Capturing the ‘ome’: the expanding molecular toolbox for RNA and DNA library construction

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

(2017) Margarita Schlackow et al.   MOLECULAR CELL

Chemical and structural effects of base modifications in messenger RNA

(2017) Emily M. Harcourt et al.   NATURE

Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

(2017) Qing Dai et al.   NATURE METHODS

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches

(2017) Daniel E. Martin-Herranz et al.   NUCLEIC ACIDS RESEARCH

An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron

(2017) Chen Zhao et al.   RNA

Targeted reduction of highly abundant transcripts using pseudo-random primers

(2016) Ophélie Arnaud et al.   BIOTECHNIQUES

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq

(2016) Yongxian Yuan et al.   BMC GENOMICS

Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing

(2016) Louise Aigrain et al.   BMC GENOMICS

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

Single-cell sequencing of the small-RNA transcriptome

(2016) Omid R Faridani et al.   NATURE BIOTECHNOLOGY

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

The ORFeome Collaboration: a genome-scale human ORF-clone resource

(2016)   NATURE METHODS

irCLIP platform for efficient characterization of protein–RNA interactions

(2016) Brian J Zarnegar et al.   NATURE METHODS

High-quality full-length immunoglobulin profiling with unique molecular barcoding

(2016) M A Turchaninova et al.   Nature Protocols

Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution

(2016) Chen Zhao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

(2016) Amanda Raine et al.   NUCLEIC ACIDS RESEARCH

RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase

(2016) Ryan M. Nottingham et al.   RNA

Synthetic evolutionary origin of a proofreading reverse transcriptase

(2016) J. W. Ellefson et al.   SCIENCE

Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution

(2016) Chen Zhao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

(2016) David E. Weinberg et al.   Cell Reports

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Library construction for next-generation sequencing: Overviews and challenges

(2016) Steven R. Head et al.   BIOTECHNIQUES

Improved transposon-based library preparation for the Ion Torrent platform

(2015) Tatyana Gorbacheva et al.   BIOTECHNIQUES

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis

(2015) Liyou Wu et al.   BMC MICROBIOLOGY

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients

(2015) Lu Wen et al.   CELL RESEARCH

Deep sequencing in library selection projects: what insight does it bring?

(2015) J Glanville et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Impact of three Illumina library construction methods on GC bias and HLA genotype calling

(2015) James H. Lan et al.   HUMAN IMMUNOLOGY

High-throughput RNA profiling via up-front sample parallelization

(2015) Azeet Narayan et al.   NATURE METHODS

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

(2015) Hongshan Guo et al.   Nature Protocols

Systematic Characteristic Exploration of the Chimeras Generated in Multiple Displacement Amplification through Next Generation Sequencing Data Reanalysis

(2015) Jing Tu et al.   PLoS One

High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases

(2015) Yidan Qin et al.   RNA

Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains

(2015) P. S. Shen et al.   SCIENCE

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

Sequencing of first-strand cDNA library reveals full-length transcriptomes

(2015) Saurabh Agarwal et al.   Nature Communications

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

(2015) Katharine Best et al.   Scientific Reports

A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors

(2015) Lior Izhar et al.   Cell Reports

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

Challenges with Using Primer IDs to Improve Accuracy of Next Generation Sequencing

(2015) Johanna Brodin et al.   PLoS One

Single Cell Transcriptome Amplification with MALBAC

(2015) Alec R. Chapman et al.   PLoS One

Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure

(2015) Ryan T. Fuchs et al.   PLoS One

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci

(2015) R. Scott Cornman et al.   PLoS One

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Influence of RNA extraction methods and library selection schemes on RNA-seq data

(2014) Marc Sultan et al.   BMC GENOMICS

Evaluating bias-reducing protocols for RNA sequencing library preparation

(2014) Thomas J Jackson et al.   BMC GENOMICS

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Advances in the profiling of DNA modifications: cytosine methylation and beyond

(2014) Nongluk Plongthongkum et al.   NATURE REVIEWS GENETICS

Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

(2014) Claire T. Deakin et al.   NUCLEIC ACIDS RESEARCH

Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases

(2014) Pawel Zajac et al.   PLoS One

Assessment of Whole Genome Amplification for Sequence Capture and Massively Parallel Sequencing

(2014) Johanna Hasmats et al.   PLoS One

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

(2014) Mandy Man-Ying Tin et al.   PLoS One

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Single-Cell Sequencing

(2014) Minfeng Chen et al.   PLoS One

Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5

(2014) G. E. Katibah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capture and Amplification by Tailing and Switching (CATS)

(2014) Andrey Turchinovich et al.   RNA Biology

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Non-random DNA fragmentation in next-generation sequencing

(2014) Maria S. Poptsova et al.   Scientific Reports

A genome scale overexpression screen to reveal drug activity in human cells

(2014) Anthony Arnoldo et al.   Genome Medicine

A Genome-Wide Tethering Screen Reveals Novel Potential Post-Transcriptional Regulators in Trypanosoma brucei

(2014) Esteban D. Erben et al.   PLoS Pathogens

Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy

(2014) Derong Xu et al.   Protein & Cell

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

populacDNA normalization by hydroxyapatite chromatography to enrich transcriptome diversity in RNA-seq applications

(2013) Victoria A. VanderNoot et al.   BIOTECHNIQUES

Identification of Human Protein Interaction Domains using an ORFeome-based Yeast Two-hybrid Fragment Library

(2013) Selma Waaijers et al.   JOURNAL OF PROTEOME RESEARCH

Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq

(2013) Maxime Wery et al.   METHODS

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA

(2013) Helena M B Seth-Smith et al.   Nature Protocols

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

Biases in small RNA deep sequencing data

(2013) Carsten A. Raabe et al.   NUCLEIC ACIDS RESEARCH

Consequences of Normalizing Transcriptomic and Genomic Libraries of Plant Genomes Using a Duplex-Specific Nuclease and Tetramethylammonium Chloride

(2013) Marta Matvienko et al.   PLoS One

Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme

(2013) Hashem Koohy et al.   PLoS One

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

(2013) S. Mohr et al.   RNA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Quantitative Transcriptomics using Designed Primer-based Amplification

(2013) Vipul Bhargava et al.   Scientific Reports

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase – engineering a thermostable ATP independent enzyme

(2012) Alexander M Zhelkovsky et al.   BMC MOLECULAR BIOLOGY

Quantitative Analysis of Hsp90-Client Interactions Reveals Principles of Substrate Recognition

(2012) Mikko Taipale et al.   CELL

Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities

(2012) Jae-Hyung Ahn et al.   JOURNAL OF MICROBIOLOGY

Non-invasive prenatal measurement of the fetal genome

(2012) H. Christina Fan et al.   NATURE

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Mechanism of RNA 2′,3′-cyclic phosphate end healing by T4 polynucleotide kinase–phosphatase

(2012) Ushati Das et al.   NUCLEIC ACIDS RESEARCH

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang et al.   NUCLEIC ACIDS RESEARCH

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Two methods for full-length RNA sequencing for low quantities of cells and single cells

(2012) X. Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

(2012) Patrick Boyle et al.   GENOME BIOLOGY

Directional, seamless, and restriction enzyme-free construction of random-primed complementary DNA libraries using phosphorothioate-modified primers

(2011) Shanshan W. Howland et al.   ANALYTICAL BIOCHEMISTRY

T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis

(2011) Sebastien Viollet et al.   BMC BIOTECHNOLOGY

New methods for next generation sequencing based microRNA expression profiling

(2011) Henk PJ Buermans et al.   BMC GENOMICS

A combinatorial method to enable detailed investigation of protein–protein interactions

(2011) Kate Maclagan et al.   Future Medicinal Chemistry

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Barcoding bias in high-throughput multiplex sequencing of miRNA

(2011) S. Alon et al.   GENOME RESEARCH

Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts

(2011) Jianzhong Su et al.   GENOMICS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

Linear amplification for deep sequencing

(2011) Wieteke A M Hoeijmakers et al.   Nature Protocols

Titration-free 454 sequencing using Y adapters

(2011) Zongli Zheng et al.   Nature Protocols

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing

(2011) Anitha D. Jayaprakash et al.   NUCLEIC ACIDS RESEARCH

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

(2011) Hana Yi et al.   NUCLEIC ACIDS RESEARCH

Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling

(2011) Felix Krueger et al.   PLoS One

Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing

(2011) Ellen Knierim et al.   PLoS One

An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs

(2011) Ru Huang et al.   PLoS One

Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing

(2011) Filip Van Nieuwerburgh et al.   PLoS One

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome

(2011) C. A. Raabe et al.   RNA

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

(2011) M. Hafner et al.   RNA

A bias-reducing strategy in profiling small RNAs using Solexa

(2011) G. Sun et al.   RNA

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Normalization of genomic DNA using duplex-specific nuclease

(2010) Irina Shagina et al.   BIOTECHNIQUES

Recent advances in DNA sequencing methods – general principles of sample preparation

(2010) Sten Linnarsson   EXPERIMENTAL CELL RESEARCH

Strand-specific deep sequencing of the transcriptome

(2010) A. P. Vivancos et al.   GENOME RESEARCH

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome

(2010) A. T. Lamm et al.   GENOME RESEARCH

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

(2010) Peng Cui et al.   GENOMICS

Whole-genome DNA methylation profiling using MethylCap-seq

(2010) Arie B. Brinkman et al.   METHODS

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

(2010) Mazhar Adli et al.   NATURE METHODS

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA

(2010) D. B. Munafo et al.   RNA

H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3

(2010) Richárd Bártfai et al.   PLoS Pathogens

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Multiple displacement amplification for complex mixtures of DNA fragments

(2009) Muhammad Shoaib et al.   BMC GENOMICS

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Genome sequence of the recombinant protein production host Pichia pastoris

(2009) Kristof De Schutter et al.   NATURE BIOTECHNOLOGY

Limitations and possibilities of small RNA digital gene expression profiling

(2009) Sam E V Linsen et al.   NATURE METHODS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

(2009) David Serre et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Mutation Rates and Intrinsic Fidelity of Retroviral Reverse Transcriptases

(2009) Luis Menéndez-Arias   Viruses-Basel

When good transcripts go bad: artifactual RT-PCR ‘splicing’ and genome analysis

(2008) Scott William Roy et al.   BIOESSAYS

Construction and characterization of a normalized yeast two-hybrid library derived from a human protein-coding clone collection

(2008) Jorja Degrado-Warren et al.   BIOTECHNIQUES

Isolation, characterization and molecular cloning of Duplex-Specific Nuclease from the hepatopancreas of the Kamchatka crab

(2008) Veronika E. Anisimova et al.   BMC BIOCHEMISTRY

A quantitative estimation of the global translational activity in logarithmically growing yeast cells

(2008) Tobias von der Haar   BMC Systems Biology

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

(2008) Mike Boxem et al.   CELL

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Normalization of full-length enriched cDNA

(2008) Ekaterina A. Bogdanova et al.   Molecular BioSystems

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Identification of soluble protein fragments by gene fragmentation and genetic selection

(2008) Michael R. Dyson et al.   NUCLEIC ACIDS RESEARCH

Novel mutations in Moloney Murine Leukemia Virus reverse transcriptase increase thermostability through tighter binding to template-primer

(2008) Bahram Arezi et al.   NUCLEIC ACIDS RESEARCH

A procedure for highly specific, sensitive, and unbiased whole-genome amplification

(2008) X. Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

(2008) Jia Qian Wu et al.   GENOME BIOLOGY