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David MacAlpine

Professor of Pharmacology and Cancer Biology
Pharmacology & Cancer Biology
Duke Box 3813, Durham, NC 27710
LSRC C333, Durham, NC 27710

Selected Publications


Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.

Journal Article Genome Res · January 5, 2026 Epigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the genome. Despite numerous studies focusing on changes in gene expression, the intricate ... Full text Link to item Cite

DNA mutagenesis driven by transcription factor competition with mismatch repair.

Journal Article Cell · October 2, 2025 Despite the remarkable fidelity of eukaryotic DNA replication, nucleotide misincorporation errors occur in every replication cycle, generating mutations that drive genetic diseases and genome evolution. Here, we show that transcription factor (TF) proteins ... Full text Link to item Cite

Spt6-Spn1 interaction is required for RNA polymerase II association and precise nucleosome positioning along transcribed genes.

Journal Article J Biol Chem · May 2025 Spt6-Spn1 is an essential histone chaperone complex that associates with RNA Polymerase II (RNAPII) and reassembles nucleosomes during gene transcription. While the interaction between Spt6 and Spn1 is important for its histone deposition and transcription ... Full text Link to item Cite

Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase.

Journal Article Genome Res · December 27, 2023 Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2 tetramers as part of the replication ... Full text Link to item Cite

Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins.

Journal Article Genes (Basel) · December 16, 2021 Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle-dependent manner. The assembly of the pre-replicative complex in G1 and the pre-initiation complex prior to activation in S phase are well characteri ... Full text Link to item Cite

Disruption of origin chromatin structure by helicase activation in the absence of DNA replication.

Journal Article Genes Dev · October 1, 2021 Prior to initiation of DNA replication, the eukaryotic helicase, Mcm2-7, must be activated to unwind DNA at replication start sites in early S phase. To study helicase activation within origin chromatin, we constructed a conditional mutant of the polymeras ... Full text Link to item Cite

RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data.

Journal Article Nucleic Acids Res · August 20, 2021 Chromatin is a tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and occupancy levels of d ... Full text Link to item Cite

Stochastic initiation of DNA replication across the human genome.

Journal Article Mol Cell · July 15, 2021 Wang et al. (2021) comprehensively map DNA replication initiation events across the human genome using single-molecule optical resolution mapping and find that initiation events are randomly distributed across broad initiation zones that are only utilized ... Full text Link to item Cite

Linking the dynamics of chromatin occupancy and transcription with predictive models.

Journal Article Genome Res · June 2021 Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins-including histones ... Full text Link to item Cite

Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication.

Journal Article Genome Res · May 2021 We interrogated at nucleotide resolution the spatiotemporal order of chromatin changes that occur immediately following a site-specific double-strand break (DSB) upstream of the PHO5 locus and its subsequent repair by nonhomologous end joining (NHEJ). We o ... Full text Link to item Cite

RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy.

Conference Res Comput Mol Biol · May 2020 Chromatin is the tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and level of occupancy ... Full text Link to item Cite

Capturing the primordial Kras mutation initiating urethane carcinogenesis.

Journal Article Nat Commun · April 14, 2020 The environmental carcinogen urethane exhibits a profound specificity for pulmonary tumors driven by an oncogenic Q61L/R mutation in the gene Kras. Similarly, the frequency, isoform, position, and substitution of oncogenic RAS mutations are often unique to ... Full text Link to item Cite

Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork.

Journal Article Genome Res · July 2019 Proper regulation and maintenance of the epigenome is necessary to preserve genome function. However, in every cell division, the epigenetic state is disassembled and then reassembled in the wake of the DNA replication fork. Chromatin restoration on nascen ... Full text Link to item Cite

Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats.

Journal Article PLoS Genet · May 2019 Repetitive DNA sequences within eukaryotic heterochromatin are poorly transcribed and replicate late in S-phase. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ... Full text Link to item Cite

Correction to: DNA copy number evolution in Drosophila cell lines.

Journal Article Genome Biol · March 11, 2019 Following publication of the original article [1], the authors reported the following errors. ... Full text Link to item Cite

Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila.

Journal Article Genome Res · November 2018 Chromatin structure has emerged as a key contributor to spatial and temporal control over the initiation of DNA replication. However, despite genome-wide correlations between early replication of gene-rich, accessible euchromatin and late replication of ge ... Full text Link to item Cite

Nucleosomes influence multiple steps during replication initiation.

Journal Article Elife · March 21, 2017 Eukaryotic replication origin licensing, activation and timing are influenced by chromatin but a mechanistic understanding is lacking. Using reconstituted nucleosomal DNA replication assays, we assessed the impact of nucleosomes on replication initiation. ... Full text Link to item Cite

Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization.

Journal Article Nucleic Acids Res · March 17, 2017 DNA replication requires the recruitment of a pre-replication complex facilitated by Origin Recognition Complex (ORC) onto the chromatin during G1 phase of the cell cycle. The ORC-associated protein (ORCA/LRWD1) stabilizes ORC on chromatin. Here, we evalua ... Full text Link to item Cite

Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila.

Journal Article Nucleic Acids Res · September 6, 2016 The methylation state of lysine 20 on histone H4 (H4K20) has been linked to chromatin compaction, transcription, DNA repair and DNA replication. Monomethylation of H4K20 (H4K20me1) is mediated by the cell cycle-regulated histone methyltransferase PR-Set7. ... Full text Link to item Cite

ORChestrating the human DNA replication program.

Journal Article Proc Natl Acad Sci U S A · August 16, 2016 Full text Link to item Cite

DNA replication origins-where do we begin?

Journal Article Genes Dev · August 1, 2016 For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) base ... Full text Link to item Cite

Noncoding Transcription Is a Driving Force for Nucleosome Instability in spt16 Mutant Cells.

Journal Article Mol Cell Biol · July 1, 2016 FACT (facilitates chromatin transcription) consists of two essential subunits, Spt16 and Pob3, and functions as a histone chaperone. Mutation of spt16 results in a global loss of nucleosomes as well as aberrant transcription. Here, we show that the majorit ... Full text Link to item Cite

Chromatin determinants of origin selection and activation

Chapter · January 1, 2016 DNA replication is an essential cell cycle-regulated process necessary for the accurate duplication of the genome. DNA replication begins at cis-acting replicator loci (replication origins) that are distributed throughout each of the eukaryotic chromosomes ... Full text Cite

Mcm2-7 Is an Active Player in the DNA Replication Checkpoint Signaling Cascade via Proposed Modulation of Its DNA Gate.

Journal Article Mol Cell Biol · June 2015 The DNA replication checkpoint (DRC) monitors and responds to stalled replication forks to prevent genomic instability. How core replication factors integrate into this phosphorylation cascade is incompletely understood. Here, through analysis of a unique ... Full text Link to item Cite

SnapShot: Origins of DNA replication.

Journal Article Cell · April 9, 2015 The fundamental unit of DNA replication, the replicon, is governed by a cis-acting replicator sequence and a trans-activating initiator factor. Despite the increased size and complexity of eukaryotic genomes, eukaryotic DNA replication continues to be guid ... Full text Link to item Cite

Dynamic loading and redistribution of the Mcm2-7 helicase complex through the cell cycle.

Journal Article EMBO J · February 12, 2015 Eukaryotic replication origins are defined by the ORC-dependent loading of the Mcm2-7 helicase complex onto chromatin in G1. Paradoxically, there is a vast excess of Mcm2-7 relative to ORC assembled onto chromatin in G1. These excess Mcm2-7 complexes exhib ... Full text Link to item Cite

Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly.

Journal Article Genes Dev · January 15, 2015 Start sites of DNA replication are marked by the origin recognition complex (ORC), which coordinates Mcm2-7 helicase loading to form the prereplicative complex (pre-RC). Although pre-RC assembly is well characterized in vitro, the process is poorly underst ... Full text Link to item Cite

Rare codons capacitate Kras-driven de novo tumorigenesis.

Journal Article J Clin Invest · January 2015 The KRAS gene is commonly mutated in human cancers, rendering the encoded small GTPase constitutively active and oncogenic. This gene has the unusual feature of being enriched for rare codons, which limit protein expression. Here, to determine the effect o ... Full text Link to item Cite

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.

Journal Article Genome Res · November 2014 Mutational heterogeneity must be taken into account when reconstructing evolutionary histories, calibrating molecular clocks, and predicting links between genes and disease. Selective pressures and various DNA transactions have been invoked to explain the ... Full text Link to item Cite

Comparative analysis of metazoan chromatin organization.

Journal Article Nature · August 28, 2014 Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our unde ... Full text Link to item Cite

DNA copy number evolution in Drosophila cell lines.

Journal Article Genome Biol · August 28, 2014 BACKGROUND: Structural rearrangements of the genome resulting in genic imbalance due to copy number change are often deleterious at the organismal level, but are common in immortalized cell lines and tumors, where they may be an advantage to cells. In orde ... Full text Link to item Cite

DNA replication and transcription programs respond to the same chromatin cues.

Journal Article Genome Res · July 2014 DNA replication is a dynamic process that occurs in a temporal order along each of the chromosomes. A consequence of the temporally coordinated activation of replication origins is the establishment of broad domains (>100 kb) that replicate either early or ... Full text Link to item Cite

Chromatin and DNA replication.

Journal Article Cold Spring Harb Perspect Biol · August 1, 2013 The size of a eukaryotic genome presents a unique challenge to the cell: package and organize the DNA to fit within the confines of the nucleus while at the same time ensuring sufficient dynamics to allow access to specific sequences and features such as g ... Full text Link to item Cite

Rare codons regulate KRas oncogenesis.

Journal Article Curr Biol · January 7, 2013 Oncogenic mutations in the small Ras GTPases KRas, HRas, and NRas render the proteins constitutively GTP bound and active, a state that promotes cancer. Ras proteins share ~85% amino acid identity, are activated by and signal through the same proteins, and ... Full text Link to item Cite

Identification of E2F target genes that are rate limiting for dE2F1-dependent cell proliferation.

Journal Article Dev Dyn · November 2012 BACKGROUND: Microarray studies have shown that the E2F transcription factor influences the expression of many genes but it is unclear how many of these targets are important for E2F-mediated control of cell proliferation. RESULTS: We assembled a collection ... Full text Link to item Cite

Genome-wide localization of replication factors.

Journal Article Methods · June 2012 Chromatin Immunoprecipitation (ChIP) is a powerful tool for the identification and characterization of protein-DNA interactions in vivo. ChIP has been utilized to study diverse nuclear processes such as transcription regulation, chromatin modification, DNA ... Full text Link to item Cite

Developmental control of gene copy number by repression of replication initiation and fork progression.

Journal Article Genome Res · January 2012 Precise DNA replication is crucial for genome maintenance, yet this process has been inherently difficult to study on a genome-wide level in untransformed differentiated metazoan cells. To determine how metazoan DNA replication can be repressed, we examine ... Full text Link to item Cite

Epigenome characterization at single base-pair resolution.

Journal Article Proc Natl Acad Sci U S A · November 8, 2011 We have combined standard micrococcal nuclease (MNase) digestion of nuclei with a modified protocol for constructing paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the ... Full text Link to item Cite

Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression.

Journal Article Genes Dev · July 1, 2011 In metazoans, how replication origins are specified and subsequently activated is not well understood. Drosophila amplicons in follicle cells (DAFCs) are genomic regions that undergo rereplication to increase DNA copy number. We identified all DAFCs by com ... Full text Link to item Cite

Defining the replication program through the chromatin landscape.

Journal Article Crit Rev Biochem Mol Biol · April 2011 DNA replication is an essential cell cycle event required for the accurate and timely duplication of the chromosomes. It is essential that the genome is replicated accurately and completely within the confines of S-phase. Failure to completely copy the gen ... Full text Link to item Cite

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Journal Article Nature · March 24, 2011 Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melan ... Full text Link to item Cite

A cis-regulatory map of the Drosophila genome.

Journal Article Nature · March 24, 2011 Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elemen ... Full text Link to item Cite

Chromatin signatures of the Drosophila replication program.

Journal Article Genome Res · February 2011 Featured Publication DNA replication initiates from thousands of start sites throughout the Drosophila genome and must be coordinated with other ongoing nuclear processes such as transcription to ensure genetic and epigenetic inheritance. Considerable progress has been made to ... Full text Link to item Cite

Developmental control of the DNA replication and transcription programs.

Journal Article Genome Res · February 2011 Polyploid or polytene cells, which have more than 2C DNA content, are widespread throughout nature and present in most differentiated Drosophila tissues. These cells also can display differential replication, that is, genomic regions of increased or decrea ... Full text Link to item Cite

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Journal Article Science · December 24, 2010 Featured Publication To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal p ... Full text Link to item Cite

Preferential re-replication of Drosophila heterochromatin in the absence of geminin.

Journal Article PLoS Genet · September 9, 2010 Featured Publication To ensure genomic integrity, the genome must be duplicated exactly once per cell cycle. Disruption of replication licensing mechanisms may lead to re-replication and genomic instability. Cdt1, also known as Double-parked (Dup) in Drosophila, is a key regul ... Full text Link to item Cite

The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin.

Journal Article Genes Dev · July 1, 2010 The origin recognition complex (ORC) binds to the specific positions on chromosomes that serve as DNA replication origins. Although ORC is conserved from yeast to humans, the DNA sequence elements that specify ORC binding are not. In particular, metazoan O ... Full text Link to item Cite

Conserved nucleosome positioning defines replication origins.

Journal Article Genes Dev · April 15, 2010 Featured Publication The origin recognition complex (ORC) specifies replication origin location. The Saccharomyces cerevisiae ORC recognizes the ARS (autonomously replicating sequence) consensus sequence (ACS), but only a subset of potential genomic sites are bound, suggesting ... Full text Link to item Cite

Expression in aneuploid Drosophila S2 cells.

Journal Article PLoS Biol · February 23, 2010 Featured Publication Extensive departures from balanced gene dose in aneuploids are highly deleterious. However, we know very little about the relationship between gene copy number and expression in aneuploid cells. We determined copy number and transcript abundance (expressio ... Full text Open Access Link to item Cite

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.

Journal Article Genome Res · February 2010 Featured Publication The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved in all eukaryotes. In Saccharomyces cerevisiae, ORC binds to specific DNA elements; however, in higher eukaryotes, ORC exhibits little sequence specificity in ... Full text Link to item Cite

Co-orientation of replication and transcription preserves genome integrity.

Journal Article PLoS Genet · January 15, 2010 In many bacteria, there is a genome-wide bias towards co-orientation of replication and transcription, with essential and/or highly-expressed genes further enriched co-directionally. We previously found that reversing this bias in the bacterium Bacillus su ... Full text Open Access Link to item Cite

Unlocking the secrets of the genome.

Journal Article Nature · June 18, 2009 Featured Publication UNLABELLED: Despite the successes of genomics, little is known about how genetic information produces complex organisms. A look at the crucial functional elements of fly and worm genomes could change that. SUPPLEMENTARY INFORMATION: The online version of t ... Full text Link to item Cite

Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila.

Journal Article EMBO J · December 12, 2007 Post-translational modifications of histones are involved in transcript initiation and elongation. Methylation of lysine 36 of histone H3 (H3K36me) resides promoter distal at transcribed regions in Saccharomyces cerevisiae and is thought to prevent spuriou ... Full text Link to item Cite

Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells.

Journal Article Genes Dev · November 15, 2007 Featured Publication Myb-MuvB (MMB)/dREAM is a nine-subunit complex first described in Drosophila as a repressor of transcription, dependent on E2F2 and the RBFs. Myb, an integral member of MMB, curiously plays no role in the silencing of the test genes previously analyzed. Mo ... Full text Link to item Cite

Drosophila follicle cell amplicons as models for metazoan DNA replication: a cyclinE mutant exhibits increased replication fork elongation.

Journal Article Proc Natl Acad Sci U S A · October 23, 2007 Featured Publication Gene clusters amplified in the ovarian follicle cells of Drosophila serve as powerful models for metazoan DNA replication. In response to developmental signals, specific genomic regions undergo amplification by repeated firing of replication origins and bi ... Full text Link to item Cite

Genome-wide analysis of re-replication reveals inhibitory controls that target multiple stages of replication initiation.

Journal Article Mol Biol Cell · May 2006 Featured Publication DNA replication must be tightly controlled during each cell cycle to prevent unscheduled replication and ensure proper genome maintenance. The currently known controls that prevent re-replication act redundantly to inhibit pre-replicative complex (pre-RC) ... Full text Link to item Cite

Temporal profile of replication of human chromosomes.

Journal Article Proc Natl Acad Sci U S A · May 3, 2005 Featured Publication Chromosomes in human cancer cells are expected to initiate replication from predictably localized origins, firing reproducibly at discrete times in S phase. Replication products obtained from HeLa cells at different stages of S phase were hybridized to cDN ... Full text Link to item Cite

A genomic view of eukaryotic DNA replication.

Journal Article Chromosome Res · 2005 Featured Publication Recent advances in DNA microarray technology have enabled eukaryotic replication to be studied at whole-chromosome and genome-wide levels. These studies have provided new insights into the mechanisms that influence origin selection and the temporally co-or ... Full text Link to item Cite

Coordination of replication and transcription along a Drosophila chromosome.

Journal Article Genes Dev · December 15, 2004 Featured Publication The mechanisms by which metazoan origins of DNA replication are defined, regulated, and influenced by chromosomal events remain poorly understood. To gain insights into these mechanisms, we developed a systematic approach using a Drosophila high-resolution ... Full text Link to item Cite

The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote.

Journal Article Genes Dev · June 1, 2004 Featured Publication The covalent modification of nucleosomal histones has emerged as a major determinant of chromatin structure and gene activity. To understand the interplay between various histone modifications, including acetylation and methylation, we performed a genome-w ... Full text Link to item Cite

Visualization of replication initiation and elongation in Drosophila.

Journal Article J Cell Biol · October 28, 2002 Featured Publication Chorion gene amplification in the ovaries of Drosophila melanogaster is a powerful system for the study of metazoan DNA replication in vivo. Using a combination of high-resolution confocal and deconvolution microscopy and quantitative realtime PCR, we foun ... Full text Link to item Cite

Replication and preferential inheritance of hypersuppressive petite mitochondrial DNA.

Journal Article EMBO J · April 2, 2001 Wild-type yeast mitochondrial DNA (mtDNA) is inherited biparentally, whereas mtDNA of hypersuppressive petite mutants is inherited uniparentally in crosses to strains with wild-type mtDNA. Genomes of hypersuppressive petites contain a conserved ori sequenc ... Full text Link to item Cite

The numbers of individual mitochondrial DNA molecules and mitochondrial DNA nucleoids in yeast are co-regulated by the general amino acid control pathway.

Journal Article EMBO J · February 15, 2000 Mitochondrial DNA (mtDNA) is inherited as a protein-DNA complex (the nucleoid). We show that activation of the general amino acid response pathway in rho(+) and rho(-) petite cells results in an increased number of nucleoids without an increase in mtDNA co ... Full text Link to item Cite

The high mobility group protein Abf2p influences the level of yeast mitochondrial DNA recombination intermediates in vivo.

Journal Article Proc Natl Acad Sci U S A · June 9, 1998 Abf2p is a high mobility group (HMG) protein found in yeast mitochondria that is required for the maintenance of wild-type (rho+) mtDNA in cells grown on fermentable carbon sources, and for efficient recombination of mtDNA markers in crosses. Here, we show ... Full text Link to item Cite

Developmental regulation of DNA replication: replication fork barriers and programmed gene amplification in Tetrahymena thermophila.

Journal Article Mol Cell Biol · October 1997 The palindromic Tetrahymena ribosomal DNA (rDNA) minichromosome is amplified 10,000-fold during development. Subsequent vegetative replication is cell cycle regulated. rDNA replication differs fundamentally in cycling vegetative and nondividing amplifying ... Full text Link to item Cite

Type I elements mediate replication fork pausing at conserved upstream sites in the Tetrahymena thermophila ribosomal DNA minichromosome.

Journal Article Mol Cell Biol · August 1997 Two-dimensional gel electrophoresis was used to study replication of the Tetrahymena thermophila ribosomal DNA (rDNA) minichromosome. During vegetative growth, the rDNA is replicated exclusively from origins in the 5' nontranscribed spacer (NTS). Whereas r ... Full text Link to item Cite

How Maize Seeds and Seedlings Cope with Oxygen Deficit

Journal Article HortScience · October 1995 Full text Cite

Differential induction of mRNAs for the glycolytic and ethanolic fermentative pathways by hypoxia and anoxia in maize seedlings.

Journal Article Plant Physiol · December 1994 Fructose-1,6-biphosphate aldolase (ALD) and enolase (ENO) from the glycolytic pathway and pyruvate decarboxylase (PDC) and alcohol dehydrogenase 2 (ADH2) from the ethanolic fermentative pathway, are enzymes previously identified as among those synthesized ... Full text Link to item Cite