Harari, S., Tahor, M., Rutsinsky, N., Meijer, S., Miller, D., Henig, O., Halutz, O., Levytskyi, K., Ben-Ami, R., Adler, A., Paran, Y., Stern, A. Drivers of adaptive evolution during chronic SARS-CoV-2 infections. medRxiv, doi:

Abu Rass R, Kustin T, Zamostiano R, Smorodinsky N, Ben Meir D, Feder D, Mishra N, Lipkin WI, Eldar A, Ehrlich M, Stern A, Bacharach E. Inferring protein function in an emerging virus: detection of the nucleoprotein in Tilapia Lake Virus. J Virol. 2022 Feb 2:JVI0175721. doi: 10.1128/JVI.01757-21.

Ganor Paz Y, Shiloh S, Brosh-Nissimov T, Grupel D, Sorek N, Kustin T, Stern A, Maklakovsky M, Polak M, Sharvit M, Neeman O, Ben Valid T, Tovbin J, Barzilay E. The association between SARS‐CoV‐2 infection and late pregnancy loss. Int J Gynaecol Obstet. 2021 Nov 14. doi: 10.1002/ijgo.14025.

Stern, A., Fleishon, S., Kustin, T., Mandelboim, M., Erster, O.,Israel Consortium of SARS-CoV-2 sequencing, Mendelson, E., Mor, O., Zuckerman, N.S. The unique evolutionary dynamics of the SARS-CoV-2 Delta variant. medRxiv, doi:

Kustin, T., Harel, N., Finkel, U., Perchik, S., Harari, S., Tahor, M, Caspi, I., Levy, R., Leschinsky, M., Ken Dror, S., Bergerzon, G., Gadban, H., Gadban, F., Eliassian, E., Shimron, O., Saleh, L., Ben-Zvi, H., Amichay, D., Ben-Dor, A., Sagas, D., Strauss, M., Shemer Avni, Y., Huppert, A., Kepten, E., Balicer, R.D., Nezer, D., Ben-Shachar, S., Stern, A. Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals. medRxiv, doi: Nature Medicine (2021).

Meijer, S.*, Harel, N.*, Ben-Ami, R., Nahari, M., Yakubovsky, M., Oster, H., Kolomansky, A., Halutz, O., Laskar, O., Henig, O., Stern, A., Paran, Y. Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole Genome Sequence Analysis. Open Forum Infectious Diseases (2021), ofab120,

Miller, D.*, Martin, M.*, Harel, N.*, Kustin, T.*, Tirosh, O.*, Meir, M., Sorek, N., Gefen-Halevi, S., Amit, S., Vorontsov, O., Wolf, D., Peretz, A., Shemer-Avni, Y., Roif-Kaminsky, D., Kopelman, N., Huppert, A., Koelle, K., Stern, A. Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. medRxiv, doi: Nature Communications volume 11, Article number: 5518 (2020). 

Gelbart, M.*, Harari, S.*, Ben-Ari, Y., Kustin T., Meir, M., Miller, D., Mor, O., Stern, A. Drivers of within-host genetic diversity in acute infections of viruses. BioRxiv, doi:, PLoS Pathog 16(11): e1009029. https:// 

Gelbart, M., Stern, A., Site-Specific evolutionary rate shifts in HIV-1 and SIV. BioRxiv, doi: Viruses 2020, 12(11), 1312;

Kustin, T. Stern, A.. Biased mutation and selection in RNA viruses. Molecular Biology and Evolution, msaa247,  

Meir, M., Harel, N., Miller, D., Gelbart, M., Eldar, A., Gophna, U., Stern, A. Competition between social cheater viruses is driven by mechanistically different cheating strategies. Science Advances, 2020, Vol. 6, no. 34, eabb7990. DOI: 10.1126/sciadv.abb7990

Harel, N.*, Meir, M.*, Gophna, U., Stern, A. Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations BioRxiv, doi: Nucleic Acids Research, 2019

Ling, G.*, Miller, D.*, Nielsen, R., Stern, A. A Bayesian framework for inferring the influence of sequence context on single base modifications. BioRxiv, doi: Molecular Biology and Evolution, Volume 37, Issue 3, March 2020, Pages 893–903, (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,

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.