Publications

 Recent Publications

 

Mazloom, S.J. Brown, A.C. Spradling and S.A. Gerbi (2020) Single-molecule sequencing of long DNA molecules allows high contiguity de novo genome assembly for the fungus fly, Sciara coprophila. BioRxiv. doi: https://doi.org/10.1101/2020.02.24.963009

S.A. Gerbi (2018) Bundling up DNA. eLIFE 7: pii: e37234. doi: 10.7554/eLife.37234.

Y. Yamamoto and S.A. Gerbi (2018) Making ends meet: targeted integration of DNA fragments by genome editing. Chromosoma. 127: 405-420.

S.A. Gerbi (2015) Beginning at the end: DNA replication within the telomere. Journal of Cell Biology 210: 177-179.

Doris SM, Smith DR, Beamesderfer JN, Raphael BJ, Nathanson JA and Gerbi SA (2015) Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics, RNA21: 1719-1730. (PMID: 26283689; PMCID: PMC4574749)

Yamamoto Y, Bliss J and Gerbi SA (2015) Whole organism genome editing: Targeted large DNA insertion via ObLiGaRe nonhomologous end-joining in vivo capture.  G3: Genes/Genomes/Genetics 5: 1843-1847. 

M.S. Foulk, J.M. Urban, C. Casella and S.A. Gerbi (2015) Characterizing and controlling intrinsic biases of Lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Research 25: 725-735.

Gerbi SA (2015) Beginning at the end: DNA replication within the telomere. Journal of Cell Biology 210: 177-179. 

Urban JM,  Foulk MS, Casella C and  Gerbi SA (2015) The hunt for origins of DNA replication in multicellular eukaryotes. F1000 7:30 (ePub). 

Urban JM, Bliss J, Lawrence CE and  Gerbi SA (2015) Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION. bioRxiv doi: http://dx.doi.org/10.1101/019281

Luan Lin, Deborah Khider, Lorraine E. Lisiecki, and Charles E. Lawrence (2014) Probabilistic sequence alignment of stratigraphic records.  Paleoceanography, 29(10): 976-9898, DOI: 10.1002/2014PA002713


Ruggieri, Eric, Lawrence, C. E. (2014)  The Bayesian Change Point and Variable Selection Algorithm: Application to the δ18O Proxy Record of the Plio-Pleistocene.  Journal of Computational and Graphical Statistics, Volume 23, Number 1, Pages 87–110 DOI:10.1080/10618600.2012.707852

Georges St. Laurent, Michael R. Tackett, Sergey Nechki, Dmitry Shtokalo, Denis Antonets, Yiannis A. Savva, Rachel Maloney, Philipp Kapranov, Charles E. Lawrence, and Robert A. Reenan (2013)  Genome-Wide Analysis of A-to-I RNA Editing via Single Molecule Sequencing in Drosophila Nature Structural and Molecular  Biology, 20(11):1333-9. doi: 10.1038/nsmb.2675.

Lauren A. Sugden, Michael R. Tackett, Yiannis A. Savva, William A. Thompson, Charles E. Lawrence (2013) Assessing the validity and reproducibility of genome scale predictions, Bioinformatics, 15;29(22):2844-51. doi: 10.1093/bioinformatics/btt508 Vol. 29 no. 22.

Yiannis A. Savva, James E.C Jepson, Asli Sahin, Arthur U. Sugden, Jacquelyn S. Dorsky, Lauren Alpert, Charles Lawrence, Robert A. Reenan (2012)  Auto-regulatory RNA editing fine-tunes mRNA re-coding and complex behavior in Drosophila,  Nature Communications   3:790 | DOI: 10.1038/ncomms1789 | https://www.nature.com/articles/ncomms1789

Eric Ruggieri, and Charles E. Lawrence, On efficient calculations for Bayesian variable selection, (2012) , Computational Statistics and Data Analysis, 56: 1319-1332, doi:10.1016/j.csda.2011.09.026

Donglai Wei, Lauren V. Alpert and Charles E. Lawrence (2011) RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. Bioinformatics, Vol. 27 no. 18, pages 2486–2493 doi:10.1093/bioinformatics/btr421