Published in Nat Rev Genet on February 01, 2014
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol (2014) 3.43
A survey of best practices for RNA-seq data analysis. Genome Biol (2016) 2.37
Ligand-dependent enhancer activation regulated by topoisomerase-I activity. Cell (2015) 1.74
Variant detection sensitivity and biases in whole genome and exome sequencing. BMC Bioinformatics (2014) 1.52
Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index. Nat Genet (2015) 1.51
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol (2016) 1.46
Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS One (2015) 1.42
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics (2015) 1.40
Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nat Commun (2015) 1.23
Inter-individual differences in the gene content of human gut bacterial species. Genome Biol (2015) 1.21
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Targeted capture in evolutionary and ecological genomics. Mol Ecol (2015) 1.01
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Potential of genotyping-by-sequencing for genomic selection in livestock populations. Genet Sel Evol (2015) 0.93
Modeling genome coverage in single-cell sequencing. Bioinformatics (2014) 0.93
Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice. BMC Immunol (2014) 0.91
Superinfection exclusion and the long-term survival of honey bees in Varroa-infested colonies. ISME J (2015) 0.91
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria. BMC Genomics (2014) 0.91
Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun (2015) 0.90
Treatment Algorithms Based on Tumor Molecular Profiling: The Essence of Precision Medicine Trials. J Natl Cancer Inst (2015) 0.90
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Resolving rates of mutation in the brain using single-neuron genomics. Elife (2016) 0.89
Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Res (2015) 0.88
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UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res (2017) 0.87
The Groucho co-repressor is primarily recruited to local target sites in active chromatin to attenuate transcription. PLoS Genet (2014) 0.86
Copy number variation detection using next generation sequencing read counts. BMC Bioinformatics (2014) 0.86
Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing. PeerJ (2015) 0.85
Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives. Oncotarget (2015) 0.85
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A reliable method for the detection of BRCA1 and BRCA2 mutations in fixed tumour tissue utilising multiplex PCR-based targeted next generation sequencing. BMC Clin Pathol (2015) 0.85
Automation of molecular-based analyses: a primer on massively parallel sequencing. Clin Biochem Rev (2014) 0.85
Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies. Hum Genet (2016) 0.84
Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach. PLoS One (2016) 0.84
Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. Mamm Genome (2015) 0.84
miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy. PLoS One (2015) 0.84
Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error. BMC Res Notes (2015) 0.84
A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases. Circ Res (2015) 0.84
Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC. PLoS One (2015) 0.84
Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol (2016) 0.84
Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies. PLoS One (2015) 0.83
Impact of three Illumina library construction methods on GC bias and HLA genotype calling. Hum Immunol (2014) 0.83
Critical evaluation of the expression of gastrin-releasing peptide in dorsal root ganglia and spinal cord. Mol Pain (2016) 0.82
Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding. PLoS One (2014) 0.81
The nephrologist of tomorrow: towards a kidney-omic future. Pediatr Nephrol (2016) 0.81
Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers. Oncologist (2016) 0.80
Exome and genome sequencing for inborn errors of immunity. J Allergy Clin Immunol (2016) 0.80
Wham: Identifying Structural Variants of Biological Consequence. PLoS Comput Biol (2015) 0.80
Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us? Cancers (Basel) (2015) 0.80
Old cell, new trick? Cnidocytes as a model for the evolution of novelty. Integr Comp Biol (2014) 0.80
Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing. BMC Genomics (2015) 0.80
Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations. J Med Genet (2014) 0.80
Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping. BMC Med Genet (2016) 0.80
Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins. Cell Rep (2016) 0.79
The role of genomics in common variable immunodeficiency disorders. Clin Exp Immunol (2017) 0.79
Differentiation of G:C vs A:T and G:C vs G:mC Base Pairs in the Latch Zone of α-Hemolysin. ACS Nano (2015) 0.79
cFinder: definition and quantification of multiple haplotypes in a mixed sample. BMC Res Notes (2015) 0.79
High throughput exome coverage of clinically relevant cardiac genes. BMC Med Genomics (2014) 0.79
BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations. Nucleic Acids Res (2015) 0.79
Estimating genomic heritabilities at the level of family-pool samples of perennial ryegrass using genotyping-by-sequencing. Theor Appl Genet (2015) 0.78
Limited resources of genome sequencing in developing countries: Challenges and solutions. Appl Transl Genom (2016) 0.78
Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death. Hum Genomics (2015) 0.78
A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Plant Cell (2016) 0.78
Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinformatics (2016) 0.78
New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis. BMC Genomics (2014) 0.78
Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells. BMC Genomics (2015) 0.78
Pediatric asthma and autism-genomic perspectives. Clin Transl Med (2015) 0.78
A Primer on Infectious Disease Bacterial Genomics. Clin Microbiol Rev (2016) 0.78
A comparison of tools for the simulation of genomic next-generation sequencing data. Nat Rev Genet (2016) 0.78
Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry. BMC Genomics (2015) 0.77
Reference standards for next-generation sequencing. Nat Rev Genet (2017) 0.77
Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes. Mol Ecol Resour (2015) 0.77
De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.). Front Plant Sci (2015) 0.77
Hepatocellular carcinoma cell lines retain the genomic and transcriptomic landscapes of primary human cancers. Sci Rep (2016) 0.77
Putative BRAF activating fusion in a medullary thyroid cancer. Cold Spring Harb Mol Case Stud (2016) 0.77
The Salivary Microbiome in Polycystic Ovary Syndrome (PCOS) and Its Association with Disease-Related Parameters: A Pilot Study. Front Microbiol (2016) 0.77
QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnol J (2016) 0.76
Sequencing and comparative analyses of the genomes of zoysiagrasses. DNA Res (2016) 0.76
Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. PLoS One (2016) 0.76
An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum). DNA Res (2016) 0.76
Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions. Biophys J (2017) 0.76
Allelic ratio of KRAS mutations in pancreatic cancer. Oncologist (2015) 0.76
Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain. Plant Physiol (2016) 0.76
Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine. J Healthc Eng (2016) 0.76
Current tools for predicting cancer-specific T cell immunity. Oncoimmunology (2016) 0.76
Human RECQ Helicase Pathogenic Variants, Population Variation and "Missing" Diseases. Hum Mutat (2016) 0.76
Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods. PLoS One (2015) 0.76
Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli. PLoS One (2016) 0.76
GROM-RD: resolving genomic biases to improve read depth detection of copy number variants. PeerJ (2015) 0.76
Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken. BMC Genomics (2015) 0.76
Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. Nat Commun (2016) 0.75
On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads. Methods (2015) 0.75
Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. BMC Genomics (2015) 0.75
Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities. BMC Genomics (2015) 0.75
Computational identification of putative lincRNAs in mouse embryonic stem cell. Sci Rep (2016) 0.75
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Landscape of transcription in human cells. Nature (2012) 20.18
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
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High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
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HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17
Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01
ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res (2012) 11.33
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17
Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol (2008) 10.10
The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature (2010) 10.04
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The long-range interaction landscape of gene promoters. Nature (2012) 9.20
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
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The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res (2009) 7.87
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Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell (2011) 6.83
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell (2011) 6.29
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol (2010) 5.98
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