud computing. Genome Biol (2009) 10.12

Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol (2010) 10.05

The case for cloud computing in genome informatics. Genome Biol (2010) 9.20

Cloud computing and the DNA data race. Nat Biotechnol (2010) 7.81

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res (2010) 7.67

Gene sequencing. The race for the $1000 genome. Science (2006) 6.76

Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res (2011) 5.60

Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol (2010) 5.32

Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30

AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71

Toward the 1,000 dollars human genome. Pharmacogenomics (2005) 4.68

Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics (2010) 3.77

Anticipating the 1,000 dollar genome. Genome Biol (2006) 2.91

The $1,000 genome, the $100,000 analysis? Genome Med (2010) 2.79

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res (2010) 2.50

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics (2010) 2.26

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Res (2011) 1.43

Network security and data integrity in academia: an assessment and a proposal for large-scale archiving. Genome Biol (2005) 1.43

Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing. Nat Rev Genet (2010) 1.40

Kryder's law. Sci Am (2005) 1.25

Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46

The genomic complexity of primary human prostate cancer. Nature (2011) 14.06

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

A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07

Unlocking the secrets of the genome. Nature (2009) 11.80

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78

Variation in transcription factor binding among humans. Science (2010) 9.33

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41

Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79

Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78

Relating three-dimensional structures to protein networks provides evolutionary insights. Science (2006) 5.50

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13

High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A (2006) 4.84

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59

Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics (2006) 4.55

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol (2009) 4.18

The GENCODE pseudogene resource. Genome Biol (2012) 4.18

An integrated approach for finding overlooked genes in yeast. Nat Biotechnol (2002) 3.88

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82

Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52

Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discov (2011) 3.43

The reality of pervasive transcription. PLoS Biol (2011) 3.41

Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A (2007) 3.35

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22

Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer (2009) 3.03

Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal (2010) 2.95

Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A (2009) 2.89

Phylogeography of Francisella tularensis: global expansion of a highly fit clone. J Bacteriol (2009) 2.85

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol (2010) 2.79

Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69

Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet (2002) 2.65

Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics (2007) 2.55

Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. Proc Natl Acad Sci U S A (2007) 2.55

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res (2010) 2.50

Molecular sampling of prostate cancer: a dilemma for predicting disease progression. BMC Med Genomics (2010) 2.40

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res (2007) 2.39

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet (2011) 2.38

Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc Natl Acad Sci U S A (2009) 2.36

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood (2009) 2.18

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res (2008) 2.17

Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics (2007) 2.08

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res (2007) 2.03

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res (2006) 1.95

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol (2010) 1.92

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res (2013) 1.83

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res (2007) 1.82

A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. J Bacteriol (2007) 1.82

Genomic islands from five strains of Burkholderia pseudomallei. BMC Genomics (2008) 1.82

Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma. Sci Transl Med (2011) 1.79

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol (2009) 1.78

A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biol (2006) 1.74

Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotechnol (2012) 1.72

N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. Neoplasia (2009) 1.68

A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. PLoS One (2007) 1.63

High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genet (2008) 1.60

The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends Genet (2007) 1.57

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Res (2012) 1.57

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56

Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem (2004) 1.55

Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics (2008) 1.54

TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Res (2004) 1.45

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Res (2011) 1.43

Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev (2009) 1.43

Network security and data integrity in academia: an assessment and a proposal for large-scale archiving. Genome Biol (2005) 1.43

Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. Cancer Res (2012) 1.40

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. Genome Biol (2014) 1.36

The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr Opin Struct Biol (2008) 1.36

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res (2010) 1.35

Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators. Sci Signal (2010) 1.35

Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol (2011) 1.35

Interleukin-29 functions cooperatively with interferon to induce antiviral gene expression and inhibit hepatitis C virus replication. J Biol Chem (2008) 1.32

Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One (2007) 1.31

Robust-linear-model normalization to reduce technical variability in functional protein microarrays. J Proteome Res (2009) 1.29

Genomics and privacy: implications of the new reality of closed data for the field. PLoS Comput Biol (2011) 1.29

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci U S A (2010) 1.24

SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions. J Biol Chem (2012) 1.24

Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem Sci (2007) 1.23

Understanding modularity in molecular networks requires dynamics. Sci Signal (2009) 1.22

Integrated assessment of genomic correlates of protein evolutionary rate. PLoS Comput Biol (2009) 1.20

Getting started in gene orthology and functional analysis. PLoS Comput Biol (2010) 1.20

Computational analysis of membrane proteins: the largest class of drug targets. Drug Discov Today (2009) 1.19

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Comput Biol (2009) 1.18

An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective. J Biomed Inform (2006) 1.15

Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. Genome Res (2010) 1.13

HingeMaster: normal mode hinge prediction approach and integration of complementary predictors. Proteins (2008) 1.13

Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds. Proteins (2002) 1.11

Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res (2004) 1.11

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics (2009) 1.10

Assays for the rapid and specific identification of North American Yersinia pestis and the common laboratory strain CO92. Biotechniques (2008) 1.09

Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC Bioinformatics (2007) 1.06