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Harari S, Miller D, Fleishon S, Burstein D, Stern A. (2024)

Using big sequencing data to identify chronic SARS-Coronavirus-2 infectionsNature Communications volume 15, Article number: 64

Caspi I, Meir M, Ben Nun N, Yakhini U, Stern A, Ram Y. (2023)

Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation. Virus Evolutionvead033

Miller D, Stern A, Burstein D. (2022)

Deciphering microbial gene function using natural language processing. Nature Communications, 29;13(1):1-1.

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. (2022)

Drivers of adaptive evolution during chronic SARS-CoV-2 infections. Nature Medicine, 28:1501–1508.

Nahmad AD, Lazzarotto CR, Zelikson N, Kustin T, Tenuta M, Huang D, Reuveni I, Nataf D, Raviv Y, Horovitz-Fried M, Dotan I, Carmi Y, Rosin-Arbesfeld R, Nemazee D, Voss JE, Stern A, Tsai SQ, Barzel A. (2022).

In vivo engineered B cells secrete high titers of broadly neutralizing anti-HIV antibodies in mice.
Nature Biotechnology, 40(8):1241-1249.

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. (2022).

Inferring Protein Function in an Emerging Virus: Detection of the Nucleoprotein in Tilapia Lake Virus. Journal of Virology, 96(6), e01757-21. 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. (2022).

The association between SARS‐CoV‐2 infection and late pregnancy loss. Int J Gynecol Obstet,157:198–209. https://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,


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. (2021)

Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals. Nature Medicine, 27:1379–1384.


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. (2021).

Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole Genome Sequence Analysis. Open Forum Infectious Diseases, 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. (2020).

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. Nat Commun 11, 5518.


Gelbart M*, Harari S*, Ben-Ari Y, Kustin T, Meir M, Miller D, Mor O, Stern A. (2020).

Drivers of within-host genetic diversity in acute infections of viruses. PLoS Pathog 16(11): e1009029.


Gelbart M, Stern A. (2020)

Site-Specific evolutionary rate shifts in HIV-1 and SIV. Viruses, 16;12(11):1312. doi: 10.3390/v12111312.


Kustin T, Stern A. (2021)

Biased mutation and selection in RNA viruses. Molecular Biology and Evolution, 38(2), 575-588,  


Meir M, Harel N, Miller D, Gelbart M, Eldar A, Gophna U, Stern A. (2020).

Competition between social cheater viruses is driven by mechanistically different cheating strategies. Science Advances, 6(34), eabb7990.

Ling G, Miller D, Nielsen R, & Stern A (2020).

A Bayesian framework for inferring the influence of sequence context on point mutations. Molecular biology and evolution, 37(3), 893-903.

Harel N*, Meir M*, Gophna U, Stern A. (2019).

Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations. Nucleic acids research, 47(22), e148-e148.


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.  (2019).

Modeling suggests that microliter volumes of contaminated blood caused an outbreak of hepatitis C during computerized tomography. Plos one, 14(1), e0210173.


Kustin T, Ling G, Sharabi S, Ram D, Friedman N, Zuckerman N, Dahan Bucris E, Glatman-Freedman A, Stern A*, Mandelboim M.* (2019).

A method to identify respiratory virus infections in clinical samples using next-generation sequencing. Scientific reports, 9(1), 1-8.


Zinger T, Gelbart M, Miller D, Pennings P, Stern A. (2019).

Inferring population genetics parameters of evolving viruses using time-series data. Virus evolution, 5(1), vez011.


Theys K*, Feder A*, Gelbart M*, Hartl M, Stern A, Pennings PS. (2018).

Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV. PLoS genetics, 14(6), e1007420.


Stern A, Yeh M.T, Zinger T, Smith M, Ling G, Nielsen R, Macadam A, Andino R. (2017).

The Evolutionary Pathway to Virulence of an RNA Virus. Cell, 169(1), 35-46.


Bar-Rogovsky H, Stern A, Penn O, Kobl I, Pupko T, Tawfik D.S. (2015). 

Assessing the prediction fidelity of ancestral reconstruction by a library approach. Protein Engineering, Design and Selection, 28(11), 507-518. doi: 10.1093/protein/gzv038



Stern A, Bianco S, Yeh MT, Wright C, Butcher K, Tang C, Nielsen R, Andino A. (2014).

Costs and benefits of mutational robustness in viruses. Cell reports, 8(4), 1026-1036.



Stern A. (2014).

CRISPR and RNA interference: similarities across immune systems: comment on" Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems" by Edwin L. Cooper and Nicola Overstreet. Physics of life reviews, 11(1), 135-151.


Mick E, Stern A, Sorek R. (2013).

Holding a grudge: Persisting anti-phage CRISPR immunity in multiple human gut microbiomes. RNA biology, 10(5), 900-906.



Mayrose I, Stern A, Burdelova E, Sabo Y, Laham-Karam N, Zamostiano R, Bacharach E, Pupko T. (2013). Synonymous site conservation in the HIV-1 genome. BMC evolutionary biology, 13(1), 1-11.



Stern A, Mick E, Tirosh I, Sagi O, Sorek R. (2012). 

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Research, 22(10):1985-94.



Stern A, Sorek R. (2011)

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



Stern A, Keren L, Amitai G, Sorek R. (2010)

Widespread targeting of self-DNA by the prokaryotic CRISPR immune system: gene regulation or auto-immunity? Trends in Genetics, 26(8):335-340.



Stern A., Mayrose I., Shaul S., Gophna U., Pupko T. (2010)

An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes. Systematic Biology, 59(2): 212-225.


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, 4(11), e1000214.



Sela N, Stern, A., Pupko, T., Ast, G. (2008)

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans. Biology Direct 3, 41.



Cohen O, Rubinstein ND, Stern A, Gophna U and Pupko, T. A. (2008)

A likelihood framework to analyze phyletic patterns. Proceedings of The Royal Society of London Series B-Biological Sciences, 363(1512):3903-11. https://doi:10.1098/rstb.2008.0177



Stern A, Doron-Faigenboim A, Erez E, Martz E, Bacharach E, Pupko T. (2007) 

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic acids research, 35(suppl_2), W506-W511. doi: 10.1093/nar/gkm382. Epub



Stern A, Privman E, Rasis M, Lavi S, Pupko T. (2007).

Evolution of the metazoan protein phosphatase 2C superfamily. Journal of molecular evolution, 64(1), 61-70.


Stern A, Pupko T. (2006)

An Evolutionary Space-Time Model with Varying Among Site Dependencies. Mol. Biol. Evol. 23: 392-400.



Doron-Faigenboim A*, Stern A*, Mayrose I, Bacharach E and Pupko, T. (2005) 

Selection: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics. 21(9): 2101-2103. https://doi:10.1093/bioinformatics/bti259

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