A J Klar

National Institutes of Health, Bethesda, MD, United States

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Publications (104)1116.15 Total impact

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    Amar J S Klar
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    ABSTRACT: Both budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccahromyces pombe have been very popular organisms used for biological research with eukaryotes for many decades. Judging from the fission yeast Schizosaccharomyces japonicus DNA sequence determined two years ago, this species is evolutionarily very much unrelated to the commonly used yeasts for research. Indicating evolutionary divergence, the S. japonicus makes 8-spored asci and mitosis occurs with a partial breakdown of nuclear membrane while the other yeasts make 4-spored asci and cells divide without nuclear breakdown. The commonly used yeast species exhibit a generation time between 1.5 and 2.0 hours and their genetic cross takes a period of over seven working days. As described here, a generation time of only 63 minutes and meiotic analysis completed in just 2.5 days, the S. japonicus fission yeast is predicted to become a choice organism for future research on the biology of eukaryotes.
    G3-Genes Genomes Genetics 08/2013; · 1.79 Impact Factor
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    Amar J S Klar, Michael J Bonaduce
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    ABSTRACT: The base complementarity feature (Watson and Crick in Nature 171(4356):737-738, 1953) and the rule of semi-conservative mode of DNA replication (Messelson and Stahl in Proc Natl Acad Sci U S A 44:671-682, 1958) dictate that two identical replicas of the parental chromosome are produced during replication. In principle, the inherent strand sequence differences could generate nonequivalent daughter chromosome replicas if one of the two strands were epigenetically imprinted during replication to effect silencing/expression of developmentally important genes. Indeed, inheritance of such a strand- and site-specific imprint confers developmental asymmetry to fission yeast sister cells by a phenomenon called mating/cell-type switching. Curiously, location of DNA strands with respect to each other at the centromere is fixed, and as a result, their selected segregation to specific sister chromatid copies occurs in eukaryotic cells. The yeast system provides a unique opportunity to determine the significance of such biased strand distribution to sister chromatids. We determined whether the cylindrical-shaped yeast cell distributes the specific chromosomal strand to the same cellular pole in successive cycles of cell division. By observing the pattern of recurrent mating-type switching in progenies of individual cells by microscopic analyses, we found that chromosome 2 strands are distributed by the random mode in successive cell divisions. We also exploited unusual "hotspot" recombination features of this system to investigate whether there is selective segregation of strands such that oldest Watson-containing strands co-segregate in the diploid cell at mitosis. Our data suggests that chromosome 2 strands are segregated independently to those of the homologous chromosome.
    Chromosome Research 05/2013; 21(3):297-309. · 2.85 Impact Factor
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    ABSTRACT: Sister chromatids contain identical DNA sequence but are chiral with respect to both their helical handedness and their replication history. Emerging evidence from various model organisms suggests that certain stem cells segregate sister chromatids nonrandomly to either maintain genome integrity or to bias cellular differentiation in asymmetric cell divisions. Conventional methods for tracing of old vs. newly synthesized DNA strands generally lack resolution for individual chromosomes and employ halogenated thymidine analogs with profound cytotoxic effects on rapidly dividing cells. Here, we present a modified chromosome orientation fluorescence in situ hybridization (CO-FISH) assay, where identification of individual chromosomes and their replication history is achieved in subsequent hybridization steps with chromosome-specific DNA probes and PNA telomere probes. Importantly, we tackle the issue of BrdU cytotoxicity and show that our method is compatible with normal mouse ES cell biology, unlike a recently published related protocol. Results from our CO-FISH assay show that mitotic segregation of mouse chromosome 7 is random in ES cells, which contrasts previously published results from our laboratory and settles a controversy. Our straightforward protocol represents a useful resource for future studies on chromatid segregation patterns of in vitro-cultured cells from distinct model organisms.
    Chromosome Research 05/2013; 21(3):311-28. · 2.85 Impact Factor
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    Chuanhe Yu, Michael J Bonaduce, Amar J S Klar
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    ABSTRACT: A key question in developmental biology addresses the mechanism of asymmetric cell division. Asymmetry is crucial for generating cellular diversity required for development in multicellular organisms. As one of the potential mechanisms, chromosomally borne epigenetic difference between sister cells that changes mating/cell-type has been demonstrated only in the Schizosaccharomyces pombe fission yeast. For technical reasons, it is nearly impossible to determine the existence of such a mechanism operating during embryonic development of multicellular organisms. Our work addresses whether such an epigenetic mechanism causes asymmetric cell division in the recently sequenced fission yeast, Schizosaccharomyces japonicus (with 36% GC content), which is highly diverged from the well-studied S. pombe species (with 44% GC content). We find that the genomic location and DNA sequences of the mating-type loci of S. japonicus differ vastly from those of the S.pombe species. Remarkably however, similar to S. pombe, the S. japonicus cells switch cell/mating type after undergoing two consecutive cycles of asymmetric cell divisions: only one among four "granddaughter" cells switches. The DNA-strand-specific epigenetic imprint at the mating-type locus1 initiates the recombination event, which is required for cellular differentiation. Therefore the S. pombe and S. japonicus mating systems provide the first two examples in which the intrinsic chirality of double helical structure of DNA forms the primary determinant of asymmetric cell division. Our results show that this unique strand-specific imprinting /segregation epigenetic mechanism for asymmetric cell division is evolutionary conserved. Motivated by these findings, we speculate that DNA-strand-specific epigenetic mechanisms might have evolved to dictate asymmetric cell division in diploid, higher eukaryotes as well.
    Genetics 11/2012; · 4.39 Impact Factor
  • Barbara A Stewart, Amar J S Klar
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    ABSTRACT: Bronchoscopic evaluations revealed that some children have double branching of bronchi (designated "doublets") in the lower lungs airways, rather than normal, single branching. Retrospective analyses revealed only one commonality in them: all subjects with doublets also had autism or autism spectrum disorder (ASD). That is, 49 subjects exhibited the presence of initial normal anatomy in upper airway followed by doublets in the lower airway. In contrast, the normal branching pattern was noted in all the remaining 410 subjects who did not have a diagnosis of autism/ASD. We propose that the presence of doublets might be an objective, reliable, and valid biologic marker of autism/ASD.
    Journal of Autism and Developmental Disorders 08/2012; · 3.06 Impact Factor
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    Chuanhe Yu, Michael J Bonaduce, Amar J S Klar
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    ABSTRACT: A novel mating-type switching-defective mutant showed a highly unstable rearrangement at the mating-type locus (mat1) in fission yeast. The mutation resulted from local amplification of a 134-bp DNA fragment by the mat1-switching phenomenon. We speculate that the rolling-circle-like replication and homologous recombination might be the general mechanisms for local genome region expansion.
    Genetics 02/2012; 191(1):285-9. · 4.39 Impact Factor
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    Stephan Sauer, Amar J S Klar
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    ABSTRACT: Ever since cloning the classic iv (inversedviscerum) mutation identified the "left-right dynein" (lrd) gene in mice, most research on body laterality determination has focused on its function in motile cilia at the node embryonic organizer. This model is attractive, as it links chirality of cilia architecture to asymmetry development. However, lrd is also expressed in blastocysts and embryonic stem cells, where it was shown to bias the segregation of recombined sister chromatids away from each other in mitosis. These data suggested that lrd is part of a cellular mechanism that recognizes and selectively segregates sister chromatids based on their replication history: old "Watson" versus old "Crick" strands. We previously proposed that the mouse left-right axis is established via an asymmetric cell division prior to/or during gastrulation. In this model, left-right dynein selectively segregates epigenetically differentiated sister chromatids harboring a hypothetical "left-right axis development 1" ("lra1") gene during the left-right axis establishing cell division. Here, asymmetry development would be ultimately governed by the chirality of the cytoskeleton and the DNA molecule. Our model predicts that randomization of chromatid segregation in lrd mutants should produce embryos with 25% situs solitus, 25% situs inversus, and 50% embryonic death due to heterotaxia and isomerism. Here we confirmed this prediction by using two distinct lrd mutant alleles. Other than lrd, thus far Nodal gene is the most upstream function implicated in visceral organs laterality determination. We next tested whether the Nodal gene constitutes the lra1 gene hypothesized in the model by testing mutant's effect on 50% embryonic lethality observed in lrd mutants. Since Nodal mutation did not suppress lethality, we conclude that Nodal is not equivalent to the lra1 gene. In summary, we describe the origin of 50% lethality in lrd mutant mice not yet explained by any other laterality-generating hypothesis.
    Frontiers in Oncology 01/2012; 2:166.
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    Chuanhe Yu, Michael J Bonaduce, Amar J S Klar
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    ABSTRACT: Schizosaccharomyces pombe, the fission yeast, cells alternate between P- and M-mating type, controlled by the alternate alleles of the mating-type locus (mat1). The mat1 switching occurs by replacing mat1 with a copy derived from a silenced "donor locus," mat2P or mat3M. The mechanism of donor choice ensuring that switching occurs primarily and productively to the opposite type, called directionality, is largely unknown. Here we identified the mat1-Mc gene, a mammalian sex-determination gene (SRY) homolog, as the primary gene that dictates directionality in M cells. A previously unrecognized, shorter swi2 mRNA, a truncated form of the swi2, was identified, and its expression requires the mat1-Mc function. We also found that the abp1 gene (human CENPB homolog) controls directionality through swi2 regulation. In addition, we implicated a cis-acting DNA sequence in mat2 utilization. Overall, we showed that switching directionality is controlled by judicious expression of two swi2 transcripts through a cell-type-regulated dual promoter. In this respect, this regulation mechanism resembles that of the Drosophila sex-determination Slx gene.
    Genetics 12/2011; 190(3):977-87. · 4.39 Impact Factor
  • Amar J S Klar
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    ABSTRACT: The majority of breast cancer cases seen in women remain unexplained by simple Mendelian genetics. It is generally hypothesized that such non-familial, so-called sporadic cases, result from exposure of the affected individuals to a cancer-causing environment and/or from stochastic cell biological errors. Clearly, adverse environment exposure can cause disease, but is that necessarily the cause of most sporadic cases? Curiously, female breast cancer patients who were selected to prefer right-hand-use reportedly exhibited a higher incidence of reversed-brain hemispheric laterality when compared to that of the public at large. Notably, such a higher level of hemispheric reversal is also found in healthy, left-handed or ambidextrous persons. Based on the association between these disparate traits, a new hypothesis for the etiology of sporadic breast cancer cases is advanced here; breast cancer predisposition and brain laterality development likely share a common genetic cause.
    Breast disease 09/2011; 33(1):49-52.
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    Amar J S Klar
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    ABSTRACT: It has been 33 years since I first presented results of genetic experiments that established the gene transposition model as the mechanism of mating-type switching in the budding yeast Saccharomyces cerevisiae at the Cold Spring Harbor Laboratory (CSHL) Yeast Genetics meeting in August 1977. Over two decades ago the Genetics Perspectives editors solicited a perspective on my participation in the studies that deciphered the mechanism of mating-type switching and revealed the phenomenon of gene silencing in yeast. Although flattered at the time, I thought that preparation of such an article called for a more seasoned researcher who had benefitted from seeing his contributions stand the test of time. Now realizing that our discovery of the transposition of a mutation from the HMα locus into the MAT (mating type) locus has provided the genetic evidence that established the gene transposition model, and having witnessed our conclusions confirmed by subsequent molecular studies, I decided that perhaps this is a good time to recount the chronology of events as they unfolded for me decades ago.
    Genetics 10/2010; 186(2):443-9. · 4.39 Impact Factor
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    Amar J S Klar
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    ABSTRACT: “The two big problems — the nature of development and the nature of the mind — are being subdued. I don’t know whether there will be beautiful, general theories to come out of this — something really nice like Watson and Crick’s double helix — or whether there will be an accumulation of more and more details. I’ll confess to a secret hope for the former” (Crow 2000).
    Journal of Biosciences 03/2010; 35(1):11-5. · 1.76 Impact Factor
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    ABSTRACT: The asymmetric cell division process is required for cellular differentiation and embryonic development. Recent evidence obtained in Drosophila and C. elegans suggest that this process occurs by non-equivalent distribution of proteins or mRNA (intrinsic factors) to daughter cells, or by their differential exposure to cell extrinsic factors. In contrast, haploid fission yeast sister cells developmentally differ by inheriting sister chromatids that are differentiated by epigenetic means. Specifically, the act of DNA replication at the mating-type locus in yeast switches it's alternate alleles only in one specific member of chromosome 2 sister chromatids in nearly every chromosome replication cycle. To employ this kind of mechanism for cellular differentiation, strictly based on Watson-Crick structure of DNA in diploid organism, selective segregation mechanism is required to coordinate distribution of potentially differentiated sister chromatids to daughter cells. Genetic evidence to this postulate was fortuitously provided by the analysis of mitotic recombinants of chromosome 7 in mouse cells. Remarkably, the biased segregation occurs in some cell types but not in others and the process seems to be chromosome-specific. This review summarizes the discovery of selective chromatid segregation phenomenon and it suggests that such a process of Somatic Sister chromatid Imprinting and Selective chromatid Segregation (SSIS model) might explain development in eukaryotes, such as that of the body axis left-right visceral organs laterality specification in mice.
    Current opinion in cell biology 12/2009; 22(1):81-7. · 14.15 Impact Factor
  • Amar J S Klar
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    ABSTRACT: Because the features of clockwise versus anti-clockwise orientation of hair-whorl coiling developed on a person's scalp is (partially, albeit significantly) correlated with that individual's right- versus left-hand-use preference (i.e., handedness) in the US and British subjects, these traits have been recently suggested to be determined biologically and through a common genetic mechanism. Here I report results of a serendipitously made observation with the Japanese population that helps to scrutinize validity of partial correlation between these attributes and to ascertain whether the underlying gene's frequency variations exist in different gene pools. Surprisingly, the whorl orientation in the Japanese individuals was found to be random, although their handedness variation is similar to that of the US population. Therefore, the whorl orientation trait is not genetically determined in the Japanese population. This result supports the idea that separate decisions must be made during embryogenesis for developing handedness and hair-whorl features at least in Japanese individuals. A recent study found the lack of association between whorl orientation and handedness in the German population, yet previous studies suggested that their scalp hair orientation is genetically determined. Therefore, pronounced genetic variation for the hair-whorl trait exists between individuals of different geographical regions. As hand preference exhibits "complex correlation" with brain hemispheric functional specialization, implications of these findings are discussed here with the goal to define biology of brain hemispheric laterality determination.
    Seminars in Cell and Developmental Biology 12/2008; 20(4):510-3. · 6.20 Impact Factor
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    ABSTRACT: The molecular mechanisms mediating eukaryotic replication termination and pausing remain largely unknown. Here we present the molecular characterization of Rtf1 that mediates site-specific replication termination at the polar Schizosaccharomyces pombe barrier RTS1. We show that Rtf1 possesses two chimeric myb/SANT domains: one is able to interact with the repeated motifs encoded by the RTS1 element as well as the elements enhancer region, while the other shows only a weak DNA binding activity. In addition we show that the C-terminal tail of Rtf1 mediates self-interaction, and deletion of this tail has a dominant phenotype. Finally, we identify a point mutation in Rtf1 domain I that converts the RTS1 element into a replication barrier of the opposite polarity. Together our data establish that multiple protein DNA and protein-protein interactions between Rtf1 molecules and both the repeated motifs and the enhancer region of RTS1 are required for site-specific termination at the RTS1 element.
    Genetics 09/2008; 180(1):27-39. · 4.39 Impact Factor
  • Gurjeet Singh, Amar J S Klar
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    ABSTRACT: The mat2,3-region of Schizosaccharomyces pombe is flanked by two inverted repeat elements, IRL and IRR, which define the boundaries of the silent domain resulting from heterochromatin assembly in the region. We employed a genetic screen to isolate factors whose mutations allowed spreading of heterochromatin across boundary elements. Surprisingly, this screen revealed that mutations in the genes required for deoxyribonucleotide biosynthesis, cdc22 (encoding the large subunit of ribonucleotide reductase) and tds1 (putative thymidylate synthase), cause silencing of marker genes inserted outside of the silent domain. Chromatin-immunoprecipitation analysis showed that histone H3 lysine 9 methylation modification, an epigenetic mark associated with gene silencing, is enriched by two- to three-fold in the cdc22 mutant as compared to the level found in the wild-type strain in regions outside the silent domain. The spreading of heterochromatin across barriers required functional Atf1/Pcr1, ATF-CREB family proteins, but not the RNA-interference Dcr1, Ago1, or Rdp1 factors, previously implicated in silencing. These results implicate the deoxyribonucleotide biosynthesis pathway in limiting epigenetic controls at barrier elements at the mating-type region, but the mechanism remains unknown.
    Yeast 03/2008; 25(2):117-28. · 1.96 Impact Factor
  • Amar J S Klar
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    ABSTRACT: The somatic DNA strand-specific imprinting to effect gene regulation and selective chromatid segregation model was previously proposed to produce developmentally nonequivalent sister cells in mitosis. Such a mechanism might explain generation of stem-cell pattern of cell division in eukaryotes. The developmentally controlled process involves a pair of homologous chromosomes at a specific cell division to establish embryonic left-right body axis asymmetry. As a result, visceral organs in the two sides of vertebrate's body develop asymmetrically. The model was specifically proposed to explain the well-known axis randomization phenotype of the left-right dynein mutant mice where one-half of animals develop with standard visceral organ's positioning and the balance develops with the inverted arrangement. The model postulated that the specific dynein, a microtubule-based molecular motor protein, promotes the selective chromatid segregation process in mitosis. Thus, random segregation involving sister chromatids of a pair of specific chromosomes leads to axis randomization of the mutant. Moreover, the model uniquely predicts that 50 percent mutant embryos should produce symmetrical cell divisions because of random segregation; consequently, their either visceral side would develop as mirror image of the other side resulting in embryonic lethality. In view of this prediction, validity of prominent body axis-determination models is scrutinized here. Results supporting the cell-type regulated chromosome 6 and chromosome 7 selective chromatids segregation phenomenon existing in mouse cells are reviewed. Published results with the mutant mice are consistent with the chromosome segregation model for axis determination.
    Breast disease 02/2008; 29:47-56.
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    Gurjeet Singh, Amar J S Klar
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    ABSTRACT: Despite extensive effort for many years, the etiology of major psychiatric diseases remains unknown. A recent study by Baysal et al. has argued against the ALG9 gene variants in causing psychosis. Due to its disruption by a balanced t(9p24;11q23) translocation that segregates with the disorder in a family, it was proposed to be a primary candidate gene causing psychosis. In addition, a recent review article by Pickard et al., entitled "Cytogenetics and gene discovery in psychiatric disorders," highlighted the importance of studies of chromosome rearrangements in finding disease-causing mutations. However, achieving the goal of finding genes by conventional association studies and by investigating chromosome rearrangements remains elusive. Here we discuss a fundamentally different explanation from the usual one considered by workers in the field concerning chromosome aberrations and psychoses etiology. We hypothesize how chromosome aberrations might cause disease but the gene at the rearrangement breakpoint is irrelevant for the etiology. Moreover, we discuss subsequently published findings that help scrutinize validity of the two very different hypotheses considered in the psychiatric genetics field. In sum, we alert the readers to the complexities of interpreting phenotypes associated with rearrangements.
    Genetics 11/2007; 177(2):1259-62. · 4.39 Impact Factor
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    ABSTRACT: Schizosaccharomyces pombe cells can switch between two mating types, plus (P) and minus (M). The change in cell type occurs due to a replication-coupled recombination event that transfers genetic information from one of the silent-donor loci, mat2P or mat3M, into the expressed mating-type determining mat1 locus. The mat1 locus can as a consequence contain DNA encoding either P or M information. A molecular mechanism, known as synthesis-dependent strand annealing, has been proposed for the underlying recombination event. A key feature of this model is that only one DNA strand of the donor locus provides the information that is copied into the mat1. Here we test the model by constructing strains that switch using two different mutant P cassettes introduced at the donor loci, mat2 and mat3. We show that in such strains wild-type P-cassette DNA is efficiently generated at mat1 through heteroduplex DNA formation and repair. The present data provide an in vivo genetic test of the proposed molecular recombination mechanism.
    Genetics 10/2007; 177(1):255-65. · 4.39 Impact Factor
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    Athanasios Armakolas, Amar J S Klar
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    ABSTRACT: During cell division, copies of mouse chromosome 7 are segregated selectively or randomly to daughter cells depending on the cell type. The mechanism for differential segregation is unknown. Because mouse left-right dynein (LRD) gene mutations result in randomization of visceral organs' laterality, we hypothesized that LRD may also function in selective chromatid segregation. Indeed, upon knock-down by RNA interference methods, LRD depletion disrupts biased segregation. LRD messenger RNA presence or absence correlates with the observed segregation patterns. This work supports the claim that LRD functions in a mechanism for selective chromatid segregation.
    Science 02/2007; 315(5808):100-1. · 31.20 Impact Factor
  • Amar J S Klar
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    ABSTRACT: Stably maintaining specific states of gene expression during cell division is crucial for cellular differentiation. In fission yeast, such patterns result from directed gene rearrangements and chromosomally inherited epigenetic gene control mechanisms that control mating cell type. Recent advances have shown that a specific DNA strand at the mat1 locus is "differentiated" by a novel strand-specific imprint so that nonequivalent sister chromatids are produced. Therefore, cellular differentiation is a natural consequence of the fact that DNA strands are complementary and nonequivalent. Another epigenetic control that "silences" library copies of mat-information is due to heterochromatin organization. This is a clear case where Mendel's gene is composed of DNA plus the associated epigenetic moiety. Following up on initial genetic studies with more recent molecular investigations, this system has become one of the prominent models to understand mechanisms of gene regulation, genome integrity, and cellular differentiation. By applying lessons learned from these studies, such epigenetic gene control mechanisms, which must be installed in somatic cells, might explain mechanisms of cellular differentiation and development in higher eukaryotes.
    Annual Review of Genetics 02/2007; 41:213-36. · 17.44 Impact Factor

Publication Stats

5k Citations
1,116.15 Total Impact Points

Institutions

  • 2002–2013
    • National Institutes of Health
      • • Gene Regulation and Chromosome Biology Laboratory
      • • Section on Developmental Genetics
      • • Center for Cancer Research
      Bethesda, MD, United States
  • 2012
    • St. Joseph's Hospital and Medical Center (AZ, USA)
      Phoenix, Arizona, United States
  • 1994–2012
    • Leidos Biomedical Research
      Maryland, United States
  • 2009
    • National and Kapodistrian University of Athens
      • Division of Experimental Physiology
      Athens, Attiki, Greece
  • 2001–2008
    • National Cancer Institute (USA)
      • • Center for Cancer Research
      • • Gene Regulation and Chromosome Biology Laboratory
      Bethesda, MD, United States
  • 2006
    • IT University of Copenhagen
      København, Capital Region, Denmark
  • 1998–2000
    • NCI-Frederick
      • Gene Regulation and Chromosome Biology Laboratory
      Maryland, United States
    • National Research and Education Network of India (ERNET)
      Bengalūru, Karnātaka, India
  • 1980–2000
    • Cold Spring Harbor Laboratory
      Cold Spring Harbor, New York, United States
  • 1977–1979
    • University of California, Berkeley
      Berkeley, California, United States