2023A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping modelGolov AK, Gavrilov AA, Kaplan N*, Razin SV*bioRxivFull text
2023KMD clustering: robust general-purpose clustering of biological dataZelig A*, Kariti H*, Kaplan NCommunications BiologyFull text
2023Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartmentsKariti H, Feld T, Kaplan NNucleic Acids ResearchFull text
2022Recruitment of transcriptional effectors by Cas9 creates cis regulatory elements and demonstrates distance-dependent transcriptional regulationBoulos J, Ehrlich I, Avidan N, Shkedi O, Haimovich-Caspi L, Kaplan N, Kehat IbioRxivFull text
2020Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and FunctionMcCoord RP, Kaplan N, Giorgetti LMolecular CellFull text
2019Attenuated chromatin compartmentalization in meiosis and its maturation in sperm developmentAlavattam KG, Maezawa S, Sakashita A, Khoury H, Barski A, Kaplan N*, Namekawa SH*Nature Structural & Molecular BiologyFull text
2018Genome organization and DNA accessibility control antigenic variation in trypanosomesMüller 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 TNNaturePubMed
2018Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patternsJavasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A, Simon IGenome ResearchPubMed
2018Three invariant Hi-C interaction patterns: applications to genome assemblyOddes S, Zelig A, Kaplan NMethodsPubMed
2016Structural organization of the inactive X chromosome in the mouseGiorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker JNaturePubMed
2015DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genomeBeh LY*, Müller MM, Muir TW, Kaplan N*, Landweber LF*Genome ResearchPubMed
2015The Hitchhiker's guide to Hi-C analysis: practical guidelinesLajoie BR, Dekker J, Kaplan NMethodsPubMed
2013High-throughput genome scaffolding from in vivo DNA interaction frequencyKaplan N, Dekker JNature BiotechnologyPubMed
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2012New insights into replication origin characteristics in metazoansCayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, Méchali MCell CyclePubMed
2010Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodologyKaplan N, Hughes TR, Lieb JD, Widom J, Segal EGenome BiologyPubMed
2010Nucleosome sequence preferences influence in vivo nucleosome organizationKaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Hughes TR, Lieb JD, Widom J, Segal ENature Structural & Molecular BiologyPubMed
2010High nucleosome occupancy is encoded at human regulatory sequencesTillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TRPLoS OnePubMed
2009Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organizationField Y, Fondufe-Mittendorf Y, Moore IK, Mieczkowski P, Kaplan N, Lubling Y, Lieb JD, Widom J, Segal ENature GeneticsPubMed
2009The DNA-encoded nucleosome organization of a eukaryotic genomeKaplan N*, Moore IK*, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal ENaturePubMed
2008Distinct modes of regulation by chromatin encoded through nucleosome positioning signalsField Y*, Kaplan N*, Fondufe-Mittendorf Y*, Moore IK, Sharon E, Lubling Y, Widom J, Segal EPLoS Computational BiologyPubMed
2007Novel families of toxin-like peptides in insects and mammals: a computational approachKaplan N, Morpurgo N, Linial MJournal of Molecular BiologyPubMed
2006Insights into social insects from the genome of the honeybee Apis melliferaHoneybee Genome Sequencing ConsortiumNaturePubMed
2006ProtoBee: hierarchical classification and annotation of the honey bee proteomeKaplan N, Linial MGenome ResearchPubMed
2006Functional annotation prediction: all for one and one for allSasson O*, Kaplan N*, Linial MProtein SciencePubMed
2005Automatic detection of false annotations via binary property clusteringKaplan N, Linial MBMC BioinformaticsPubMed
2005ProtoNet 4.0: a hierarchical classification of one million protein sequencesKaplan N, Sasson O, Inbar U, Friedlich M, Fromer M, Fleischer H, Portugaly E, Linial N, Linial MNucleic Acids ResearchPubMed
2004A functional hierarchical organization of the protein sequence spaceKaplan N, Friedlich M, Fromer M, Linial MBMC BioinformaticsPubMed
2003PANDORA: keyword-based analysis of protein sets by integration of annotation sourcesKaplan N, Vaaknin A, Linial MNucleic Acids ResearchPubMed