Curriculum vitae

Jonas Ibn-Salem

Personal data

Date of birth

24.07.1987

Place of birth

Mamers (France)

Nationality

German

Education

2014–2018

PhD in Computational Biology, Johannes Gutenberg University Mainz and Institute of Molecular Biology (IMB), Mainz, Germany

2011–2014

MSc Bioinformatics, Freie Universität Berlin, Germany

2008–2011

BSc Bioinformatics, Freie Universität Berlin, Germany

1994–2007

Abitur (A level), Rudolf-Steiner-Schule Loheland, Fulda, Germany

Publications

  • Zepeda-Mendoza CJ*, Ibn-Salem J*, Kammin T, Harris DJ, Rita D, Gripp KW, MacKenzie JJ, Gropman A, Graham B, Shaheen R, Alkuraya FS, Brasington CK, Spence EJ, Masser-Frye D, Bird LM, Spiegel E, Sparkes RL, Ordulu Z, Talkowski ME, Andrade-Navarro MA, Robinson PN, Morton CC.
    Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements.
    Am J Hum Genet. 2017 Aug 3;101(2):206-217. doi: 10.1016/j.ajhg.2017.06.011.

  • Ibn-Salem J, Muro EM, Andrade-Navarro MA.
    Co-regulation of paralog genes in the three-dimensional chromatin architecture.
    Nucleic Acids Research 2017 Jan 9;45(1):81-91. doi: 10.1093/nar/gkw813.

  • Ibn-Salem, J., Meiers, S., Eigenbrod, O., Sehlke, R., Talyan, S., Schwahn, K., Otto, R., Pataskar, A., Metge, F., & Angerer, P.
    Highlights of the 1st Student Symposium on Computational Genomics.
    Genomics And Computational Biology. 2017 2(1), e59. doi:10.18547/gcb.2016.vol2.iss1.e59

  • Hansen P, Hecht J, Ibn-Salem J, Menkuec BS, Roskosch S, Truss M, Robinson PN.
    Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.
    BMC Genomics. 2016 Nov 4;17(1):873. https://doi.org/10.1186/s12864-016-3164-6  

  • Piacentino ML, Zuch DT, Fishman J, Rose S, Speranza EE, Li C, Yu J, Chung O, Ramachandran J, Ferrell P, Patel V, Reyna A, Hameeduddin H, Chaves J, Hewitt FB, Bardot E, Lee D, Core AB, Hogan JD, Keenan JL, Luo L, Coulombe-Huntington J, Blute TA, Oleinik E, Ibn-Salem J, Poustka AJ, Bradham CA.
    RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins.
    Development. 2016 Jan 11. doi: 10.1242/dev.129312  

  • Starick SR*, Ibn-Salem J*, Jurk M, Hernandez C, Love MI, Chung HR, Vingron M, Thomas-Chollier M, Meijsing SH.
    ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors.
    Genome Research. 2015 Jun;25(6):825-35. doi:10.1101/gr.185157.114

  • Köhler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA, Robinson PN.
    Clinical interpretation of CNVs with cross-species phenotype data.
    J Med Genet. 2014 Nov;51(11):766-772. doi: 10.1136/jmedgenet-2014-102633.

  • Ibn-Salem J*, Köhler S*, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN.
    Deletions of chromosomal regulatory boundaries are associated with congenital disease.
    Genome Biology. 2014 Sep 4;15(9):423. doi: 10.1186/s13059-014-0423-1.

* equal contributions

Preprints

  • Krefting J, Andrade-Navarro MA, Ibn-Salem J#.
    Evolutionary stability of topologically associating domains is associated with conserved gene regulation.
    bioRxiv. 2017. doi:10.1101/231431.

  • Ibn-Salem J#, Andrade-Navarro MA#.
    Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.
    bioRxiv. February 2018:257584. doi:10.1101/257584.

# corresponding author

Invited Talks

  • Imperial College London, MRC London Institute of Medical Sciences, 19 May. 2017, London, UK
    Title: Evolution of TADs and prediction of chromatin looping

  • Humboldt University Berlin, Humboldt University Berlin, 19 Dez. 2016, Berlin, Germany
    Title: ChIP-seq and related techniques to analyze protein-DNA interactions and predict chromatin looping interactions.

  • Max-Planck-Institute for Molecular Genetics, 04 Dez. 2015, Berlin, Germany
    Title: Co-regulation of paralog genes in the 3D chromatin architecture

Conference Presentations

  • Basel Computational Biology Conference BC\(^{2}\), 12-15 Sept 2017, Basel, Switzerland
    Title: Prediction of chromatin looping interactions from ChIP-seq profiles at CTCF motifs

  • ISCB European Student Council Symposium 2016, 3 Sept 2016, The Hauge, Netherlands
    Title: Prediction of Chromatin Looping Events

  • ISCB Student Council Symposium 2015, 10 July 2015, Dublin, Ireland
    Title: Co-regulation of human paralog genes in the three-dimensional chromatin architecture

Poster Presentations

  • 2017 IMB Conference: Gene Regulation by The Numbers, 19 - 21 June 2017, Mainz, Germany
    Title: Prediction of chromatin looping interactions from ChIP-seq profiles at CTCF motifs

  • 15th European Conference on Computational Biology, 4-7 Sept 2016, The Hauge, Netherlands
    Title: Co-regulation of paralog genes in the three-dimensional chromatin architecture

  • German Conference on Bioinformatics 2016, 12-15 Sept 2016, Berlin, Germany
    Title: Prediction of three-dimensional chromatin looping from sequence motifs and protein binding signals

  • EMBO Conference: From Functional Genomics to Systems Biology, 12-15 Nov 2016, Heidelberg, Germany
    Title: Three-dimensional chromatin looping predicted by CTCF motifs and ChIP-seq signals

  • RECOMB Comparative Genomics 2015, 04-07 Oct. 2015, Frankfurt, Germany
    Title: Co-regulation of paralog genes in the three-dimensional chromatin architecture

  • ISMB/ECCB Conference 2015, 12-14 July, Dublin, Ireland
    Title: Co-regulation of human paralog genes in the three-dimensional chromatin architecture

  • Regulatory Genomics Special Interest Group, 11 July 2015, Dublin, Ireland
    Title: Co-regulation of human paralog genes in the three-dimensional chromatin architecture

  • ISCB Student Council Symposium 2015, 10 July 2015, Dublin, Ireland
    Title: Co-regulation of human paralog genes in the three-dimensional chromatin architecture

  • Genome Regulation in 3D Conference, June 28-30, 2015, Rehovot, Israel
    Title: Co-regulation of human paralog genes in the three-dimensional chromatin architecture

  • German Conference on Bioinformatics 2014, Sept. 29 - Oct. 1, 2014, Bielefeld, Germany
    Title: Deletions of chromosomal regulatory boundaries are associated with congenital disease

  • Annual Meeting of the AGD 2014, Oct 10-11, Potsdam, Germany
    Title: Deletions of chromosomal regulatory boundaries are associated with congenital disease

Grants and Awards

  • Travel Grant from gsk Stiftung (350 EUR) for “`Genomic Regulation 2018”’ workshop, 15-18 March 2018, Nendaz, Switzerland.
  • Digital Future Scholarship free admission (900 EUR) to “`The Digital Future”’ conference on May 13th, 2017 in Berlin
  • Scientific Event Grant 3,500 Euro from Boehringer Ingelheim Stiftung for Student Symposium on Computational Genomics, Nov 30, 2016, Mainz
  • Scientific Meeting Grant 1,500 GBP (~1,750 EUR) from The Company of Biologists (EA1228) for Student Symposium on Computational Genomics, Nov 30, 2016, Mainz
  • Travel Fellowship Award for 4th ISCB European Student Council Symposium 2016, Sept 2016, The Hauge, Netherlands
  • Digital Future Scholarship free admission (900 EUR) to “`The Digital Future”’ conference on May 11th, 2016 in Berlin
  • F1000Research Poster Awards from ISMB/ECCB
  • Runner-up Poster Presentation Award form ISCB Student Council Symposium 2015
  • Travel Award to the Genome regulation in 3D meeting, June 28-30, Weizmann Institute of Science, Rehovot, Israel
  • Third poster price of Annual Meeting of the AGD 2014

Organizational Experience

  • Student Symposium on Computational Genomics, Nov 30, 2016, IMB, Mainz, Germany (main organizer and symposium chair)

Research Experience

Sep 2014 – Feb 2018

Research assistant and doctoral student, Johannes Gutenberg University Mainz and Institute of Molecular Biology (IMB), Mainz, Germany

May 2017 (for two weeks)

Lab visit, Imperial College London, London, UK. Invited by Boris Lehnert and Matthias Merkenschlager.
Computational analysis of gene expression and 3D genome organization upon knock-down of cohesin in mouse macrophages and thymocytes

Jun 2014 – August 2014

Research assistant, Computational Biology Group at Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin, Berlin, Germany.
Computational analysis of structural variations and phenotype associations.

Sep 2013 – Jun 2014

Student assistant (Master thesis project), Department Vingron at Max Planck Institute for Molecular Genetics, Berlin, Germany and Institut de Biologie de l’ Ecole Normale Superieure, Paris, France
Transcription factor binding profiles in ChIP-exo data

Apr 2013 – Dec 2013

Student assistant, Computational Biology Group at Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin, Berlin
Modeling the effect of genomic deletions of regulatory barriers in the chromatin structure on gene regulation and phenotypes.

Jan 2011 – Aug 2013

Student assistant, Max Planck Institute for Molecular Genetics, Department Lehrarch, Group: Evolution and Development, Berlin