Research Topics
| S KarlinSummaryAffiliation: Stanford University Country: USA Publications
Research Grants
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Detail Information
Publications
Amino acid runs in eukaryotic proteomes and disease associationsSamuel 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...- Genomics. Annotation of the Drosophila genomeS Karlin
Mathematics Department, Stanford University, Serra Street, California 94305, USA
Nature 411:259-60. 2001 - Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomesS 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... - Characterizations of highly expressed genes of four fast-growing bacteriaS 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... - Statistical signals in bioinformaticsSamuel 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... - John Maynard Smith and recombinationSamuel Karlin
Department of Mathematics, Stanford University, Stanford, CA 94305-2125, USA
Theor Popul Biol 68:3-5. 2005 - Predicted highly expressed genes in archaeal genomesSamuel 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... - Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomesSamuel 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... - Associations between human disease genes and overlapping gene groups and multiple amino acid runsSamuel Karlin
Departments of Mathematics and Pathology, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 99:17008-13. 2002.... - Predicting gene expression levels from codon biases in alpha-proteobacterial genomesSamuel 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... - Genome comparisons and analysisSamuel 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... - Comparative analysis of gene expression among low G+C gram-positive genomesSamuel 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... - Heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolutionS 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... - Distinguishing features of delta-proteobacterial genomesSamuel 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... - Codon usages in different gene classes of the Escherichia coli genomeS 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... - Predicted highly expressed genes of diverse prokaryotic genomesS 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... - Genome-scale compositional comparisons in eukaryotesA 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... - Highly expressed and alien genes of the Synechocystis genomeJ 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... - Molecular evolution of herpesviruses: genomic and protein sequence comparisonsS 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).. - Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organismsV 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... - Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damageS 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... - The extended environment of mononuclear metal centers in protein structuresS 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... - Conservation among HSP60 sequences in relation to structure, function, and evolutionL 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... - Applications and statistics for multiple high-scoring segments in molecular sequencesS Karlin
Department of Mathematics, Stanford University, CA 94305
Proc Natl Acad Sci U S A 90:5873-7. 1993.... - Charge configurations in viral proteinsS 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... - Classification of mononuclear zinc metal sites in protein structuresS 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... - Predicting coding potential from genome sequence: application to betaherpesviruses infecting rats and miceLuciano 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... - Methods and algorithms for statistical analysis of protein sequencesV 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)... - Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structuresJiong 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... - Extended metal environments of cytochrome c oxidase structuresS 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... - Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotesSamuel 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... - Genomic comparisons among gamma-proteobacteriaJan 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... - Frequent oligonucleotide motifs in genomes of three streptococciJan 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... - Protein length in eukaryotic and prokaryotic proteomesLuciano 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... - Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22Chingfer 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... - Distinctive features of large complex virus genomes and proteomesJan 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 Grants
- STOCHASTIC MODELS IN MEDICINE AND BIOLOGYSamuel 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...
- ANALYSIS OF MOLECULAR SEQUENCE DATASamuel 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...
- COMPARATIVE GENOMIC AND EVOLUTIONARY STUDIESSamuel 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. ..
- MOLECULAR SEQUENCE DATASamuel Karlin; Fiscal Year: 2001..by spacings between repeats, and by properties of repeat families (intergenic, coding, direct, inverted, mixed). ..
- MOLECULAR SEQUENCE DATASamuel 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)...
- THEORY & APPLIED STUDIES IN EVOLUTIONARY GENETICSSamuel 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...
- Gene Expression Levels Across Diverse GenomesSamuel 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. ..