I am maintaining an up-to-date annotated bibliography of *Seq assays (functional genomics assays based on high-througphput sequencing) on this page. The bibliography is also available in BibTeX. I also maintain a page with a list of reviews and survey papers about *Seq.

RNA structure

dsRNA-Seq: Qi Zheng et al., “Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis,” PLoS Genet 6, no. 9 (September 30, 2010): e1001141, doi:10.1371/journal.pgen.1001141.

FRAG-Seq: Jason G. Underwood et al., “FragSeq: Transcriptome-wide RNA Structure Probing Using High-throughput Sequencing,” Nature Methods 7, no. 12 (December 2010): 995–1001, doi:10.1038/nmeth.1529.

SHAPE-Seq: (a) Julius B. Lucks et al., “Multiplexed RNA Structure Characterization with Selective 2′-hydroxyl Acylation Analyzed by Primer Extension Sequencing (SHAPE-Seq),” Proceedings of the National Academy of Sciences 108, no. 27 (July 5, 2011): 11063–11068, doi:10.1073/pnas.1106501108.
(b) Sharon Aviran et al., “Modeling and Automation of Sequencing-based Characterization of RNA Structure,” Proceedings of the National Academy of Sciences (June 3, 2011), doi:10.1073/pnas.1106541108.

PARTE-Seq: Yue Wan et al., “Genome-wide Measurement of RNA Folding Energies,” Molecular Cell 48, no. 2 (October 26, 2012): 169–181, doi:10.1016/j.molcel.2012.08.008.

PARS-Seq: Michael Kertesz et al., “Genome-wide Measurement of RNA Secondary Structure in Yeast,” Nature 467, no. 7311 (September 2, 2010): 103–107, doi:10.1038/nature09322.

Structure-Seq: Yiliang Ding et al., “In Vivo Genome-wide Profiling of RNA Secondary Structure Reveals Novel Regulatory Features,” Nature advance online publication (November 24, 2013), doi:10.1038/nature12756.

DMS-Seq: Silvi Rouskin et al., “Genome-wide Probing of RNA Structure Reveals Active Unfolding of mRNA Structures in Vivo,” Nature advance online publication (December 15, 2013), doi:10.1038/nature12894.

Viral RNA

Cir-Seq: Ashley Acevedo, Leonid Brodsky, and Raul Andino, “Mutational and Fitness Landscapes of an RNA Virus Revealed through Population Sequencing,” Nature 505, no. 7485 (January 30, 2014): 686–690, doi:10.1038/nature12861.

DNA

Dup-Seq: Schmitt, Michael W., Scott R. Kennedy, Jesse J. Salk, Edward J. Fox, Joseph B. Hiatt, and Lawrence A. Loeb. “Detection of Ultra-rare Mutations by Next-generation Sequencing.” Proceedings of the National Academy of Sciences 109, no. 36 (September 4, 2012): 14508–14513. doi:10.1073/pnas.1208715109.

IMS-MDA-Seq: Helena M. B. Seth-Smith et al., “Generating Whole Bacterial Genome Sequences of Low-abundance Species from Complex Samples with IMS-MDA,” Nature Protocols 8, no. 12 (December 2013): 2404–2412, doi:10.1038/nprot.2013.147.

Chromatin structure, accessibility and nucleosome positioning

Nucleo-Seq: Anton Valouev et al., “Determinants of Nucleosome Organization in Primary Human Cells,” Nature 474, no. 7352 (June 23, 2011): 516–520, doi:10.1038/nature10002.

DNAse-Seq: Gregory E. Crawford et al., “Genome-wide Mapping of DNase Hypersensitive Sites Using Massively Parallel Signature Sequencing (MPSS),” Genome Research 16, no. 1 (January 1, 2006): 123–131, doi:10.1101/gr.4074106.

DNAseI-Seq: Jay R. Hesselberth et al., “Global Mapping of protein-DNA Interactions in Vivo by Digital Genomic Footprinting,” Nature Methods 6, no. 4 (April 2009): 283–289, doi:10.1038/nmeth.1313.

Sono-Seq: Raymond K. Auerbach et al., “Mapping Accessible Chromatin Regions Using Sono-Seq,” Proceedings of the National Academy of Sciences 106, no. 35 (September 1, 2009): 14926–14931, doi:10.1073/pnas.0905443106.

Hi-C-Seq: Erez Lieberman-Aiden et al., “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome,” Science 326, no. 5950 (October 9, 2009): 289–293, doi:10.1126/science.1181369.

ChIA-PET-Seq: Melissa J. Fullwood et al., “An Oestrogen-receptor-α-bound Human Chromatin Interactome,” Nature 462, no. 7269 (November 5, 2009): 58–64, doi:10.1038/nature08497.

FAIRE-Seq: Hironori Waki et al., “Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation,” PLoS Genet 7, no. 10 (October 20, 2011): e1002311,

NOMe-Seq: Theresa K. Kelly et al., “Genome-wide Mapping of Nucleosome Positioning and DNA Methylation Within Individual DNA Molecules,” Genome Research 22, no. 12 (December 1, 2012): 2497–2506, doi:10.1101/gr.143008.112.

ATAC-Seq: Jason D. Buenrostro et al., “Transposition of Native Chromatin for Fast and Sensitive Epigenomic Profiling of Open Chromatin, DNA-binding Proteins and Nucleosome Position,” Nature Methods advance online publication (October 6, 2013), doi:10.1038/nmeth.2688.

Genome variation

RAD-Seq: Nathan A. Baird et al., “Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers,” PLoS ONE 3, no. 10 (October 13, 2008): e3376, doi:10.1371/journal.pone.0003376.

Freq-Seq: Lon M. Chubiz et al., “FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations,” PLoS ONE 7, no. 10 (October 31, 2012): e47959, doi:10.1371/journal.pone.0047959.

CNV-Seq: Chao Xie and Martti T. Tammi, “CNV-seq, a New Method to Detect Copy Number Variation Using High-throughput Sequencing,” BMC Bioinformatics 10, no. 1 (March 6, 2009): 80, doi:10.1186/1471-2105-10-80.

Novel-Seq: Iman Hajirasouliha et al., “Detection and Characterization of Novel Sequence Insertions Using Paired-end Next-generation Sequencing,” Bioinformatics 26, no. 10 (May 15, 2010): 1277–1283, doi:10.1093/bioinformatics/btq152.

TAm-Seq: Tim Forshew et al., “Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA,” Science Translational Medicine 4, no. 136 (May 30, 2012): 136ra68, doi:10.1126/scitranslmed.3003726.

DNA replication

Repli-Seq: R. Scott Hansen et al., “Sequencing Newly Replicated DNA Reveals Widespread Plasticity in Human Replication Timing,” Proceedings of the National Academy of Sciences 107, no. 1 (January 5, 2010): 139–144, doi:10.1073/pnas.0912402107

ARS-Seq: Ivan Liachko et al., “High-resolution Mapping, Characterization, and Optimization of Autonomously Replicating Sequences in Yeast,” Genome Research 23, no. 4 (April 1, 2013): 698–704, doi:10.1101/gr.144659.112.

Sort-Seq: Carolin A. Müller et al., “The Dynamics of Genome Replication Using Deep Sequencing,” Nucleic Acids Research (October 1, 2013): gkt878, doi:10.1093/nar/gkt878.

Transposable element discovery

Pool-Seq: Robert Kofler, Andrea J. Betancourt, and Christian Schlötterer, “Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila Melanogaster,” PLoS Genet 8, no. 1 (January 26, 2012): e1002487, doi:10.1371/journal.pgen.1002487.

Replication

Bubble-Seq: Larry D. Mesner et al., “Bubble-seq Analysis of the Human Genome Reveals Distinct Chromatin-mediated Mechanisms for Regulating Early- and Late-firing Origins,” Genome Research (July 16, 2013), doi:10.1101/gr.155218.113.

Transcription

RNA-Seq: Ali Mortazavi et al., “Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq,” Nature Methods 5, no. 7 (July 2008): 621–628, doi:10.1038/nmeth.1226.

GRO-Seq: Leighton J. Core, Joshua J. Waterfall, and John T. Lis, “Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters,” Science 322, no. 5909 (December 19, 2008): 1845–1848, doi:10.1126/science.1162228.

Quartz-Seq: Yohei Sasagawa et al., “Quartz-Seq: a Highly Reproducible and Sensitive Single-cell RNA-Seq Reveals Non-genetic Gene Expression Heterogeneity,” Genome Biology 14, no. 4 (April 17, 2013): R31, doi:10.1186/gb-2013-14-4-r31.

CAGE-Seq: Hazuki Takahashi et al., “5′ End-centered Expression Profiling Using Cap-analysis Gene Expression and Next-generation Sequencing,” Nature Protocols 7, no. 3 (March 2012): 542–561, doi:10.1038/nprot.2012.005.

Nascent-Seq: Joseph Rodriguez, Jerome S. Menet, and Michael Rosbash, “Nascent-Seq Indicates Widespread Cotranscriptional RNA Editing in Drosophila,” Molecular Cell 47, no. 1 (July 13, 2012): 27–37, doi:10.1016/j.molcel.2012.05.002.

Precapture RNA-Seq: Tim R. Mercer et al., “Targeted RNA Sequencing Reveals the Deep Complexity of the Human Transcriptome,” Nature Biotechnology 30, no. 1 (January 2012): 99–104, doi:10.1038/nbt.2024.

Cel-Seq: Tamar Hashimshony et al., “CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification,” Cell Reports 2, no. 3 (September 27, 2012): 666–673, doi:10.1016/j.celrep.2012.08.003.

3P-Seq: Calvin H. Jan et al., “Formation, Regulation and Evolution of Caenorhabditis Elegans 3′UTRs,” Nature 469, no. 7328 (January 6, 2011): 97–101, doi:10.1038/nature09616.

NET-Seq: L. Stirling Churchman and Jonathan S. Weissman, “Nascent Transcript Sequencing Visualizes Transcription at Nucleotide Resolution,” Nature 469, no. 7330 (January 20, 2011): 368–373, doi:10.1038/nature09652.

SS3-Seq: Oh Kyu Yoon and Rachel B. Brem, “Noncanonical Transcript Forms in Yeast and Their Regulation During Environmental Stress,” RNA 16, no. 6 (June 1, 2010): 1256–1267, doi:10.1261/rna.2038810.

FRT-Seq: Lira Mamanova et al., “FRT-seq: Amplification-free, Strand-specific Transcriptome Sequencing,” Nature Methods 7, no. 2 (February 2010): 130–132, doi:10.1038/nmeth.1417.

3-Seq: Andrew H. Beck et al., “3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples,” PLoS ONE 5, no. 1 (January 19, 2010): e8768, doi:10.1371/journal.pone.0008768.

PRO-Seq: Hojoong Kwak et al., “Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing,” Science 339, no. 6122 (February 22, 2013): 950–953, doi:10.1126/science.1229386.

Bru-Seq: Artur Veloso et al., “Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin,” PLoS ONE 8, no. 10 (October 23, 2013): e78190, doi:10.1371/journal.pone.0078190.

TIF-Seq: Vicent Pelechano, Wu Wei, and Lars M. Steinmetz, “Extensive Transcriptional Heterogeneity Revealed by Isoform Profiling,” Nature 497, no. 7447 (May 2, 2013): 127–131, doi:10.1038/nature12121.

3′-Seq: Steve Lianoglou et al., “Ubiquitously Transcribed Genes Use Alternative Polyadenylation to Achieve Tissue-specific Expression,” Genes & Development 27, no. 21 (November 1, 2013): 2380–2396, doi:10.1101/gad.229328.113.

TIVA-Seq: Ditte Lovatt et al., “Transcriptome in Vivo Analysis (TIVA) of Spatially Defined Single Cells in Live Tissue,” Nature Methods 11, no. 2 (February 2014): 190–196, doi:10.1038/nmeth.2804.

Smart-Seq: Simone Picelli et al., “Full-length RNA-seq from Single Cells Using Smart-seq2,” Nature Protocols 9, no. 1 (January 2014): 171–181, doi:10.1038/nprot.2014.006.

Post-transcriptional modification of RNA

PAS-Seq: Peter J. Shepard et al., “Complex and Dynamic Landscape of RNA Polyadenylation Revealed by PAS-Seq,” RNA 17, no. 4 (April 1, 2011): 761–772, doi:10.1261/rna.2581711.

PAL-Seq: Alexander O. Subtelny et al., “Poly(A)-tail Profiling Reveals an Embryonic Switch in Translational Control,” Nature advance online publication (January 29, 2014), doi:10.1038/nature13007.

Translation

Ribo-Seq: Nicholas T. Ingolia et al., “Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling,” Science 324, no. 5924 (April 10, 2009): 218–223, doi:10.1126/science.1168978.

Frac-Seq: Timothy Sterne-Weiler et al., “Frac-seq Reveals Isoform-specific Recruitment to Polyribosomes,” Genome Research (June 19, 2013), doi:10.1101/gr.148585.112.

GTI-Seq: Ji Wan and Shu-Bing Qian, “TISdb: a Database for Alternative Translation Initiation in Mammalian Cells,” Nucleic Acids Research (November 6, 2013), doi:10.1093/nar/gkt1085.

TFBS and Enhancer activity

SELEX-Seq: Matthew Slattery et al., “Cofactor Binding Evokes Latent Differences in DNA Binding Specificity Between Hox Proteins,” Cell 147, no. 6 (December 9, 2011): 1270–1282, doi:10.1016/j.cell.2011.10.053.

CRE-Seq: Jamie C. Kwasnieski et al., “Complex Effects of Nucleotide Variants in a Mammalian Cis-regulatory Element,” Proceedings of the National Academy of Sciences 109, no. 47 (November 20, 2012): 19498–19503, doi:10.1073/pnas.1210678109.

STARR-Seq: Cosmas D. Arnold et al., “Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq,” Science 339, no. 6123 (March 1, 2013): 1074–1077, doi:10.1126/science.1232542.

SRE-Seq: Robin P. Smith et al., “Massively Parallel Decoding of Mammalian Regulatory Sequences Supports a Flexible Organizational Model,” Nature Genetics 45, no. 9 (September 2013): 1021–1028, doi:10.1038/ng.2713.

HITS-KIN-Seq: Ulf-Peter Guenther et al., “Hidden Specificity in an Apparently Nonspecific RNA-binding Protein,” Nature 502, no. 7471 (October 17, 2013): 385–388, doi:10.1038/nature12543.

Capture-C-Seq: Jim R. Hughes et al., “Analysis of Hundreds of Cis-regulatory Landscapes at High Resolution in a Single, High-throughput Experiment,” Nature Genetics 46, no. 2 (February 2014): 205–212, doi:10.1038/ng.2871.

RNA-RNA interaction

CLASH-Seq: Aleksandra Helwak et al., “Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding,” Cell 153, no. 3 (April 2013): 654–665, doi:10.1016/j.cell.2013.03.043.

RNA-DNA binding

ChIRP-Seq: Ci Chu et al., “Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions,” Molecular Cell 44, no. 4 (November 18, 2011): 667–678, doi:10.1016/j.molcel.2011.08.027.

CHART-Seq: Matthew D. Simon et al., “The Genomic Binding Sites of a Noncoding RNA,” Proceedings of the National Academy of Sciences 108, no. 51 (December 20, 2011): 20497–20502, doi:10.1073/pnas.1113536108.

RAP-Seq: Jesse M. Engreitz et al., “The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome,” Science 341, no. 6147 (August 16, 2013): 1237973, doi:10.1126/science.1237973.

RNA-protein interaction

RIP-Seq: Ci Chu et al., “Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions,” Molecular Cell 44, no. 4 (November 18, 2011): 667–678, doi:10.1016/j.molcel.2011.08.027.

PAR-Clip-Seq: Markus Hafner et al., “Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP,” Cell 141, no. 1 (April 2, 2010): 129–141, doi:10.1016/j.cell.2010.03.009.

iCLIP-Seq: Julian König et al., “iCLIP Reveals the Function of hnRNP Particles in Splicing at Individual Nucleotide Resolution,” Nature Structural & Molecular Biology 17, no. 7 (July 2010): 909–915, doi:10.1038/nsmb.1838.

PTB-Seq: Yuanchao Xue et al., “Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping,” Molecular Cell 36, no. 6 (December 24, 2009): 996–1006, doi:10.1016/j.molcel.2009.12.003.

Protein-DNA binding

ChIP-Seq: David S. Johnson et al., “Genome-Wide Mapping of in Vivo Protein-DNA Interactions,” Science 316, no. 5830 (June 8, 2007): 1497–1502, doi:10.1126/science.1141319.

ChIP-Seq: Tarjei S. Mikkelsen et al., “Genome-wide Maps of Chromatin State in Pluripotent and Lineage-committed Cells,” Nature 448, no. 7153 (August 2, 2007): 553–560, doi:10.1038/nature06008.

HiTS-Flip-Seq: Razvan Nutiu et al., “Direct Measurement of DNA Affinity Landscapes on a High-throughput Sequencing Instrument,” Nature Biotechnology 29, no. 7 (July 2011): 659–664, doi:10.1038/nbt.1882.

Chip-exo-Seq: Ho Sung Rhee and B. Franklin Pugh, “Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution,” Cell 147, no. 6 (December 9, 2011): 1408–1419, doi:10.1016/j.cell.2011.11.013.

PB-Seq: Michael J. Guertin et al., “Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo,” PLoS Genet 8, no. 3 (March 29, 2012): e1002610, doi:10.1371/journal.pgen.1002610.

AHT-ChIP-Seq: Sarah Aldridge et al., “AHT-ChIP-seq: a Completely Automated Robotic Protocol for High-throughput Chromatin Immunoprecipitation,” Genome Biology 14, no. 11 (November 7, 2013): R124, doi:10.1186/gb-2013-14-11-r124.

Protein-protein interaction

PDZ-Seq: Andreas Ernst et al., “Coevolution of PDZ Domain–ligand Interactions Analyzed by High-throughput Phage Display and Deep Sequencing,” Molecular BioSystems 6, no. 10 (2010): 1782, doi:10.1039/c0mb00061b. 

Small molecule-protein interaction

PD-Seq: Daniel Arango et al., “Molecular Basis for the Action of a Dietary Flavonoid Revealed by the Comprehensive Identification of Apigenin Human Targets,” Proceedings of the National Academy of Sciences 110, no. 24 (June 11, 2013): E2153–E2162, doi:10.1073/pnas.1303726110.

Small molecule-DNA interaction

Chem-Seq: Lars Anders et al., “Genome-wide Localization of Small Molecules,” Nature Biotechnology 32, no. 1 (January 2014): 92–96, doi:10.1038/nbt.2776.

Methylation

CAB-Seq: Xingyu Lu et al., “Chemical Modification-Assisted Bisulfite Sequencing (CAB-Seq) for 5-Carboxylcytosine Detection in DNA,” Journal of the American Chemical Society 135, no. 25 (June 26, 2013): 9315–9317, doi:10.1021/ja4044856.

HELP-Seq: Mayumi Oda et al., “High-resolution Genome-wide Cytosine Methylation Profiling with Simultaneous Copy Number Analysis and Optimization for Limited Cell Numbers,” Nucleic Acids Research 37, no. 12 (July 1, 2009): 3829–3839, doi:10.1093/nar/gkp260.

TAB-Seq: Miao Yu et al., “Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome,” Cell 149, no. 6 (June 8, 2012): 1368–1380, doi:10.1016/j.cell.2012.04.027.

TAmC-Seq: Liang Zhang et al., “Tet-mediated Covalent Labelling of 5-methylcytosine for Its Genome-wide Detection and Sequencing,” Nature Communications 4 (February 26, 2013): 1517, doi:10.1038/ncomms2527.

fCAB-Seq: Chun-Xiao Song et al., “Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming,” Cell 153, no. 3 (April 25, 2013): 678–691, doi:10.1016/j.cell.2013.04.001.

MeDIP-Seq: Thomas A. Down et al., “A Bayesian Deconvolution Strategy for Immunoprecipitation-based DNA Methylome Analysis,” Nature Biotechnology 26, no. 7 (July 2008): 779–785, doi:10.1038/nbt1414.

Methyl-Seq: Alayne L. Brunner et al., “Distinct DNA Methylation Patterns Characterize Differentiated Human Embryonic Stem Cells and Developing Human Fetal Liver,” Genome Research 19, no. 6 (June 1, 2009): 1044–1056, doi:10.1101/gr.088773.108.

oxBS-Seq: Michael J. Booth et al., “Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution,” Science 336, no. 6083 (May 18, 2012): 934–937, doi:10.1126/science.1220671.

RBBS-Seq: Zachary D. Smith et al., “High-throughput Bisulfite Sequencing in Mammalian Genomes,” Methods 48, no. 3 (July 2009): 226–232, doi:10.1016/j.ymeth.2009.05.003.

BS-Seq: Ryan Lister et al., “Human DNA Methylomes at Base Resolution Show Widespread Epigenomic Differences,” Nature 462, no. 7271 (November 19, 2009): 315–322, doi:10.1038/nature08514.

BisChIP-Seq: Aaron L. Statham et al., “Bisulfite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq) Directly Informs Methylation Status of Histone-modified DNA,” Genome Research 22, no. 6 (June 1, 2012): 1120–1127, doi:10.1101/gr.132076.111.

Phenotyping

Bar-Seq: Andrew M. Smith et al., “Quantitative Phenotyping via Deep Barcode Sequencing,” Genome Research (July 21, 2009), doi:10.1101/gr.093955.109.

TraDI-Seq: Gemma C. Langridge et al., “Simultaneous Assay of Every Salmonella Typhi Gene Using One Million Transposon Mutants,” Genome Research (October 13, 2009), doi:10.1101/gr.097097.109.

Tn-Seq: Tim van Opijnen, Kip L. Bodi, and Andrew Camilli, “Tn-seq; High-throughput Parallel Sequencing for Fitness and Genetic Interaction Studies in Microorganisms,” Nature Methods 6, no. 10 (October 2009): 767–772, doi:10.1038/nmeth.1377.

IN-Seq: Andrew L. Goodman et al., “Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat,” Cell Host & Microbe 6, no. 3 (September 17, 2009): 279–289, doi:10.1016/j.chom.2009.08.003.

Immuno-Seq: Harlan S. Robins et al., “Comprehensive Assessment of T-cell Receptor Β-chain Diversity in Αβ T Cells,” Blood 114, no. 19 (November 5, 2009): 4099–4107, doi:10.1182/blood-2009-04-217604.

mutARS-Seq: Ivan Liachko et al., “High-resolution Mapping, Characterization, and Optimization of Autonomously Replicating Sequences in Yeast,” Genome Research 23, no. 4 (April 1, 2013): 698–704, doi:10.1101/gr.144659.112.

Ig-Seq: Vollmers, Christopher, Rene V. Sit, Joshua A. Weinstein, Cornelia L. Dekker, and Stephen R. Quake. “Genetic Measurement of Memory B-cell Recall Using Antibody Repertoire Sequencing” Proceedings of the National Academy of Sciences 110, no. 33 (August 13, 2013): 13463–13468. doi:10.1073/pnas.1312146110.

Ig-seq: Busse, Christian E., Irina Czogiel, Peter Braun, Peter F. Arndt, and Hedda Wardemann. “Single-cell Based High-throughput Sequencing of Full-length Immunoglobulin Heavy and Light Chain Genes.” European Journal of Immunology (2013): n/a–n/a. doi:10.1002/eji.201343917.

Ren-Seq: Florian Jupe et al., “Resistance Gene Enrichment Sequencing (RenSeq) Enables Reannotation of the NB-LRR Gene Family from Sequenced Plant Genomes and Rapid Mapping of Resistance Loci in Segregating Populations,” The Plant Journal 76, no. 3 (2013): 530–544, doi:10.1111/tpj.12307.

Mu-Seq: Donald R. McCarty et al., “Mu-seq: Sequence-Based Mapping and Identification of Transposon Induced Mutations,” PLoS ONE 8, no. 10 (October 23, 2013): e77172, doi:10.1371/journal.pone.0077172.

Stable-Seq: Ikjin Kim et al., “High-throughput Analysis of in Vivo Protein Stability,” Molecular & Cellular Proteomics: MCP 12, no. 11 (November 2013): 3370–3378, doi:10.1074/mcp.O113.031708.

Proposed but not yet implemented

WIMP-Seq: Andrzej Drukier et al., “New Dark Matter Detectors Using DNA for Nanometer Tracking,” arXiv:1206.6809 (June 28, 2012), http://arxiv.org/abs/1206.6809.

BOINC-Seq: Anthony M. Zador et al., “Sequencing the Connectome,” PLoS Biol 10, no. 10 (October 23, 2012): e1001411, doi:10.1371/journal.pbio.1001411.

The *Seq List (in chronological order)

  1. Gregory E. Crawford et al., “Genome-wide Mapping of DNase Hypersensitive Sites Using Massively Parallel Signature Sequencing (MPSS),” Genome Research 16, no. 1 (January 1, 2006): 123–131, doi:10.1101/gr.4074106.
  2. David S. Johnson et al., “Genome-Wide Mapping of in Vivo Protein-DNA Interactions,” Science 316, no. 5830 (June 8, 2007): 1497–1502, doi:10.1126/science.1141319.
  3. Tarjei S. Mikkelsen et al., “Genome-wide Maps of Chromatin State in Pluripotent and Lineage-committed Cells,” Nature 448, no. 7153 (August 2, 2007): 553–560, doi:10.1038/nature06008.
  4. Thomas A. Down et al., “A Bayesian Deconvolution Strategy for Immunoprecipitation-based DNA Methylome Analysis,” Nature Biotechnology 26, no. 7 (July 2008): 779–785, doi:10.1038/nbt1414.
  5. Ali Mortazavi et al., “Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq,” Nature Methods 5, no. 7 (July 2008): 621–628, doi:10.1038/nmeth.1226.
  6. Nathan A. Baird et al., “Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers,” PLoS ONE 3, no. 10 (October 13, 2008): e3376, doi:10.1371/journal.pone.0003376.
  7. Leighton J. Core, Joshua J. Waterfall, and John T. Lis, “Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters,” Science 322, no. 5909 (December 19, 2008): 1845–1848, doi:10.1126/science.1162228.
  8. Chao Xie and Martti T. Tammi, “CNV-seq, a New Method to Detect Copy Number Variation Using High-throughput Sequencing,” BMC Bioinformatics 10, no. 1 (March 6, 2009): 80, doi:10.1186/1471-2105-10-80.
  9. Jay R. Hesselberth et al., “Global Mapping of protein-DNA Interactions in Vivo by Digital Genomic Footprinting,” Nature Methods 6, no. 4 (April 2009): 283–289, doi:10.1038/nmeth.1313.
  10. Nicholas T. Ingolia et al., “Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling,” Science 324, no. 5924 (April 10, 2009): 218–223, doi:10.1126/science.1168978.
  11. Alayne L. Brunner et al., “Distinct DNA Methylation Patterns Characterize Differentiated Human Embryonic Stem Cells and Developing Human Fetal Liver,” Genome Research 19, no. 6 (June 1, 2009): 1044–1056, doi:10.1101/gr.088773.108.
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  92. Silvi Rouskin et al., “Genome-wide Probing of RNA Structure Reveals Active Unfolding of mRNA Structures in Vivo,” Nature advance online publication (December 15, 2013), doi:10.1038/nature12894.
  93. Lars Anders et al., “Genome-wide Localization of Small Molecules,” Nature Biotechnology 32, no. 1 (January 2014): 92–96, doi:10.1038/nbt.2776.
  94. Simone Picelli et al., “Full-length RNA-seq from Single Cells Using Smart-seq2,” Nature Protocols 9, no. 1 (January 2014): 171–181, doi:10.1038/nprot.2014.006.
  95. Alexander O. Subtelny et al., “Poly(A)-tail Profiling Reveals an Embryonic Switch in Translational Control,” Nature advance online publication (January 29, 2014), doi:10.1038/nature13007.
  96. Ashley Acevedo, Leonid Brodsky, and Raul Andino, “Mutational and Fitness Landscapes of an RNA Virus Revealed through Population Sequencing,” Nature 505, no. 7485 (January 30, 2014): 686–690, doi:10.1038/nature12861.
  97. Ditte Lovatt et al., “Transcriptome in Vivo Analysis (TIVA) of Spatially Defined Single Cells in Live Tissue,” Nature Methods 11, no. 2 (February 2014): 190–196, doi:10.1038/nmeth.2804.
  98. Jim R. Hughes et al., “Analysis of Hundreds of Cis-regulatory Landscapes at High Resolution in a Single, High-throughput Experiment,” Nature Genetics 46, no. 2 (February 2014): 205–212, doi:10.1038/ng.2871.

If you believe there is an error in the list or know of an assay that is missing please send me a comment using the form below.

Most recent update: November 23, 2013.