Salzman Lab Publications

Selected Publications

R. Dehghannasiri, M. Jordanski, D. Freeman, G. Hsieh, J. Howard, E. Lehnert, J. Salzman (2019). “Towards precise and cost-effective fusion discovery: A landscape of druggable gene fusions across TCGA cancers”, Cancer Research, DOI: 10.1158/1538-7445.AM2019-2468.

R. Dehghannasiri, D. Freeman, M. Jordanski, G. Hsieh, A. Damljanovic, E. Lehnert, J. Salzman (2019). “Improved detection of gene fusions by applying statistical methods reveals new oncogenic RNA cancer drivers”, bioRxiv.

R. Dehghannasiri, L. Szabo, J. Salzman (2018). “Ambiguous splice sites distinguish circRNA and linear splicing in the human genome”, Bioinformatics.

Barrett SP*, Parker KR*, Horn C, Mata M, Salzman J (2017). ciRS-7 exonic sequence is embedded in a long non-coding RNA locus. DOI 10.1371/journals.pgen.1007114. PMID 29236709. 

G Hsieh, R Bierman, L Szabo, AG Lee, DE Freeman, N Watson, EA Sweet-Cordero, J Salzman (2017). Statistical algorithms improve accuracy of gene fusion detection. DOI 10.1093/nar/gkx453     PDF

L Szabo, J Salzman (2016). Detecting Circular RNAs: bioinformatic and experimental challenges. doi:10.1038/nrg.2016.114   PDF

S.P. Barrett, J Salzman (2016). Circular RNAs: analysis, expressions and potential functions. DOI 10.1242/dev.128074   PDF

J Salzman (2016). Circular RNA Expression: Its Potential Regulation and Function. Trends in Genetics: DOI 10.1016/j.tig.2016.03.002   PDF Copy

S.P. Barrett, P.L. Wang, J. Salzman (2015). Circular RNA biogenesis can proceed through an exon-containing lariat precursor. eLife 4: e07540.

L. Szabo, R. Morey, N.J. Palpant, P.L. Wang, N. Afari, C. Jiang, M.M. Parast, C.E. Murry, L.C. Laurent, J. Salzman (2015). Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during fetal development. Genome Biology 16(126): DOI 10.1186/s13059-015-0690-5

H. Jiang, J. Salzman (2014) A penalized likelihood approach for robust estimation of isoform expression. Statistics and Its Interface. 8, 437-445. PDF  

P.L. Wang, Y. Bao, M.C. Yee, S.P. Barrett, G.J. Hogan, M.N. Olsen, J.R. Dinneny, P.O. Brown, J. Salzman (2014). Circular RNA Is Expressed across the Eukaryotic Tree of Life. PLoS ONE 9(3): e90859. doi:10.1371/journal.pone.0090859.

J. Salzman, R.E. Chen, M.N. Olsen, P.L. Wang, P.O. Brown (2013). Cell type specific features of circular RNA expression. PLoS Genetics, doi:10.1371/journal.pgen.1003777

B. Rajaratnam and J. Salzman (2013). “Best Permutation Analysis”, Journal of Multivariate Analysis 121: 193-223.

H. Jiang, J. Salzman (2012) Statistical properties of an early stopping rule for resampling-based multiple testing. Biometrika, doi: 10.1093/biomet/ass051.

J. Salzman, C. Gawad, P. L. Wang, N. Lacayo and P. O. Brown (2012). Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One. 7(2). — Faculty of 1000; features in Nature, Biotechniques and other scientific press venues.

J. Salzman, R. J. Marinelli, P. L. Wang, A. Greene, J. Nielsen, B. Nelsen, C. Dresher and P. O. Brown (2011). ESRRA-C11orf20 is a Recurrent Gene Fusion in Serous Ovarian Carcinoma. PLoS Biology, 9(9).

J. Salzman, H. Jiang, and W. Wong (2011). Statistical Modeling of RNA-Seq Data. Statistical Science. 26 (1).

D. T. Pride, C. Sun, J. Salzman, N. Rao, P. Loomer, G. C. Armitage, J. Banfield, and D. A. Relman (2010). Analysis of Streptococcal CRISPRs from Human Saliva Reveals Substantial Sequence Diversity Within and Between Subjects Over Time. Genome Research. 21.

N. Tsvetanova, D. Klass, J. Salzman and P.O. Brown (2010). Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces Cerevisiae. PLoS One. 5(9).

M. Rabinowitz, D.S. Johnson, J. Salzman, M. Banjevic, C. Cinnioglu, B. Behr (2008). Reliable Concurrent Calling of Multiple Genetic Alleles and 24-Chromosome Ploidy Without Embryo Freezing Using Parental Support Technology (PS). Fertility and Sterility, Volume 90, Page S23.

A. Nayak and J. Salzman (2006). Limits on the Ability of Quantum States to Convey Classical Messages. Journal of the ACM. 52, No. 1, 184-206.

P. Diaconis and J. Salzman (2006). Projection Pursuit for Discrete Data. Festschrift for David Freedman, IMS Lecture Notes.

M. Jablonski, J. Salzman, A. Wierman and A. P. Godbole (2004). An Improved Upper Bound for the Pebbling Threshold of the n-path. Discrete Mathematics. 275, 367-373.

Refereed Conference Proceedings
Ashwin Nayak and Julia Salzman (2002). “On Communication Over an Entanglement-Assisted Quantum Channel”. In Proceedings of the Thirty-Fourth Annual ACM Symposium on the Theory of Computing, pages 698-704. In the joint session with the 17th Annual IEEE Conference on Computational Comp lexity, 2002.

J. Salzman (2007). “Spectral Analysis with Markov Chains." Ph. D. Dissertation, Department of Statistics, Stanford University.

J. Salzman (2002). “Distinct knots with the same Jones Polynomial.” Princeton University Underdergraduate Thesis.