S Karlin

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Protein length in eukaryotic and prokaryotic proteomes
    Luciano Brocchieri
    Department of Mathematics, Stanford University Stanford, CA 94305 2125, USA
    Nucleic Acids Res 33:3390-400. 2005
  2. ncbi request reprint Genomics. Annotation of the Drosophila genome
    S Karlin
    Mathematics Department, Stanford University, Serra Street, California 94305, USA
    Nature 411:259-60. 2001
  3. ncbi request reprint Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
    S Karlin
    Dept of Mathematics, Stanford University, 94305 2125, Stanford, CA, USA
    Trends Microbiol 9:335-43. 2001
  4. pmc Statistical signals in bioinformatics
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 102:13355-62. 2005
  5. pmc Amino acid runs in eukaryotic proteomes and disease associations
    Samuel Karlin
    Department of Mathematics, and Center for Computational Genetics and Biological Modeling, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 99:333-8. 2002
  6. ncbi request reprint John Maynard Smith and recombination
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Theor Popul Biol 68:3-5. 2005
  7. pmc Characterizations of highly expressed genes of four fast-growing bacteria
    S Karlin
    Department of Mathematics, Stanford University, Stanford, California 94305 2125, USA
    J Bacteriol 183:5025-40. 2001
  8. pmc Predicted highly expressed genes in archaeal genomes
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 102:7303-8. 2005
  9. pmc Associations between human disease genes and overlapping gene groups and multiple amino acid runs
    Samuel Karlin
    Departments of Mathematics and Pathology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:17008-13. 2002
  10. pmc Predicting gene expression levels from codon biases in alpha-proteobacterial genomes
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:7313-8. 2003

Research Grants

  1. STOCHASTIC MODELS IN MEDICINE AND BIOLOGY
    Samuel Karlin; Fiscal Year: 1980
  2. ANALYSIS OF MOLECULAR SEQUENCE DATA
    Samuel Karlin; Fiscal Year: 1992
  3. Gene Expression Levels Across Diverse Genomes
    Samuel Karlin; Fiscal Year: 2006
  4. COMPARATIVE GENOMIC AND EVOLUTIONARY STUDIES
    Samuel Karlin; Fiscal Year: 2002
  5. MOLECULAR SEQUENCE DATA
    Samuel Karlin; Fiscal Year: 1993
  6. THEORY & APPLIED STUDIES IN EVOLUTIONARY GENETICS
    Samuel Karlin; Fiscal Year: 1993
  7. MOLECULAR SEQUENCE DATA
    Samuel Karlin; Fiscal Year: 2001

Detail Information

Publications37

  1. pmc Protein length in eukaryotic and prokaryotic proteomes
    Luciano Brocchieri
    Department of Mathematics, Stanford University Stanford, CA 94305 2125, USA
    Nucleic Acids Res 33:3390-400. 2005
    ..These differences are interpreted with respect to evolutionary trends and prevailing environmental conditions within the two prokaryotic groups...
  2. ncbi request reprint Genomics. Annotation of the Drosophila genome
    S Karlin
    Mathematics Department, Stanford University, Serra Street, California 94305, USA
    Nature 411:259-60. 2001
  3. ncbi request reprint Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
    S Karlin
    Dept of Mathematics, Stanford University, 94305 2125, Stanford, CA, USA
    Trends Microbiol 9:335-43. 2001
    ..Additionally, G+C variation and genome signature differences of the Mycobacterium tuberculosis genome indicate two pA gene clusters...
  4. pmc Statistical signals in bioinformatics
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 102:13355-62. 2005
    ..Bioinformatics is highly interdisciplinary, using knowledge from mathematics, statistics, computer science, biology, medicine, physics, chemistry, and engineering...
  5. pmc Amino acid runs in eukaryotic proteomes and disease associations
    Samuel Karlin
    Department of Mathematics, and Center for Computational Genetics and Biological Modeling, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 99:333-8. 2002
    ..There are striking differences in amino acid runs for glutamine, asparagine, and leucine among the five proteomes...
  6. ncbi request reprint John Maynard Smith and recombination
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Theor Popul Biol 68:3-5. 2005
  7. pmc Characterizations of highly expressed genes of four fast-growing bacteria
    S Karlin
    Department of Mathematics, Stanford University, Stanford, California 94305 2125, USA
    J Bacteriol 183:5025-40. 2001
    ..Relationships of PHX genes with stoichiometry, multifunctionality, and operon structures are also examined. The spatial distribution of PHX genes within each genome reveals clusters and significantly long regions without PHX genes...
  8. pmc Predicted highly expressed genes in archaeal genomes
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 102:7303-8. 2005
    ..RadA is a major DNA repair and recombination protein of Archaea. Archaeal genomes feature a strong Shine-Dalgarno ribosome-binding motif more pronounced in Euryarchaea compared with Crenarchaea...
  9. pmc Associations between human disease genes and overlapping gene groups and multiple amino acid runs
    Samuel Karlin
    Departments of Mathematics and Pathology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:17008-13. 2002
    ....
  10. pmc Predicting gene expression levels from codon biases in alpha-proteobacterial genomes
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:7313-8. 2003
    ..CAUCR stands out among available prokaryotic genomes with 25 PHX TonB-dependent receptors. These are putatively involved in uptake of iron ions and other nonsoluble compounds...
  11. ncbi request reprint Genome comparisons and analysis
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305, USA
    Curr Opin Struct Biol 13:344-52. 2003
    ..The next phase of research will be increasingly dominated by efforts to integrate the deluge of data into our understanding of biological systems...
  12. pmc Comparative analysis of gene expression among low G+C gram-positive genomes
    Samuel Karlin
    Department of Mathematics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:6182-7. 2004
    ..The various substrate specificities among phosphotransferase systems in different genomes apparently reflect on differences in habitat, lifestyle, and nutrient sources...
  13. pmc Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 102:7309-14. 2005
    ..Where the numbers are approximately commensurate, a facultative growth behavior prevails...
  14. pmc Heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution
    S Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 97:11348-53. 2000
    ..Evolutionary relations are confounded by differential selection pressures, convergence, variable mutational rates, site variability, and lateral gene transfer...
  15. pmc Distinguishing features of delta-proteobacterial genomes
    Samuel Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:11352-7. 2006
    ..The predicted highly expressed genes from delta genomes reflect their different ecologies, metabolic strategies, and adaptations...
  16. ncbi request reprint Codon usages in different gene classes of the Escherichia coli genome
    S Karlin
    Department of Mathematics, Stanford University, CA 94305 2125, USA
    Mol Microbiol 29:1341-55. 1998
    ..These are identified, including four clusters (operons). The bulk of these genes have no known function...
  17. pmc Predicted highly expressed genes of diverse prokaryotic genomes
    S Karlin
    Department of Mathematics, Stanford University, California 94305 2125, USA
    J Bacteriol 182:5238-50. 2000
    ..Relationships of PHX genes with stoichiometry, multifunctionality, and operon structures are discussed. Our methodology may be used complementary to experimental expression analysis...
  18. pmc Genome-scale compositional comparisons in eukaryotes
    A J Gentles
    Mathematics Department, Stanford University, Stanford, California 94305, USA
    Genome Res 11:540-6. 2001
    ..We detail the relations between species genome signatures and suggest possible mechanisms for their origin and maintenance...
  19. ncbi request reprint Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms
    V Brendel
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    J Mol Evol 44:528-41. 1997
    ..We propose that RecA-like proteins derive evolutionarily from an assortment of independent domains and that the functional homologs of RecA in noneubacteria comprise an array of RecA-like proteins acting in series or cooperatively...
  20. pmc Highly expressed and alien genes of the Synechocystis genome
    J Mrazek
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Nucleic Acids Res 29:1590-601. 2001
    ..The proteins encoded by PHX and PA genes are described with respect to functional classifications, their organization in the genome and their stoichiometry in multi-subunit complexes...
  21. pmc Molecular evolution of herpesviruses: genomic and protein sequence comparisons
    S Karlin
    Department of Mathematics, Stanford University, California 94305
    J Virol 68:1886-902. 1994
    ..e., among EHV1, herpes simplex virus type 1, varicella-zoster virus, pseudorabies virus type 1 and Marek's disease virus) and within gammaherpesviruses (EBV versus herpesvirus saimiri).(ABSTRACT TRUNCATED AT 400 WORDS)..
  22. pmc Evolutionary conservation of RecA genes in relation to protein structure and function
    S Karlin
    Department of Mathematics, Stanford University, Stanford, California 94305 2125, USA
    J Bacteriol 178:1881-94. 1996
    ..The conservation of various RecA positions and regions suggests a model for RecA-double-stranded DNA interaction and other functional and structural assignments...
  23. pmc Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage
    S Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 98:5240-5. 2001
    ..The top PHX gene of DEIRA is the multifunctional tricarboxylic acid (TCA) gene aconitase, which, apart from its role in respiration, also alerts the cell to oxidative damage...
  24. pmc The extended environment of mononuclear metal centers in protein structures
    S Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 94:14225-30. 1997
    ..v) The extended environment of mononuclear Fe sites often is associated with histidine-tyrosine or histidine-acidic clusters...
  25. pmc Classification of mononuclear zinc metal sites in protein structures
    S Karlin
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 94:14231-6. 1997
    ..Mononuclear zinc sites can be classified into six types depending on the ligand composition and geometry. Implications of the results are discussed in terms of divergent and convergent evolution...
  26. pmc Conservation among HSP60 sequences in relation to structure, function, and evolution
    L Brocchieri
    Department of Mathematics, Stanford University, California 94305 2125, USA
    Protein Sci 9:476-86. 2000
    ..The evolutionary information of the multiple alignment proffers attractive sites for mutational studies...
  27. pmc Applications and statistics for multiple high-scoring segments in molecular sequences
    S Karlin
    Department of Mathematics, Stanford University, CA 94305
    Proc Natl Acad Sci U S A 90:5873-7. 1993
    ....
  28. pmc Charge configurations in viral proteins
    S Karlin
    Department of Mathematics, Stanford University, CA 94305
    Proc Natl Acad Sci U S A 85:9396-400. 1988
    ..This contrast might reflect the role of protein charge structures in facilitating competitive virus-host interactions involving the cellular transcription, translation, protein sorting, and transport apparatus...
  29. pmc Predicting coding potential from genome sequence: application to betaherpesviruses infecting rats and mice
    Luciano Brocchieri
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    J Virol 79:7570-96. 2005
    ..This expanded set of candidate genes provides an additional basis for investigation in cytomegalovirus biology and pathogenesis...
  30. pmc Methods and algorithms for statistical analysis of protein sequences
    V Brendel
    Department of Mathematics, Stanford University, CA 94305 2125
    Proc Natl Acad Sci U S A 89:2002-6. 1992
    ..B. (volker/genomic@stanford.edu)...
  31. pmc Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures
    Jiong Ma
    Department of Biological Sciences, Stanford University, Stanford, California 94305 2125, USA
    J Bacteriol 184:5733-45. 2002
    ..In light of these results, we discuss the role of the SD sequence in translation initiation and its relationship with predicted gene expression levels and with operon structure in both bacterial and archaeal genomes...
  32. ncbi request reprint Extended metal environments of cytochrome c oxidase structures
    S Karlin
    Department of Mathematics, Stanford University, California 94305 2125, USA
    Biochemistry 37:17726-34. 1998
    ..Many hydrogen bonding relations along the interface of subunits I and II demarcate this surface as a potential participant in proton pumping...
  33. ncbi request reprint Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotes
    Samuel Karlin
    Department of Mathematics, Stanford University, California 94305 2125, USA
    Theor Popul Biol 61:367-90. 2002
    ..Differences among genomes are influenced by lifestyle, habitat, physiology, energy sources, and other factors...
  34. ncbi request reprint Genomic comparisons among gamma-proteobacteria
    Jan Mrazek
    Department of Mathematics, Stanford University, CA 94305, USA
    Environ Microbiol 8:273-88. 2006
    ..Comparative analysis of PHX genes from complex environmental genomic sequences as well as from uncultured pathogenic microbes can provide a novel, useful tool to predict global flux of matter and key intermediates...
  35. pmc Frequent oligonucleotide motifs in genomes of three streptococci
    Jan Mrazek
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Nucleic Acids Res 30:4216-21. 2002
    ..Two regions of the L.lactis genome feature an intriguing pattern of several periodically occurring HRMs separated by precisely 59 bp. In a striking contrast to S.pneumoniae and L.lactis, S.pyogenes contains hardly any frequent words...
  36. pmc Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22
    Chingfer Chen
    Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
    Proc Natl Acad Sci U S A 99:2930-5. 2002
    ..Other assessments concern comparisons of intergenic lengths, properties of Psig sequences, and correlations between Alu and Psig sequences...
  37. pmc Distinctive features of large complex virus genomes and proteomes
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 104:5127-32. 2007
    ..iii) Frequent oligonucleotides and peptides are characterized in the large viral genomes. The frequent words may provide structural flexibility to interact with host proteins...

Research Grants40

  1. STOCHASTIC MODELS IN MEDICINE AND BIOLOGY
    Samuel Karlin; Fiscal Year: 1980
    ..Parallel simulation studies are also in progress which complement the combined empirical and model buttressed exploratory methodology that we are developing...
  2. ANALYSIS OF MOLECULAR SEQUENCE DATA
    Samuel Karlin; Fiscal Year: 1992
    ..The unique collaboration between our group and members of the biology and medical departments provides an ideal framework for achieving the research objectives defined in this grant...
  3. Gene Expression Levels Across Diverse Genomes
    Samuel Karlin; Fiscal Year: 2006
    ..A third major objective of our research will be to extend our codon usage methods for predicting gene expression levels to eukaryotic genomes, including yeast, D. melanogaster, C. elegans, and human. ..
  4. COMPARATIVE GENOMIC AND EVOLUTIONARY STUDIES
    Samuel Karlin; Fiscal Year: 2002
    ..We will further investigate rare and frequent words, motifs, or compositional biases. Finally, we will continue the development of versatile code that implements all our computational and statistical methods for sequence analysis. ..
  5. MOLECULAR SEQUENCE DATA
    Samuel Karlin; Fiscal Year: 1993
    ..Intensive detailed studies on large genomic sequences will be conducted for comparative purposes and to identify special regions (origin of replications, regulatory sequences, and structural elements)...
  6. THEORY & APPLIED STUDIES IN EVOLUTIONARY GENETICS
    Samuel Karlin; Fiscal Year: 1993
    ..The unique collaboration between our groups and members of the biology and medical departments provides an ideal framework for achieving the research objectives defined in this grant...
  7. MOLECULAR SEQUENCE DATA
    Samuel Karlin; Fiscal Year: 2001
    ..by spacings between repeats, and by properties of repeat families (intergenic, coding, direct, inverted, mixed). ..