Selected Publications - Full list at Google Scholar

Ten Hacken E et al. Convergent evolutionary paths and therapeutic vulnerabilities revealed by in vivo modeling of CLL clonal heterogeneity and transformation to Richter syndrome. Blood Cancer Discovery, accepted.

Parry E et al. Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome,
Nature Medicine, accepted.

​

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. PDF
Nature Genetics, 2022.

Gutierrez C et al.
Multi-functional barcoding with ClonMapper enables high resolution study of clonal dynamics during tumor evolution and treatment.
Nature Cancer, 2021.

Ouspenskaia T et al.
Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer.

Nature Biotechnology, 2021.

Barak M et al.
Selection Against Long dsRNA Structures is the First Line of Defense Against False Activation of Innate Immunity. Genome Biology, 2020.

Ray DA, et al.
Simultaneous TE analysis of 19 Heliconiine butterflies yields novel insights into rapid TE-based genome diversification and multiple SINE births and deaths.

Gen Biol Evol, 2019.

Jacob-Hirsch J et al. 
Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders.
2018. Cell Research, 10.1038/cr.2018.8.

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.

Porath HT et al.
Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance. 2017.
Genome Biology, 18, 185.

Kipper S et al.
Control and Automation of Multilayered Integrated Microfluidic Device Fabrication.
Lab Chip, 2017,17, 557-566.

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.

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.

Knisbacher BA, Gerber D, Levanon EY.
DNA editing by APOBECs: a genomic preserver and transformer.
Trends in Genetics 2016, 32(1), 16–28. (Review)

Paz-Yaacov N, et al.
Elevated RNA Editing Activity Is a Major Contributor to Transcriptomic Diversity in Tumors.
Cell Rep 2015, 13:267–76.

Knisbacher BA, Levanon EY.
DNA and RNA editing of retrotransposons accelerate mammalian genome evolution.
Ann N Y Acad Sci 2015, 1341:115–25. (Review)

Fang X, et al. 
Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.
Nature Communications 2014, 5:3966.

Lindič N, et al.
Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins.
Retrovirology 2013, 10:156.