ד"ר שחר אלון

ראשי מעבדות מחקר
טלפון
דוא"ל
shaharalon.mail@gmail.com
    קורות חיים

    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)
    Page 2
    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.
    Page 3
    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
    Page 4
    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.
    Page 5
    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.
    Page 6
    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.

    תאריך עדכון אחרון : 06/08/2023