Marc Suchard

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Fully Bayesian tests of neutrality using genealogical summary statistics
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Genet 9:68. 2008
  2. pmc Dating the time of viral subtype divergence
    John D O'Brien
    Department of Biomathematics, UCLA, Los Angeles, CA 90095, USA
    BMC Evol Biol 8:172. 2008
  3. pmc Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
    Benjamin D Redelings
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
    BMC Evol Biol 7:40. 2007
  4. pmc Bayesian random local clocks, or one rate to rule them all
    Alexei J Drummond
    Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand
    BMC Biol 8:114. 2010
  5. pmc Many-core algorithms for statistical phylogenetics
    Marc A Suchard
    Department of Biomathematics, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 25:1370-6. 2009
  6. pmc General practitioners' views on genetic screening for common diseases
    M A Suchard
    Howard Hughes Medical Institute, USA
    Br J Gen Pract 49:45-6. 1999
  7. ncbi request reprint BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny
    Marc A Suchard
    Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Bioinformatics 22:2047-8. 2006
  8. ncbi request reprint Models for estimating bayes factors with applications to phylogeny and tests of monophyly
    Marc A Suchard
    Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
    Biometrics 61:665-73. 2005
  9. pmc Stochastic models for horizontal gene transfer: taking a random walk through tree space
    Marc A Suchard
    Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, 90095 1766, USA
    Genetics 170:419-31. 2005
  10. pmc Bayesian estimation of recent migration rates after a spatial expansion
    Grant Hamilton
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, Switzerland
    Genetics 170:409-17. 2005

Research Grants

Collaborators

Detail Information

Publications33

  1. pmc Fully Bayesian tests of neutrality using genealogical summary statistics
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Genet 9:68. 2008
    ..Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome...
  2. pmc Dating the time of viral subtype divergence
    John D O'Brien
    Department of Biomathematics, UCLA, Los Angeles, CA 90095, USA
    BMC Evol Biol 8:172. 2008
    ..We show a time of divergence approximately 100 years ago, substantially more recent than previous estimates which range from 250 to 3800 years ago...
  3. pmc Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
    Benjamin D Redelings
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
    BMC Evol Biol 7:40. 2007
    ..Joint estimation of alignment and phylogeny sidesteps biases that stem from conditioning on a single alignment by taking into account the ensemble of near-optimal alignments...
  4. pmc Bayesian random local clocks, or one rate to rule them all
    Alexei J Drummond
    Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand
    BMC Biol 8:114. 2010
    ..Thus, including both the global molecular clock and the unconstrained model results, there are a total of 2(2n-2) possible rate models available for averaging with 1, 2, ..., 2n - 2 different rate categories...
  5. pmc Many-core algorithms for statistical phylogenetics
    Marc A Suchard
    Department of Biomathematics, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 25:1370-6. 2009
    ....
  6. pmc General practitioners' views on genetic screening for common diseases
    M A Suchard
    Howard Hughes Medical Institute, USA
    Br J Gen Pract 49:45-6. 1999
    ..Nevertheless, as many as 76% had referred patients to a genetics unit in the past year, and 50% had counselled about genetics...
  7. ncbi request reprint BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny
    Marc A Suchard
    Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Bioinformatics 22:2047-8. 2006
    ..AVAILABILITY: Software is available for download at http://www.biomath.ucla.edu/msuchard/bali-phy...
  8. ncbi request reprint Models for estimating bayes factors with applications to phylogeny and tests of monophyly
    Marc A Suchard
    Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
    Biometrics 61:665-73. 2005
    ..The second example focuses on HIV recombination detection. For potential clinical application, these types of analyses must be completed as efficiently as possible...
  9. pmc Stochastic models for horizontal gene transfer: taking a random walk through tree space
    Marc A Suchard
    Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, 90095 1766, USA
    Genetics 170:419-31. 2005
    ....
  10. pmc Bayesian estimation of recent migration rates after a spatial expansion
    Grant Hamilton
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, Switzerland
    Genetics 170:409-17. 2005
    ..Estimates based on both markers suggest that expansion occurred <10,000 years ago, after the most recent glaciation, and that migration rates are strongly male biased...
  11. ncbi request reprint Hierarchical phylogenetic models for analyzing multipartite sequence data
    Marc A Suchard
    Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095 1766, USA
    Syst Biol 52:649-64. 2003
    ..Preliminary results suggest evolution and not reemergence...
  12. ncbi request reprint Pomegranate juice ellagitannin metabolites are present in human plasma and some persist in urine for up to 48 hours
    Navindra P Seeram
    Departments of Biomathematics and Human Genetics, University of California, Los Angeles, CA, USA
    J Nutr 136:2481-5. 2006
    ..Whether genetic polymorphisms in EA-metabolizing enzymes (e.g., catechol-O-methyl transferase and glucuronosyl transferase) are related to variations in response to PJ remains to be established...
  13. ncbi request reprint Joint Bayesian estimation of alignment and phylogeny
    Benjamin D Redelings
    Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 1766, USA
    Syst Biol 54:401-18. 2005
    ..Our software implementation can estimate alignment uncertainty and we describe a method for summarizing this uncertainty in a single plot...
  14. ncbi request reprint Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage
    Marc A Suchard
    Department of Biomathematics, School of Medicine, University of California, Los Angeles, California 90095 1766, USA
    Syst Biol 51:715-28. 2002
    ..We employed scaled regeneration quantile plots to assess convergence and found this approach convenient to use even for our variable dimensional model parameter space...
  15. ncbi request reprint Testing a molecular clock without an outgroup: derivations of induced priors on branch-length restrictions in a Bayesian framework
    Marc A Suchard
    Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, California 90095 1766, USA
    Syst Biol 52:48-54. 2003
    ..These derivations also have more general applicability to the examination of prior assumptions in Bayesian phylogenetics...
  16. pmc Pomegranate juice and extracts provide similar levels of plasma and urinary ellagitannin metabolites in human subjects
    Navindra P Seeram
    Center for Human Nutrition, David Geffen School of Medicine, Los Angeles California, USA
    J Med Food 11:390-4. 2008
    ..This study demonstrates that ellagitannin metabolites, delivered from pomegranate fruits, as PJ, POMxl, and POMxp, reach equivalent levels with a delay in time of maximum concentration of POMxp compared to PJ and POMxl...
  17. ncbi request reprint Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics
    Maria R D'Orsogna
    Department of Physics and Astronomy, University of California, Los Angeles, California 90095 1547, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 68:021925. 2003
    ..Cell positional distributions and the associated moments are computed in this feedback system. Average drift and mean squared displacements are found. Crossover behaviors among different diffusion regimes are found...
  18. pmc Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics
    Vladimir N Minin
    Department of Statistics, University of Washington, USA
    Mol Biol Evol 25:1459-71. 2008
    ..Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons...
  19. doi request reprint Alignment uncertainty and genomic analysis
    Karen M Wong
    Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, CA 92093, USA
    Science 319:473-6. 2008
    ..Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions...
  20. ncbi request reprint Pomegranate ellagitannin-derived metabolites inhibit prostate cancer growth and localize to the mouse prostate gland
    Navindra P Seeram
    Center for Human Nutrition, Greater Los Angeles VA Medical Center, Los Angeles, California, USA
    J Agric Food Chem 55:7732-7. 2007
    ..This warrants future human tissue bioavailability studies and further clinical studies in men with CaP...
  21. ncbi request reprint Early nodal response as a predictor for necessity of functional neck dissection after chemoradiation
    Roy Vongtama
    Department of Radiation Oncology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
    Cancer J 10:339-42. 2004
    ..In this study, we retrospectively analyzed a cohort of node-positive patients to examine pathological response as well as clinical outcome after chemoradiation with or without functional neck dissection...
  22. ncbi request reprint Dual multiple change-point model leads to more accurate recombination detection
    Vladimir N Minin
    Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, CA 90095 1766, USA
    Bioinformatics 21:3034-42. 2005
    ..Statistical analysis is done in a Bayesian framework using reversible jump Markov chain Monte Carlo sampling to approximate the joint posterior distribution of all model parameters...
  23. ncbi request reprint Continued evolution in gp41 after interruption of enfuvirtide in subjects with advanced HIV type 1 disease
    Christina M R Kitchen
    Department of Biostatistics, University of California, Los Angeles, Los Angeles, California 90095, Section of Retroviral Therapeutics, Brigham and Women s Hospital, Boston, MA 02115, USA
    AIDS Res Hum Retroviruses 22:1260-6. 2006
    ..In contrast to observations when all drugs are interrupted, loss of resistance during enfuvirtide interruption is most likely due to ongoing viral evolution (and back-mutation), rather than emergence of an archived virus...
  24. pmc Evolution of human immunodeficiency virus type 1 coreceptor usage during antiretroviral Therapy: a Bayesian approach
    Christina M R Kitchen
    Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA 90095 1772
    J Virol 78:11296-302. 2004
    ..This model is not limited to analyses of HIV-1 but can be used to elucidate evolutionary processes for other organisms as well...
  25. ncbi request reprint Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains
    Janet S Sinsheimer
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 1766, USA
    Appl Bioinformatics 2:131-44. 2003
    ....
  26. pmc Molecular evolution and mosaicism of leptospiral outer membrane proteins involves horizontal DNA transfer
    David A Haake
    Division of Infectious Diseases, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
    J Bacteriol 186:2818-28. 2004
    ....
  27. ncbi request reprint Time squared: repeated measures on phylogenies
    Hua Guo
    Department of Biostatistics, School of Public Health, University of California, Los Angeles, USA
    Mol Biol Evol 24:352-62. 2007
    ..To demonstrate PR model applicability more generally, we conclude with a short examination of variation in brain development across 4 primate species...
  28. ncbi request reprint cBrother: relaxing parental tree assumptions for Bayesian recombination detection
    Fang Fang
    Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
    Bioinformatics 23:507-8. 2007
    ..Availability: cBrother can be freely downloaded from http://www.biomath.org/dormanks/ and can be compiled on Linux, Macintosh and Windows operating systems. Online documentation and a tutorial are also available at the site...
  29. pmc Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes
    Vladimir N Minin
    Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genetics 175:1773-85. 2007
    ..We then proceed with the analysis of 42 human immunodeficiency virus (HIV) intersubtype gag recombinants and identify a putative recombination hotspot...
  30. ncbi request reprint A nonparametric method for accommodating and testing across-site rate variation
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
    Syst Biol 56:975-87. 2007
    ....
  31. pmc Leptospira interrogans endostatin-like outer membrane proteins bind host fibronectin, laminin and regulators of complement
    Brian Stevenson
    Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, United States of America
    PLoS ONE 2:e1188. 2007
    ..These characteristics suggest that Len proteins together facilitate invasion and colonization of host tissues, and protect against host immune responses during mammalian infection...
  32. pmc Use of electrochemical DNA biosensors for rapid molecular identification of uropathogens in clinical urine specimens
    Joseph C Liao
    Division of Infectious Diseases, 111F, VA Greater LA Healthcare, Los Angeles, CA 90073, USA
    J Clin Microbiol 44:561-70. 2006
    ..When combined with a microfluidics-based sample preparation module, the integrated system could serve as a point-of-care device for rapid diagnosis of urinary tract infections...
  33. pmc Development of an advanced electrochemical DNA biosensor for bacterial pathogen detection
    Joseph C Liao
    Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
    J Mol Diagn 9:158-68. 2007
    ..These results demonstrate the importance of target-probe and probe-probe interactions in the detection of bacterial 16S rRNA using an electrochemical DNA sensor approach...

Research Grants3

  1. Bayesian Joint Estimation of Alignment and Phylogeny
    Marc Suchard; Fiscal Year: 2009
    ....
  2. Bayesian Joint Estimation of Alignment and Phylogeny
    Marc A Suchard; Fiscal Year: 2010
    ....