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Selected Publications

2021     Alon  S*, Goodwin DR*, Sinha A*, Wassie AT*, Chen F*, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao C-C, Suk H-J, Wang R, Yu C-C, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rosen RO, Regev A, IMAXT Consortium, Church GM, Marblestone AH, Boyden ES. Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems. Science, Vol. 371, Issue 6528, eaax2656. *Equal contribution. [Full Text] [Supplementary Materials

Covered by: Nature Methods, NatureNIH Director's Blog, GenomeWeb, BusinessWire, GEN, The Jerusalem Post,, MIT news, SpectrumRNA-Seq, Times of Israel, GLZ radio (Hebrew), KAN radio (Hebrew) and more.


2018     Alon S*, Huynh GH*, Boyden ES. Expansion Microscopy: Enabling Single Cell Analysis In Intact Biological Systems. FEBS Journal. *Equal contribution. 

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 Genetics, New York Times, Washington Post, Daily Mail, Scientific American, WIRED, The Atlantic and more. 


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. 

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, NHGRI, NSF, and more. 

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     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, 10.7554/eLife.09991. *Equal contribution.

Covered by eLife Insight: ‘Sex under the moon’, and more.


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.


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      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 ChangesJ Immunol. 189:4890-4899. Appear in the 'Issue Highlights' section.

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.


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.

Granted Patents

2021      Chen F, Payne AC, Buenrostro JD, Reginato P, Boyden ES, Alon SIn situ ATAC sequencing. US Patent No. 11180804. 

2021      Chen F, Wassie A, Alon S, Marblestone AH, Sinha A, Payne A, Boyden ES. Multiplexed Signal Amplified FISH via Splinted Ligation
Amplification and Sequencing
US Patent No. 10995361.

2020      Alon S, Chen F, Payne A, Wassie A, Goodwin D, Boyden ES. Augmenting In Situ Nucleic Acid Sequencing of Expanded Biological Samples with In Vitro Sequence Information. US Patent No. 10526649.


2019      Wassie A, Chen F, Boyden ES, Alon S. Nanoscale Imaging of Proteins and Nucleic Acids via Expansion Microscopy. US Patent No. 10364457.


2018      Alon S, Boyden ES, Chen F, Church GM, Daugharthy E, Marblestone A, Tillberg PW. In situ nucleic acid sequencing of expanded biological samples. US patent No. 10059990.

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