Li San Wang

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. pmc Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
    Qi Zheng
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS Genet 6:e1001141. 2010
  2. pmc Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential
    Jay E Johnson
    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 38:1114-22. 2010
  3. pmc High-throughput identification of long-range regulatory elements and their target promoters in the human genome
    Yih Chii Hwang
    Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 41:4835-46. 2013
  4. pmc Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6
    Paul E Turner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    BMC Evol Biol 12:153. 2012
  5. pmc Comparison of xMAP and ELISA assays for detecting cerebrospinal fluid biomarkers of Alzheimer's disease
    Li San Wang
    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
    J Alzheimers Dis 31:439-45. 2012
  6. doi request reprint The impact of multiple protein sequence alignment on phylogenetic estimation
    Li San Wang
    Department of Pathology and Laboratory Medicine and Penn Center for Bioinformatics, 1424 Blockley Hall, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104, USA
    IEEE/ACM Trans Comput Biol Bioinform 8:1108-19. 2011
  7. pmc Population-based study of genetic variation in individuals with autism spectrum disorders from Croatia
    Li San Wang
    Department of Pathology, Laboratory Medicine, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia 19104, USA
    BMC Med Genet 11:134. 2010
  8. doi request reprint Global analysis of RNA secondary structure in two metazoans
    Fan Li
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell Rep 1:69-82. 2012
  9. pmc Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach
    Liying Cui
    Department of Biology, Institute of Molecular Evolutionary Genetics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Evol Biol 6:13. 2006
  10. pmc Comparison of cerebrospinal fluid levels of tau and Aβ 1-42 in Alzheimer disease and frontotemporal degeneration using 2 analytical platforms
    David J Irwin
    Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
    Arch Neurol 69:1018-25. 2012

Detail Information

Publications40

  1. pmc Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
    Qi Zheng
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS Genet 6:e1001141. 2010
    ..Overall, our findings highlight the importance of base-paired RNAs in eukaryotes and present an approach that should be widely applicable for the analysis of this key structural feature of RNA...
  2. pmc Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential
    Jay E Johnson
    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 38:1114-22. 2010
    ..These findings indicate that, like Sgs1, WRN and BLM can regulate transcription globally by targeting G4-DNA...
  3. pmc High-throughput identification of long-range regulatory elements and their target promoters in the human genome
    Yih Chii Hwang
    Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 41:4835-46. 2013
    ..In total, our study presents a novel high-throughput workflow for confident, genome-wide discovery of enhancer-target promoter pairs, which will significantly improve our understanding of these regulatory interactions...
  4. pmc Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6
    Paul E Turner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    BMC Evol Biol 12:153. 2012
    ..The resulting tree yielded 32 clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits (fitness on original and novel hosts)...
  5. pmc Comparison of xMAP and ELISA assays for detecting cerebrospinal fluid biomarkers of Alzheimer's disease
    Li San Wang
    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
    J Alzheimers Dis 31:439-45. 2012
    ....
  6. doi request reprint The impact of multiple protein sequence alignment on phylogenetic estimation
    Li San Wang
    Department of Pathology and Laboratory Medicine and Penn Center for Bioinformatics, 1424 Blockley Hall, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104, USA
    IEEE/ACM Trans Comput Biol Bioinform 8:1108-19. 2011
    ..We discuss these observations and implications for future work...
  7. pmc Population-based study of genetic variation in individuals with autism spectrum disorders from Croatia
    Li San Wang
    Department of Pathology, Laboratory Medicine, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia 19104, USA
    BMC Med Genet 11:134. 2010
    ..Genome-wide studies on autism spectrum disorders (ASDs) have mostly focused on large-scale population samples, but examination of rare variations in isolated populations may provide additional insights into the disease pathogenesis...
  8. doi request reprint Global analysis of RNA secondary structure in two metazoans
    Fan Li
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell Rep 1:69-82. 2012
    ..Overall, our findings provide a global assessment of RNA folding in animals...
  9. pmc Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach
    Liying Cui
    Department of Biology, Institute of Molecular Evolutionary Genetics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Evol Biol 6:13. 2006
    ....
  10. pmc Comparison of cerebrospinal fluid levels of tau and Aβ 1-42 in Alzheimer disease and frontotemporal degeneration using 2 analytical platforms
    David J Irwin
    Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
    Arch Neurol 69:1018-25. 2012
    ..To use values of cerebrospinal fluid tau and β-amyloid obtained from 2 different analytical immunoassays to differentiate Alzheimer disease (AD) from frontotemporal lobar degeneration (FTLD)...
  11. pmc Genomic landscape of a three-generation pedigree segregating affective disorder
    Shuzhang Yang
    Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 4:e4474. 2009
    ..Our analysis suggests that family based studies of the combined effect of common and rare CNVs at many loci may represent a useful approach in the genetic analysis of disease susceptibility of mental disorders...
  12. ncbi request reprint Transcriptional target prediction using qualitative reasoning
    Li San Wang
    Dept of Biol, Univ of Pennsylvania, Philadelphia, PA 19104, USA
    Conf Proc IEEE Eng Med Biol Soc 1:3138-41. 2006
    ..Our new algorithm performed comparably to published approaches and allowed rapid analysis of complex, multiple gene selection criteria...
  13. pmc Comparative survey of the topographical distribution of signature molecular lesions in major neurodegenerative diseases
    Steven E Arnold
    Penn Memory Center, Departments of Psychiatry and Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104
    J Comp Neurol 521:4339-55. 2013
    ....
  14. ncbi request reprint Enhanced position weight matrices using mixture models
    Sridhar Hannenhalli
    Department of Genetics, University of Pennsylvania Philadelphia, PA 19104, USA
    Bioinformatics 21:i204-12. 2005
    ..Intuitively, the subclasses correspond to either distinct binding preference of the same transcription factor in different contexts or distinct subtypes of the transcription factor...
  15. pmc Analysis of nonlinear gene expression progression reveals extensive pathway and age-specific transitions in aging human brains
    Kajia Cao
    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e74578. 2013
    ..Our study reveals age-correlated expression changes at particular age points and allows one to estimate the age of an individual with better accuracy than previously published methods. ..
  16. ncbi request reprint Dense subgraph computation via stochastic search: application to detect transcriptional modules
    Logan Everett
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Bioinformatics 22:e117-23. 2006
    ..This is just one context in which an efficient computation of dense subgraphs in a multi-partite graph is needed...
  17. pmc The cobweb of life revealed by genome-scale estimates of horizontal gene transfer
    Fan Ge
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    PLoS Biol 3:e316. 2005
    ..We propose that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches...
  18. pmc Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study
    Mi Ryung Han
    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Neurol 10:90. 2010
    ..We carried out a genome-wide association study (GWAS) in order to better define the genetic backgrounds to these three states in relation to CSF levels...
  19. pmc SAVoR: a server for sequencing annotation and visualization of RNA structures
    Fan Li
    Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
    Nucleic Acids Res 40:W59-64. 2012
    ..These values can then be visualized on a customizable secondary structure model. SAVoR is freely available at http://tesla.pcbi.upenn.edu/savor...
  20. pmc DRAW+SneakPeek: analysis workflow and quality metric management for DNA-seq experiments
    Chiao Feng Lin
    Department of Pathology and Laboratory Medicine and Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA, Department of Physics, University of Washington, Seattle, WA 98105, USA, Genomics and Computational Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA and Department of Pathology and Laboratory Medicine, The Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
    Bioinformatics 29:2498-500. 2013
    ..Both DRAW and SneakPeek are freely available under the MIT license, and are available as Amazon machine images to be used directly on Amazon cloud with minimal installation...
  21. pmc Correcting population stratification in genetic association studies using a phylogenetic approach
    Mingyao Li
    Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Bioinformatics 26:798-806. 2010
    ....
  22. pmc CoRAL: predicting non-coding RNAs from small RNA-sequencing data
    Yuk Yee Leung
    Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 41:e137. 2013
    ..The ability to reliably annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using small RNA sequencing data in less well-characterized organisms. ..
  23. pmc Frequency and clinicopathological characteristics of presenilin 1 Gly206Ala mutation in Puerto Rican Hispanics with dementia
    Steven E Arnold
    Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Alzheimers Dis 33:1089-95. 2013
    ..Considered together with the increased prevalence and mortality of AD reported in Puerto Rico, these high rates may reflect hereditary risk concentrated in the island which warrants further study...
  24. pmc Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs
    Paul Ryvkin
    Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Methods 67:28-35. 2014
    ..CoRAL is available at http://wanglab.pcbi.upenn.edu/coral/. ..
  25. pmc Computational approaches to the detection and analysis of sequences with intramolecular G-quadruplex forming potential
    Paul Ryvkin
    Department of Pathology, Penn Center for Bioinformatics, and Graduate Group in Genomics and Computational Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    Methods Mol Biol 608:39-50. 2010
    ..We also discuss methods for assessing the significance and specificity of associations between the sequences and different biological functions...
  26. pmc Fine mapping of genetic variants in BIN1, CLU, CR1 and PICALM for association with cerebrospinal fluid biomarkers for Alzheimer's disease
    John S K Kauwe
    Department of Biology, Brigham Young University, Provo, Utah, United States of America
    PLoS ONE 6:e15918. 2011
    ..Our results suggest that these variants do not affect risk via a mechanism that results in a strong additive effect on CSF levels of Aβ(42) or ptau(181)...
  27. pmc Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence
    Jesse M Platt
    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genes Dev 27:1406-20. 2013
    ..Rap1 relocalization is thus a novel mechanism connecting DNA damage responses (DDRs) at telomeres to global changes in chromatin and gene expression while driving the pace of senescence. ..
  28. pmc Cellular, synaptic, and biochemical features of resilient cognition in Alzheimer's disease
    Steven E Arnold
    Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
    Neurobiol Aging 34:157-68. 2013
    ..These data characterize cellular and synaptic features and identify novel biochemical targets that may be associated with resilient cognitive brain aging in the setting of pathological AD...
  29. pmc TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance
    Larry N Singh
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 35:7360-71. 2007
    ..The application of TREMOR on human muscle-specific, liver-specific and cell-cycle-related genes reveals TFs and TMs that were validated from literature and also reveals additional related genes...
  30. ncbi request reprint Distance-based genome rearrangement phylogeny
    Li San Wang
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Mol Evol 63:473-83. 2006
    ..Our study shows that tree reconstruction under these two methods is much more accurate when based on EDE distances than when based on other distances previously suggested for whole genomes...
  31. pmc The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila
    Nan Liu
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Nature 482:519-23. 2012
    ....
  32. pmc Design of comprehensive Alzheimer's disease centers to address unmet national needs
    John Q Trojanowski
    Institute on Aging, Philadelphia, PA, USA
    Alzheimers Dement 6:150-5. 2010
    ..The intent of this position paper is to stimulate thinking and foster the development of other or alternative models for a systematic approach to the study of dementia and movement disorders...
  33. pmc Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae
    Steve G Hershman
    College of Arts and Sciences and Vagelos Scholars Program, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 36:144-56. 2008
    ..These findings raise the possibility that QFP sequences form bona fide G-quadruplexes in vivo and thus regulate transcription...
  34. pmc Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions
    Vivianna M Van Deerlin
    1 Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA 2 These authors contributed equally to this work
    Nat Genet 42:234-9. 2010
    ..TMEM106B variants also contribute to genetic risk for FTLD-TDP in individuals with mutations in GRN. Our data implicate variants in TMEM106B as a strong risk factor for FTLD-TDP, suggesting an underlying pathogenic mechanism...
  35. pmc Selection of individual VH genes occurs at the pro-B to pre-B cell transition
    Wenzhao Meng
    Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Immunol 187:1835-44. 2011
    ....
  36. pmc Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis
    David C Whitcomb
    Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
    Nat Genet 44:1349-54. 2012
    ..These results could partially explain the high frequency of alcohol-related pancreatitis in men (male hemizygote frequency is 0.26, whereas female homozygote frequency is 0.07)...
  37. pmc A Bayesian approach to efficient differential allocation for resampling-based significance testing
    Shane T Jensen
    Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Bioinformatics 10:198. 2009
    ..Using resampling-based procedures for multiple testing is computationally intensive and typically requires large numbers of resamples...
  38. pmc Analyzing Copy Number Variation Using SNP Array Data: Protocols for Calling CNV and Association Tests
    Chiao Feng Lin
    Department of Pathology and Laboratory Medicine and Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
    Curr Protoc Hum Genet 79:1.27.1-1.27.15. 2013
    ..Curr. Protoc. Hum. Genet. 79:1.27.1-1.27.15. © 2013 by John Wiley & Sons, Inc. ..
  39. pmc Potent obatoclax cytotoxicity and activation of triple death mode killing across infant acute lymphoblastic leukemia
    Karen A Urtishak
    Division of Oncology, Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
    Blood 121:2689-703. 2013
    ..This in vitro obatoclax activity and its multiple killing mechanisms across molecular cytogenetic subsets provide a rationale to incorporate a similarly acting compound into combination strategies to combat infant ALL...