D E Wildman

Summary

Affiliation: Wayne State University
Country: USA

Publications

  1. pmc Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation
    Zuogang Peng
    School of Biology, Institute of Bioscience and Bioengineering, Institute of Biosystems, Georgia Institute of Technology, Atlanta, GA 30332, USA
    BMC Genomics 10:247. 2009
  2. pmc Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees
    Donna M Toleno
    Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
    BMC Bioinformatics 10:77. 2009
  3. pmc Genomics, biogeography, and the diversification of placental mammals
    Derek E Wildman
    Perinatology Research Branch, National Institute of Child Health and Human Development National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 104:14395-400. 2007
  4. pmc Sources for comparative studies of placentation. II. Genomic resources
    D E Wildman
    Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
    Placenta 29:144-7. 2008
  5. pmc OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
    Guozhen Liu
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine Detroit, MI 48201, USA
    Source Code Biol Med 2:5. 2007
  6. doi request reprint A fully resolved genus level phylogeny of neotropical primates (Platyrrhini)
    Derek E Wildman
    Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, 540 E Canfield Ave, Detroit, MI 48201, USA
    Mol Phylogenet Evol 53:694-702. 2009
  7. pmc Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles
    Monica Uddin
    Center for Molecular Medicine and Genetics, Department of Anatomy and Cell Biology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 101:2957-62. 2004
  8. pmc Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates
    Timothy R Schmidt
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 102:6379-84. 2005
  9. pmc Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data
    Zhuo Cheng Hou
    Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development NIH DHHS, Detroit, MI 48201, USA
    Mol Phylogenet Evol 52:660-4. 2009
  10. ncbi request reprint Coadaptive evolution in cytochrome c oxidase: 9 of 13 subunits show accelerated rates of nonsynonymous substitution in anthropoid primates
    Jeffrey W Doan
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Mol Phylogenet Evol 33:944-50. 2004

Collaborators

Detail Information

Publications40

  1. pmc Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation
    Zuogang Peng
    School of Biology, Institute of Bioscience and Bioengineering, Institute of Biosystems, Georgia Institute of Technology, Atlanta, GA 30332, USA
    BMC Genomics 10:247. 2009
    ..Advances in genomics have the potential to alleviate the shortage of neutral markers. Here we present a method to develop numerous markers from putatively neutral regions of primate genomes...
  2. pmc Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees
    Donna M Toleno
    Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
    BMC Bioinformatics 10:77. 2009
    ..In this process, only data from oligonucleotide probes predicted to have robust hybridization sensitivity and specificity for both transcriptomes are retained for analysis...
  3. pmc Genomics, biogeography, and the diversification of placental mammals
    Derek E Wildman
    Perinatology Research Branch, National Institute of Child Health and Human Development National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 104:14395-400. 2007
    ..Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades...
  4. pmc Sources for comparative studies of placentation. II. Genomic resources
    D E Wildman
    Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
    Placenta 29:144-7. 2008
    ..Additionally, museums, zoos, and commercial entities are available to provide genomic resources to the placental research community. Recommendations for tissue storage conditions of placentas in genomic research are given...
  5. pmc OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
    Guozhen Liu
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine Detroit, MI 48201, USA
    Source Code Biol Med 2:5. 2007
    ..Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence...
  6. doi request reprint A fully resolved genus level phylogeny of neotropical primates (Platyrrhini)
    Derek E Wildman
    Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, 540 E Canfield Ave, Detroit, MI 48201, USA
    Mol Phylogenet Evol 53:694-702. 2009
    ..With a fully resolved platyrrhine phylogeny in place it is now possible to design and test hypotheses regarding the evolution and diversification of platyrrhine phenotypes and life histories...
  7. pmc Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles
    Monica Uddin
    Center for Molecular Medicine and Genetics, Department of Anatomy and Cell Biology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 101:2957-62. 2004
    ....
  8. pmc Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates
    Timothy R Schmidt
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 102:6379-84. 2005
    ..We suggest that reducing the electrostatic interaction between COX and CYC was part of the adaptive evolution underlying the emergence of anthropoid primates...
  9. pmc Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data
    Zhuo Cheng Hou
    Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development NIH DHHS, Detroit, MI 48201, USA
    Mol Phylogenet Evol 52:660-4. 2009
    ....
  10. ncbi request reprint Coadaptive evolution in cytochrome c oxidase: 9 of 13 subunits show accelerated rates of nonsynonymous substitution in anthropoid primates
    Jeffrey W Doan
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Mol Phylogenet Evol 33:944-50. 2004
  11. ncbi request reprint A map of the common chimpanzee genome
    Derek E Wildman
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E Canfield Ave, Detroit, MI 48201, USA
    Bioessays 24:490-3. 2002
    ..77%) between humans and chimpanzees, while highlighting intriguing areas of potential difference. If we wish to understand the genetic basis of humankind, the completion of the chimpanzee genome deserves high priority...
  12. pmc Molecular evolution of the cytochrome c oxidase subunit 5A gene in primates
    Monica Uddin
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit MI 48201, USA
    BMC Evol Biol 8:8. 2008
    ..Here, we test the hypothesis that COX5A, the ETC gene that encodes cytochrome c oxidase subunit 5A, shows a pattern of anthropoid-specific adaptive evolution, and investigate the distribution of this protein in catarrhine brains...
  13. pmc Severe preeclampsia is characterized by increased placental expression of galectin-1
    Nandor Gabor Than
    Perinatology Research Branch, NICHD, NIH, DHHS, Detroit, Michigan 48201, USA
    J Matern Fetal Neonatal Med 21:429-42. 2008
    ..To test this hypothesis, we studied placental galectin-1 mRNA and protein expression and localization in women with preeclampsia (PE) and in those who delivered a small-for-gestational age (SGA) neonate...
  14. pmc Chorioamnionitis and increased galectin-1 expression in PPROM --an anti-inflammatory response in the fetal membranes?
    Nandor Gabor Than
    Perinatology Research Branch, NICHD NIH DHHS, Wayne State University Hutzel Women s Hospital, 3990 John R, Box 4, Detroit, MI 48201, USA
    Am J Reprod Immunol 60:298-311. 2008
    ..Galectin-1 can regulate immune responses upon infection and inflammation. We determined galectin-1 expression in the chorioamniotic membranes and its changes during histological chorioamnionitis...
  15. pmc Emergence of hormonal and redox regulation of galectin-1 in placental mammals: implication in maternal-fetal immune tolerance
    Nandor Gabor Than
    Perinatology Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, and Department of Health and Human Services, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 105:15819-24. 2008
    ....
  16. pmc Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries
    Morris Goodman
    Center for Molecular Medicine and Genetics, Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 106:20824-9. 2009
    ....
  17. ncbi request reprint Mitochondrial evidence for the origin of hamadryas baboons
    Derek E Wildman
    Department of Anthropology, New York Univesity, USA
    Mol Phylogenet Evol 32:287-96. 2004
    ..The mitochondrial paraphyly of Ethiopian hamadryas and anubis (P. anubis) baboons suggests an extensive and complex history of sex-specific introgression...
  18. pmc Ancient origin of placental expression in the growth hormone genes of anthropoid primates
    Zack Papper
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 106:17083-8. 2009
    ..e., the roles played by placenta-expressed GHs in human pregnancy may have a longer evolutionary history than previously appreciated)...
  19. ncbi request reprint Accelerated evolution of the electron transport chain in anthropoid primates
    Lawrence I Grossman
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201, USA
    Trends Genet 20:578-85. 2004
    ..Two important questions are: (i) how has evolution altered ETC function? and; (ii) how might functional changes in the ETC be linked to evolution of an expanded neocortical brain?..
  20. ncbi request reprint Moving primate genomics beyond the chimpanzee genome
    Morris Goodman
    Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
    Trends Genet 21:511-7. 2005
    ..Some of these traits have been discovered recently, particularly in genes encoding proteins that are important for brain function...
  21. doi request reprint Comparative analysis of encephalization in mammals reveals relaxed constraints on anthropoid primate and cetacean brain scaling
    A M Boddy
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
    J Evol Biol 25:981-94. 2012
    ..We propose both neutral drift and selective factors may have played a role in the evolution of brain-body allometry...
  22. pmc Review: Toward an integrated evolutionary understanding of the mammalian placenta
    D E Wildman
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Placenta 32:S142-5. 2011
    ....
  23. pmc Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates
    Allon Goldberg
    Center for Molecular Medicine and Genetics and Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 100:5873-8. 2003
    ..We argue that these changes were linked to the evolution of an expanded neocortex in anthropoid primates...
  24. pmc Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo
    Derek E Wildman
    Center for Molecular Medicine and Genetics and Department of Anatomy and Cell Biology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 100:7181-8. 2003
    ....
  25. pmc The human progesterone receptor shows evidence of adaptive evolution associated with its ability to act as a transcription factor
    Caoyi Chen
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Mol Phylogenet Evol 47:637-49. 2008
    ..Positive selection provides the basis for the hypothesis that changes in structure and function of the progesterone receptor during evolution contribute to the diversity of primate reproductive biology, especially in parturition...
  26. pmc Over-expression of the thrombin receptor (PAR-1) in the placenta in preeclampsia: a mechanism for the intersection of coagulation and inflammation
    Offer Erez
    Perinatology Research Branch, NICHD, NIH, DHHS, Bethesda, Maryland, USA
    J Matern Fetal Neonatal Med 21:345-55. 2008
    ..The aim of this study was to determine whether preterm PE is associated with changes in placental expression of PAR-1...
  27. ncbi request reprint Rapid nonsynonymous evolution of the iron-sulfur protein in anthropoid primates
    Jeffrey W Doan
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E Canfield Avenue, Detroit, MI 48201, USA
    J Bioenerg Biomembr 37:35-41. 2005
    ..Nevertheless, we find that the catalytically active ISP has an accelerated rate of amino acid replacement in anthropoid primates whereas the catalytically inactive subunit 9 does not...
  28. pmc Evolution of the mammalian placenta revealed by phylogenetic analysis
    Derek E Wildman
    Perinatology Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 103:3203-8. 2006
    ..The influence of these factors on placental development needs further investigation...
  29. pmc Adaptive history of single copy genes highly expressed in the term human placenta
    Zhuocheng Hou
    Perinatology Research Branch, NICHD NIH DHHS Wayne State University, Detroit, MI 48201, USA
    Genomics 93:33-41. 2009
    ..Adaptations in genes highly expressed in human placenta are attractive candidates for functional and clinical studies...
  30. ncbi request reprint Molecular evolution of aerobic energy metabolism in primates
    L I Grossman
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
    Mol Phylogenet Evol 18:26-36. 2001
    ..Discovering the biochemical adaptations suggested by molecular evolutionary analysis will be an exciting challenge...
  31. ncbi request reprint Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates)
    Juan C Opazo
    Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
    Mol Phylogenet Evol 40:274-80. 2006
    ..Divergence time estimations using both local molecular clock and Bayesian approaches suggest the families diverged from one another over a short period of geological time in the late Oligocene-early Miocene...
  32. pmc Distinct genomic signatures of adaptation in pre- and postnatal environments during human evolution
    Monica Uddin
    Center for Molecular Medicine and Genetics and Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 105:3215-20. 2008
    ..Comparing adaptively evolving genes from pre- and postnatal-stage tissues suggests that different selective pressures act on the development vs. the maintenance of the human phenotype...
  33. pmc A primate subfamily of galectins expressed at the maternal-fetal interface that promote immune cell death
    Nandor Gabor Than
    Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 106:9731-6. 2009
    ....
  34. ncbi request reprint The phylogenetic history of New World monkey beta globin reveals a platyrrhine beta to delta gene conversion in the atelid ancestry
    Tom Prychitko
    Department of Anatomy and Cell Biology, Wayne State University, Detroit, MI, USA
    Mol Phylogenet Evol 35:225-34. 2005
    ..This phylogeny generally agreed with results from other nuclear genes. The one exception was that the beta sequences did not place the callitrichine clade within the Cebidae but weakly joined the callitrichine and atelid clades...
  35. pmc Phylogenetic comparisons suggest that distance from the locus control region guides developmental expression of primate beta-type globin genes
    Robert M Johnson
    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 103:3186-91. 2006
    ....
  36. ncbi request reprint Relationship between maternal and fetal plasma glucose and insulin concentrations during graded maternal hyperglycemic states in primates
    Joaquin Santolaya-Forgas
    Perinatology Research Branch, NICHD NIH DHHS, Bethesda, Maryland 20892, USA
    Am J Perinatol 23:369-75. 2006
    ....
  37. pmc New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate
    Purvesh Khatri
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 34:W626-31. 2006
    ..Currently, Onto-Translate allows arbitrary mappings between 28 types of IDs for 53 organisms. Onto-Tools are freely available at http://vortex.cs.wayne.edu/Projects.html...
  38. ncbi request reprint Episodic positive selection in ape cytochrome c oxidase subunit IV
    Derek E Wildman
    Mol Biol Evol 19:1812-5. 2002
  39. pmc Evolution of increased glia-neuron ratios in the human frontal cortex
    Chet C Sherwood
    Department of Anthropology, The George Washington University, Washington, DC 20052, USA
    Proc Natl Acad Sci U S A 103:13606-11. 2006
    ....
  40. pmc Functionally important glycosyltransferase gain and loss during catarrhine primate emergence
    Chihiro Koike
    Department of Surgery and Thomas E Starzl Transplantation Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
    Proc Natl Acad Sci U S A 104:559-64. 2007
    ..However, we emphasize that positively selected regulatory changes in sugar chain metabolism might well have contributed in a major way to catarrhine origins...