| Year | Title | Authors | Journal | Links |
|---|---|---|---|---|
| 2023 | A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model | Golov AK, Gavrilov AA, Kaplan N*, Razin SV* | bioRxiv | Full text |
| 2023 | KMD clustering: robust general-purpose clustering of biological data | Zelig A*, Kariti H*, Kaplan N | Communications Biology | Full text |
| 2023 | Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments | Kariti H, Feld T, Kaplan N | Nucleic Acids Research | Full text |
| 2022 | Recruitment of transcriptional effectors by Cas9 creates cis regulatory elements and demonstrates distance-dependent transcriptional regulation | Boulos J, Ehrlich I, Avidan N, Shkedi O, Haimovich-Caspi L, Kaplan N, Kehat I | bioRxiv | Full text |
| 2020 | Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function | McCoord RP, Kaplan N, Giorgetti L | Molecular Cell | Full text |
| 2019 | Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development | Alavattam KG, Maezawa S, Sakashita A, Khoury H, Barski A, Kaplan N*, Namekawa SH* | Nature Structural & Molecular Biology | Full text |
| 2018 | Genome organization and DNA accessibility control antigenic variation in trypanosomes | Müller LSM, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba AE, Sebra RP, Siegel TN | Nature | PubMed |
| 2018 | Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns | Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A, Simon I | Genome Research | PubMed |
| 2018 | Three invariant Hi-C interaction patterns: applications to genome assembly | Oddes S, Zelig A, Kaplan N | Methods | PubMed |
| 2016 | Structural organization of the inactive X chromosome in the mouse | Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J | Nature | PubMed |
| 2015 | DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome | Beh LY*, Müller MM, Muir TW, Kaplan N*, Landweber LF* | Genome Research | PubMed |
| 2015 | The Hitchhiker's guide to Hi-C analysis: practical guidelines | Lajoie BR, Dekker J, Kaplan N | Methods | PubMed |
| 2013 | High-throughput genome scaffolding from in vivo DNA interaction frequency | Kaplan N, Dekker J | Nature Biotechnology | PubMed Nat. Rev. Genet. Nat. Methods |
| 2012 | New insights into replication origin characteristics in metazoans | Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, Méchali M | Cell Cycle | PubMed F1000 |
| 2010 | Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology | Kaplan N, Hughes TR, Lieb JD, Widom J, Segal E | Genome Biology | PubMed |
| 2010 | Nucleosome sequence preferences influence in vivo nucleosome organization | Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Hughes TR, Lieb JD, Widom J, Segal E | Nature Structural & Molecular Biology | PubMed |
| 2010 | High nucleosome occupancy is encoded at human regulatory sequences | Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR | PLoS One | PubMed |
| 2009 | Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization | Field Y, Fondufe-Mittendorf Y, Moore IK, Mieczkowski P, Kaplan N, Lubling Y, Lieb JD, Widom J, Segal E | Nature Genetics | PubMed F1000 |
| 2009 | The DNA-encoded nucleosome organization of a eukaryotic genome | Kaplan N*, Moore IK*, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E | Nature | PubMed F1000 |
| 2008 | Distinct modes of regulation by chromatin encoded through nucleosome positioning signals | Field Y*, Kaplan N*, Fondufe-Mittendorf Y*, Moore IK, Sharon E, Lubling Y, Widom J, Segal E | PLoS Computational Biology | PubMed |
| 2007 | Novel families of toxin-like peptides in insects and mammals: a computational approach | Kaplan N, Morpurgo N, Linial M | Journal of Molecular Biology | PubMed |
| 2006 | Insights into social insects from the genome of the honeybee Apis mellifera | Honeybee Genome Sequencing Consortium | Nature | PubMed F1000 |
| 2006 | ProtoBee: hierarchical classification and annotation of the honey bee proteome | Kaplan N, Linial M | Genome Research | PubMed |
| 2006 | Functional annotation prediction: all for one and one for all | Sasson O*, Kaplan N*, Linial M | Protein Science | PubMed |
| 2005 | Automatic detection of false annotations via binary property clustering | Kaplan N, Linial M | BMC Bioinformatics | PubMed |
| 2005 | ProtoNet 4.0: a hierarchical classification of one million protein sequences | Kaplan N, Sasson O, Inbar U, Friedlich M, Fromer M, Fleischer H, Portugaly E, Linial N, Linial M | Nucleic Acids Research | PubMed |
| 2004 | A functional hierarchical organization of the protein sequence space | Kaplan N, Friedlich M, Fromer M, Linial M | BMC Bioinformatics | PubMed |
| 2003 | PANDORA: keyword-based analysis of protein sets by integration of annotation sources | Kaplan N, Vaaknin A, Linial M | Nucleic Acids Research | PubMed Science |