Research Topics
Genomes and Genes | Stephan C SchusterSummaryAffiliation: Pennsylvania State University Country: USA Publications
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Detail Information
Publications
Sequencing and analysis of a South Asian-Indian personal genomeRavi Gupta
SciGenom Labs Pvt Ltd, Kakkanad, Cochin, Kerala, India
BMC Genomics 13:440. 2012..In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala...- Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validationElizabeth A Tindall
Cancer Genetics Group, Children s Cancer Institute Australia for Medical Research, Sydney Children s Hospital, High Street, Randwick, NSW 2031, Australia
BMC Res Notes 3:39. 2010..We highlight applications for interpretation of Illumina generated genotype cluster plots to maximise data inclusion and reduce genotyping errors... - Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaeaChristian Lange
Institute for Molecular Biosciences, Johann Wolfgang Goethe University, Max von Laue Strasse 9, 60438 Frankfurt a, M, Germany
BMC Genomics 8:415. 2007..Additional species have not been investigated yet. Particularly, until now no global study of translational control with any prokaryotic species was available... - Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolutionEske Willerslev
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100, Denmark
BMC Evol Biol 9:95. 2009..One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments... - Methods for comparative metagenomicsDaniel H Huson
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
BMC Bioinformatics 10:S12. 2009..Increasingly, there is a need for new ways of comparing multiple metagenomics datasets, and for fast and user-friendly implementations of such approaches... 
Next-generation sequencing transforms today's biologyStephan C Schuster
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA
Nat Methods 5:16-8. 2008..However, before stepping into the limelight, next-generation sequencing had to overcome the inertia of a field that relied on Sanger-sequencing for 30 years...- Complete Khoisan and Bantu genomes from southern AfricaStephan C Schuster
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Lab, University Park, Pennsylvania 16802, USA
Nature 463:943-7. 2010..Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data... - Sequencing the nuclear genome of the extinct woolly mammothWebb Miller
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA
Nature 456:387-90. 2008..This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction... - A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genomeTravis N Mavrich
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 18:1073-83. 2008..3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping... - Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restorationWeisheng Wu
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 21:1659-71. 2011..These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors... - Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiaeJi Qi
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA
BMC Genomics 10:475. 2009..Differences at the nucleotide level associated with COs and NCOs enable us to detect these recombination events and their distributions... - Nucleosome organization in the Drosophila genomeTravis N Mavrich
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Nature 453:358-62. 2008..At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines... - Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)Webb Miller
Pennsylvania State University, University Park, PA 16802, USA
Proc Natl Acad Sci U S A 108:12348-53. 2011..Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations... - Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate changeWebb Miller
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA
Proc Natl Acad Sci U S A 109:E2382-90. 2012.... - Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum AcidobacteriaAmaya M Garcia Costas
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
Environ Microbiol 14:177-90. 2012..Some transposases were homologous to those of mat community members from other phyla... - inGAP: an integrated next-generation genome analysis pipelineJi Qi
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA
Bioinformatics 26:127-9. 2010..inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly. AVAILABILITY: inGAP is available at http://sites.google.com/site/nextgengenomics/ingap.. - Polymorphic integrations of an endogenous gammaretrovirus in the mule deer genomeDaniel Elleder
Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
J Virol 86:2787-96. 2012..The discovery of a novel transcriptionally active and insertionally polymorphic retrovirus in mammals could provide a useful model system to study the dynamic interaction between the host genome and an invading retrovirus... - The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)Webb Miller
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA
Genome Res 19:213-20. 2009..This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes... - Ancestral polyploidy in seed plants and angiospermsYuannian Jiao
Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Nature 473:97-100. 2011.... - Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in DictyosteliumGue Su Chang
Center for Eukaryotic Gene Regulation and Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
Genome Res 22:1098-106. 2012..Indeed, we find a strong phylogenetic relationship between the presence of the NELF pausing factor and positioning of the +1 nucleosome. Pausing and +1 nucleosome positioning may have coevolved in animals... - Calling SNPs without a reference sequenceAakrosh Ratan
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA
BMC Bioinformatics 11:130. 2010.... - Tracking the past: interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigeniusFangqing Zhao
Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 19:1384-92. 2009..Comparisons of the transposable elements (TEs) between mammoth and other mammals may shed light on the evolutionary history of TEs in various mammalian lineages... - Nodeomics: pathogen detection in vertebrate lymph nodes using meta-transcriptomicsNicola E Wittekindt
Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
PLoS ONE 5:e13432. 2010..Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals... - Aye-aye population genomic analyses highlight an important center of endemism in northern MadagascarGeorge H Perry
Departments of Anthropology and Biology and Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802
Proc Natl Acad Sci U S A 110:5823-8. 2013..To help facilitate future ecological- and conservation-motivated population genomic analyses by noncomputational biologists, the analytical toolkit used in this study is available on the Galaxy Web site... - Chestnut resistance to the blight disease: insights from transcriptome analysisAbdelali Barakat
The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA
BMC Plant Biol 12:38. 2012.... - Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial matZhenfeng Liu
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
ISME J 5:1279-90. 2011.... - Comparison of next generation sequencing technologies for transcriptome characterizationP Kerr Wall
Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
BMC Genomics 10:347. 2009..19). We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica) and the magnoliid avocado (Persea americana) using a variety of methods for cDNA synthesis... - Comparison of sequencing platforms for single nucleotide variant calls in a human sampleAakrosh Ratan
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, USA
PLoS ONE 8:e55089. 2013.... - Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environmentJennifer F Biddle
Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA
Proc Natl Acad Sci U S A 105:10583-8. 2008..These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups... - Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expressionYong Cheng
Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 19:2172-84. 2009..More broadly, these studies illustrate how a "master regulator" transcription factor coordinates tissue differentiation through a panoply of DNA and protein interactions... - Poor Man's 1000 Genome Project: Recent Human Population Expansion Confounds the Detection of Disease Alleles in 7,098 Complete Mitochondrial GenomesHie Lim Kim
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University University Park, PA, USA
Front Genet 4:13. 2013..This result showed the difficulty of detecting a pathogenic mutation within an abundance of rare variants in the human population, even with a large number of genomes available for study... - Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogensJihye Park
Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, USA
BMC Genomics 13:545. 2012..The compelling picture from previous comparisons of the three sequenced genomes was of genome degradation, with substantial loss of genome content (up to 24%) associated with adaptation to humans... 
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genomeIstvan Albert
Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Nature 446:572-6. 2007..Transcriptional start sites tended to reside about one helical turn inside the nucleosome border. These findings reveal an intimate relationship between chromatin architecture and the underlying DNA sequence it regulates...- Whole-genome shotgun sequencing of mitochondria from ancient hair shaftsM Thomas P Gilbert
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
Science 317:1927-30. 2007..The method therefore sets the stage for molecular-genetic analysis of museum collections... - Microbial community gene expression in ocean surface watersJorge Frias-Lopez
Departments of Civil and Environmental Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 105:3805-10. 2008..Thus, microbial community transcriptomic analyses revealed not only indigenous gene- and taxon-specific expression patterns but also gene categories undetected in previous DNA-based metagenomic surveys... - Characterization of large-insert DNA libraries from soil for environmental genomic studies of ArchaeaAlexander H Treusch
Institute of Microbiology and Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
Environ Microbiol 6:970-80. 2004..We thereby extend the genomic information of uncultivated crenarchaeota from soil and offer hints to specific metabolic traits present in this group... - Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegansKwang-Zin Lee
, , Spemannstrasse 37, , Germany
Nucleic Acids Res 31:2553-60. 2003..Thus, intrachromosomal rearrange ments occur frequently in nematodes, limiting the likelihood of identifying orthologous genes of P.pacificus and C.elegans based on positional information within the two genomes... - Transcriptional regulation by antitermination. Interaction of RNA with NusB protein and NusB/NusE protein complex of Escherichia coliHolger Lüttgen
Lehrstuhl fur Organische Chemie und Biochemie, Technische Universitat Munchen, Garching, Germany
J Mol Biol 316:875-85. 2002..Replacement of bases in the terminal segments of the boxA RNA motif caused minor chemical shift changes as compared to base exchanges in the central part of the dodecameric boxA motif... - Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomesM Thomas P Gilbert
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
Proc Natl Acad Sci U S A 105:8327-32. 2008..Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep... - Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcaniiAlexander Zaigler
, Biozentrum Niederursel, , Marie-Curie-Str 9, D-60439 Frankfurt, Germany
Mol Microbiol 48:1089-105. 2003..Analysis of the results revealed that onefold-coverage shotgun DNA microarrays are well suited to characterize the regulation of metabolic pathways as well as protein complexes in response to changes in environmental conditions... - A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspectiveSnjezana Rendulic
Max-Planck-Institute for Developmental Biology, , Germany
Science 303:689-92. 2004..A plethora of paralogous gene families coding for enzymes, such as hydrolases and transporters, are used throughout the life cycle of B. bacteriovorus for prey entry, prey killing, and the uptake of complex molecules... - Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical dataBettina Siebers
Department of Microbiology, Universitat Duisburg Essen, 45117 Essen, Germany
J Bacteriol 186:2179-94. 2004..Almost all genes necessary for glycogen and trehalose metabolism were identified in the T. tenax genome... - Whole-genome prokaryotic phylogenyStefan R Henz
, Sand 14, , Germany
Bioinformatics 21:2329-35. 2005..In this approach, first Blast is used to compare genomes, then a distance matrix is computed, and finally a tree- or network-reconstruction method such as UPGMA, Neighbor-Joining, BioNJ or Neighbor-Net is applied... - Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factorsHenri L Saenz
Focal Area Infection Biology, Biozentrum, University of Basel, CH 4056 Basel, Switzerland
Nat Genet 39:1469-76. 2007..bacilliformis, and one has been lost by deletion. The 14 pathogenicity genes specific for the radiating lineage encode two laterally acquired type IV secretion systems, suggesting that these systems have a role in host adaptability... - Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequenceFrank Thieme
, , Weinbergweg 10, D-06120 Halle (Saale, Germany
J Bacteriol 187:7254-66. 2005..Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides... - Metagenomics to paleogenomics: large-scale sequencing of mammoth DNAHendrik N Poinar
McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada
Science 311:392-4. 2006..The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics... - Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestorGregory J Velicer
Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
Proc Natl Acad Sci U S A 103:8107-12. 2006..These results provide insight into the genetic basis of two large adaptive transitions in a social bacterium... - OSLay: optimal syntenic layout of unfinished assembliesDaniel C Richter
Center for Bioinformatics ZBIT, Institute for Computer Science, Tubingen University, 72076 Tubingen, Germany
Bioinformatics 23:1573-9. 2007..Related genome sequences can be used to layout contigs in an assembly. AVAILABILITY: OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay... - Complete genome sequence of the myxobacterium Sorangium cellulosumSusanne Schneiker
Department of Genetics, Bielefeld University, PO Box 100131, D 33501 Bielefeld, Germany
Nat Biotechnol 25:1281-9. 2007..Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry... - BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparisonDaniela Bartels
, Center for Biotechnology (CeBiTec) D-33594 Bielefeld, Germany
Bioinformatics 21:853-9. 2005..The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries...