Assaf Gordon's Scientific Publications

1. Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing

   Timour Baslan, Jude Kendall, Konstantin Volyanskyy, Katherine McNamara, Hilary Cox, Sean D'Italia, Frank Ambrosio, Michael Riggs, Linda Rodgers, Anthony Leotta, Junyan Song, Yong Mao, Jie Wu, Ronak Shah, Rodrigo Gularte-Mérida, Kalyani Chadalavada, Gouri Nanjangud, Vinay Varadan, Assaf Gordon, Christina Curtis, Alex Krasnitz, Nevenka Dimitrova, Lyndsay Harris, Michael Wigler, James Hicks

   Elife 9:e51480 (May 2020)

   PMID: 32401198 DOI: 10.7554/eLife.51480
2. DNA.Land: A Digital Biobank Using A Massive Crowdsourcing Approach

   Jie Yuan*, Assaf Gordon*, Daniel Speyer, Richard Aufrichtig, Dina Zielinski, Joseph Pickrell, Yaniv Erlich
   * these authors equally contributed to this manuscript

   Nature Genetics volume 50, pages160–165 (2018)

   PMID: 29374253 DOI: 10.1038/s41588-017-0021-8
3. Quantitative analysis of population-scale family trees

   Joanna Kaplanis, Assaf Gordon, Mary Wahl, Michael Gershovits, Barak Markus, Mona Sheikh, Melissa Gymrek, Gaurav Bhatia, Daniel G MacArthur, Alkes Price, and Yaniv Erlich

   Science 13 Apr 2018: Vol. 360, Issue 6385, pp. 171-175

   DOI: 10.1126/science.aam9309
4. Rapid re-identification of human samples using portable DNA sequencing

   Sophie Zaaijer, Assaf Gordon, Daniel Speyer, Robert Piccone, Simon Cornelis Groen, Yaniv Erlich

   eLife 6:e27798 (Nov 2017)

   PMID: 29182147 DOI: 10.7554/eLife.27798
5. Genome-wide profiling of heritable and de novo STR variations

   Thomas Willems, Dina Zielinski, Assaf Gordon, Melissa Gymrek, and Yaniv Erlich

   Nature Methods 14, 590592 (2017). doi:10.1038/nmeth.4267 Epub 22-17 April 24

   PMID: 28436466
6. DNA Compass: a secure, client-side site for navigating personal genetic information

   Charles Curnin, Assaf Gordon, and Yaniv Erlich

   Bioinformatics, 2017. doi: 10.1093/bioinformatics/btx135 Epub 2017 March 11

   PMID: 28334237
7. Democratizing DNA fingerprinting

   Sophie Zaaijer, Assaf Gordon, Robert Piccone, Daniel Speyer, and Yaniv Erlich

   bioRxiv (pre-print). 2016
8. A Computational Algorithm to Predict shRNA Potency.

   Knott SR, Maceli AR, Erard N, Chang K, Marran K, Zhou X, Gordon A, El Demerdash O, Wagenblast E, Kim S, Fellmann C, Hannon GJ.

   Mol Cell. 2014 Dec 18;56(6):796-807. doi: 10.1016/j.molcel.2014.10.025. Epub 2014 Nov 26.

   PMID: 25435137 [PubMed - in process]
9. A Genome-Wide Survey of Sexually Dimorphic Expression of Drosophila miRNAs Identifies the Steroid Hormone-Induced miRNA let-7 as a Regulator of Sexual Identity.

   Fagegaltier D, König A, Gordon A, Lai EC, Gingeras TR, Hannon GJ, Shcherbata HR.

   Genetics. 2014 Oct;198(2):647-68. doi: 10.1534/genetics.114.169268. Epub 2014 Jul 31.

   PMID: 25081570
10. iPipet: sample handling using a tablet.

    Zielinski D, Gordon A, Zaks BL, Erlich Y.

    Nat Methods. 2014 Aug;11(8):784-5. doi: 10.1038/nmeth.3028.

    PMID: 25075904
11. An integrated encyclopedia of DNA elements in the human genome.

    ENCODE Project Consortium

    Nature. 2012 Sep 6;489(7414):57-74.

    PMID: 22955616
12. Landscape of transcription in human cells

    Djebali, Sarah, Davis, Carrie A. et al.

    Nature, 2012 Sep 6;489(7414):101-8.

    PMID: 22955620
13. Production of artificial piRNAs in flies and mice.

    Muerdter F, Olovnikov I, Molaro A, Rozhkov NV, Czech B, Gordon A, Hannon GJ, Aravin AA.

    RNA. 2012 Jan;18(1):42-52. doi: 10.1261/rna.029769.111. Epub 2011 Nov 17.

    PMID: 22096018
14. Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila.

    Haase AD, Fenoglio S, Muerdter F, Guzzardo PM, Czech B, Pappin DJ, Chen C, Gordon A, Hannon GJ.

    Genes Dev. 2010 Nov 15;24(22):2499-504. doi: 10.1101/gad.1968110. Epub 2010 Oct 21.

    PMID: 20966049
15. Manipulation of FASTQ data with Galaxy.

    Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team.

    Bioinformatics. 2010 Jul 15;26(14):1783-5.

    PMID: 20562416
16. Compressed Genotyping.

    Erlich Y, Gordon A, Brand M, Hannon GJ, Mitra PP.

    EEE Trans Inf Theory. 2010 Feb;56(2):706-723.

    PMID: 21451737
17. Hierarchical rules for Argonaute loading in Drosophila.

    Czech B, Zhou R, Erlich Y, Brennecke J, Binari R, Villalta C, Gordon A, Perrimon N, Hannon GJ.

    Mol Cell. 2009 Nov 13;36(3):445-56. doi: 10.1016/j.molcel.2009.09.028.

    PMID: 19917252
18. DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis.

    Erlich Y, Chang K, Gordon A, Ronen R, Navon O, Rooks M, Hannon GJ.

    Genome Res. 2009 Jul;19(7):1243-53. doi: 10.1101/gr.092957.109. Epub 2009 May 15.

    PMID: 19447965
19. Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs.

    Fejes-Toth K, Sotirova V, Sachidanandam R, Assaf G, Hannon GJ, Kapranov P, Foissac S, Willingham AT, Duttagupta R, Dumais E, Gingeras TR.

    Nature. 2009 Feb 19;457(7232):1028-32.

    PMID: 19169241