Mark R Segal

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi Validation in genomics: CpG island methylation revisited
    Mark R Segal
    University of California, San Francisco, CA, USA
    Stat Appl Genet Mol Biol 5:Article29. 2006
  2. ncbi Relating HIV-1 sequence variation to replication capacity via trees and forests
    Mark R Segal
    University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 3:Article2; discussion article 7, article 9. 2004
  3. pmc Reconstruction of 3D genome architecture via a two-stage algorithm
    Mark R Segal
    Division of Bioinformatics, Department of Epidemiology and Biostatistics, University of California, 550 16th Street, San Francisco, 94158, CA, USA
    BMC Bioinformatics 16:373. 2015
  4. pmc Reproducibility of 3D chromatin configuration reconstructions
    Mark R Segal
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94143, USADepartment of Mathematics, San Francisco State University, San Francisco, CA 94132, USA
    Biostatistics 15:442-56. 2014
  5. pmc Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis
    Michael P Cummings
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742 3360, USA
    BMC Bioinformatics 5:137. 2004
  6. ncbi Relating amino acid sequence to phenotype: analysis of peptide-binding data
    M R Segal
    Division of Biostatistics, University of California, San Francisco 94143 0560, USA
    Biometrics 57:632-42. 2001
  7. doi Clustering with exclusion zones: genomic applications
    Mark R Segal
    Division of Biostatistics, University of California, San Francisco, CA 94107, USA
    Biostatistics 12:234-46. 2011
  8. pmc A novel topology for representing protein folds
    Mark R Segal
    Division of Biostatistics, University of California, San Francisco, California 94107, USA
    Protein Sci 18:686-93. 2009
  9. doi Re-cracking the nucleosome positioning code
    Mark R Segal
    University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 7:Article14. 2008
  10. ncbi Microarray gene expression data with linked survival phenotypes: diffuse large-B-cell lymphoma revisited
    Mark R Segal
    Division of Biostatistics, University of California, San Francisco, CA 94143 0560, USA
    Biostatistics 7:268-85. 2006

Detail Information

Publications44

  1. ncbi Validation in genomics: CpG island methylation revisited
    Mark R Segal
    University of California, San Francisco, CA, USA
    Stat Appl Genet Mol Biol 5:Article29. 2006
    ....
  2. ncbi Relating HIV-1 sequence variation to replication capacity via trees and forests
    Mark R Segal
    University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 3:Article2; discussion article 7, article 9. 2004
    ..Other approaches including logic regression, support vector machines and neural networks are also applied. We interpret results in terms of HIV-1 reverse transcriptase structure and function...
  3. pmc Reconstruction of 3D genome architecture via a two-stage algorithm
    Mark R Segal
    Division of Bioinformatics, Department of Epidemiology and Biostatistics, University of California, 550 16th Street, San Francisco, 94158, CA, USA
    BMC Bioinformatics 16:373. 2015
    ..However, only limited, low-resolution reconstructions have been realized for mammals due to computational bottlenecks...
  4. pmc Reproducibility of 3D chromatin configuration reconstructions
    Mark R Segal
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94143, USADepartment of Mathematics, San Francisco State University, San Francisco, CA 94132, USA
    Biostatistics 15:442-56. 2014
    ..Our methods of reproducibility assessment provide a means for comparing 3D reconstruction solutions so that we can discern between local and global optima by contrasting solutions under perturbed inputs. ..
  5. pmc Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis
    Michael P Cummings
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742 3360, USA
    BMC Bioinformatics 5:137. 2004
    ..Such a model might provide the basis for quantifying rifampin resistance status based exclusively on DNA sequence data and thus eliminate the requirements for time consuming culturing and antibiotic testing of clinical isolates...
  6. ncbi Relating amino acid sequence to phenotype: analysis of peptide-binding data
    M R Segal
    Division of Biostatistics, University of California, San Francisco 94143 0560, USA
    Biometrics 57:632-42. 2001
    ..We further tackle the question of whether observed associations are attributable to amino acid properties as well as addressing the assessment and implications of between-position covariation...
  7. doi Clustering with exclusion zones: genomic applications
    Mark R Segal
    Division of Biostatistics, University of California, San Francisco, CA 94107, USA
    Biostatistics 12:234-46. 2011
    ..In several instances, dramatic changes to unadjusted inference that does not accommodate exclusions are evidenced...
  8. pmc A novel topology for representing protein folds
    Mark R Segal
    Division of Biostatistics, University of California, San Francisco, California 94107, USA
    Protein Sci 18:686-93. 2009
    ..Furthermore, unlike existing topologies, the proposed geometry exhibits fine scale structure with respect to sequence position along the chain, potentially providing insights into folding initiation and/or nucleation sites...
  9. doi Re-cracking the nucleosome positioning code
    Mark R Segal
    University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 7:Article14. 2008
    ....
  10. ncbi Microarray gene expression data with linked survival phenotypes: diffuse large-B-cell lymphoma revisited
    Mark R Segal
    Division of Biostatistics, University of California, San Francisco, CA 94143 0560, USA
    Biostatistics 7:268-85. 2006
    ..These indicate that gene expression data, in turn, only delivers modest predictions of posttherapy DLBCL survival. We conclude by outlining possibilities for further work...
  11. ncbi Dependence estimation for marginal models of multivariate survival data
    M R Segal
    Division of Biostatistics, University of California, San Francisco 94143 0560, USA
    Lifetime Data Anal 3:251-68. 1997
    ..An alternate, ad hoc approach to dependence estimation, based on design effects, is proposed and evaluated via simulation and illustrative examples...
  12. ncbi Regression approaches for microarray data analysis
    Mark R Segal
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143 0560, USA
    J Comput Biol 10:961-80. 2003
    ..Model selection and solution multiplicity issues are also discussed. The methods are evaluated using a microarray-based study of cardiomyopathy in transgenic mice...
  13. ncbi Persistence of primary drug resistance among recently HIV-1 infected adults
    Jason D Barbour
    Gladstone Institute of Virology and Immunology, San Francisco, California 94141 9100, USA
    AIDS 18:1683-9. 2004
    ..We sought to determine if primary drug resistance would be lost at a rapid rate, and viral pol replication capacity would increase, in the absence of treatment...
  14. pmc Identification of yeast transcriptional regulation networks using multivariate random forests
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, California, USA
    PLoS Comput Biol 5:e1000414. 2009
    ..These include intriguing instances of differing motif dosages and differing combinatorial motif control that promote regulatory specificity in rRNA metabolism under differing physiological processes...
  15. ncbi Greater CD4 T-cell gains after one year of antiretroviral therapy are associated with lower HIV-1 pol replication capacity
    Jason D Barbour
    Positive Health Program, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California, USA
    AIDS 20:2123-5. 2006
    ..Viral polRC was measured before starting ART in all subjects. We examined 243 individuals for a median 260 days after initiating ART. Low baseline polRC was associated with greater CD4 T-cell gains independent of virological responses...
  16. ncbi Higher CD4+ T cell counts associated with low viral pol replication capacity among treatment-naive adults in early HIV-1 infection
    Jason D Barbour
    Gladstone Institute of Virology and Immunology, University of California, San Francisco, USA
    J Infect Dis 190:251-6. 2004
    ....
  17. ncbi A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94107, USA
    Bioinformatics 23:1459-67. 2007
    ..Affymetrix SNP arrays, e.g. use multiple sets of short oligonucleotide probes for each known SNP, and require effective statistical methods to combine these probe intensities in order to generate reliable and accurate genotype calls...
  18. pmc Sequence-based classification using discriminatory motif feature selection
    Hao Xiong
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 6:e27382. 2011
    ..Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is available at http://www.epibiostat.ucsf.edu/biostat/sen/dmfs/...
  19. ncbi Identifying differentially expressed genes from microarray experiments via statistic synthesis
    Yee Hwa Yang
    Departments of Medicine, Center for Bioinformatics and Molecular Biostatistics, University of California San Francisco, CA 94143, USA
    Bioinformatics 21:1084-93. 2005
    ..We further evaluate performance on one other microarray study...
  20. pmc 1H nuclear magnetic resonance brain metabolomics in neonatal mice after hypoxia-ischemia distinguished normothermic recovery from mild hypothermia recoveries
    Jia Liu
    Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, California, USA
    Pediatr Res 74:170-9. 2013
    ....
  21. pmc Evolution of phenotypic drug susceptibility and viral replication capacity during long-term virologic failure of protease inhibitor therapy in human immunodeficiency virus-infected adults
    Jason D Barbour
    Gladstone Institute of Virology and Immunology, Department of Medicine, University of California, San Francisco, California, USA
    J Virol 76:11104-12. 2002
    ....
  22. pmc Assessment of differential gene expression in human peripheral nerve injury
    Yuanyuan Xiao
    Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
    BMC Genomics 3:28. 2002
    ....
  23. pmc Analysis of a splice array experiment elucidates roles of chromatin elongation factor Spt4-5 in splicing
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, California, United States of America
    PLoS Comput Biol 1:e39. 2005
    ..Our results suggest that the Spt4-Spt5 complex may help coordinate splicing with transcription under conditions that present kinetic challenges to spliceosome assembly or function...
  24. doi Analytical validation of a practical molecular assay prognostic of survival in nonsquamous non-small cell lung cancer
    Johannes R Kratz
    Thoracic Oncology Program, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
    Diagn Mol Pathol 22:65-9. 2013
    ....
  25. pmc A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome
    Daniel Capurso
    Department of Bioengineering and Therapeutic Sciences, San Francisco, CA, USA
    BMC Genomics 13:630. 2012
    ..Performance assessments are based on accuracy and interpretative yield...
  26. doi Biological sequence classification utilizing positive and unlabeled data
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94107, USA
    Bioinformatics 24:1198-205. 2008
    ..Traditional two-class classification methods do not effectively handle such data...
  27. pmc Simple, defensible sample sizes based on cost efficiency
    Peter Bacchetti
    Division of Biostatistics, Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94143 0560, USA
    Biometrics 64:577-85; discussion 586-94. 2008
    ..These methods are easy to implement, based on reliable inputs, and well justified, so they should be regarded as acceptable alternatives to current conventional approaches...
  28. pmc Metabolomics of oxidative stress in recent studies of endogenous and exogenously administered intermediate metabolites
    Jia Liu
    Department of Anesthesia, University of California, San Francisco, CA 94143, USA E Mails J L M K
    Int J Mol Sci 12:6469-501. 2011
    ..All, however, shared the common goal of ultimately developing "omics"-based, diagnostic tests to help influence therapies...
  29. ncbi Plasticity of gene expression in injured human dorsal root ganglia revealed by GeneChip oligonucleotide microarrays
    Douglas Rabert
    Neurobiology Unit, Roche Bioscience, Palo Alto, CA, USA
    J Clin Neurosci 11:289-99. 2004
    ..This study represents an important step in identifying new genes and molecular mechanisms in human DRG, with potential therapeutic relevance for nerve repair and relief of chronic neuropathic pain...
  30. pmc Site-specific translocation and evidence of postnatal origin of the t(1;19) E2A-PBX1 fusion in childhood acute lymphoblastic leukemia
    Joseph L Wiemels
    Department of Epidemiology and Biostatistics, University of California, San Francisco 94143, USA
    Proc Natl Acad Sci U S A 99:15101-6. 2002
    ....
  31. ncbi Ethics and sample size
    Peter Bacchetti
    Division of Biostatistics, Department of Epidemiology and Biostatistics, School of Medicine, Box 0560, University of California, San Francisco, CA 94143, USA
    Am J Epidemiol 161:105-10. 2005
    ..Lower power does not make a study unethical. The analysis addresses only ethical acceptability, not optimality; large studies may be desirable for other than ethical reasons...
  32. pmc A practical molecular assay to predict survival in resected non-squamous, non-small-cell lung cancer: development and international validation studies
    Johannes R Kratz
    University of California, San Francisco, CA 94143 1724, USA
    Lancet 379:823-32. 2012
    ..We aimed to develop and validate a practical, reliable assay that improves risk stratification compared with conventional staging...
  33. pmc Regulated gene expression in cultured type II cells of adult human lung
    Philip L Ballard
    Department of Pediatrics, University of California San Francisco, San Francisco, USA
    Am J Physiol Lung Cell Mol Physiol 299:L36-50. 2010
    ..Our results further define the adult human type II cell molecular phenotype and demonstrate that a subset of genes remains hormone responsive in cultured adult cells...
  34. ncbi Stepwise normalization of two-channel spotted microarrays
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 4:Article4. 2005
    ..In addition, we evaluate the effectiveness of STEPNORM and other commonly used normalization methods utilizing a set of specially constructed splicing arrays...
  35. pmc Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains
    Libusha Kelly
    Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, California, USA
    Protein Sci 19:2110-21. 2010
    ..Our analysis provides a structural and evolutionary framework for rationalizing and predicting the functional effects of nsSNPs in this clinically important membrane transporter superfamily...
  36. ncbi Prediction of genomewide conserved epitope profiles of HIV-1: classifier choice and peptide representation
    Yuanyuan Xiao
    University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 4:Article25. 2005
    ..Once again, amino acid sequence representation was at least as effective as using properties. Assessment of novel epitope predictions awaits experimental verification...
  37. pmc Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions
    Daniel Capurso
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
    Nucleic Acids Res 44:2028-35. 2016
    ..This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions. ..
  38. pmc Distance-based assessment of the localization of functional annotations in 3D genome reconstructions
    Daniel Capurso
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94107, USA
    BMC Genomics 15:992. 2014
    ..We propose an alternative approach that avoids dichotomization of the data and instead directly estimates the significance of distances within the 3D reconstruction...
  39. pmc Outcome-related metabolomic patterns from 1H/31P NMR after mild hypothermia treatments of oxygen-glucose deprivation in a neonatal brain slice model of asphyxia
    Jia Liu
    Department of Anesthesia, University of California, San Francisco, California 94143 0648, USA
    J Cereb Blood Flow Metab 31:547-59. 2011
    ..The findings suggest a potential role for metabolomic monitoring during therapeutic hypothermia...
  40. ncbi Residual-based tree-structured survival analysis
    Sunduz Keles
    Group in Biostatistics, University of California, Berkeley, CA 94720, USA
    Stat Med 21:313-26. 2002
    ..Further investigation is provided by simulation and an illustrative example using time to AIDS with data deriving from a Western Australian HIV cohort study...
  41. ncbi Inclusion body formation reduces levels of mutant huntingtin and the risk of neuronal death
    Montserrat Arrasate
    Gladstone Institute of Neurological Disease, University of California, San Francisco, California 94141, USA
    Nature 431:805-10. 2004
    ..Surprisingly, inclusion body formation predicts improved survival and leads to decreased levels of mutant huntingtin elsewhere in a neuron. Thus, inclusion body formation can function as a coping response to toxic mutant huntingtin...
  42. doi On E-values for tandem MS scoring schemes
    Mark R Segal
    Bioinformatics 24:1652-3; author reply 1654. 2008
  43. ncbi Genomic anatomy of the specific reciprocal translocation t(15;17) in acute promyelocytic leukemia
    Andreas Reiter
    III Medizinische Universitätsklinik, Klinikum Mannheim, Fakultät für Klinische Medizin der Universität Heidelberg, Germany
    Genes Chromosomes Cancer 36:175-88. 2003
    ..These findings are consistent with the hypothesis that the t(15;17) occurs by nonhomologous recombination of DNA after processing of the double-strand breaks by a dysfunctional DNA damage-repair mechanism...
  44. ncbi DNA topoisomerase II in therapy-related acute promyelocytic leukemia
    Anita R Mistry
    Department of Medical and Molecular Genetics, Guy s, King s, and St Thomas School of Medicine, London
    N Engl J Med 352:1529-38. 2005
    ..We studied acute promyelocytic leukemia (APL) with the t(15;17) translocation that developed after treatment of breast or laryngeal cancer with chemotherapeutic agents that poison topoisomerase II...