Publications

Harel, N.*, Meir, M.*, Gophna, U., Stern, A. Sequencing Complete Genomes of RNA Viruses With MinION Nanopore:

Finding Associations Between Mutations. BioRxiv, doi: https://doi.org/10.1101/575480. Nucleic Acids Research, 2019 https://doi.org/10.1093/nar/gkz907

Ling, G.*, Miller, D.*, Nielsen, R., Stern, A. A Bayesian framework for inferring the influence of sequence context on single base modifications. BioRxiv, doi: https://doi.org/10.1101/571646. Molecular Biology and Evolution, 2019.

Shteyer E., Shekhtman L., Zinger T., Harari S., Gafanovich, I., Wolf, D., Ivgi, H., Barsuk, R., Dery, I., Armoni, D., Rivkin, M., Pipalia, R., Cohen Eliav, M., Skorochod, Y., Breuer, G.S., Tur-kaspa, R., Weil Wiener, Y., Stern, A., Cotler, S.J., Dahari, H., Lurie Y.  Modeling suggests that microliter volumes of contaminated blood caused an outbreak of hepatitis C during computerized tomography. PLoS ONE 14(1): e0210173 (2018)

Kustin, T., Ling, G., Sharabi, S., Ram, D., Friedman, N., Zuckerman, N., Dahan Bucris, E., Glatman-Freedman, A., Stern, A.*, Mandelboim, M.* ​A method to identify respiratory virus infections in clinical samples using next-generation sequencing. Scientific Reports, volume 9, Article number: 2606 (2019) 

Zinger, T., Gelbart, M., Miller, D., Pennings, P., Stern, A. Inferring Population Genetics Parameters of Evolving Viruses Using Time-series Data. Virus Evolution, Vol 5, Issue 1, January 2019, vez011, https://doi.org/10.1093/ve/vez011.

Gelbart, M.*, Harari, S.*, Ben-Ari, Y., Kustin T., Meir, M., Miller, D., Mor, O., Stern, A. Accurate in vivo population sequencing uncovers drivers of within-host genetic diversity in viruses. BioRxiv, doi: https://doi.org/10.1101/349498v3

Gelbart, M., Stern, A., Evolutionary rate shifts suggest species-specific adaptation events in HIV-1 and SIV. BioRxiv, doi: https://doi.org/10.1101/190769

Theys K.*, Feder, A.*, Gelbart, M.*, Hartl, M., Stern, A., Pennings PS. Within-patient HIV mutation frequencies reveal fitness costs of CpG dinucleotides, drastic amino acid changes and G→A mutations. PLoS Genetics, Jun 28;14(6):e1007420 (2018). 

Stern, A., Yeh, M.T., Zinger, T., Smith, M., Ling, G., Nielsen, R., Macadam, A,, Andino, R. The Evolutionary Pathway to Virulence of an RNA Virus. Cell, Volume 169, Issue 1, 23 March 2017, Pages 35–46.e19

Bar-Rogovsky, H. Stern, A. Penn, O. Kobl, I. Pupko, T. Tawfik, D.S. Assessing the prediction fidelity of ancestral reconstruction by a library approach. Protein Engineering Design and Selection (2015). doi: 10.1093/protein/gzv038

 

Stern, A. Bianco, S., Yeh, M.T., Wright, C., Butcher, K., Tang,. C., Nielsen, R., Andino, A. Costs and benefits of mutational robustness in viruses. Cell Reports, 8(4): 1026-1036 (2014) 

 

Stern, A. CRISPR and RNA interference: similarities across immune systems. Physics of Life Reviews. pii: S1571-0645(13)00181-4. (2013)

 

Mick E., Stern A., Sorek R. Holding a grudge: Persisting anti-phage CRISPR immunity in multiple human gut microbiomes. RNA Biology, 10(5):1-7 (2013)

 

Mayrose, I., Stern, A., Burdelova, E., Sabo, Y., Laham-Karam, N., Zamostiano, R., Bacharach, E., Pupko, T. Synonymous site conservation in the HIV-1 genome. BMC Evolutionary Biology 13:164 (2013)

 

Stern, A., Mick, E., Tirosh, I., Sagi, O., Sorek, R. CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Research, 22(10):1985-94 (2012)

 

Stern A., Sorek R. The phage-host arms race: shaping the evolution of microbes. Bioessays, 33(1): 43-51 (2011)

 

Stern, A., Keren, L., Amitai, G., Sorek, R.. Widespread targeting of self-DNA by the prokaryotic CRISPR immune system: gene regulation or auto-immunity? Trends in Genetics, 26(8):335-340 (2010)

 

Stern A., Mayrose I., Shaul S., Gophna U., Pupko T. An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes. Systematic Biology, 59(2): 212-225, (2010)

 

Penn O.* , Stern A.*, , Rubinstein N., Dutheil J., Bacharach E., Galtier N., Pupko T. 2008. Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Computational Biology. Nov;4(11):e1000214 (2008) *Authors contributed equally.

 

Sela N, Stern, A., Pupko, T., Ast, G. Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans. Biology Direct. Oct 8;3:41 (2008)

 

Cohen, O., Rubinstein, ND., Stern, A., Gophna, U., and Pupko, T. A likelihood framework to analyze phyletic patterns. Proceedings of The Royal Society of London Series B-Biological Sciences. Dec 27;363(1512):3903-11. (2008)

 

Stern, A., Doron-Faigenboim, A., Erez, E., Martz, E., Bacharach, E., Pupko, T. Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Research. 35: W506-W511 (2007)

 

Stern, A., Privman, E., Rasis, M., Lavi, S., Pupko, T. Evolution of the metazoan protein phosphatase 2C superfamily. J. Mol. Evol. 64(1):61-70, (2007)

 

Stern, A., Pupko, T. An Evolutionary Space-Time Model with Varying Among Site Dependencies. Mol. Biol. Evol. 23: 392-400 (2006)

 

Doron-Faigenboim, A.*, Stern, A.*, Mayrose, I., Bacharach, E., and Pupko, T. Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics. 21(9): 2101-2103 (2005) *Authors contributed equally. 

© 2014 Adi Stern laboratory at Tel-Aviv University

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