Research Topics
| Marc SuchardSummaryAffiliation: University of California Country: USA Publications
Research Grants
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Detail Information
Publications
Fully Bayesian tests of neutrality using genealogical summary statisticsAlexei 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...- Dating the time of viral subtype divergenceJohn 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... - Incorporating indel information into phylogeny estimation for rapidly emerging pathogensBenjamin 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... - Bayesian random local clocks, or one rate to rule them allAlexei 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... - Many-core algorithms for statistical phylogeneticsMarc A Suchard
Department of Biomathematics, University of California, Los Angeles, CA 90095, USA
Bioinformatics 25:1370-6. 2009.... - General practitioners' views on genetic screening for common diseasesM 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... 
BAli-Phy: simultaneous Bayesian inference of alignment and phylogenyMarc 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...- Models for estimating bayes factors with applications to phylogeny and tests of monophylyMarc 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... - Stochastic models for horizontal gene transfer: taking a random walk through tree spaceMarc A Suchard
Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, 90095 1766, USA
Genetics 170:419-31. 2005.... - Bayesian estimation of recent migration rates after a spatial expansionGrant 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... - Hierarchical phylogenetic models for analyzing multipartite sequence dataMarc 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... - Pomegranate juice ellagitannin metabolites are present in human plasma and some persist in urine for up to 48 hoursNavindra 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... - Joint Bayesian estimation of alignment and phylogenyBenjamin 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... - Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritageMarc 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... - Testing a molecular clock without an outgroup: derivations of induced priors on branch-length restrictions in a Bayesian frameworkMarc 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... - Pomegranate juice and extracts provide similar levels of plasma and urinary ellagitannin metabolites in human subjectsNavindra 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... - Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamicsMarc A Suchard
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... - Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamicsVladimir 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... 
Alignment uncertainty and genomic analysisKaren 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...- Pomegranate ellagitannin-derived metabolites inhibit prostate cancer growth and localize to the mouse prostate glandNavindra 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... - Early nodal response as a predictor for necessity of functional neck dissection after chemoradiationRoy 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... - Dual multiple change-point model leads to more accurate recombination detectionVladimir N Minin
Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, CA 90095-1766, USA
Bioinformatics 21:3034-42. 2005..We also analyze two real HIV sequences to identify recombination break-points using the dual MCP model... - Continued evolution in gp41 after interruption of enfuvirtide in subjects with advanced HIV type 1 diseaseChristina 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... - Evolution of human immunodeficiency virus type 1 coreceptor usage during antiretroviral Therapy: a Bayesian approachChristina 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... - Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strainsJanet 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.... - Molecular evolution and mosaicism of leptospiral outer membrane proteins involves horizontal DNA transferDavid A Haake
Division of Infectious Diseases, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
J Bacteriol 186:2818-28. 2004.... - Time squared: repeated measures on phylogeniesHua 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... - cBrother: relaxing parental tree assumptions for Bayesian recombination detectionFang 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... - Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processesVladimir 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... - A nonparametric method for accommodating and testing across-site rate variationJohn P Huelsenbeck
Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
Syst Biol 56:975-87. 2007.... - Leptospira interrogans endostatin-like outer membrane proteins bind host fibronectin, laminin and regulators of complementBrian 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... - Use of electrochemical DNA biosensors for rapid molecular identification of uropathogens in clinical urine specimensJoseph 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... - Development of an advanced electrochemical DNA biosensor for bacterial pathogen detectionJoseph 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 Grants
- Bayesian Joint Estimation of Alignment and PhylogenyMarc Suchard; Fiscal Year: 2009....
- Bayesian Joint Estimation of Alignment and PhylogenyMarc A Suchard; Fiscal Year: 2010....