2009    Alon S, Eisenberg E, Jacob-Hirsch J, Rechavi G, Vatine G, Toyama R, Coon SL, Klein DC, Gothilf Y. A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland. Bioinformatics, 25(5):559-62.

2009    Toyama R, Chen X, Jhawar N, Aamar E, Epstein J, Reany N, Alon S, Gothilf Y, Klein DC, Dawid IB. Transcriptome analysis of the zebrafish pineal gland. Dev Dyn, 238(7):1813-1826.

2010    Ben-Moshe Z, Vatine G, Alon S, Tovin A, Mracek P, Foulkes N, Gothilf Y. Multiple PAR and E4BP4 bZIP transcription factors in zebrafish: diverse spatial and temporal expression patterns. Chronobiology Int. 27(8):1509-31.

2011    Levy O*, Kaniewska P*, Alon S, Eisenberg E, Karako-Lampert S, Bay LK, Reef R, Rodriguez-Lanetty M, Miller DJ, Hoegh-Guldberg O. Complex diel cycles of gene expression in the coral-algal symbiosis. Science, 331:175. *Equal contribution. 

2011    Alon S*, Vigneault F*, Eminaga S, Christodoulou D, Seidman J, Church GM, Eisenberg E. Bar-coding bias in high-throughput multiplex sequencing of miRNA. Genome Research, 21:1506–1511. *Equal contribution.

2012    Alon S*, Mor E*, Vigneault F*, Gallo A, Locatelli F, Church GM, Shomron N, Eisenberg E. Systematic identification of edited microRNAs in the human brain. Genome Research, 22:1533-1540. *Equal contribution.

2012    Dresner E, Zemel A, Arviv C, Barak SL, Alon S, Ofir R, Gothilf Y, Gozes I. Novel Evolutionary-Conserved Role for the ADNP Protein Family that is Important for Erythropoiesis. J Biol Chem. 287(48):40173-40185.

2012    Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, Christodoulou D, Seidman J, Eisenberg E, Church GM. High-throughput multiplex sequencing of miRNA. Current Protocols in Human Genetics. 11.12:1-10.

2012    Tovin A*, Alon S*, Ben-Moshe Z, Mracek P, Vatine G, Foulkes N, Jacob-Hirsch J, Rechavi G, Coon SL, Klein DC, Eisenberg E, Gothilf Y. Systematic identification of rhythmic genes reveals camk1gb as a new element in the circadian clockwork. PLOS Genetics. 8(12):e1003116. *Equal contribution.

2012    Sela-Culang I, Alon S, Ofran Y. A Systematic Comparison of Free and Bound Antibodies Reveals Binding-Related Conformational Changes. J Immunol. 189:4890-4899. Appear in the 'Issue Highlights' section.

2012    Smadja-Storz S, Tovin A, Mracek P, Alon S, Foulkes NS, Gothilf Y. Casein kinase 1delta activity: a key element in the zebrafish circadian timing system. PLOS One 8(1):e54189.

2013    Alon S, Eisenberg E. Identifying RNA editing sites in miRNAs by deep sequencing. Methods in Molecular Biology, 1038:159-170.

2014    Ben-Moshe Z*, Alon S*, Mracek P, Faigenbloom L, Tovin A, Vatine G, Eisenberg E, Foulkes SN, Gothilf Y (2014). The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light. Nucleic Acids Research; doi: 10.1093/nar/gkt1359. *Equal contribution

2015    Alon S, Eisenberg E. Using deep sequencing data for identification of editing sites in mature miRNAs. Methods in Molecular Biology 1269:231-42.

2015    Alon S, Garrett SC, Levanon EY, Olson S, Graveley BR, Rosenthal JJC, Eisenberg E. The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. eLife 4:e05198. Covered by: Science Magazine Editor’s Choice, Science Daily, IFLScience, SciGuru, ScienceNews, The Scientist, NHGRI, NSF, and more.

2015    Tomaselli S, Galeano F, Alon S, Raho S, Galardi S, Polito VA, Presutti C, Vincenti S, Eisenberg E, Locatelli F, Gallo A. Modulation of microRNA editing, expression and processing through ADAR2 deaminase in glioblastoma. Genome Biology, 16:5.

2015    Alon S, Erew M, Eisenberg E. DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data. Bioinformatics, 31:2568-2570. 

2015    Oren M*, Tarrant AM*, Alon S, Simon-Blecher N, Elbaz I, Appelbaum L, Levy O. Profiling molecular and behavioral circadian rhythms in the non-symbiotic sea anemone Nematostella vectensis. Scientific Reports 5:11418. *Equal contribution

2015    Bekerman LY, Elbaz I, Diber A, Dahary D, Bar LG, Alon S, Goldshtein TL, Appelbaum L. Hypocretin neuron-specific transcriptome profiling identifies the sleep modulator Kcnh4a. eLife 4:e08638. Covered by eLife Insight Transcriptomics: Resting easy with a sleep regulator.

2015    Kaniewska P*, Alon S*, Karako-Lampert S, Hoegh-Guldberg O, Levy O. Signaling cascades and the importance of moonlight in coral broadcast mass spawning. eLife 4:e09991. Covered by: eLife Cover Story, eLife Insight Mass spawning: Sex under the moon,, BBC radio *Equal contribution

2016    Rainy N, Etzion T, Alon S, Pomeranz A, Nisgav Y, Livnat T, Bach M, Gerstner CD, Baehr W, Gothilf Y, Stiebel-Kalish H. Unc119c knockdown results in visual impairment and early-onset retinal dystrophy in zebrafish. Biochemical and Biophysical Research Communications. 473:1211-1217. 

2016    Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES. Nanoscale Imaging of RNA with Expansion Microscopy. Nature Methods, 13:679–684. 

2016    Ben-Moshe Z, Alon S, Vallone D, Bayleyen Y, Tovin A, Shainer I, Nisembaum LG, Aviram I, Smadja SS, Fuentes M, Falcón J, Eisenberg E, Klein DC, Burgess HA , Foulkes NS, Gothilf Y. Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior. PLOS Genetics, 12(11): e1006445.

2017 Porath HT, Schaffer A, Kaniewska P, Alon S, Eisenberg E, Rosenthal J, Levanon EY, Levy O. A-to-I RNA editing in the earliest-diverging eumetazoan phyla. Molecular Biology and Evolution, msx125.

2017 Liscovitch-Brauer N, Alon S, Porath HT, Elstein B, Unger R, Ziv T, Admon A, Levanon EY, Rosenthal JJC, Eisenberg E. Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods. Cell, 169:191–202. Covered by: Cell Journal Cover, Nature, Nature Reviews GeneticsNew York Times, Washington Post, Daily MailScientific American, WIREDThe Atlantic and more.