• 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
• New Frontiers in Plant Functional Genomics Using Next Generation Sequencing Technologies Publication: New Frontiers in Plant Functional Genomics Using Next Generation Sequencing Technologies Authors: R. Nutter, G. Kahl et. al. (2008) Wiley, pages 431-444

• 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.
• Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using nextgeneration sequencer Publication: Human Genetics (2010) Authors: Mitsui, et al.

• 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.

• 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.
• 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.
• ParMap, an Algorithm for the Identification of Complex Genomic Variations in Nextgen Sequencing Data. Publication: Available from Nature Precedings, 2010 Authors: Khiabanian, 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.
• 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.
• 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.
• 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.
• The Uniqueome: A mappability resource for short-tag sequencing Publication: Bioinformatics (2010) Authors: Koehler R. 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.
• Low coverage sequencing: Implications for the design of complex trait association studies Publication: Genome Research (2011) Authors: Li Y. et al.
• Sniper: Improved SNP discovery by multiply mapping deep sequenced reads Publication: Genome Biology (2011) Authors: Simola D. et al

• Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline Publication: Human Molecular Genetics (2011) Authors: Kloosterman, et al.
• Next-generation sequencing of Coccidioides immitis isolated during cluster investigation Publication: Emerging Infectious Deiseases (2011) Authors: Engelthaler, et al.
• 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.
• Next‐generation sequencing of Coccidioides immitis Isolated during cluster Investigation Publication: Emerging Infectious Diseases (2011) Authors: Engelthaler, 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
• 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.
• 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.
• Fast Forward Genetics Publication: Nature Biotechnology 26, 1248 - 1249, 2008 Authors: Darby and Hall
• The developmental transcriptome of Drosophila melanogaster Publication: Nature (2010) Authors: Graveley, et al.
• Whole-Exome Sequencing Identifies FAM20A Mutations as a Cause of Amelogenesis Imperfecta and Gingival Hyperplasia Syndrome Publication: American Journal Human Genetics, (2011) Authors: O'Sullivan J. et al.
• Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms Publication: PLoS ONE (2011) Authors: Suzuki S. 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 populations Publication: PNAS 2011 Authors: Gravel S et al

• Carrier testing for severe childhood recessive diseases by next-generation sequencing Publication: 2011Science Translational Medicine (2011) Authors: Bell, 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.
• Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors Publication: Genome Research (2010) Authors: Robbins, 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.
• 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.
• Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples Publication: Nature Methods (2010) Authors: Nijman, 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.
• De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome Publication: Nature Genetics (2011) Authors: Hoischen A. et al
• Integrated genomic analyses of ovarian carcinoma Publication: Nature (2011) Authors: Cancer Genome Atlas Research Network

• Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter Kashmirensis Ghosh W. et al, 2011, Journal of Bacteriology
• Whole Genome Sequencing of Environmental Vibrio Cholerae 01 from 10 Nanograms of DNA Using Short Reads Chaparro P. et al, 2011, Journal Microbiological Methods
• 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.
• First complete genome sequence of infectious laryngotracheitis virus Publication: BMC Genomics (2011) Authors: Lee S. et al
• Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study Publication: Journal of Microbiological Methods (2011) Authors: Cerdeira L. et al.

• Chromosome length influences replication-induced topological stress Publication: Nature (2011) Authors: Kegel, et al.
• Efficient double fragmentation ChIP-Seq provides nucleotide resolution protein-DNA binding profiles Publication: PLoS One (2010) Authors: Mokry, 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.

• 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.
• 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.
• Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Publication: Genome Research, 2010 Authors: Edwards, et al.
• Increased methylation variation in epigenetic domains across cancer types Publication: Nature Genetics (2011) Authors: Hansen K. et al.
• High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology Publication: PLoS One, 2011 Authors: Lan L. 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.
• RNA-Seq analysis of two closely related leukemia clones that differ in their self-renewal capacity Publication: Blood (2010) Authors: Wilhelm, 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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 Journal (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 RNAseq analysis from minute amount of total RNA Publication: Nucleic Acids Research Authors: Tariq M. et al, 2011
• XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast Publication: Nature Authors: Dijk E. et al, 2011
• Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis Publication: Cell Authors: Autran. D et al, 2011

• Deep Sequencing of Virus-infected Cells Reveals HIV-encoded small RNAs Shopman N. et al, 2011, Nucleic Acids Research
• 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.
• 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.

• 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.

• Genome-wide measurement of RNA secondary structure in yeast Publication: Nature (2010) Authors: Kertesz, et al.
• Long noncoding RNA as modular scaffold of histone modification complexes Publication: Science, Published online (July 8, 2010) Authors: Tsai, 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.

• SOLiD™ Software: Data Analysis and Management
• SOLiD™ System Barcoding

• Whole Genome Resequencing
• Whole Genome Sequencing of E. coli Bacteria
• Mate-Paired Libraries Detect/Define Genetic Rearrangements

• Microdroplet-based PC R enrichment of genomic regions for targeted sequencing on the SO LiD® System
• Array-based Enrichment of Specific Genomic Regions using the SOLiD™ System
• Targeted Resequencing and Rare Allele Detection
• SureSelect™ Solution-Based Enrichment of Genomic Regions for Targeted Resequencing on the SOLiD™ System

• Whole Genome Sequencing of E. coli Bacteria
• First complete genome sequence of infectious laryngotracheitis virus Publication: BMC Genomics (2011) Authors: Lee S. et al.

• SOLiD™ High Throughput Analysis of Differential Gene Expression

• miRNA Discovery and Profiling with the SOLiD™ Small RNA Expression Kit
• Whole Genome Analysis of Small RNA

• Analysis of Protein-DNA Interactions With the SOLiD™ ChIP-Seq Kit

• 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

• Fractionation of Differentially Methylated Regions with the MethylMinerâ„¢ Methylated DNA Enrichment Kit and Deep Sequencing with the SOLiD™ System

Application Fact Sheet

• SOLiD™ System Accuracy

Brochures

• Product Bulletin: SOLiD™ Total RNA-Seq Kit
• TarqetSeq™ Exome Custom Enrichment Kit Product Bulletin

Quarterly Newsletter

• The SOLiD Read August 2011
• The SOLiD Read February 2011

Specification Sheet

• 5500 Series Genetic Analyzer System Specification Sheet
• Library Builder Specification Sheet
• SOLiD™ EZ Bead™ System Specification Sheet
• LifeScope Genomic Analysis Solutions Specification Sheet

White Papers

• SOLiD™ System Accuracy with the Exact Call Chemistry Module
• 2-Base Color Codes and Its Application to Annotation, Error Detection, and Error Correction

• 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

• ABRF 2011 - Robotic scripts, methods, reagents, and devices for high throughput automated production of next generation sequencing DNA fragment libraries
• AGBT 2011 - Methods and reagents for automating DNA fragment library construction on commonly available liquid handling robotic platforms
• AGBT 2011 - A New protocol for next gen library construction increases yield / complexity and simplifies parallel sample handling

• 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.
• Genome-wide discovery of copy number variations in cancer patients using SOLiD™ sequencing

• 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
• Targeted sequence enrichment for the SOLiD™ System

• AGBT 2011 - Single molecule real-time DNA squencing using FRET-based reagents
• Increased Read Length on the SOLiD™ Sequencing Platform.
• Finding Indels with Short Sequencing Reads and De Novo Assembly with SOLiD Reads
• Genome completion by SOLiD™ System Next Generation Sequencing.
• Rapid, Short-Read Sequencing and Comparison of 8 Different Listeria Strains.

• Rapid chromatin oreparation 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.

• AGBT 2011 - RNA-seq for identifying gene expression changes associated with relapse in acute lymphoblastic leukemia (ALL)
• Multiplex sequencing on the SOLiD™ platform with 10, 16, or 96 barcodes
• Gene Expression in human samples using SOLiD™ Next Generation Sequencing.
• ESAT 2011 - Comparative Analysis of CHO Cell Transcriptional Dynamics under Different Cell Culture Conditions using Next Generation RNA Sequencing Technology

• 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

• 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
• SOLiD™ sequencing unravels transcriptome
• 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

• AGBT 2011 - Sequencing of methylated human DNA enriched through MBD-Affinity is a cost-effective alternative to whole genome bisulfite conversion
• Genome-wide methylation data analysis on the SOLiD™ System
• Efficient whole-genome DNA methylation analysis of the Human Reference Genome
• Sequencing of Methylated DNA Enriched with Methyl-CpG-binding domains.