Dr. Binyamin Knisbacher

Email
binyamin.knisbacher@biu.ac.il
Research

Cancer Genomics and Immunogenomics 

The lab develops and applies computational tools to study DNA and RNA aberrations that drive cancer and how these produce novel therapeutic opportunities. The lab uses bioinformatics and machine learning methods to characterize alterations in cancer cells and advance precision medicine for cancer patients. Our expertise can be applied to any tumor type, but we have special interest in cancers arising from immune cells and specifically chronic lymphocytic leukemia (CLL), a common B-cell leukemia. Thus, on the intersection of cancer genomics and immunology, we study the relationship between cancerous and normal immune cells and use computational genomics to identify new targets for immunotherapy.

The lab is launching in October 2022! We are recruiting highly motivated individuals for all training stages – MSc, PhD and Postdocs. MDs or individuals from other fields with programming experience that are enthusiastic about bioinformatics are welcome to apply.

 

 

Publications
  1. Knisbacher BA*, Lin Z*, Hahn CK*, Nadeu F*, Duran-Ferrer F*, Stevenson KE, Tausch E, Delgado J, Barbera-Mourelle A, Taylor-Weiner A, Bousquets-Muñoz P, Diaz-Navarro A, Dunford A, Anand A, Kretzmer H, Gutierrez-Abril J, López-Tamargo S, Fernandes SM, Sun C, Sivina M, Rassenti LZ, Schneider C, Li S, Parida L, Meissner A, Aguet F, Burger JA, Wiestner A, Kipps TJ, Brown JR, Hallek M, Stewart C, Neuberg DS, Martín-Subero JI, Puente XS, Stilgenbauer S, Wu CJ, Campo E and Getz G. Molecular map of chronic lymphocytic leukemia and its impact on outcome. Nature Genetics, Accepted.
  2. Gutierrez C, Al’Khafaji AM, Brenner E, Johnson KE, Gohil SH, Lin Z, Knisbacher BA, Durrett RE, Li S, Parvin S, Biran A, Zhang W, Rassenti L, Kipps TJ, Livak KJ, Neuberg D, Letai A, Getz G, Wu CJ and Brock A. Multi-functional barcoding with ClonMapper enables high resolution study of clonal dynamics during tumor evolution and treatment. Nature Cancer, 2021.
  3. Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A. Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer. Nature Biotechnology, 2021.
  4. Barak M, Porath HT, Finkelstein G, Knisbacher BA, Buchumenski I, Roth SH, Levanon EY, Eisenberg E. Selection Against Long dsRNA Structures is the First Line of Defense Against False Activation of Innate Immunity. Genome Biology, 2020.
  5. Ray DA, Grimshaw JR, Halsey MK, Korstian JM, Osmanski AB, Sullivan KAM, Wolf KA, Reddy H, Foley N, Stevens RD, Knisbacher BA, Levy O, Counterman B, Edelman NB, Mallet J. Simultaneous TE analysis of 19 Heliconiine butterflies yields novel insights into rapid TE-based genome diversification and multiple SINE births and deaths. Genome Biology and Evolution, 2019.
  6. Jacob-Hirsch J, Eyal E, Knisbacher BA, Roth J, Cesarkas K, Dor C, Farage-Barhom S, Kunik V, Simon AJ, Gal M, et al.  Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders. 2018. Cell Research, 10.1038/cr.2018.8.
  7. Levy O*, Knisbacher BA*, Levanon EY and Havlin S. Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes. 2017. Science Advances, 3, e1701256.
  8. Porath HT, Knisbacher BA, Eisenberg E, Levanon EY. Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance. 2017. Genome Biology, 18, 185.
  9. Kipper S, Frolov L, Guy O, Pellach M, Glick Y, Malichi A, Knisbacher BA, et al. 2017. Control and Automation of Multilayered Integrated Microfluidic Device Fabrication. Lab on a Chip, 2017,17, 557-566.
  10. Li K*, Wang L*, Knisbacher BA*, Xu Q*, et al. Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax. PNAS 2016, doi:10.1073/pnas.1607497113.
  11. Knisbacher BA, Levanon EY. DNA editing of LTR retrotransposons reveals the impact of APOBECs on vertebrate genomes. Molecular Biology and Evolution 2016, 33(2), 554–67.
  12. Knisbacher BA, Gerber D, Levanon EY. DNA editing by APOBECs: a genomic preserver and transformer. Trends in Genetics 2016, 32(1), 16–28. (Review)
  13. Paz-Yaacov N, Bazak L, Buchumenski I, Porath HT, Danan-Gotthold M, Knisbacher BA, Eisenberg E, Levanon EY. Elevated RNA Editing Activity Is a Major Contributor to Transcriptomic Diversity in Tumors. Cell Reports 2015, 13:267–76.
  14. Knisbacher BA, Levanon EY. DNA and RNA editing of retrotransposons accelerate mammalian genome evolution. Ann N Y Acad Sci 2015, 1341:115–25. (Review)
  15. Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, Larkin D, Jiang X, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, Huang Z, Gorbunova V, Zhang L, Zhao W, Wildman DE, Xiong Y, Gudkov A, Zheng Q, Rechavi G, Liu S, Bazak L, Chen J, Knisbacher BA, et al. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications 2014, 5:3966.
  16. Lindič N, Budič M, Petan T, Knisbacher BA, Levanon EY, Lovšin N. Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins. Retrovirology 2013, 10:156.

Last Updated Date : 05/12/2022