Bring back Yagev Buchshtab, (brother of PhD student Nufar),
held hostage in Gaza for over 150 days!!!
Publications
Harari S, Miller D, Fleishon S, Burstein D, Stern A. (2024)
Using big sequencing data to identify chronic SARS-Coronavirus-2 infections. Nature Communications volume 15, Article number: 64 https://www.nature.com/articles/s41467-024-44803-4
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 Evolution, vead033. https://academic.oup.com/ve/article/9/1/vead033/7175026
Miller D, Stern A, Burstein D. (2022)
Deciphering microbial gene function using natural language processing. Nature Communications, 29;13(1):1-1.
https://www.nature.com/articles/s41467-022-33397-4
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. https://www.nature.com/articles/s41591-022-01882-4
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. https://pubmed.ncbi.nlm.nih.gov/35681059/
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.
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. https://www.nature.com/articles/s41591-021-01413-7
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, https://doi.org/10.1093/ofid/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. https://doi.org/10.1038/s41467-020-19248-0
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. https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009029
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, https://doi.org/10.1093/molbev/msaa247
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. https://www.science.org/doi/10.1126/sciadv.abb7990
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. https://doi.org/10.1093/nar/gkz907
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. https://www.nature.com/articles/s41598-018-37483-w
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. https://academic.oup.com/ve/article/5/1/vez011/5512690
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. https://doi.org/10.1371/journal.pgen.1007420
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. https://doi.org/10.1016/j.cell.2017.03.013
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. https://doi.org/10.1016/j.celrep.2014.07.011
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. https://doi.org/10.1016/j.plrev.2013.11.004
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. https://doi.org/10.4161/rna.23929
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. https://doi.org/10.1186/1471-2148-13-16
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. http://www.genome.org/cgi/doi/10.1101/gr.138297.112.
Stern A, Sorek R. (2011)
The phage-host arms race: shaping the evolution of microbes. Bioessays, 33(1): 43-51. https://doi.org/10.1002/bies.201000071
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. https://doi.org/10.1093/sysbio/syp104
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. https://doi.org/10.1371/journal.pcbi.1000214
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. https://doi.org/10.1186/1745-6150-3-41
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. https://doi.org/10.1007/s00239-006-0033-y
Stern A, Pupko T. (2006)
An Evolutionary Space-Time Model with Varying Among Site Dependencies. Mol. Biol. Evol. 23: 392-400. https://doi.org/10.1093/molbev/msj044
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