Methods
Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen
- First Published February 9, 2010
Methods
A new strategy for genome assembly using short sequence reads and reduced representation libraries
- First Published February 1, 2010
Methods
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
- First Published January 5, 2010
Methods
Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error
- First Published December 1, 2009
Methods
Targeted chromosomal deletions in human cells using zinc finger nucleases
- First Published December 1, 2009
Methods
Detection of nonneutral substitution rates on mammalian phylogenies
- First Published October 26, 2009
Methods
High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
- First Published October 21, 2009
Methods
Salmonella Typhi gene using one million transposon mutants" > Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
- First Published October 13, 2009
Methods
Rapid inexpensive genome-wide association using pooled whole blood
- First Published October 3, 2009
Methods
Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time
- First Published October 1, 2009
Methods
Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)
- First Published October 1, 2009
Methods
Predictable dynamic program of timing of DNA replication in human cells
- First Published September 18, 2009
Methods
Two-parameter characterization of chromosome-scale recombination rate
- First Published September 14, 2009
Methods
An ensemble model of competitive multi-factor binding of the genome
- First Published August 31, 2009
Methods
Sensitive and accurate detection of copy number variants using read depth of coverage
- First Published August 5, 2009
Methods
Distinguishing direct versus indirect transcription factor–DNA interactions
- First Published August 3, 2009
Methods
Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing
- First Published July 28, 2009
Methods
Direct multiplex sequencing (DMPS)—a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA
- First Published July 27, 2009
Methods
A probabilistic approach for SNP discovery in high-throughput human resequencing data
- First Published July 15, 2009
Methods
Identification of deleterious mutations within three human genomes
- First Published July 14, 2009
Methods
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
- First Published July 6, 2009
Methods
Transcriptional and post-transcriptional profile of human chromosome 21
- First Published July 6, 2009
Methods
Identification of rare cancer driver mutations by network reconstruction
- First Published July 2, 2009
Methods
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
- First Published June 22, 2009
Methods
Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations
- First Published June 22, 2009
Methods
Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
- First Published June 18, 2009
Methods
Next-generation tag sequencing for cancer gene expression profiling
- First Published June 18, 2009
Methods
Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
- First Published June 18, 2009
Methods
Genome-wide comparisons of variation in linkage disequilibrium
- First Published June 18, 2009
Methods
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
- First Published June 12, 2009
Methods
A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease
- First Published June 8, 2009
Methods
Genome-wide screen of promoter methylation identifies novel markers in melanoma
- First Published June 2, 2009
Methods
Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly
- First Published May 21, 2009
Methods
Drosophila melanogaster" > Conserved introns reveal novel transcripts in Drosophila melanogaster
- First Published May 20, 2009
Methods
Incorporating nucleosomes into thermodynamic models of transcription regulation
- First Published May 18, 2009
Methods
DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis
- First Published May 15, 2009
Methods
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
- First Published May 15, 2009
Methods
Shifted Transversal Design smart-pooling for high coverage interactome mapping
- First Published May 15, 2009
Methods
MS-qFRET: A quantum dot-based method for analysis of DNA methylation
- First Published May 14, 2009
Methods
Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing
- First Published May 7, 2009
Methods
The difficulty of avoiding false positives in genome scans for natural selection
- First Published May 1, 2009
Methods
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
- First Published March 9, 2009
Methods
Integrating siRNA and protein–protein interaction data to identify an expanded insulin signaling network
- First Published March 4, 2009
Methods
Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
- First Published February 23, 2009
Methods
Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system
- First Published February 18, 2009
Methods
Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
- First Published February 9, 2009
Methods
A transcription factor affinity-based code for mammalian transcription initiation
- First Published January 13, 2009
Methods
Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy
- First Published January 13, 2009
Methods
Genome-wide profiling of salt fractions maps physical properties of chromatin
- First Published December 16, 2008
Methods
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
- First Published December 11, 2008
Methods
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
- First Published November 26, 2008
Methods
Pseudomonas syringae pv. oryzae" > De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
- First Published November 17, 2008
Methods
A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements
- First Published November 17, 2008
Methods
High-resolution human core-promoter prediction with CoreBoost_HM
- First Published November 7, 2008
Methods
Hox cis-regulatory elements" > Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- First Published November 3, 2008
Methods
cis-regulatory variation in human haplotypes" > Targeted screening of cis-regulatory variation in human haplotypes
- First Published October 29, 2008
Methods
DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression
- First Published October 29, 2008
Methods
Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
- First Published October 27, 2008
Methods
Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes
- First Published October 10, 2008
Methods
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- First Published October 10, 2008
Methods
Genome-wide nucleotide-level mammalian ancestor reconstruction
- First Published October 10, 2008
Methods
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
- First Published October 2, 2008
Methods
cis-regulatory elements" > Ab initio identification of functionally interacting pairs of cis-regulatory elements
- First Published September 17, 2008
Methods
Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification
- First Published September 16, 2008
Methods
Rapid whole-genome mutational profiling using next-generation sequencing technologies
- First Published September 4, 2008
Methods
MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
- First Published September 2, 2008
Methods
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
- First Published August 29, 2008
Methods
An MCMC algorithm for haplotype assembly from whole-genome sequence data
- First Published August 1, 2008
Methods
C. elegans gene annotations" > Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
- First Published July 24, 2008
Methods
Confounding between recombination and selection, and the Ped/Pop method for detecting selection
- First Published July 10, 2008
Methods
Inferring causal relationships among different histone modifications and gene expression
- First Published June 18, 2008
Methods
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
- First Published June 11, 2008
Methods
A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations
- First Published May 23, 2008
Methods
Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
- First Published April 25, 2008
Methods
Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions
- First Published April 25, 2008
Methods
Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
- First Published April 21, 2008
Methods
Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
- First Published April 16, 2008
Methods
Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
- First Published March 27, 2008
Methods
Power and SNP tagging in whole mitochondrial genome association studies
- First Published March 20, 2008
Methods
Mapping translocation breakpoints by next-generation sequencing
- First Published March 7, 2008
Methods
Arabidopsis thaliana with resequencing microarrays" > Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- First Published March 6, 2008
Methods
Comprehensive high-throughput arrays for relative methylation (CHARM)
- First Published March 3, 2008
Methods
Large-scale screening for novel low-affinity extracellular protein interactions
- First Published February 22, 2008
Methods
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
- First Published February 19, 2008