Cohen Y and Hershberg R (2022) Rapid adaptation often occurs through mutations to the most highly conserved positions of the RNA polymerase core enzyme, Genome Biology and Evolution, evac105
Pennings PS, Ogbunugafor CB and Hershberg R (2022) Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs, G3 Genes|Genomes|Genetics, 12: jkac190
Katz S*, Avrani S*, Yavneh M, Hilau S, Gross Y and Hershberg R (2021) Dynamics of mutation accumulation and adaptation during three years of evolution under long-term stationary phase. Molecular Biology and Evolution, 38:2778–2790,
Hilau S, Katz S, Wasserman T, Hershberg R and Savir Y (2021) Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains. biorxiv preprint
Gross J, Avrani S, Katz S, Hilau S and Hershberg R (2020) Culture volume influences the dynamics of adaptation under long-term stationary phase. Genome Biology and Evolution 12: 2292-2301
Avrani S*, Katz S* and Hershberg R (2020) Adaptations Accumulated under Prolonged Resource Exhaustion Are Highly Transient. mSphere 5:e00388-20.
Yannai A, Katz S and Hershberg R (2018) The codon usage of lowly expressed genes is subject to natural selection. Genome Biology and Evolution. evy084
Karasov TL, Barrett L, Hershberg R* and Bergelson J* (2017) Similar levels of gene content variation observed for Pseudomonas syringae populations extracted from single and multiple host species. PLoS ONE. 2: e0184195. (*Equal contribution)
Bolotin E and Hershberg R (2017) Horizontally Acquired Genes Are Often Shared Between Closely Related Bacterial Species. Frontiers in Microbiology. 8, 1536
Hershberg R (2017) Antibiotic-Independent Adaptive Effects of Antibiotic Resistance Mutations. Trends in Genetics. 8: 521-528
Avrani S, Bolotin E, Katz S and Hershberg R (2017) Rapid genetic adaptation during the first four months of survival under resource exhaustion. Molecular Biology and Evolution. 7: 1758–1769
Hershberg R (2016) Human host range of Mycobacterium tuberculosis. Nature Genetics. 48: 1453-1454. (Invited News and Views article)
Bolotin E and Hershberg R (2016) Bacterial Intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes. Scientific Reports. 6:35168.
Ostrow SL and Hershberg R (2016) The somatic nature of cancer allows it to affect highly constrained genes. Genome Biology and evolution, 8(5):1614-1620.
Lan Y, Rosen G* and Hershberg R* (2016) Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains. Microbiome, 4:18 (Co-last authors, co-contributing authors).
Hershberg R (2016) Codon usage and translational selection. In: Kliman RM (ed.), Encyclopaedia of Evolutionary Biology, Vol. 1, pp. 293-298. Oxford: Academic Press. (Book chapter, full text will be provided upon request)
Ostrow SL†, Simon E†, Prinz E, Bick T, Shentzer T, Nagawkar SS, Sabo E, Ben-Itzhak O, Hershberg R* and Hershkovitz D* (2016) Variation in KRAS driver substitution distributions between tumor types is determined by both mutation and natural selection. Scientific reports. 6:21927 (†Equal contributors, *Co-last authors, co-contributing authors)
Hershberg R (2015) Mutation – the engine of evolution: studying mutation and its role in the evolution of bacteria. Cold Spring Harbor Perspectives in Biology. 7(9):a018077
Bolotin E and Hershberg R (2015) Gene loss dominates as a source of genetic variation within clonal bacterial species. Genome Biology and Evolution. 7(8): 2173-2187
Field W and Hershberg R (2015) Alarmingly high segregation frequencies of quinolone resistance alleles within human and animal microbiomes are not explained by direct clinical antibiotic exposure. Genome Biology and Evolution. 7(6):1728-1742
Reichenberger ER, Rosen G, Hershberg U* and Hershberg R* (2015) Prokaryotic nucleotide composition is shaped by both phylogeny and the environment. Genome Biology and Evolution. 7(5): 1380-1389 (*co-last authors, paper was highlighted by the journal).
Ostrow SL, Barshir R, DeGregori J, Yeger-Lotem E and Hershberg R (2014) Cancer evolution is associated with pervasive positive selection on globally expressed genes. PLoS Genetics. 10(3): e1004239 (Article was featured in the Research Highlight section of Nature Reviews Genetics
Lan Y, Morrison C, Hershberg R*, and Rosen G* (2014) POGO-DB – a database of Pairwise-comparisons Of Genomes and conserved Orthologous genes. Nucleic Acids Research. doi: 10.1093/nar/gkt1094. (*Co-last authors, co-corresponding authors).
Katz S and Hershberg R (2013) Elevated mutagenesis does not explain the increased frequency of antibiotic resistant mutants in starved aging colonies. PLoS Genetics. 9(11): e1003968.
Lawrie DS, Messer PW, Hershberg R, and Petrov DA (2013) Strong Purifying Selection at Synonymous Sites in D. melanogaster. PLoS Genetics 9(5): e1003527
Hershberg R and Petrov DA (2012) On the Limitations of Using Ribosomal Genes as References for the Study of Codon Usage: A Rebuttal. PLoS One 7(12): e49060
Hershberg R and Petrov DA (2010) Evidence That Mutation Is Universally Biased towards AT in Bacteria. PLoS Genetics 6(9):e1001115 (Article was featured with a perspective in PLoS Genetics, and was also selected as a ‘must read’ article by Faculty of 1000).
Hershberg R and Petrov DA (2009) General rules for optimal codon choice. PLoS Genetics 5(7):e1000556 (Article was featured in the Research Highlight section of Nature Reviews Genetics).
Hershberg R*, Lipatov M*, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S (2008) High Functional Diversity in M. tuberculosis Driven by Genetic Drift and Human Demography. PLoS Biology 6(12):e311 (*Equal contributors, article was featured as a Science Magazine Editor’s Choice)
Hershberg R and Petrov DA (2008) Selection on codon bias. Annual Reviews in Genetics 42:287-99
Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I, Margalit, H, Altuvia S (2008) Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Research. 36(6):1913-27
Hershberg R, Tang H, Petrov DA (2007) Reduced selection leads to accelerated gene loss in Shigella. Genome Biology. 8(8):R164
Hershberg R, Margalit H (2006) Co-evolution of transcription factors and their targets depends on mode of regulation. Genome Biology. 7(7):R62 (Article was featured in the “What the papers say” section of Bioassays)
Hershberg R, Yeger-Lotem E, Margalit H (2005) Chromosomal organization is shaped by the transcriptional regulatory network. Trends in Genetics. 21(3):138-42
Zlotorynski E, Rahat A, Skaug J, Ben-Porat N, Ozeri E, Hershberg R, Levi A, Scherer, SW, Margalit H, Kerem B (2003) Molecular basis for expression of common and rare fragile sites. Mol. Ce ll. Biol. 23(20):7143-7151
Hershberg R, Altuvia S, Margalit H (2003) A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Research 31(7):1813-1820
Argaman L*, Hershberg R*, Vogel J*, Bejerano G, Wagner EGH, Margalit H, Altuvia S (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biology 11(12):941-950. (*Equal contributors, cover article, selected as a ‘must read article by Faculty of 1000).
Hershberg R, Bejerano G, Santos-Zavaleta A, Margalit H (2001) PromEC: an updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Research. 29(1):277.