Dr. Shahar Alon

CURRICULUM VITAE
Shahar Alon
January 2020
Affiliation The Alexander Kofkin Faculty of Engineering,
The Gonda Brain Research Center,
The Institute for Nanotechnology and Advanced Materials,
Bar-Ilan University
& MIT Media Lab Research Affiliated
E-mail: shahar.alon@biu.ac.il
Mobile: +972-54-9304406; Office: +972-3-7384636
Personal Born Jul. 1979, Israeli Citizenship
Address HaTomer Street 25, Savyon, Israel, zip code 5654225
Education
2014-2019 Postdoctoral Fellow, Synthetic Neurobiology Group
Advisor: Prof. Ed Boyden. McGovern Institute for Brain Research,
Massachusetts Institute of Technology (MIT)
2016-2019 Howard Hughes Medical Institute Fellow of the Life Sciences
Research Foundation
2009-2014 Ph.D. in Neuroscience,
The Interdisciplinary Doctoral Program in Neuroscience for
Outstanding Students at Tel Aviv University.
Faculty of Life Sciences and School of Physics, Tel Aviv University.
Title: ‘Revealing new functional roles of RNA editing in the brain’
Advisors: Prof. Eli Eisenberg, School of Physics and Astronomy
Prof. Yoav Gothilf, Department of Neurobiology
2006-2008 M.Sc. in Neurobiology, Summa cum laude,
Faculty of Life Sciences and School of Physics, Tel Aviv University.
Title: ‘Genome-wide analysis of spatial and temporal expression in the
context of the circadian clock’
Advisors: Prof. Eli Eisenberg, School of Physics and Astronomy
Prof. Yoav Gothilf, Department of Neurobiology
1997-2000 B.Sc. The Department of Physics, Bar-Ilan University
Additional Scientific Experience
2012 Visitor Scientist, Harvard Medical School, Department of Genetics,
George Church lab (November 2012-January 2013)
2000-2005 Computational Physicist, Nuclear Research Center - Negev,
Department of Physics
Notable Academic Awards
2016-2019 Life Science Research Foundation Fellowship (~25 Ph.D. from all the
Life Sciences fields receive this scholarship in U.S. each year from
more than 1000 applicants)
2014-2016 Rothschild Postdoctoral Fellowship (12 Ph.D. from all STEM fields
receive this scholarship in Israel each year)
2011-2014 Clore Foundation Fellowship for Outstanding Scholars (10 Ph.D.
students from all STEM fields receive this scholarship in Israel each
year)
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Other Academic Awards
2014 Best Poster Award, First Sagol School of Neuroscience Retreat, Tel
Aviv University
2013 Adams Super Center Student Travel Grant, Tel Aviv University
2013 Best Publication Award, the Sagol School of Neuroscience, Tel Aviv
University
2012 Award for Excellence in Research, The George S. Wise Faculty of Life
Sciences, Tel Aviv University
2012 Best Poster Award, Seventh Edmond J. Safra Center for
Bioinformatics Retreat, Tel Aviv University
2011 Best Grant Proposal Award, the Sagol School of Neuroscience, Tel
Aviv University
2011 The Constantiner Institute for Molecular Genetics Travel Scholarship,
Tel Aviv University
2009-2011 The Dean Scholarship for Excellent Students, Tel Aviv University
2008 Award for 'trainees who have demonstrated exceptional research
success and potential through their presentation': Gordon Research
Conference on 'Pineal Cell Biology – Mechanisms of Circadian
Rhythmicity'
2008 Award for Excellence in Teaching and Research, Tel Aviv University
2008 M.Sc. Summa cum laude, Tel Aviv University
1998 Distinction award for B.Sc. students. The Department of Physics,
Bar-Ilan University
List of Publications (27 manuscripts, 1284 citations, h-index 19)
2018 Alon S*, Huynh GH*, Boyden ES. Expansion Microscopy: Enabling
Single Cell Analysis In Intact Biological Systems. Review Article.
FEBS Journal. *Equal contribution. Impact factor: 4.5.
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.
Impact factor: 30.4.
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.
Impact factor: 6.2.
2017 Cesarini V, Silvestris DA, Tassinari V, Tomaselli S, Alon S, Eisenberg
E, Locatelli F, Gallo A. ADAR2/miR-589-3p axis controls
glioblastoma cell migration/invasion. Nucleic Acids Research; doi:
10.1093/nar/gkx1257. Impact factor: 10.2.
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. Impact factor: 2.3.
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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. Impact factor: 25.1.
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. Impact factor: 6.1.
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, Phys.org and more. Impact factor: 7.7.
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. Impact factor:
11.9.
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. Impact factor: 7.3.
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. Impact factor: 4.2.
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,
10.7554/eLife.08638. Impact factor: 7.7.
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. Covered by
eLife Insight: ‘Sex under the moon’. *Equal contribution. Impact
factor: 7.7.
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. Impact factor: 10.2.
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. Impact factor: 11.3.
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. Impact factor: 4.2.
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
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Y. Systematic identification of rhythmic genes reveals camk1gb as a
new element in the circadian clockwork. PLOS Genetics,
8(12):e1003116. *Equal contribution. Impact factor: 6.1.
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.
Impact factor: 4.9.
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. Impact factor: 2.8.
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. Impact factor: 37.2.
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. Impact factor: 11.3.
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. Impact factor: 3.3.
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. Impact factor: 7.3.
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. Impact factor:
2.1.
Peer Reviewed Book Chapters
2015 Alon S, Eisenberg E. Using deep sequencing data for identification of
editing sites in mature miRNAs. Methods in Molecular Biology
1269:231-42.
2013 Alon S, Eisenberg E. Identifying RNA editing sites in miRNAs by
deep sequencing. Methods in Molecular Biology, 1038:159-170.
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. *Equal contribution.
Manuscript in final preparations
2019 Alon S, Goodwin D, Sinha A, Wassie A, Chen F, Daugharthy ER,
Bando Y, Kajita A, Marrett K, Wassie A, Payne AC, Sinha A, Suk HJ,
Wang R, Yu C-C, Tillberg P, Reginato P, Pak N, Kohman RE,
IMAXT Consortium, Church GM, Marblestone AH, Boyden ES.
Untargeted and targeted in situ transcriptomic sequencing in physically
expanded tissue. Was reviewed by Science and will be submitted again
soon.
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Granted Patents
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.
Patent Applications
2018 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 App. 15/876,347.
2018 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 App.
15/789,419.
2017 Wassie A, Chen F, Boyden ES, Alon S. Nanoscale Imaging of Proteins
and Nucleic Acids via Expansion Microscopy. US Patent App.
15/229,539.
Oral Presentations
2017 'Comprehensive in Situ Transcriptome Characterization Throughout
Intact Brain Circuits', NHGRI/NIH Centers of Excellence in Genomic
Science, Seattle, WA, October 3. Invited Speaker.
2016 ‘Expansion Sequencing (ExSEQ): Comprehensive In Situ
Transcriptome Characterization Throughout Intact Brain Circuits’,
Pittcon Conference, Atlanta, Georgia, March 10. Invited Speaker.
2016 ‘Expansion Microscopy & Expansion Sequencing’, Focus on
Microscopy Conference (FOM), Taipei, Taiwan, March 20. Invited
Speaker. Plenary Session.
2015 ‘ExSEQ: Expansion microscopy in-situ sequencing’, Physics of Brain
Activity Mapping III (PoBAM III), Massachusetts Institute of
Technology, February 25. Invited Speaker.
2015 'Expansion Sequencing (ExSEQ): Towards Comprehensive In Situ
Transcriptome Characterization Throughout Intact Brain Circuits’,
McGovern Institute Retreat, Falmouth, Massachusetts, May 31. Invited
Speaker.
2014 ‘Genome-wide measurements of the circadian clock’, Two lectures
given in a course at the Interuniversity Institute for Marine Sciences
‘Periodicity & Rhytmicity in Marine Ecosystems’, Eilat – Israel,
January 12-16.
2014 'New functional roles of RNA editing in the brain', Bar-Ilan University
– Israel, January 20.
2014 'Glass half full: on true understanding of the human brain, Barack
Obama, and beer', Lecture giving to the general audience as part of the
Wize project, Beer Garden, Tel Aviv – Israel, January 29.
2014 'Edited microRNA regulates daily locomotor rhythms in zebrafish',
FISEB/ILANIT Congress, Eilat – Israel, February 10-13.
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2012-2013 'High-Throughput methods in circadian biology', Lecture given in a
course at the Bar-Ilan University 'Biological Clocks', Bar-Ilan
University – Israel, May 13, 2012 and May 19, 2013.
2012 ‘Genome-wide measurements of the circadian clock’, Lecture given in
a course at the Interuniversity Institute for Marine Sciences
‘Periodicity & Rhytmicity in Marine Ecosystems’, Eilat – Israel,
January 8-13.
2012 'Editing of microRNAs in the human brain', SINS Congress 2012,
Catania - Italy, April 19-22. Invited Speaker.
2011 'Systematic identification of A-to-I editing in miRNAs', Gordon
Research Conference on 'RNA editing', Galveston, TX - USA, January
8-14.
2011 'Multiplexing in miRNA deep-sequencing: doing it wrong, doing it
right', the 3rd Annual TAU microRNA Consortium Conference, Tel
Aviv University – Israel, January 27.
2011 'Measuring the circadian clock', Lecture given in a course at the Bar-
Ilan University 'Biological Clocks', Bar-Ilan University - Israel, May 1.
2011 'Diving Deep into miRNAs: Identifying Editing Sites and Removing
Deep-Sequencing Biases', Sixth Edmond J. Safra Bioinformatics
Retreat, Hagoshrim – Israel, May 18-19.
2011 'Next Generation Sequencing of the Nematostella', Conference on
Nematostella as a model organism, Shadot Yam - Israel, December 4.
2011 'Systematic identification of edited miRNAs in the brain', the 4rd
Annual TAU microRNA Consortium Conference, Tel Aviv University
– Israel, December 18.
2010 ‘High-throughput multiplex sequencing of miRNA: bias and solution’,
Conference of the Institute of Biotechnology, Maalot – Israel, June 22-
24.
2010 ‘Using genome-wide tools for the analysis of the circadian clock’,
Lecture given in a course at the Interuniversity Institute for Marine
Sciences ‘Periodicity & Rhytmicity in Marine Ecosystems’, Eilat –
Israel, October 17-26.
2008 'In-silico identification and in-vivo validation of a new regulatory
element governing pineal-specific expression', Gordon Research
Conference on 'Pineal Cell Biology – Mechanisms of Circadian
Rhythmicity', Il Ciocco – Italy, April 20-25.
Teaching Experience and Additional Academic Activities
2016 Teaching Certificate from MIT Kaufman Teaching Certificate Program
2009-2018 Writing referee reports for Bioinformatics and Nucleic Acids Research.
2013-2014 Lecturer in the course 'Matlab Programming for Neuroscience' (over
100 registered students), Tel Aviv University.
2010-2012 Teaching assistant (TA) in the course 'Lab in Molecular Biology', Tel
Aviv University.
2008-2009 TA in the course 'Bioinformatics', Bar-Ilan University.
2008-2009 TA in the course 'Biochemistry', Bar-Ilan University.
2007 TA in the course 'Lab in Molecular Biology', Tel Aviv University.