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

Routh et al. JMB 2015

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.