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SOLiD® Next Generation Sequencing Publications & Literature
All the latest scientific publications using the SOLiD System, as well as brochures, application notes, protocols, and other product literature from Applied Biosystems.
Platform/Technology
- NGSQC: cross‐platform quality analysis pipeline for deep sequencing data
Publication: BMC Genomics
Authors: Dai, et al. - Applied Biosystems SOLiD™ System: Ligation-Based Sequencing
Publication: Next Generation Genome Sequencing: Towards Personalized Medicine
Authors: Pandey V, Nutter RC, Prediger E (2008), Wiley, pages 29-41
Accuracy of the SOLiD ™ System
- Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing
Publication: Acids Research (2010)
Authors: Picardi, et al. - U87MG Decoded: The genomic sequence of a cytogenetically aberrant human cancer cell line
Publication: PLoS Genetics (2010)
Authors: Smith, et al.
- Evaluation of next generation sequencing platforms for population targeted sequencing studies
Publication: Genome Biology (2009)
Authors: Harismendy, et al. - Modeling non-uniformity in short-read rates in RNA-Seq data
Publication: Genome Biology (2010)
Authors: Li, et al. - Limitations and possibilities of small RNA digital gene expression profiling
Publication: Nature Methods (2009)
Authors: Linsen, et al. - Rapid whole-genome mutational profiling using next-generation sequencing technologies
Publication: Genome Res. (2008)
Authors: Smith, et al. - High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs
Publication: BMC Genomics (2009)
Authors: Walter, et al. - Comparing platforms for c. elegans mutant identification using high-throughput whole-genome sequencing
Publication: PLoS ONE
Authors: Shen, et al. - SNP discovery performance of two second generation sequencing platforms in the NOD2 gene region
Publication: Human Mutation (2010)
Authors: Melum, et al. - Whole-genome resequencing reveals loci under selection during chicken domestication
Publication: Nature (2010)
Authors: Rubin, et al. - Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma
Publication: Nucleic Acids Research (2010)
Authors: Nucleic Acids Research, et al. - A small-cell lung cancer genome with complex signatures of tobacco exposure
Publication: Nature (2010)
Authors: Pleasance, et al. - Polymorphism discovery in high-throughput resequenced microarray-enriched human genomic loci
Publication: Journal of Biomolecular Techniques
Authors: Antipova, et al. - Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms
Publication: Forensic Sci. Int. Gene. Suppl. (2009)
Authors: Cummings, et al. - Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding
Publication: Genome Res (2009)
Authors: McKernan, et al. - Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries
Publication: Nucleic Acids Research (2010)
Authors: Mokry, et al.
Automation
- Semi-Automated library preparation for high-throughput DNA sequencing platforms
Publication: Journal of Biomedicine and Biotechnology, Volume 2010, Article ID 617469
Authors: Farias-Hesson, et al.
Bioinformatics
- ZOOM Lite: next-generation sequencing data mapping and visualization software
Publication: Nucleic Acids Research (2011)
Authors: Zhang Z. et al. - Sniper: Improved SNP discovery by multiply mapping deep sequenced reads
Publication: Genome Biology (2011)
Authors: Simola D. et al - A framework for variation discovery and genotyping using next-generation DNA sequencing data
Publication: Nature Genetics (2011)
Authors: De Pristo M. A, et al. - HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies
Publication: Nucleic Acids Research (2011)
Authors: Kim et al. - Analysis of quality raw data of second generation sequencers with Quality Assessment Software
Publication: BMC Research Notes (2011)
Authors: Ramos R. et al. - SHRiMP2: Sensitive yet Practical Short Read Mapping
Publication: Bioinformatics (2011)
Authors: David M. et al. - ComB: SNP Calling and Mapping Analysis for Color and Nucleotide Space Platforms
Publication: Journal of Computational Biology (2011)
Authors: Souaiaiai T. et al. - Low coverage sequencing: Implications for the design of complex trait association studies
Publication: Genome Research (2011)
Authors: Li Y. et al. - Efficient study design for next generation sequencing
Publication: Genetic epidemiology (2011)
Authors: Sampson, et al. - Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads
Publication: BMC Bioinformatics (2011)
Authors: Duitama J, et al.
- Improving RNA-Seq expression estimates by correcting for fragment bias
Publication: Genome Biology (2011)
Authors: Roberts A., et al. - Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
Publication: BMC Genomics (2011)
Authors: You, et al. - A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing
Publication: Biosystems (2011)
Authors: Guo, et al. - NGSQC: cross-platform quality analysis pipeline for deep sequencing data
Publication: BMC Genomics (2011)
Authors: Dai, et al. - Technology-specific error signatures in the 1000 Genomes Project data
Publication: Human Genetics (2011)
Authors: Nothangel, et al. - The Uniqueome: A mappability resource for short-tag sequencing
Publication: Bioinformatics (2010)
Authors: Koehler R. et al. - A survey of sequence alignment algorithms for next-generation sequencing
Publication: Briefings in Bioinformatics (2010)
Authors: Li, et al. - Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA
Publication: Genome Biology (2010)
Authors: Homer, et al. - Designing efficient spaced seeds for SOLiD™ read mapping
Publication: Advances in Bioinformatics (2010)
Authors: Noe, et al. - SV SVDetect: A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
Publication: Bioinformatics, Vol. 26 no. 15 , pages 1895–1896 (2010)
Authors: Zeitouni, et al. - The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
Publication: Genome Res. published online (July 19, 2010)
Authors: McKenna, et al. - SOPRA: Scaffolding algorithm for paired reads via statistical optimization
Publication: BMC Bioinformatics, 11:345 (2010)
Authors: Dayarian, et al. - Filtering error from SOLiD™ Output
Publication: Bioinformatics, Vol. 26 no. 6, pages 849–850 (2010)
Authors: Sasson, et al. - VARiD: A variation detection framework for color-space and letter-space platforms
Publication: Bioinformatics, Vol. 26 ISMB, pages i343–i349 (2010)
Authors: Dalca, et al. - Intensity normalization improves color calling in SOLiD™ sequencing.
Publication: Nature Methods 7, 336-337 (2010)
Authors: Wu, et al. - Modeling non-uniformity in short-read rates in RNA-Seq data
Publication: Genome Biology 2010, 11:R50
Authors: Li, et al. - Correction of sequencing errors in a mixed set of reads.
Publication: Bioinformatics Advance Access published April 8, 2010
Authors: Salmela - Global and unbiased detection of splice junctions from RNA-seq data.
Publication: Genome Biology 2010, 11:R34
Authors: Ameur, et al. - A scaling normalization method for differential expression analysis of RNA-seq Data.
Publication: Genome Biology 2010, 11:R25
Authors: Robinson and Oshlack - PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
Publication: Genome Biology 2009, 10:R23
Authors: Korbel, et al. - Archiving next generation sequencing data.
Publication: Nucleic Acids Research, 2009, 1–2
Authors: Shumway, et al. - PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.
Publication: Bioinformatics 2009 25(19):2514-2521
Authors: Chen, et al. - Local alignment of two-base encoded DNA sequence.
Publication: BMC Bioinformatics 2009, 10:175
Authors: Homer, et al. - SHRiMP: Accurate Mapping of Short Color-space Reads.
Publication: PLoS Comput Biol 5(5): e1000386. (2009)
Authors: Rumble, et al. - Crystallizing short-read assemblies around seeds.
Publication: BMC Bioinformatics 2009, 10 (Suppl 1):S16
Authors: Hossain, et al. - RNA-MATE: A recursive mapping strategy for high-throughput RNA-sequencing data.
Publication: Bioinformatics, 2009
Authors: Cloonan, et al. - Efficient mapping of Applied Biosystems SOLiD™ sequence data to a reference genome for functional genomic applications.
Publication: Bioinformatics 2008 24(23):2776-2777
Authors: Ondov, et al.
Whole Genome Resequencing
- Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of single individual haplotyping techniques
Publication: Nucleic Acids Research (2011)
Authors: Duitama J. et al. - Comparative analysis of the complete genome sequences of two Australian origin live attenuated vaccines of infectious laryngotracheitis virus
Publication: Vaccine (2011)
Authors: Lee Sang-Won et al. - Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage
Publication: PNAS (2011)
Authors: Farrer R.A. et al - Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline
Publication: Human Molecular Genetics (2011)
Authors: Kloosterman, et al. - Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
Publication: Nature Genetics (2011)
Authors: Ju. et al. - Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole genome-based clinical diagnostics
Publication: Genetics in Medicine (2011)
Authors: Moore. et al. - Demographic history and rare allele sharing among human population
Publication: Gravel S et al, 2011
Authors: PNAS
- Mapping copy number variation by population-scale genome sequencing
Publication: Nature (2011)
Authors: Mills, et al. - Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
Publication: Virology journal (2011)
Authors: Legendre M, et al. - Full genome re-sequencing reveals a novel circadian clock mutation inArabidopsis
Publication: Genome Biology (2011)
Authors: Ashelford, et al. - Comprehensive long span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
Publication: Genome Research (2011)
Authors: Hillmer A.M., et al. - The genome of the woodland strawberry, Fragaria vesca
Publication: Nature Genetics (2010)
Authors: Shulaev, et al. - The developmental transcriptome of Drosophila melanogaster
Publication: Nature (2010)
Authors: Graveley, et al. - SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools
Publication: BMC Genomics (2010)
Authors: Marklund, et al. - An Alport syndrome mutation in mouse Col4a4 identified by whole genome sequencing and bulk segregation analysis
Publication: Genetics (2010)
Authors: Arnold, et al. - A map of human genome variation from population-scale sequencing
Publication: Nature (2010)
Authors: The 1000 Genomes Project Consortium - SOLiD™ sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes
Publication: BMC Genomics (2010)
Authors: Gulig, et al - Bulk segregation mapping of mutations in closely related strains of mice
Publication: Genetics (2010)
Authors: Xia, et al - Complete genome sequence of Staphylococcus aureus fifl strain JKD6008, a ST239 clone of methicillin-resistant Staphylococcus aureus with intermediate level vancomycin resistance
Publication: J. of Bacteriology (2010)
Authors: Howden et al - The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse
Publication: J. of Bacteriology Online 190(7): 2597-2606
Authors: Durfee, T., et al - The developmental transcriptome of Drosophila melanogaster
Publication: Nature (2010)
Authors: Graveley, et al. - Whole-genome resequencing reveals loci under selection during chicken domestication
Publication: Nature 464, 587-591 25 March 2010
Authors: Rubin C., et al. - Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy
Publication: N Eng J Med 10 March 2010
Authors: Lupski J., et al. - Development of personalized tumor biomarkers using massively parallel sequencing
Publication: Science Translational Medicine, February 24, 2010
Authors: Leary R., et al. - Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples
Publication: Nucleic Acids Research, 2010, 1–7
Authors: Smith et al. - Complete Khoisan and Bantu genomes from southern Africa
Publication: Nature, Vol 463, February 18, 2010
Authors: Schuster et al. - U87MG Decoded: The genomic sequence of a cytogenetically aberrant human cancer cell line
Publication: PLoS Genetics, January 2010, volume 6, issue 1
Authors: Clark, et al. - Maternal Plasma DNA Analysis with Massively Parallel Sequencing by Ligation for Noninvasive Prenatal Diagnosis of Trisomy 21
Publication: Clinical Chemistry 56:3 ,2010
Authors: Chiu, et al. - Digital fetal aneuploidy diagnosis by next-generation sequencing
Publication: Clinical Chemistry 56:3 336–338, 2010
Authors: Voelkerding and Lyon - A small-cell lung cancer genome with complex signatures of tobacco exposure.
Publication: Nature, 463, 184-190, January 14, 2010
Authors: Pleasance, et al. - Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing
Publication: European Journal of Human Genetics, December 2, 2009
Authors: Chen, et al. - Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms
Publication: Forensic Sci. Int. Gene. Suppl., 2009
Authors: Cummings, et al. - Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding
Publication: Genome Res. Published online June 22, 2009
Authors: McKernan, et al. - Rapid whole-genome mutational profiling using next-generation sequencing technologies
Publication: Genome Res. 2008. 18: 1638-1642
Authors: Smith et al. - Comparing platforms for c. elegans mutant identification using high-throughput whole-genome sequencing
Publication: PLoS ONE 3(12): e4012. doi:10.1371/journal.pone.0004012 I (2008)
Authors: Shen et al. - Fast Forward Genetics
Publication: Nature Biotechnology 26, 1248 - 1249, 2008
Authors: Darby and Hall
Targeted Resequencing
- Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing
Publication: Nature Protocols (2011)
Authors: Harakalova M. et al. - Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing
Publication: Nature Genetics (2011)
Authors: Stark M.S. et al. - Decoding cell lineage from acquired mutations using arbitrary deep sequencing
Publication: Nature Methods (2011)
Authors: Carlson C. A. et al. - Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform
Publication: Plos One (2011)
Authors: Hedges D.J. et al. - Population genetics in non- model organisms: II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms
Publication: Molecular Biology and Evolution (2011)
Authors: Zhou R. et al. - Carrier testing for severe childhood recessive diseases by next-generation sequencing
Publication: 2011Science Translational Medicine (2011)
Authors: Bell, et al. - De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome
Publication: Nature Genetics (2011)
Authors: Hoischen A. et al. - Ultra-deep sequencing of Mouse Mitochondrial DNA: mutational patterns and their origin
Publication: PLoS Genetics (2011)
Authors: Ameur A., et al.
- Genomic DNA pooling strategy for next-generation sequencing-based rare variant discovery in Abdominal Aortic Aneurysm regions of interest—challenges and limitations
Publication: , J. of Cardiovasc. Trans. Res. (2011)
Authors: Haraklova, et al. - Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors
Publication: Genome Research (2010)
Authors: Robbins, et al. - Targeted resequencing of candidate genes using selector probes
Publication: Nature Genetics (2010)
Authors: Johansson, et al. - New mutations and intellectual function
Publication: Nature Genetics (2010)
Authors: Lupski, et al. - Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples
Publication: Nucleic Acids Research (2010)
Authors: Smith, et al. - A de novo paradigm for mental retardation
Publication: Nature Genetics (2010)
Authors: Vissers, et al. - Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency
Publication: Nature Genetics (2010)
Authors: Haack, et al. - Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples
Publication: Nature Methods (2010)
Authors: Nijman, et al. - Ultra high throughput sequencing in human DNA variation detection: A comparative study on the NDUFA3-PRPF31 region
Publication: PLoS ONE (2010)
Authors: Benaglio, et al. - Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome
Publication: Nature Genetics (2010)
Authors: Krawitz, et al. - Exome sequencing identifies WDR35 variants involved in sensenbrenner syndrome
Publication: The American Journal of Human Genetics (2010)
Authors: Glissen et al. - Whole exome capture in solution with 3Gbp of data
Publication: Genome Biology, 11:R62 (2010)
Authors: Bainbridge, et al. - SNP discovery performance of two second generation sequencing platforms in the NOD2 gene region
Publication: Human Mutation Volume 9999 Issue 999A, published online (May 18, 2010)
Authors: Melum, et al. - Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer.
Publication: Journal of Human Genetics, May 2010
Authors: Mitsui, et al. - PHF6 mutations in T-cell acute lymphoblastic leukemia.
Publication: Nature Genetics 42, 338-342. 14 March 2010
Authors: Van Vlierberghe, P., et al. - Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.
Publication: 25 Jan 2010
Authors: Mokry, M., et al. - GC-Biased Evolution Near Human Accelerated Regions
Publication: PLoS Genetics, 2010
Authors: Katzman, et al. - De novo mutations of SETBP1 cause Schinzel-Giedion syndrome.
Publication: Nature Genetics, May 2010
Authors: Hoischen, et al. - Targeted resequencing of candidate genes using selector probes
Publication: Nucleic Acids Research (2010)
Authors: Johansson, et al. - Polymorphism Discovery in High-Throughput Resequenced Microarray-Enriched Human Genomic Loci.
Publication: Journal of Biomolecular Techniques 20:253–257
Authors: Antipova, et al. - High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs.
Publication: BMC Genomics 2009, 10:379
Authors: Walter, et al. - Evaluation of next generation sequencing platforms for population targeted sequencing studies.
Publication: Genome Biology 2009, 10:R32
Authors: Harismendy, et al.
De Novo Sequencing
- First complete genome sequence of infectious laryngotracheitis virus
Publication: BMC Genomics (2011)
Authors: Lee S. et al - Whole-Genome Shotgun Sequencing of the Sulfur-Oxidixing Chemoautotroph Tetrathiobacter kashmirensis
Publication: Journal of Bacteriology (2011)
Authors: Ghosh W et al - Whole genome sequencing of environmental Vibrio cholerae 01 from 10 nanograms of DNA using short reads
Publication: Journal of Microbiological Methods (2011)
Authors: Chaparro P, et al. - Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis l19 as a case study
Publication: Journal of Microbiological Methods (2011)
Authors: Cerdeira L, et al. - Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
Publication: BMC Genomics (2010)
Authors: den Bakker, et al. - Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism
Publication: Science (2010)
Authors: Spanu, et al.
- Complete genome sequence of corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis
Publication: J. Bacteriology (2010)
Authors: Silva, et al.
Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
- Chromosome length influences replication-induced topological stress
Publication: Nature (2011)
Authors: Kegel, et al.
- ATP hydrolysis is required for relocating cohesin from sites occupied by its Scc2/4
Publication: Current Biology (2010)
Authors: Hu, et al. - A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion
Publication: The EMBO Journal (2010)
Authors: Kurze, et al. - The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection
Publication: Nature Immunology (2010)
Authors: Satoh, et al. - A downstream intergenic cluster of regulatory enhancers contributes to the induction of CYP24A1 expression by 1α,25-dihydroxyvitamin D3
Publication: The Journal of Biological Chemistry (2010)
Authors: Meyer, et al. - A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells
Publication: Genome Res, published online (May 27, 2010)
Authors: Tallack, et al. - Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ System
Publication: Nature Methods 6, (2009)
Authors: Shah et.al. - A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.
Publication: Genome Research. 2008 Jul;18(7):1051-63.
Authors: Valoeuv, A., et al. - Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.
Publication: Bioinformatics. 5 March 2010
Authors: Johannes, F., et al. - ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth.
Publication: PLoS Biol 7(12): e1000256
Authors: Markljung, et al. - A novel mechanism of epigenetic regulation: Nucleosome-space occupancy.
Publication: Biochem. Biophys. Res. Commun (2009)
Authors: Ciu, et al. - Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.
Publication: Genome Biology 2009, 10:R129
Authors: Motallebipour, et al. - A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome.
Publication: Genome Biology 2009, 10:R109
Authors: Jiang and Pugh - Interaction of transcriptional regulators with specific nucleosomes across the saccharomyces genome.
Publication: Molecular Cell Volume 35, Issue 6, 889-902, 24 September 2009
Authors: Koerber, et.al. - Nucleosomes are well positioned in exons and carry characteristic histone modifications.
Publication: Genome Research 2009. 19:1732-1741.
Authors: Andersson, et al. - The human TTAGGG repeat factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats
Publication: Cell Research (2011)
Authors: Simonet T. et al.
Methylation Analysis
- Increased methylation variation in epigenetic domains across cancer types
Publication: Nature Genetics (2011)
Authors: Edwards, et al. - High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology
Publication: PLoS One (2011)
Authors: Lan L, et al. - Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing data
Publication: Electrophoresis (2010)
Authors: Yang, et al. - An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD™ System
Publication: Bioinformatics Advance Access (June 18, 2010)
Authors: Ondov, et al.
- Whole methylome analysis by ultra-deep sequencing using two-base encoding.
Publication: PLoS ONE 5(2):e9320 22 Feb 2010
Authors: Chung, C., et al. - Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns.
Publication: Genome Research, 2010
Authors: Edwards, et al. - Preparation of genome-wide DNA fragment libraries using bisulfite in polyacrylamide gel electrophoresis slices with formamide denaturation and quality control for massively parallel sequencing by oligonucleotide ligation and detection.
Publication: ScienceDirect. Published online April 18, 2009.
Whole Transcriptome Analysis
- Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell
Publication: Journal of Virology (2012)
Authors: Lefebvre G. et al - Genome wide full-length transcript analysis using 5'and 3' paired-end-tag next generation sequencing (RNA-PET)
Publication: Methods in Molecular Biology, vol. 809 (2012)
Authors: Xiaoan Ruan and Yijun Ruan - Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe
Publication: Molecular Systems Biology (2011)
Authors: Bitton D. A. et al. - Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
Publication: Genome Research (2011)
Authors: Kolle G. et al. - Whole-Genome Sequencing for Optimized Patient Management
Publication: Science Translational Medicine (2011)
Authors: Bainbridge M. et al. - Genome-wide Analysis of the 5’ and 3’ Ends of Vaccinia Virus Early mRNAs Delineates Regulatory Sequences of Annotated and Anomalous Transcripts
Publication: Journal of Virology (2011)
Authors: Yang Z., et al. - The Cluster 1 Type VI Secretion System Is a Major Virulence Determinant in Burkholderia pseudomallei
Publication: Infection and Immunity (2011)
Authors: Burtnick M., et al. - Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis
Publication: Cell (2011) Authors: Autran D. et al. - NanoRNAs Prime Transcription Initiation In Vivo
Publication: Molecular Cell (2011)
Authors: Goldman et al. - Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
Publication: Bioinformatics (2011)
Authors: Labaj P. et al. - A tissue-specific landscape of sense/antisense transcription in the mouse intestine
Publication: BMC Genomics (2011)
Authors: Klostermeier U. et al. - Metatranscriptomics of a hot-spring microbial mat
Publication: The ISME Journals (2011)
Authors: Z Liu et al. - Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres
Publication: PloS One (2011)
Authors: Tang F. et al. - Whole-transcriptome RNSseq analysis from minute amount of total RNA
Publication: Nucleic Acids Research (2011)
Authors: Tariq M. et al. - XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast
Publication: Nature (2011)
Authors: Dijk E. et al. - Zebrafish mRNA sequencing decipher novelties in transcriptome dynamics during maternal to zygotic transition
Publication: Genome Research (2011)
Authors: Aanes H. et al. - Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome
Publication: Molecular Ecology Resources (2011)
Authors: Everett M.V. et al. - Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
Publication: PLos One (2011)
Authors: Costa V. et al. - Development and applications of single-cell transcriptome analysis
Publication: Nature Methods (2011)
Authors: Tang F. et al. - Transcriptional consequences of genomic structural aberrations in breast cancer
Publication: Genome Research (2011)
Authors: Inaki K. et al. - Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Publication: BMC Genomics (2011)
Authors: Isabella V. M., et al. - Hyperactivation of anandamide synthesis and regulation of cell-cycle progression via cannabinoid type 1 (CB1) receptors in the regenerating liver
Publication: PNAS (2011)
Authors: Mukhopadhyay B. et al. - Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
Publication: Virology journal (2011)
Authors: Legendre M. et al. - Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss
Publication: Science (2010)
Authors: Mitrovich, et al. - FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
Publication: Nature Methods (2010)
Authors: Underwood, et al. - The exon junction complex controls the splicing of mapk and other long intron-containing transcripts in drosophila
Publication: Cell (2010)
Authors: Ashton-Beaucage, et al. - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk
Publication: Nature (2010)
Authors: Heinig, et al. - Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing
Publication: Genome Biology (2010)
Authors: Wetterbom, et al. - Constitutively active androgen receptor splice variants expressed in castration-resistant prostate cancer require full-length androgen receptor
Publication: PNAS (2010)
Authors: Watson, et al. - Roles of xanthophyll carotenoids in protection against photoinhibition and oxidative stress in the cyanobacterium Synechococcus sp. strain PCC 7002
Publication: Archives of Biochemistry and Biophysics (2010)
Authors: Zhu et al. - Functional and structural characterization of the 2/2 hemoglobin from Synechococcus sp. PCC 7002
Publication: Biochemistry (2010)
Authors: Scott et al. - The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation
Publication: PLoS Genetics, (2010)
Authors: Tuch, et al. - Simultaneous high-resolution analysis of vaccinia virus and host cell transcriptomes by deep RNA sequencing
Publication: PNAS, published online (June 7, 2010)
Authors: Yang, et al. - Genome-wide misexpression of X-linked versus autosomal genes associated with hybrid male sterility
Publication: Genome Res., published online (May 28, 2010)
Authors: Lu, et al. - Widespread transcription at neuronal activity-regulated enhancers
Publication: Nature (2010)
Authors: Kim et al. - RNA-Seq analysis to capture the transcriptome landscape of a single cell.
Publication: Nature Protocols, 5, -516-535. 25 Feb 2010
Authors: Tang, F., et al. - Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations.
Publication: PLoS ONE 5(2): e9317. 19 Feb 2010
Authors: Tuch, T., et al. - A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling.
Publication: BMC Genomics 2010, 11:282
Authors: Bradford et al. - Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNASeq Analysis.
Publication: Cell Stem Cell, 6, May 7, 2010
Authors: Tang et al. - Widespread transcription at neuronal activity-regulated enhancers.
Publication: Nature, 14 April 2010
Authors: Kim et al. - Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.
Publication: Nucleic Acids Research, 2010, 1–13
Authors: Picardi et al. - The Structure and Complexity of a Bacterial Transcriptome
Publication: Bacteriol. 2009 : JB.00122-09v1
Authors: Passalacqua, K., et al. - mRNA-Seq whole-transcriptome analysis of a single cell
Publication: Nature Methods, published online: 6 April 2009.
Authors: Tang et al. - Stem cell transcriptome profiling via massive-scale mRNA sequencing.
Publication: Nature Methods Online. 2008 Jul;5(7):613-9.
Authors: Cloonan, N., et al.
Small RNA Analysis
- Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis
Publication: BMC Genomics (2012)
Authors: Tu J. et al. - Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs
Publication: RNA (2012)
Authors: Voellenkle C. et al - Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing
Publication: Molecular Plant Pathology, (2012)
Authors: Stassen J. et al. - Sequencing circulating miRNA in maternal plasma with modified library preparation
Publication: Clinica Chimica Acta(2011)
Authors: Ge Q. et al. - Assessment of nanomaterial cytotoxicity with SOLiD sequencing-based microRNA expression profiling
Publication: Biomaterials (2011)
Authors: Li S. et al. - Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana
Publication: PLoS One (2011)
Authors: Norden-Krichmar T. et al - Deep Sequencing of virus-infected cells reveals HIV-encoded small RNAs
Publication: Nucleic Acids Research (2011)
Authors: Shopman N, et al. - A Comprehensive Survey of miRNA Repertoire and 39 Addition Events in the Placentas of Patients with Pre- Eclampsia from High-Throughput Sequencing
Publication: PloS One (2011)
Authors: Guo, et al. - Next-Generation Sequencing of MicroRNAs for Breast Cancer Detection
Publication: Journal of Biomedicine and Biotechnology (2011)
Authors: Qu Q, et al. - Sequencing circulating miRNA in maternal plasma with modified library preparation
Publication: Clinica Chimica Acta(2011)
Authors: Ge Q. et al. - Assessment of nanomaterial cytotoxicity with SOLiD sequencing-based microRNA expression profiling
Publication: Biomaterials (2011)
Authors: Li S. et al. - Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana
Publication: PLoS One (2011)
Authors: Norden-Krichmar T. et al - Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti- viral defense
Publication: BMC Microbiology (2011)
Authors: Hess A.M. et al. - MicroRNAs as participants in cytotoxicity of CdTe quantum dots in NIH/3T3 cells
Publication: Biomaterials (2011)
Authors: Li, et al. - Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread Intron loss
Publication: Science (2010)
Authors: Quinn, et al.
- Discovery and characterization of medaka miRNA genes by next generation sequencing platform
Publication: BMC Genomics (2010)
Authors: Li, et al. - Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells
Publication: PLoS Genetics (2010)
Authors: Hanina, et al. - Next-generation sequencing identifies the natural killer cell microRNA transcriptome
Publication: Genome Res. (2010)
Authors: Fehniger, et al. - Ultra-deep sequencing reveals the microRNA expression pattern of the human stomach
Publication: PLoS ONE (2010)
Authors: Ribeiro-dos-Santos, et al. - Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs
Publication: RNA (2010)
Authors: Lin, et al. - Arabidopsis lyrata small RNAs: Transient MIRNA and small interfering RNA loci within the Arabidopsis Genus
Publication: Publication: The Plant Cell (2010)
Authors: Ma et al. - Identification of homologous microRNAs in 56 animal genomes
Publication: Publication: Genomics; 96(1): 1-9 (July 2010)
Authors: Li, et al. - RNA deep sequencing of the Atlantic cod transcriptome.
Publication: Comparative Biochemistry and Physiology, May 2010
Authors: Johansen, et al. - Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma.
Publication: Nucleic Acids Research, 2010, 1–10
Authors: Schulte et al. - High Throughput Sequencing of MicroRNAs in Adenovirus Type 3 Infected Human Laryngeal Epithelial Cells.
Publication: Journal of Biomedicine and Biotechnology, 2010
Authors: Qi, et al. - Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila.
Publication: Nature Structural & Molecular Biology 17, 24 - 30 (2010)
Authors: Marques, et al. - Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome
Publication: RNA (2009)
Authors: Addo-Quaye, et al. - Ago2 Immunoprecipitation Identifies Predicted MicroRNAs in Human Embryonic Stem Cells and Neural Precursors.
Publication: PLoS ONE (2009) 4(9): e7192.
Authors: Goff, et al. - Limitations and possibilities of small RNA digital gene expression profiling.
Publication: Nature Methods 6, 474-476 (2009)
Authors: Linsen, et al.
Gene Expression
- Variation in the Large-Scale Organization of Gene Expression Levels in the Hippocampus Relates to Stable Epigenetic Variability in Behavior.
Publication: PLoS ONE (2008) 3(10): e3344.
Authors: Alter et al. - High-Resolution Analysis of the 5'-End Transcriptome Using a Next Generation DNA Sequencer.
Publication: PLoS ONE. 2009; 4(1): e4108
Authors: Hashimoto, et al.
RNA Structure
- Long noncoding RNA as modular scaffold of histone modification complexes
Publication: Science, Published online (July 8, 2010)
Authors: Tsai, et al.
Metagenomics
- Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat
Publication: The ISME Journal (2011)
Authors: Liu Z. et al. - Confirmation of the Sequence of 'Candidatus Liberibacter asiaticus' and Assessment of Microbial Diversity in Huanglongbing-Infected Citrus Phloem Using a Metagenomic Approach.
Publication: Molecular Plant-Microbe Interactions, Vol. 22, No. 12, 2009
Authors: Tyler et al. - The carnivorous bladderwort (Utricularia, Lentibulaiceae) a system inflates.
Publication: Journal of Experimental Botany, vol. 61, No1, pp 5-9, 2010
Authors: Albert, et al.
How the SOLiD™ System Works
Whole Genome Sequencing
- Whole Genome Resequencing
- Whole Genome Sequencing of E. coli Bacteria
- Mate-Paired Libraries Detect/Define Genetic Rearrangements
Targeted Resequencing
- Array-based Enrichment of Specific Genomic Regions using the SOLiD™ System
- SureSelect™ Solution-Based Enrichment of Genomic Regions for Targeted Resequencing on the SOLiD™ System
De Novo Sequencing
- Whole Genome Sequencing of E. coli Bacteria
- First complete genome sequence of infectious laryngotracheitis virus
Publication: BMC Genomics (2011)
Authors: Lee S. et al.
Gene Expression Profiling
Small RNA Analysis
- miRNA Discovery and Profiling with the SOLiD™ Small RNA Expression Kit
- Whole Genome Analysis of Small RNA
Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
Whole Transcriptome Analysis
- Effective Strategies for Exon/Exon Junction Mapping and Fusion Transcript Detection
- Whole Transcriptome Profiling Using the SOLiD™ 3 System
- Single-Cell Whole Transcriptome Profiling with the SOLiD™ System
Methylation Analysis
Application Fact Sheet
Quarterly Newsletter
- The SOLID Read
August 2011 - The SOLID Read
February 2011
Specification Sheet
White Papers
How the SOLiD™ System Works
- AGBT 2011 - Accurate detection of insertions and deletions
- AGBT 2011 - Getting personal: improved throughput and accuracy toward enhanced understanding of human genome biology
- AGBT 2011 - Towards a pushbutton human genome
- AGBT 2011 - Low input mate-paired sequencing and its application on FFPE tumor samples
- AGBT 2011 - Real-time data quality feedback for the 5500 Series SOLiD™ Sequencers
- AGBT 2011 - High accuracy base space sequencing: results from error-correction ligation chemistry
- AGBT 2011 - Accuracy and performance breakthroughs with the 5500 Series SOLiD™ Sequencers
- AGBT 2011 - Analysis of a Southern African genome using SOLiD™ System error correction codes
- Increased read length on the SOLiD™ Sequencing platform
- Multiplex sequencing on the SOLiD™ platform with 10, 16, or 96 barcodes
- SOLiD™ System Sequencing and 2 Base Encoding
- Accurate genome-wide SNP detection with low and medium coverage with next-generation sequencing
- Paired end sequencing on the SOLiD™ platform
- Enhanced Throughput and Accuracy on the SOLiD™ System.
- BioScope™ 1.2: An Applications Framework for SOLiD™ Sequence Data Analysis.
- Application specific accuracy with SOLiD™ System high throughput sequencing
- ESHG 2011 - Simultaneous Evaluation of Small RNA, Whole Transcriptome, Whole Genome, ChipSeq and Targeted Resequencing on Next Generation Sequencing Platforms
- ESHG 2011- P12.045 Detection of low frequency variation in heterogeneous samples using the accuracy and sensitivity of a SOLiDTM System
Automation
- A new protocol for next gen library construction increases yield / complexity and simplifies parallel sample handling
- ABRF 2011 - Robotic scripts, methods, reagents, and devices for high throughput automated production of next generation sequencing DNA fragment libraries
Whole Genome Sequencing
- Lorne 2011 - Preliminary description of the genome of the single individual from northern Europe
- AGBT 2011 - Accessing the inaccessible genome
- Paired end sequencing of human genomes on the SOLiD™ platform
- Increased Read Length on the SOLiD™ Sequencing Platform.
- The Detectable Genome: How much of the human genome is accessible to variant discovery by next-generation sequencing?
- Large-Scale SNP Detection via Ligation-based Dibase Sequencing Across Multiple HapMap Individuals: NA18507, NA19240, and NA12878
- Accurate genome-wide SNP detection with low and medium coverage with next-generation sequencing
- Dibase sequencing allows accurate SNP detection at moderate and low coverage with diBayes algorithm
- Functional analysis of the genetic variation within the genomes of three HapMap individuals obtained by whole-genome, second-generation sequencing
- Sequence and Structural Variation in a Human Genome
- Resolving Structural Variations Using SOLiD™ Mate Pair Sequencing Technology
- A high-resolution structural variation map of human germline genomes by next-generation, high-throughput paired end sequencing with the SOLiD™ System
- Whole Genome Resequencing with Short Reads: Accurate Mutation Discovery with Mate Pairs and Quality Values
- Finding Indels with Short Sequencing Reads and De Novo Assembly with SOLiD™ Reads
- Genome Variablility Analysis of Yoruba in Ibadan, Nigeria (NA18507) by SOLiD™ Mediated Whole Genome Re-Sequencing
- Next-generation Sequencing for Detection of Rare Variants and Heterozygosity
- Single Base-pair Breakpoint Resolution Map of Small to Large Indels Using a Split Read Technique with High-throughput Mate-pair and Fragment Sequencing
- Whole-Genome SNP Detection and Haplotype Phasing with Mate Pairs via Ligation-Based Dibase Sequencing
- The normal and tumor spectrum of copy number variation: Copy number alterations correlate with changes in gene expression in tumor transcriptome.
Targeted Resequencing
- AGBT 2011 - Multiplex exome enrichment from pooled barcoded libraries yields efficient SNP and indel detection on the SOLiD™ System
- PCR-based targeted sequence enrichment for next generation sequencing platform.
- DiBayes: A SNP Detection Algorithm for Next-Generation Dibase Sequencing
- Applications of Next Generation Sequencing in Genetic Epidemiology
- SNP discovery in high-throughput resequenced microarray-enriched human genomic loci.
- Multiplexed Target Enrichment for SOLiD™ System Sequencing
- Solution-Based Enrichment of Genomic Loci for Massively Parallel Sequencing on the SOLiD™ System
- MHC Haplotype Sequencing: An Integrated Approach to Common Disease
De Novo Sequencing
- AGBT 2011 - Single molecule real-time DNA squencing using FRET-based reagents
- Increased Read Length on the SOLiD™ Sequencing Platform.
Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
- Rapid chromatin preparation from solid mammalian tissues for low cell ChIP assays
- SOLiD™ ChIP-Seq kit for ChIP & ChIP-sequencing from low number of cell & tissue samples
- SOLiD™ ChIP-Seq Kit for ChIP and ChIP-Seq with Low Cell Number Samples.
Gene Expression Profiling
Small RNA Analysis
- ABRF 2011 - MicroRNA analysis using RNA extracted from matched formalin-fixed paraffin-embedded (FFPE) and fresh frozen samples on SOLiD™ system
- AGBT 2011 - SOLiD™ System approaches for small RNA expression profiling of formalin-fixed, paraffin-embedded (FFPE) tissue samples
- An Expression Atlas of small RNAs generated using the SOLiD™ Sequencing System
- Multiplex Sequencing on the SOLiD™ Platform with 10, 16, or 96 Barcodes
- A novel approach for miRNA profiling using massively parallel, ligation-based sequencing
- Analysis of the Molecular Factors Controlling Human Osteosarcoma Response to Chemotherapy
Whole Transcriptome Analysis
- ABRF 2011 - Improvements in SOLiD™ whole transcriptome library preparation workflow to enable low input RNA amounts
- ABRF 2011 - Development of ERCC RNA spike-in control mixes
- ABRF 2011 - Use of synthetic transcript pools to evaluate RNA-Seq performance and analytical methods
- AGBT 2011 - RNA-Seq for identifying gene expression changes associated with relapse in Acute Lymphoblastic Leukemia (ALL)
- Identifying novel expressed gene fusions in MCF-7 cell line using next generation sequencing
- Multiplex sequencing on the SOLiD™ platform with 10, 16, or 96 barcodes
- Whole transcriptome analysis of total human RNAs by massively parallel sequencing on the SOLiD™ system
- Single cell transcriptome analysis on the SOLiD™ system
- A comparison of next generation sequencing and microarrays for whole transcriptome expression profiling
- mRNA-Seq Whole Transcriptome Analysis of a Single Cell
- Whole transcriptome sequencing of three oral cancers
- Multiplex Single Cell RNA-Seq Transcriptome Analysis of Pluripotent Cells both in vitro and in vivo
- IADR 2011 - The Saliva RNA Interactome
Methylation Analysis
Platform/Technology
- NGSQC: cross‐platform quality analysis pipeline for deep sequencing data
Publication: BMC Genomics
Authors: Dai, et al. - Applied Biosystems SOLiD™ System: Ligation-Based Sequencing
Publication: Next Generation Genome Sequencing: Towards Personalized Medicine
Authors: Pandey V, Nutter RC, Prediger E (2008), Wiley, pages 29-41
Accuracy of the SOLiD ™ System
- Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing
Publication: Acids Research (2010)
Authors: Picardi, et al. - U87MG Decoded: The genomic sequence of a cytogenetically aberrant human cancer cell line
Publication: PLoS Genetics (2010)
Authors: Smith, et al.
- Evaluation of next generation sequencing platforms for population targeted sequencing studies
Publication: Genome Biology (2009)
Authors: Harismendy, et al. - Modeling non-uniformity in short-read rates in RNA-Seq data
Publication: Genome Biology (2010)
Authors: Li, et al. - Limitations and possibilities of small RNA digital gene expression profiling
Publication: Nature Methods (2009)
Authors: Linsen, et al. - Rapid whole-genome mutational profiling using next-generation sequencing technologies
Publication: Genome Res. (2008)
Authors: Smith, et al. - High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs
Publication: BMC Genomics (2009)
Authors: Walter, et al. - Comparing platforms for c. elegans mutant identification using high-throughput whole-genome sequencing
Publication: PLoS ONE
Authors: Shen, et al. - SNP discovery performance of two second generation sequencing platforms in the NOD2 gene region
Publication: Human Mutation (2010)
Authors: Melum, et al. - Whole-genome resequencing reveals loci under selection during chicken domestication
Publication: Nature (2010)
Authors: Rubin, et al. - Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma
Publication: Nucleic Acids Research (2010)
Authors: Nucleic Acids Research, et al. - A small-cell lung cancer genome with complex signatures of tobacco exposure
Publication: Nature (2010)
Authors: Pleasance, et al. - Polymorphism discovery in high-throughput resequenced microarray-enriched human genomic loci
Publication: Journal of Biomolecular Techniques
Authors: Antipova, et al. - Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms
Publication: Forensic Sci. Int. Gene. Suppl. (2009)
Authors: Cummings, et al. - Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding
Publication: Genome Res (2009)
Authors: McKernan, et al. - Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries
Publication: Nucleic Acids Research (2010)
Authors: Mokry, et al.
Automation
- Semi-Automated library preparation for high-throughput DNA sequencing platforms
Publication: Journal of Biomedicine and Biotechnology, Volume 2010, Article ID 617469
Authors: Farias-Hesson, et al.
Bioinformatics
- ZOOM Lite: next-generation sequencing data mapping and visualization software
Publication: Nucleic Acids Research (2011)
Authors: Zhang Z. et al. - Sniper: Improved SNP discovery by multiply mapping deep sequenced reads
Publication: Genome Biology (2011)
Authors: Simola D. et al - A framework for variation discovery and genotyping using next-generation DNA sequencing data
Publication: Nature Genetics (2011)
Authors: De Pristo M. A, et al. - HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies
Publication: Nucleic Acids Research (2011)
Authors: Kim et al. - Analysis of quality raw data of second generation sequencers with Quality Assessment Software
Publication: BMC Research Notes (2011)
Authors: Ramos R. et al. - SHRiMP2: Sensitive yet Practical Short Read Mapping
Publication: Bioinformatics (2011)
Authors: David M. et al. - ComB: SNP Calling and Mapping Analysis for Color and Nucleotide Space Platforms
Publication: Journal of Computational Biology (2011)
Authors: Souaiaiai T. et al. - Low coverage sequencing: Implications for the design of complex trait association studies
Publication: Genome Research (2011)
Authors: Li Y. et al. - Efficient study design for next generation sequencing
Publication: Genetic epidemiology (2011)
Authors: Sampson, et al. - Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads
Publication: BMC Bioinformatics (2011)
Authors: Duitama J, et al.
- Improving RNA-Seq expression estimates by correcting for fragment bias
Publication: Genome Biology (2011)
Authors: Roberts A., et al. - Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
Publication: BMC Genomics (2011)
Authors: You, et al. - A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing
Publication: Biosystems (2011)
Authors: Guo, et al. - NGSQC: cross-platform quality analysis pipeline for deep sequencing data
Publication: BMC Genomics (2011)
Authors: Dai, et al. - Technology-specific error signatures in the 1000 Genomes Project data
Publication: Human Genetics (2011)
Authors: Nothangel, et al. - The Uniqueome: A mappability resource for short-tag sequencing
Publication: Bioinformatics (2010)
Authors: Koehler R. et al. - A survey of sequence alignment algorithms for next-generation sequencing
Publication: Briefings in Bioinformatics (2010)
Authors: Li, et al. - Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA
Publication: Genome Biology (2010)
Authors: Homer, et al. - Designing efficient spaced seeds for SOLiD™ read mapping
Publication: Advances in Bioinformatics (2010)
Authors: Noe, et al. - SV SVDetect: A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
Publication: Bioinformatics, Vol. 26 no. 15 , pages 1895–1896 (2010)
Authors: Zeitouni, et al. - The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
Publication: Genome Res. published online (July 19, 2010)
Authors: McKenna, et al. - SOPRA: Scaffolding algorithm for paired reads via statistical optimization
Publication: BMC Bioinformatics, 11:345 (2010)
Authors: Dayarian, et al. - Filtering error from SOLiD™ Output
Publication: Bioinformatics, Vol. 26 no. 6, pages 849–850 (2010)
Authors: Sasson, et al. - VARiD: A variation detection framework for color-space and letter-space platforms
Publication: Bioinformatics, Vol. 26 ISMB, pages i343–i349 (2010)
Authors: Dalca, et al. - Intensity normalization improves color calling in SOLiD™ sequencing.
Publication: Nature Methods 7, 336-337 (2010)
Authors: Wu, et al. - Modeling non-uniformity in short-read rates in RNA-Seq data
Publication: Genome Biology 2010, 11:R50
Authors: Li, et al. - Correction of sequencing errors in a mixed set of reads.
Publication: Bioinformatics Advance Access published April 8, 2010
Authors: Salmela - Global and unbiased detection of splice junctions from RNA-seq data.
Publication: Genome Biology 2010, 11:R34
Authors: Ameur, et al. - A scaling normalization method for differential expression analysis of RNA-seq Data.
Publication: Genome Biology 2010, 11:R25
Authors: Robinson and Oshlack - PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
Publication: Genome Biology 2009, 10:R23
Authors: Korbel, et al. - Archiving next generation sequencing data.
Publication: Nucleic Acids Research, 2009, 1–2
Authors: Shumway, et al. - PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.
Publication: Bioinformatics 2009 25(19):2514-2521
Authors: Chen, et al. - Local alignment of two-base encoded DNA sequence.
Publication: BMC Bioinformatics 2009, 10:175
Authors: Homer, et al. - SHRiMP: Accurate Mapping of Short Color-space Reads.
Publication: PLoS Comput Biol 5(5): e1000386. (2009)
Authors: Rumble, et al. - Crystallizing short-read assemblies around seeds.
Publication: BMC Bioinformatics 2009, 10 (Suppl 1):S16
Authors: Hossain, et al. - RNA-MATE: A recursive mapping strategy for high-throughput RNA-sequencing data.
Publication: Bioinformatics, 2009
Authors: Cloonan, et al. - Efficient mapping of Applied Biosystems SOLiD™ sequence data to a reference genome for functional genomic applications.
Publication: Bioinformatics 2008 24(23):2776-2777
Authors: Ondov, et al.
Whole Genome Resequencing
- Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of single individual haplotyping techniques
Publication: Nucleic Acids Research (2011)
Authors: Duitama J. et al. - Comparative analysis of the complete genome sequences of two Australian origin live attenuated vaccines of infectious laryngotracheitis virus
Publication: Vaccine (2011)
Authors: Lee Sang-Won et al. - Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage
Publication: PNAS (2011)
Authors: Farrer R.A. et al - Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline
Publication: Human Molecular Genetics (2011)
Authors: Kloosterman, et al. - Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
Publication: Nature Genetics (2011)
Authors: Ju. et al. - Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole genome-based clinical diagnostics
Publication: Genetics in Medicine (2011)
Authors: Moore. et al. - Demographic history and rare allele sharing among human population
Publication: Gravel S et al, 2011
Authors: PNAS
- Mapping copy number variation by population-scale genome sequencing
Publication: Nature (2011)
Authors: Mills, et al. - Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
Publication: Virology journal (2011)
Authors: Legendre M, et al. - Full genome re-sequencing reveals a novel circadian clock mutation inArabidopsis
Publication: Genome Biology (2011)
Authors: Ashelford, et al. - Comprehensive long span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
Publication: Genome Research (2011)
Authors: Hillmer A.M., et al. - The genome of the woodland strawberry, Fragaria vesca
Publication: Nature Genetics (2010)
Authors: Shulaev, et al. - The developmental transcriptome of Drosophila melanogaster
Publication: Nature (2010)
Authors: Graveley, et al. - SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools
Publication: BMC Genomics (2010)
Authors: Marklund, et al. - An Alport syndrome mutation in mouse Col4a4 identified by whole genome sequencing and bulk segregation analysis
Publication: Genetics (2010)
Authors: Arnold, et al. - A map of human genome variation from population-scale sequencing
Publication: Nature (2010)
Authors: The 1000 Genomes Project Consortium - SOLiD™ sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes
Publication: BMC Genomics (2010)
Authors: Gulig, et al - Bulk segregation mapping of mutations in closely related strains of mice
Publication: Genetics (2010)
Authors: Xia, et al - Complete genome sequence of Staphylococcus aureus fifl strain JKD6008, a ST239 clone of methicillin-resistant Staphylococcus aureus with intermediate level vancomycin resistance
Publication: J. of Bacteriology (2010)
Authors: Howden et al - The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse
Publication: J. of Bacteriology Online 190(7): 2597-2606
Authors: Durfee, T., et al - The developmental transcriptome of Drosophila melanogaster
Publication: Nature (2010)
Authors: Graveley, et al. - Whole-genome resequencing reveals loci under selection during chicken domestication
Publication: Nature 464, 587-591 25 March 2010
Authors: Rubin C., et al. - Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy
Publication: N Eng J Med 10 March 2010
Authors: Lupski J., et al. - Development of personalized tumor biomarkers using massively parallel sequencing
Publication: Science Translational Medicine, February 24, 2010
Authors: Leary R., et al. - Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples
Publication: Nucleic Acids Research, 2010, 1–7
Authors: Smith et al. - Complete Khoisan and Bantu genomes from southern Africa
Publication: Nature, Vol 463, February 18, 2010
Authors: Schuster et al. - U87MG Decoded: The genomic sequence of a cytogenetically aberrant human cancer cell line
Publication: PLoS Genetics, January 2010, volume 6, issue 1
Authors: Clark, et al. - Maternal Plasma DNA Analysis with Massively Parallel Sequencing by Ligation for Noninvasive Prenatal Diagnosis of Trisomy 21
Publication: Clinical Chemistry 56:3 ,2010
Authors: Chiu, et al. - Digital fetal aneuploidy diagnosis by next-generation sequencing
Publication: Clinical Chemistry 56:3 336–338, 2010
Authors: Voelkerding and Lyon - A small-cell lung cancer genome with complex signatures of tobacco exposure.
Publication: Nature, 463, 184-190, January 14, 2010
Authors: Pleasance, et al. - Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing
Publication: European Journal of Human Genetics, December 2, 2009
Authors: Chen, et al. - Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms
Publication: Forensic Sci. Int. Gene. Suppl., 2009
Authors: Cummings, et al. - Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding
Publication: Genome Res. Published online June 22, 2009
Authors: McKernan, et al. - Rapid whole-genome mutational profiling using next-generation sequencing technologies
Publication: Genome Res. 2008. 18: 1638-1642
Authors: Smith et al. - Comparing platforms for c. elegans mutant identification using high-throughput whole-genome sequencing
Publication: PLoS ONE 3(12): e4012. doi:10.1371/journal.pone.0004012 I (2008)
Authors: Shen et al. - Fast Forward Genetics
Publication: Nature Biotechnology 26, 1248 - 1249, 2008
Authors: Darby and Hall
Targeted Resequencing
- Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing
Publication: Nature Protocols (2011)
Authors: Harakalova M. et al. - Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing
Publication: Nature Genetics (2011)
Authors: Stark M.S. et al. - Decoding cell lineage from acquired mutations using arbitrary deep sequencing
Publication: Nature Methods (2011)
Authors: Carlson C. A. et al. - Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform
Publication: Plos One (2011)
Authors: Hedges D.J. et al. - Population genetics in non- model organisms: II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms
Publication: Molecular Biology and Evolution (2011)
Authors: Zhou R. et al. - Carrier testing for severe childhood recessive diseases by next-generation sequencing
Publication: 2011Science Translational Medicine (2011)
Authors: Bell, et al. - De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome
Publication: Nature Genetics (2011)
Authors: Hoischen A. et al. - Ultra-deep sequencing of Mouse Mitochondrial DNA: mutational patterns and their origin
Publication: PLoS Genetics (2011)
Authors: Ameur A., et al.
- Genomic DNA pooling strategy for next-generation sequencing-based rare variant discovery in Abdominal Aortic Aneurysm regions of interest—challenges and limitations
Publication: , J. of Cardiovasc. Trans. Res. (2011)
Authors: Haraklova, et al. - Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors
Publication: Genome Research (2010)
Authors: Robbins, et al. - Targeted resequencing of candidate genes using selector probes
Publication: Nature Genetics (2010)
Authors: Johansson, et al. - New mutations and intellectual function
Publication: Nature Genetics (2010)
Authors: Lupski, et al. - Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples
Publication: Nucleic Acids Research (2010)
Authors: Smith, et al. - A de novo paradigm for mental retardation
Publication: Nature Genetics (2010)
Authors: Vissers, et al. - Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency
Publication: Nature Genetics (2010)
Authors: Haack, et al. - Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples
Publication: Nature Methods (2010)
Authors: Nijman, et al. - Ultra high throughput sequencing in human DNA variation detection: A comparative study on the NDUFA3-PRPF31 region
Publication: PLoS ONE (2010)
Authors: Benaglio, et al. - Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome
Publication: Nature Genetics (2010)
Authors: Krawitz, et al. - Exome sequencing identifies WDR35 variants involved in sensenbrenner syndrome
Publication: The American Journal of Human Genetics (2010)
Authors: Glissen et al. - Whole exome capture in solution with 3Gbp of data
Publication: Genome Biology, 11:R62 (2010)
Authors: Bainbridge, et al. - SNP discovery performance of two second generation sequencing platforms in the NOD2 gene region
Publication: Human Mutation Volume 9999 Issue 999A, published online (May 18, 2010)
Authors: Melum, et al. - Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer.
Publication: Journal of Human Genetics, May 2010
Authors: Mitsui, et al. - PHF6 mutations in T-cell acute lymphoblastic leukemia.
Publication: Nature Genetics 42, 338-342. 14 March 2010
Authors: Van Vlierberghe, P., et al. - Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.
Publication: 25 Jan 2010
Authors: Mokry, M., et al. - GC-Biased Evolution Near Human Accelerated Regions
Publication: PLoS Genetics, 2010
Authors: Katzman, et al. - De novo mutations of SETBP1 cause Schinzel-Giedion syndrome.
Publication: Nature Genetics, May 2010
Authors: Hoischen, et al. - Targeted resequencing of candidate genes using selector probes
Publication: Nucleic Acids Research (2010)
Authors: Johansson, et al. - Polymorphism Discovery in High-Throughput Resequenced Microarray-Enriched Human Genomic Loci.
Publication: Journal of Biomolecular Techniques 20:253–257
Authors: Antipova, et al. - High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs.
Publication: BMC Genomics 2009, 10:379
Authors: Walter, et al. - Evaluation of next generation sequencing platforms for population targeted sequencing studies.
Publication: Genome Biology 2009, 10:R32
Authors: Harismendy, et al.
De Novo Sequencing
- First complete genome sequence of infectious laryngotracheitis virus
Publication: BMC Genomics (2011)
Authors: Lee S. et al - Whole-Genome Shotgun Sequencing of the Sulfur-Oxidixing Chemoautotroph Tetrathiobacter kashmirensis
Publication: Journal of Bacteriology (2011)
Authors: Ghosh W et al - Whole genome sequencing of environmental Vibrio cholerae 01 from 10 nanograms of DNA using short reads
Publication: Journal of Microbiological Methods (2011)
Authors: Chaparro P, et al. - Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis l19 as a case study
Publication: Journal of Microbiological Methods (2011)
Authors: Cerdeira L, et al. - Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
Publication: BMC Genomics (2010)
Authors: den Bakker, et al. - Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism
Publication: Science (2010)
Authors: Spanu, et al.
- Complete genome sequence of corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis
Publication: J. Bacteriology (2010)
Authors: Silva, et al.
Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
- Chromosome length influences replication-induced topological stress
Publication: Nature (2011)
Authors: Kegel, et al.
- ATP hydrolysis is required for relocating cohesin from sites occupied by its Scc2/4
Publication: Current Biology (2010)
Authors: Hu, et al. - A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion
Publication: The EMBO Journal (2010)
Authors: Kurze, et al. - The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection
Publication: Nature Immunology (2010)
Authors: Satoh, et al. - A downstream intergenic cluster of regulatory enhancers contributes to the induction of CYP24A1 expression by 1α,25-dihydroxyvitamin D3
Publication: The Journal of Biological Chemistry (2010)
Authors: Meyer, et al. - A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells
Publication: Genome Res, published online (May 27, 2010)
Authors: Tallack, et al. - Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ System
Publication: Nature Methods 6, (2009)
Authors: Shah et.al. - A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.
Publication: Genome Research. 2008 Jul;18(7):1051-63.
Authors: Valoeuv, A., et al. - Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.
Publication: Bioinformatics. 5 March 2010
Authors: Johannes, F., et al. - ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth.
Publication: PLoS Biol 7(12): e1000256
Authors: Markljung, et al. - A novel mechanism of epigenetic regulation: Nucleosome-space occupancy.
Publication: Biochem. Biophys. Res. Commun (2009)
Authors: Ciu, et al. - Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.
Publication: Genome Biology 2009, 10:R129
Authors: Motallebipour, et al. - A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome.
Publication: Genome Biology 2009, 10:R109
Authors: Jiang and Pugh - Interaction of transcriptional regulators with specific nucleosomes across the saccharomyces genome.
Publication: Molecular Cell Volume 35, Issue 6, 889-902, 24 September 2009
Authors: Koerber, et.al. - Nucleosomes are well positioned in exons and carry characteristic histone modifications.
Publication: Genome Research 2009. 19:1732-1741.
Authors: Andersson, et al. - The human TTAGGG repeat factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats
Publication: Cell Research (2011)
Authors: Simonet T. et al.
Methylation Analysis
- Increased methylation variation in epigenetic domains across cancer types
Publication: Nature Genetics (2011)
Authors: Edwards, et al. - High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology
Publication: PLoS One (2011)
Authors: Lan L, et al. - Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing data
Publication: Electrophoresis (2010)
Authors: Yang, et al. - An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD™ System
Publication: Bioinformatics Advance Access (June 18, 2010)
Authors: Ondov, et al.
- Whole methylome analysis by ultra-deep sequencing using two-base encoding.
Publication: PLoS ONE 5(2):e9320 22 Feb 2010
Authors: Chung, C., et al. - Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns.
Publication: Genome Research, 2010
Authors: Edwards, et al. - Preparation of genome-wide DNA fragment libraries using bisulfite in polyacrylamide gel electrophoresis slices with formamide denaturation and quality control for massively parallel sequencing by oligonucleotide ligation and detection.
Publication: ScienceDirect. Published online April 18, 2009.
Whole Transcriptome Analysis
- Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell
Publication: Journal of Virology (2012)
Authors: Lefebvre G. et al - Genome wide full-length transcript analysis using 5'and 3' paired-end-tag next generation sequencing (RNA-PET)
Publication: Methods in Molecular Biology, vol. 809 (2012)
Authors: Xiaoan Ruan and Yijun Ruan - Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe
Publication: Molecular Systems Biology (2011)
Authors: Bitton D. A. et al. - Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
Publication: Genome Research (2011)
Authors: Kolle G. et al. - Whole-Genome Sequencing for Optimized Patient Management
Publication: Science Translational Medicine (2011)
Authors: Bainbridge M. et al. - Genome-wide Analysis of the 5’ and 3’ Ends of Vaccinia Virus Early mRNAs Delineates Regulatory Sequences of Annotated and Anomalous Transcripts
Publication: Journal of Virology (2011)
Authors: Yang Z., et al. - The Cluster 1 Type VI Secretion System Is a Major Virulence Determinant in Burkholderia pseudomallei
Publication: Infection and Immunity (2011)
Authors: Burtnick M., et al. - Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis
Publication: Cell (2011) Authors: Autran D. et al. - NanoRNAs Prime Transcription Initiation In Vivo
Publication: Molecular Cell (2011)
Authors: Goldman et al. - Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
Publication: Bioinformatics (2011)
Authors: Labaj P. et al. - A tissue-specific landscape of sense/antisense transcription in the mouse intestine
Publication: BMC Genomics (2011)
Authors: Klostermeier U. et al. - Metatranscriptomics of a hot-spring microbial mat
Publication: The ISME Journals (2011)
Authors: Z Liu et al. - Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres
Publication: PloS One (2011)
Authors: Tang F. et al. - Whole-transcriptome RNSseq analysis from minute amount of total RNA
Publication: Nucleic Acids Research (2011)
Authors: Tariq M. et al. - XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast
Publication: Nature (2011)
Authors: Dijk E. et al. - Zebrafish mRNA sequencing decipher novelties in transcriptome dynamics during maternal to zygotic transition
Publication: Genome Research (2011)
Authors: Aanes H. et al. - Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome
Publication: Molecular Ecology Resources (2011)
Authors: Everett M.V. et al. - Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
Publication: PLos One (2011)
Authors: Costa V. et al. - Development and applications of single-cell transcriptome analysis
Publication: Nature Methods (2011)
Authors: Tang F. et al. - Transcriptional consequences of genomic structural aberrations in breast cancer
Publication: Genome Research (2011)
Authors: Inaki K. et al. - Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Publication: BMC Genomics (2011)
Authors: Isabella V. M., et al. - Hyperactivation of anandamide synthesis and regulation of cell-cycle progression via cannabinoid type 1 (CB1) receptors in the regenerating liver
Publication: PNAS (2011)
Authors: Mukhopadhyay B. et al. - Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
Publication: Virology journal (2011)
Authors: Legendre M. et al. - Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss
Publication: Science (2010)
Authors: Mitrovich, et al. - FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
Publication: Nature Methods (2010)
Authors: Underwood, et al. - The exon junction complex controls the splicing of mapk and other long intron-containing transcripts in drosophila
Publication: Cell (2010)
Authors: Ashton-Beaucage, et al. - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk
Publication: Nature (2010)
Authors: Heinig, et al. - Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing
Publication: Genome Biology (2010)
Authors: Wetterbom, et al. - Constitutively active androgen receptor splice variants expressed in castration-resistant prostate cancer require full-length androgen receptor
Publication: PNAS (2010)
Authors: Watson, et al. - Roles of xanthophyll carotenoids in protection against photoinhibition and oxidative stress in the cyanobacterium Synechococcus sp. strain PCC 7002
Publication: Archives of Biochemistry and Biophysics (2010)
Authors: Zhu et al. - Functional and structural characterization of the 2/2 hemoglobin from Synechococcus sp. PCC 7002
Publication: Biochemistry (2010)
Authors: Scott et al. - The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation
Publication: PLoS Genetics, (2010)
Authors: Tuch, et al. - Simultaneous high-resolution analysis of vaccinia virus and host cell transcriptomes by deep RNA sequencing
Publication: PNAS, published online (June 7, 2010)
Authors: Yang, et al. - Genome-wide misexpression of X-linked versus autosomal genes associated with hybrid male sterility
Publication: Genome Res., published online (May 28, 2010)
Authors: Lu, et al. - Widespread transcription at neuronal activity-regulated enhancers
Publication: Nature (2010)
Authors: Kim et al. - RNA-Seq analysis to capture the transcriptome landscape of a single cell.
Publication: Nature Protocols, 5, -516-535. 25 Feb 2010
Authors: Tang, F., et al. - Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations.
Publication: PLoS ONE 5(2): e9317. 19 Feb 2010
Authors: Tuch, T., et al. - A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling.
Publication: BMC Genomics 2010, 11:282
Authors: Bradford et al. - Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNASeq Analysis.
Publication: Cell Stem Cell, 6, May 7, 2010
Authors: Tang et al. - Widespread transcription at neuronal activity-regulated enhancers.
Publication: Nature, 14 April 2010
Authors: Kim et al. - Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.
Publication: Nucleic Acids Research, 2010, 1–13
Authors: Picardi et al. - The Structure and Complexity of a Bacterial Transcriptome
Publication: Bacteriol. 2009 : JB.00122-09v1
Authors: Passalacqua, K., et al. - mRNA-Seq whole-transcriptome analysis of a single cell
Publication: Nature Methods, published online: 6 April 2009.
Authors: Tang et al. - Stem cell transcriptome profiling via massive-scale mRNA sequencing.
Publication: Nature Methods Online. 2008 Jul;5(7):613-9.
Authors: Cloonan, N., et al.
Small RNA Analysis
- Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis
Publication: BMC Genomics (2012)
Authors: Tu J. et al. - Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs
Publication: RNA (2012)
Authors: Voellenkle C. et al - Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing
Publication: Molecular Plant Pathology, (2012)
Authors: Stassen J. et al. - Sequencing circulating miRNA in maternal plasma with modified library preparation
Publication: Clinica Chimica Acta(2011)
Authors: Ge Q. et al. - Assessment of nanomaterial cytotoxicity with SOLiD sequencing-based microRNA expression profiling
Publication: Biomaterials (2011)
Authors: Li S. et al. - Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana
Publication: PLoS One (2011)
Authors: Norden-Krichmar T. et al - Deep Sequencing of virus-infected cells reveals HIV-encoded small RNAs
Publication: Nucleic Acids Research (2011)
Authors: Shopman N, et al. - A Comprehensive Survey of miRNA Repertoire and 39 Addition Events in the Placentas of Patients with Pre- Eclampsia from High-Throughput Sequencing
Publication: PloS One (2011)
Authors: Guo, et al. - Next-Generation Sequencing of MicroRNAs for Breast Cancer Detection
Publication: Journal of Biomedicine and Biotechnology (2011)
Authors: Qu Q, et al. - Sequencing circulating miRNA in maternal plasma with modified library preparation
Publication: Clinica Chimica Acta(2011)
Authors: Ge Q. et al. - Assessment of nanomaterial cytotoxicity with SOLiD sequencing-based microRNA expression profiling
Publication: Biomaterials (2011)
Authors: Li S. et al. - Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana
Publication: PLoS One (2011)
Authors: Norden-Krichmar T. et al - Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti- viral defense
Publication: BMC Microbiology (2011)
Authors: Hess A.M. et al. - MicroRNAs as participants in cytotoxicity of CdTe quantum dots in NIH/3T3 cells
Publication: Biomaterials (2011)
Authors: Li, et al. - Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread Intron loss
Publication: Science (2010)
Authors: Quinn, et al.
- Discovery and characterization of medaka miRNA genes by next generation sequencing platform
Publication: BMC Genomics (2010)
Authors: Li, et al. - Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells
Publication: PLoS Genetics (2010)
Authors: Hanina, et al. - Next-generation sequencing identifies the natural killer cell microRNA transcriptome
Publication: Genome Res. (2010)
Authors: Fehniger, et al. - Ultra-deep sequencing reveals the microRNA expression pattern of the human stomach
Publication: PLoS ONE (2010)
Authors: Ribeiro-dos-Santos, et al. - Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs
Publication: RNA (2010)
Authors: Lin, et al. - Arabidopsis lyrata small RNAs: Transient MIRNA and small interfering RNA loci within the Arabidopsis Genus
Publication: Publication: The Plant Cell (2010)
Authors: Ma et al. - Identification of homologous microRNAs in 56 animal genomes
Publication: Publication: Genomics; 96(1): 1-9 (July 2010)
Authors: Li, et al. - RNA deep sequencing of the Atlantic cod transcriptome.
Publication: Comparative Biochemistry and Physiology, May 2010
Authors: Johansen, et al. - Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma.
Publication: Nucleic Acids Research, 2010, 1–10
Authors: Schulte et al. - High Throughput Sequencing of MicroRNAs in Adenovirus Type 3 Infected Human Laryngeal Epithelial Cells.
Publication: Journal of Biomedicine and Biotechnology, 2010
Authors: Qi, et al. - Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila.
Publication: Nature Structural & Molecular Biology 17, 24 - 30 (2010)
Authors: Marques, et al. - Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome
Publication: RNA (2009)
Authors: Addo-Quaye, et al. - Ago2 Immunoprecipitation Identifies Predicted MicroRNAs in Human Embryonic Stem Cells and Neural Precursors.
Publication: PLoS ONE (2009) 4(9): e7192.
Authors: Goff, et al. - Limitations and possibilities of small RNA digital gene expression profiling.
Publication: Nature Methods 6, 474-476 (2009)
Authors: Linsen, et al.
Gene Expression
- Variation in the Large-Scale Organization of Gene Expression Levels in the Hippocampus Relates to Stable Epigenetic Variability in Behavior.
Publication: PLoS ONE (2008) 3(10): e3344.
Authors: Alter et al. - High-Resolution Analysis of the 5'-End Transcriptome Using a Next Generation DNA Sequencer.
Publication: PLoS ONE. 2009; 4(1): e4108
Authors: Hashimoto, et al.
RNA Structure
- Long noncoding RNA as modular scaffold of histone modification complexes
Publication: Science, Published online (July 8, 2010)
Authors: Tsai, et al.
Metagenomics
- Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat
Publication: The ISME Journal (2011)
Authors: Liu Z. et al. - Confirmation of the Sequence of 'Candidatus Liberibacter asiaticus' and Assessment of Microbial Diversity in Huanglongbing-Infected Citrus Phloem Using a Metagenomic Approach.
Publication: Molecular Plant-Microbe Interactions, Vol. 22, No. 12, 2009
Authors: Tyler et al. - The carnivorous bladderwort (Utricularia, Lentibulaiceae) a system inflates.
Publication: Journal of Experimental Botany, vol. 61, No1, pp 5-9, 2010
Authors: Albert, et al.
How the SOLiD™ System Works
Whole Genome Sequencing
- Whole Genome Resequencing
- Whole Genome Sequencing of E. coli Bacteria
- Mate-Paired Libraries Detect/Define Genetic Rearrangements
Targeted Resequencing
- Array-based Enrichment of Specific Genomic Regions using the SOLiD™ System
- SureSelect™ Solution-Based Enrichment of Genomic Regions for Targeted Resequencing on the SOLiD™ System
De Novo Sequencing
- Whole Genome Sequencing of E. coli Bacteria
- First complete genome sequence of infectious laryngotracheitis virus
Publication: BMC Genomics (2011)
Authors: Lee S. et al.
Gene Expression Profiling
Small RNA Analysis
- miRNA Discovery and Profiling with the SOLiD™ Small RNA Expression Kit
- Whole Genome Analysis of Small RNA
Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
Whole Transcriptome Analysis
- Effective Strategies for Exon/Exon Junction Mapping and Fusion Transcript Detection
- Whole Transcriptome Profiling Using the SOLiD™ 3 System
- Single-Cell Whole Transcriptome Profiling with the SOLiD™ System
Methylation Analysis
Application Fact Sheet
Quarterly Newsletter
- The SOLID Read
August 2011 - The SOLID Read
February 2011
Specification Sheet
White Papers
How the SOLiD™ System Works
- AGBT 2011 - Accurate detection of insertions and deletions
- AGBT 2011 - Getting personal: improved throughput and accuracy toward enhanced understanding of human genome biology
- AGBT 2011 - Towards a pushbutton human genome
- AGBT 2011 - Low input mate-paired sequencing and its application on FFPE tumor samples
- AGBT 2011 - Real-time data quality feedback for the 5500 Series SOLiD™ Sequencers
- AGBT 2011 - High accuracy base space sequencing: results from error-correction ligation chemistry
- AGBT 2011 - Accuracy and performance breakthroughs with the 5500 Series SOLiD™ Sequencers
- AGBT 2011 - Analysis of a Southern African genome using SOLiD™ System error correction codes
- Increased read length on the SOLiD™ Sequencing platform
- Multiplex sequencing on the SOLiD™ platform with 10, 16, or 96 barcodes
- SOLiD™ System Sequencing and 2 Base Encoding
- Accurate genome-wide SNP detection with low and medium coverage with next-generation sequencing
- Paired end sequencing on the SOLiD™ platform
- Enhanced Throughput and Accuracy on the SOLiD™ System.
- BioScope™ 1.2: An Applications Framework for SOLiD™ Sequence Data Analysis.
- Application specific accuracy with SOLiD™ System high throughput sequencing
- ESHG 2011 - Simultaneous Evaluation of Small RNA, Whole Transcriptome, Whole Genome, ChipSeq and Targeted Resequencing on Next Generation Sequencing Platforms
- ESHG 2011- P12.045 Detection of low frequency variation in heterogeneous samples using the accuracy and sensitivity of a SOLiDTM System
Automation
- A new protocol for next gen library construction increases yield / complexity and simplifies parallel sample handling
- ABRF 2011 - Robotic scripts, methods, reagents, and devices for high throughput automated production of next generation sequencing DNA fragment libraries
Whole Genome Sequencing
- Lorne 2011 - Preliminary description of the genome of the single individual from northern Europe
- AGBT 2011 - Accessing the inaccessible genome
- Paired end sequencing of human genomes on the SOLiD™ platform
- Increased Read Length on the SOLiD™ Sequencing Platform.
- The Detectable Genome: How much of the human genome is accessible to variant discovery by next-generation sequencing?
- Large-Scale SNP Detection via Ligation-based Dibase Sequencing Across Multiple HapMap Individuals: NA18507, NA19240, and NA12878
- Accurate genome-wide SNP detection with low and medium coverage with next-generation sequencing
- Dibase sequencing allows accurate SNP detection at moderate and low coverage with diBayes algorithm
- Functional analysis of the genetic variation within the genomes of three HapMap individuals obtained by whole-genome, second-generation sequencing
- Sequence and Structural Variation in a Human Genome
- Resolving Structural Variations Using SOLiD™ Mate Pair Sequencing Technology
- A high-resolution structural variation map of human germline genomes by next-generation, high-throughput paired end sequencing with the SOLiD™ System
- Whole Genome Resequencing with Short Reads: Accurate Mutation Discovery with Mate Pairs and Quality Values
- Finding Indels with Short Sequencing Reads and De Novo Assembly with SOLiD™ Reads
- Genome Variablility Analysis of Yoruba in Ibadan, Nigeria (NA18507) by SOLiD™ Mediated Whole Genome Re-Sequencing
- Next-generation Sequencing for Detection of Rare Variants and Heterozygosity
- Single Base-pair Breakpoint Resolution Map of Small to Large Indels Using a Split Read Technique with High-throughput Mate-pair and Fragment Sequencing
- Whole-Genome SNP Detection and Haplotype Phasing with Mate Pairs via Ligation-Based Dibase Sequencing
- The normal and tumor spectrum of copy number variation: Copy number alterations correlate with changes in gene expression in tumor transcriptome.
Targeted Resequencing
- AGBT 2011 - Multiplex exome enrichment from pooled barcoded libraries yields efficient SNP and indel detection on the SOLiD™ System
- PCR-based targeted sequence enrichment for next generation sequencing platform.
- DiBayes: A SNP Detection Algorithm for Next-Generation Dibase Sequencing
- Applications of Next Generation Sequencing in Genetic Epidemiology
- SNP discovery in high-throughput resequenced microarray-enriched human genomic loci.
- Multiplexed Target Enrichment for SOLiD™ System Sequencing
- Solution-Based Enrichment of Genomic Loci for Massively Parallel Sequencing on the SOLiD™ System
- MHC Haplotype Sequencing: An Integrated Approach to Common Disease
De Novo Sequencing
- AGBT 2011 - Single molecule real-time DNA squencing using FRET-based reagents
- Increased Read Length on the SOLiD™ Sequencing Platform.
Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
- Rapid chromatin preparation from solid mammalian tissues for low cell ChIP assays
- SOLiD™ ChIP-Seq kit for ChIP & ChIP-sequencing from low number of cell & tissue samples
- SOLiD™ ChIP-Seq Kit for ChIP and ChIP-Seq with Low Cell Number Samples.
Gene Expression Profiling
Small RNA Analysis
- ABRF 2011 - MicroRNA analysis using RNA extracted from matched formalin-fixed paraffin-embedded (FFPE) and fresh frozen samples on SOLiD™ system
- AGBT 2011 - SOLiD™ System approaches for small RNA expression profiling of formalin-fixed, paraffin-embedded (FFPE) tissue samples
- An Expression Atlas of small RNAs generated using the SOLiD™ Sequencing System
- Multiplex Sequencing on the SOLiD™ Platform with 10, 16, or 96 Barcodes
- A novel approach for miRNA profiling using massively parallel, ligation-based sequencing
- Analysis of the Molecular Factors Controlling Human Osteosarcoma Response to Chemotherapy
Whole Transcriptome Analysis
- ABRF 2011 - Improvements in SOLiD™ whole transcriptome library preparation workflow to enable low input RNA amounts
- ABRF 2011 - Development of ERCC RNA spike-in control mixes
- ABRF 2011 - Use of synthetic transcript pools to evaluate RNA-Seq performance and analytical methods
- AGBT 2011 - RNA-Seq for identifying gene expression changes associated with relapse in Acute Lymphoblastic Leukemia (ALL)
- Identifying novel expressed gene fusions in MCF-7 cell line using next generation sequencing
- Multiplex sequencing on the SOLiD™ platform with 10, 16, or 96 barcodes
- Whole transcriptome analysis of total human RNAs by massively parallel sequencing on the SOLiD™ system
- Single cell transcriptome analysis on the SOLiD™ system
- A comparison of next generation sequencing and microarrays for whole transcriptome expression profiling
- mRNA-Seq Whole Transcriptome Analysis of a Single Cell
- Whole transcriptome sequencing of three oral cancers
- Multiplex Single Cell RNA-Seq Transcriptome Analysis of Pluripotent Cells both in vitro and in vivo
- IADR 2011 - The Saliva RNA Interactome
Methylation Analysis
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.
Connect with Sequencing Groups
- Twitter: @SOLiDSequencing
- SOLiD® Community
For Research Use Only. Not for use in diagnostic procedures.