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 ClickSeq Publications

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ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3′-Azido cDNAs:

Routh et al. JMB 2015

ClickSeq was originally published in 2015 in the Journal of Molecular Biology as a method to make RNAseq libraries that do not contain artifactual chimeric reads to allow the detailed analysis of rare recombination events in RNA viruses. 

Ciesla, J., Huang, K-L., Wagner, E.J., Munger, J.

A UL26-PIAS1 complex antagonizes anti-viral gene expression during Human Cytomegalovirus infection

Haugen, R.J., Barnier, C., Elrod, N.D., Luo, H., Jensen, M.K., Ji, P., Smibert, C.A., Lipshitz, H.D., Wagner, E.J., Freddolino, P.L., Goldstrohm, A.C.

Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex

Sung, P.-y.;  Zhou, Y.;  Kao, C. C.;  Aburigh, A. A.;  Routh, A.; Roy, P., 

A multidisciplinary approach to the identification of the protein–RNA connectome in double-stranded RNA virus capsids. 

Sotcheff, S.;  Zhou, Y.;  Yeung, J.;  Sun, Y.;  Johnson, J. E.;  Torbett, B. E.; Routh, A. L., 

ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids. 

Radnaa, E.;  Urrabaz-Garza, R.;  Elrod, N. D.;  de Castro Silva, M.;  Pyles, R.;  Han, A.; Menon, R., 

Generation and characterization of human Fetal membrane and Decidual cell lines for reproductive biology experiments. 

Mascibroda, L. G.;  Shboul, M.;  Elrod, N. D.;  Colleaux, L.;  Hamamy, H.;  Huang, K.-L.;  Peart, N.;  Singh, M. K.;  Lee, H.; Merriman, B., 

INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex. 

Funk, O. H.;  Qalieh, Y.;  Doyle, D. Z.;  Lam, M. M.; Kwan, K. Y., 

Postmitotic accumulation of histone variant H3. 3 in new cortical neurons establishes neuronal chromatin, transcriptome, and identity. 

Soto-Acosta, R.;  Edwards, T. C.;  Dreis, C. D.;  Krishna, V. D.;  Cheeran, M. C.;  Qiu, L.;  Xie, J.;  Bonnac, L. F.; Geraghty, R. J., 

Enhancing the Antiviral Potency of Nucleobases for Potential Broad-Spectrum Antiviral Therapies. 

Langsjoen, R. M.;  Zhou, Y.;  Holcomb, R. J.; Routh, A. L., 

Chikungunya Virus Infects the Heart and Induces Heart-Specific Transcriptional Changes in an Immunodeficient Mouse Model of Infection. 

Doyle, D. Z.;  Lam, M. M.;  Qalieh, A.;  Qalieh, Y.;  Sorel, A.;  Funk, O. H.; Kwan, K. Y., 

Chromatin remodeler Arid1a regulates subplate neuron identity and wiring of cortical connectivity. 

Zhou, Y.; Routh, A., 

Mapping RNA–capsid interactions and RNA secondary structure within virus particles using next-generation sequencing. 

Langsjoen, R.;  Muruato, A.;  Kunkel, S.;  Jaworski, E.; Routh, A.,

 Differential alphavirus defective RNA diversity between intracellular and extracellular compartments is driven by subgenomic recombination events. 

Keil, J. M.;  Doyle, D. Z.;  Qalieh, A.;  Lam, M. M.;  Funk, O. H.;  Qalieh, Y.;  Shi, L.;  Mohan, N.;  Sorel, A.; Kwan, K. Y., 

Symmetric neural progenitor divisions require chromatin-mediated homologous recombination DNA repair by Ino80. 

Kautz, T. F.;  Jaworski, E.;  Routh, A.; Forrester, N. L., 

A low fidelity virus shows increased recombination during the removal of an alphavirus reporter gene. 

Huang, K.-L.;  Jee, D.;  Stein, C. B.;  Elrod, N. D.;  Henriques, T.;  Mascibroda, L. G.;  Baillat, D.;  Russell, W. K.;  Adelman, K.; Wagner, E. J.,

 Integrator recruits protein phosphatase 2A to prevent pause release and facilitate transcription termination. 

Shi, L.;  Qalieh, A.;  Lam, M. M.;  Keil, J. M.; Kwan, K. Y., 

Robust elimination of genome-damaged cells safeguards against brain somatic aneuploidy following Knl1 deletion. 

Reyes-Ruiz, J. M.;  Osuna-Ramos, J. F.;  Bautista-Carbajal, P.;  Jaworski, E.;  Soto-Acosta, R.;  Cervantes-Salazar, M.;  Angel-Ambrocio, A. H.;  Castillo-Munguía, J. P.;  Chávez-Munguía, B.; De Nova-Ocampo, M., 

Mosquito cells persistently infected with dengue virus produce viral particles with host-dependent replication. 

Elrod, N. D.;  Henriques, T.;  Huang, K.-L.;  Tatomer, D. C.;  Wilusz, J. E.;  Wagner, E. J.; Adelman, K., 

The integrator complex attenuates promoter-proximal transcription at protein-coding genes. 

Jaworski, E.; Routh, A., 

ClickSeq: replacing fragmentation and enzymatic ligation with click-chemistry to prevent sequence chimeras. 

Jaworski, E.; Routh, A., 

Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus. 

Routh, A.;  Head, S. R.;  Ordoukhanian, P.; Johnson, J. E., 

ClickSeq: fragmentation-free next-generation sequencing via click ligation of adaptors to stochastically terminated 3′-azido cDNAs. 

Routh, A.;  Chang, M. W.;  Okulicz, J. F.;  Johnson, J. E.; Torbett, B. E., 

CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data. 


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