Dr Emre Karakoc | Principal Bioinformatician

Karakoc, Emre

Emre is interested in the development of novel computational methods for the analysis of large-scale functional genomics datasets to understand the effects of the somatic variants in cancer evolution, development and response to therapies. He is also interested in the identifaciton of the key genetic dependencies in cancer and related therapeutic markers.

Emre completed his Ph.D. on Computer Science at Simon Fraser University, Canada on combinatorial algorithms, focusing on the development of novel algorithms for RNA structure prediction and functional clustering, with an application to the classification of biomolecules and small chemical compounds. During his postdoctoral studies at the University of Washington, he worked on structural variants and copy number variants in the context of complex diseases, such as Autism. Later in Max Planck Institute, he worked on evolutionary genetics and computational methods for admixture and introgression.

Publications

  • Dual-stressor selection alters eco-evolutionary dynamics in experimental communities.

    Hiltunen T, Cairns J, Frickel J, Jalasvuori M, Laakso J et al.

    Nature ecology & evolution 2018;2;12;1974-1981

  • Population size changes and selection drive patterns of parallel evolution in a host-virus system.

    Frickel J, Feulner PGD, Karakoc E and Becks L

    Nature communications 2018;9;1;1706

  • Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus.

    Harr B, Karakoc E, Neme R, Teschke M, Pfeifle C et al.

    Scientific data 2016;3;160075

  • The evolution and functional impact of human deletion variants shared with archaic hominin genomes.

    Lin YL, Pavlidis P, Karakoc E, Ajay J and Gokcumen O

    Molecular biology and evolution 2015;32;4;1008-19

  • ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

    Dao P, Numanagić I, Lin YY, Hach F, Karakoc E et al.

    Bioinformatics (Oxford, England) 2014;30;5;644-51

  • Transmission disequilibrium of small CNVs in simplex autism.

    Krumm N, O'Roak BJ, Karakoc E, Mohajeri K, Nelson B et al.

    American journal of human genetics 2013;93;4;595-606

  • Altered splicing of ATP6AP2 causes X-linked parkinsonism with spasticity (XPDS).

    Korvatska O, Strand NS, Berndt JD, Strovas T, Chen DH et al.

    Human molecular genetics 2013;22;16;3259-68

  • The bonobo genome compared with the chimpanzee and human genomes.

    Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR et al.

    Nature 2012;486;7404;527-31

  • Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.

    O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N et al.

    Nature 2012;485;7397;246-50

  • Insights into hominid evolution from the gorilla genome sequence.

    Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I et al.

    Nature 2012;483;7388;169-75

  • Detection of structural variants and indels within exome data.

    Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L et al.

    Nature methods 2011;9;2;176-8

  • Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.

    O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ et al.

    Nature genetics 2011;43;6;585-9

  • Dual-stressor selection alters eco-evolutionary dynamics in experimental communities.

    Hiltunen T, Cairns J, Frickel J, Jalasvuori M, Laakso J et al.

    Nature ecology & evolution 2018;2;12;1974-1981

  • Population size changes and selection drive patterns of parallel evolution in a host-virus system.

    Frickel J, Feulner PGD, Karakoc E and Becks L

    Nature communications 2018;9;1;1706

  • Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus.

    Harr B, Karakoc E, Neme R, Teschke M, Pfeifle C et al.

    Scientific data 2016;3;160075

  • The evolution and functional impact of human deletion variants shared with archaic hominin genomes.

    Lin YL, Pavlidis P, Karakoc E, Ajay J and Gokcumen O

    Molecular biology and evolution 2015;32;4;1008-19

  • ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

    Dao P, Numanagić I, Lin YY, Hach F, Karakoc E et al.

    Bioinformatics (Oxford, England) 2014;30;5;644-51

  • Transmission disequilibrium of small CNVs in simplex autism.

    Krumm N, O'Roak BJ, Karakoc E, Mohajeri K, Nelson B et al.

    American journal of human genetics 2013;93;4;595-606

  • Altered splicing of ATP6AP2 causes X-linked parkinsonism with spasticity (XPDS).

    Korvatska O, Strand NS, Berndt JD, Strovas T, Chen DH et al.

    Human molecular genetics 2013;22;16;3259-68

  • The bonobo genome compared with the chimpanzee and human genomes.

    Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR et al.

    Nature 2012;486;7404;527-31

  • Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.

    O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N et al.

    Nature 2012;485;7397;246-50

  • Insights into hominid evolution from the gorilla genome sequence.

    Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I et al.

    Nature 2012;483;7388;169-75

  • Detection of structural variants and indels within exome data.

    Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L et al.

    Nature methods 2011;9;2;176-8

  • Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.

    O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ et al.

    Nature genetics 2011;43;6;585-9

Karakoc, Emre