Zhiping Weng

Summary

Affiliation: Boston University
Country: USA

Publications

  1. ncbi request reprint FAST: a novel protein structure alignment algorithm
    Jianhua Zhu
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 58:618-27. 2005
  2. ncbi request reprint Computational determination of the structure of rat Fc bound to the neonatal Fc receptor
    Z Weng
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    J Mol Biol 282:217-25. 1998
  3. ncbi request reprint Managing biological sequence and protein structure data
    Zhiping Weng
    Department of Biomedical Engineering, Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    OMICS 7:25-6. 2003
  4. ncbi request reprint A novel shape complementarity scoring function for protein-protein docking
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 51:397-408. 2003
  5. ncbi request reprint Protein-Protein Docking Benchmark 2.0: an update
    Julian Mintseris
    Boston University Bioinformatics Program, Boston, Massachusetts 02215, USA
    Proteins 60:214-6. 2005
  6. ncbi request reprint ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 60:207-13. 2005
  7. ncbi request reprint The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 69:719-25. 2007
  8. pmc CARRIE web service: automated transcriptional regulatory network inference and interactive analysis
    Peter M Haverty
    Bioinformatics Program and Biomedical Engineering Department, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W213-6. 2004
  9. ncbi request reprint M-ZDOCK: a grid-based approach for Cn symmetric multimer docking
    Brian Pierce
    Bioinformatics Program, Boston University, Boston, MA, USA
    Bioinformatics 21:1472-8. 2005
  10. pmc SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
    Zhenjun Hu
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W235-41. 2004

Collaborators

Detail Information

Publications75

  1. ncbi request reprint FAST: a novel protein structure alignment algorithm
    Jianhua Zhu
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 58:618-27. 2005
    ..Typical pairwise alignments take FAST less than a second with a Pentium III 1.2GHz CPU. FAST software and a web server are available at http://biowulf.bu.edu/FAST/...
  2. ncbi request reprint Computational determination of the structure of rat Fc bound to the neonatal Fc receptor
    Z Weng
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    J Mol Biol 282:217-25. 1998
    ....
  3. ncbi request reprint Managing biological sequence and protein structure data
    Zhiping Weng
    Department of Biomedical Engineering, Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    OMICS 7:25-6. 2003
  4. ncbi request reprint A novel shape complementarity scoring function for protein-protein docking
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 51:397-408. 2003
    ..Our docking program ZDOCK has been parallelized and the average computing time is 4 minutes using sixteen IBM SP3 processors. Both ZDOCK and the benchmark are freely available to academic users (http://zlab.bu.edu/~ rong/dock)...
  5. ncbi request reprint Protein-Protein Docking Benchmark 2.0: an update
    Julian Mintseris
    Boston University Bioinformatics Program, Boston, Massachusetts 02215, USA
    Proteins 60:214-6. 2005
    ..The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2...
  6. ncbi request reprint ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 60:207-13. 2005
    ..These results are evidence that ZDOCK in combination with RDOCK is capable of making accurate predictions on a diverse set of protein complexes...
  7. ncbi request reprint The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 69:719-25. 2007
    ..Here we outline a practical and successful docking strategy, given limited prior biological knowledge of the complex to be predicted...
  8. pmc CARRIE web service: automated transcriptional regulatory network inference and interactive analysis
    Peter M Haverty
    Bioinformatics Program and Biomedical Engineering Department, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W213-6. 2004
    ..Our service also provides Gene Ontology annotation to aid the user in forming hypotheses about the role of each gene in the cellular response. The CARRIE web service is freely available at http://zlab.bu.edu/CARRIE-web...
  9. ncbi request reprint M-ZDOCK: a grid-based approach for Cn symmetric multimer docking
    Brian Pierce
    Bioinformatics Program, Boston University, Boston, MA, USA
    Bioinformatics 21:1472-8. 2005
    ..In addition, the running times are 30-40% faster for M-ZDOCK. AVAILABILITY: M-ZDOCK is freely available to academic users at http://zlab.bu.edu/m-zdock/ CONTACT: zhiping@bu.edu SUPPLEMENTARY INFORMATION: http://zlab.bu.edu/m-zdock...
  10. pmc SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
    Zhenjun Hu
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W235-41. 2004
    ..bu.edu/SeqVISTA/web.jnlp, provided that Java Web Start has been installed. In addition, a stand-alone version of the program can be downloaded and run locally. It can be obtained at http://zlab.bu.edu/SeqVISTA...
  11. ncbi request reprint Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum
    Liqun Yu
    Department of Neurology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
    Physiol Genomics 23:89-102. 2005
    ..Taken together, these results strongly support the existence of an Egr-2-directed transcriptional regulatory network controlled by striatal A2ARs...
  12. ncbi request reprint Identification of conserved structural features at sequentially degenerate locations in transcription factor binding sites
    Heather E Burden
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Genome Inform 16:49-58. 2005
    ..Availability: ICSF is freely available to academic users at http://zlab.bu.edu/ICSF . Supplementary information: http://zlab.bu.edu/ICSF ...
  13. ncbi request reprint Protein-protein docking: overview and performance analysis
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, MA, USA
    Methods Mol Biol 413:283-314. 2008
    ..Finally, we perform regression analysis to better understand the strengths and weaknesses of ZDOCK and to suggest areas of future development for protein-docking algorithms in general...
  14. pmc MotifViz: an analysis and visualization tool for motif discovery
    Yutao Fu
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 32:W420-3. 2004
    ..For comparison, we have also implemented the simple motif-matching program Possum. MotifViz provides uniform and intuitive input and output formats for all four programs. It can be accessed at http://biowulf.bu.edu/MotifViz...
  15. ncbi request reprint A protein-protein docking benchmark
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 52:88-91. 2003
    ..The benchmark is available at (http://zlab.bu.edu/~rong/dock/benchmark.shtml)...
  16. ncbi request reprint Integrating statistical pair potentials into protein complex prediction
    Julian Mintseris
    Bioinformatics Program, Boston University, Massachusetts 02215, USA
    Proteins 69:511-20. 2007
    ..Furthermore, we show that the new potential performs well on antibody-antigen complexes, with most predictions clustering around the Complementarity Determining Regions of antibodies without any manual intervention...
  17. ncbi request reprint Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences
    Yutao Fu
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Genome Inform 16:68-72. 2005
    ..One of the alignment programs, GLAM, produced comparable matrices in terms of the average ranking of true positive sites across the whole test set of sequences...
  18. ncbi request reprint Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering
    Dmitriy Leyfer
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Bioinformatics 21:ii197-203. 2005
    ..We set out to devise a method that would identify TMs while avoiding arbitrary thresholds on TM sizes and number...
  19. ncbi request reprint Site2genome: locating short DNA sequences in whole genomes
    Martin C Frith
    Bioinformatics Program, Boston University, MA 02215, USA
    Bioinformatics 20:1468-9. 2004
    ..AVAILABILITY: http://zlab.bu.edu/site2genome/..
  20. ncbi request reprint Limited agreement among three global gene expression methods highlights the requirement for non-global validation
    Peter M Haverty
    Bioinformatics Program, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
    Bioinformatics 20:3431-41. 2004
    ..Furthermore, analyses of mRNA abundance distributions indicate limitations in the EBE and SAGE methods at both high- and low-expression levels...
  21. pmc Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling
    Liqun Yu
    Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
    Physiol Genomics 37:199-210. 2009
    ....
  22. pmc Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome
    Hualin Xi
    Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
    PLoS Genet 3:e136. 2007
    ..Finally, we found that approximately 8% of the genome overlaps a DNaseI HS site in at least one the six cell lines studied, indicating that a significant percentage of the genome is potentially functional...
  23. doi request reprint Performance of ZDOCK and ZRANK in CAPRI rounds 13-19
    Howook Hwang
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 78:3104-10. 2010
    ....
  24. ncbi request reprint RDOCK: refinement of rigid-body protein docking predictions
    Li Li
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 53:693-707. 2003
    ..RDOCK is freely available to academic users at http://zlab.bu.edu/ approximately rong/dock...
  25. ncbi request reprint ZDOCK: an initial-stage protein-docking algorithm
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts, USA
    Proteins 52:80-7. 2003
    ..All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/~ rong/dock...
  26. pmc Protein-protein docking benchmark version 3.0
    Howook Hwang
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 73:705-9. 2008
    ..0 will facilitate the development of new algorithms that require a large number of training examples. Benchmark 3.0 is available to the public at http://zlab.bu.edu/benchmark...
  27. ncbi request reprint Less is more: towards an optimal universal description of protein folds
    Joseph D Szustakowski
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Bioinformatics 21:ii66-71. 2005
    ..Here we focus on an intermediate level of regularity. We have developed automated methods to systematically construct a dictionary of supersecondary structures that can be used as 'protein parts' to describe fold-sized structures...
  28. pmc An avidin-like domain that does not bind biotin is adopted for oligomerization by the extracellular mosaic protein fibropellin
    Itai Yanai
    Biomedical Engineering Department, 44 Cummington Street, Boston University, Boston, MA 02215, USA
    Protein Sci 14:417-23. 2005
    ..Finally, based upon the oligomerization of the avidin-like domain, we propose a model for the overall structure of the apical lamina...
  29. pmc Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains
    Brian G Pierce
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Biochemistry 49:7050-9. 2010
    ..These results highlight the complex nature of TCR association and binding and will be informative in future design efforts that combine multiple mutant residues...
  30. pmc Transcription factor binding and modified histones in human bidirectional promoters
    Jane M Lin
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, USA
    Genome Res 17:818-27. 2007
    ....
  31. pmc Cluster-Buster: Finding dense clusters of motifs in DNA sequences
    Martin C Frith
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 31:3666-8. 2003
    ..Cluster-Buster is the third incarnation of our software for finding clusters of pre-specified motifs in DNA sequences. We offer a Cluster-Buster web server at http://zlab.bu.edu/cluster-buster/...
  32. pmc Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification
    Peter M Haverty
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:179-88. 2004
    ..The predicted networks were validated with comparisons to literature sources, experimental TF binding data, and gene ontology biological process information...
  33. pmc Finding functional sequence elements by multiple local alignment
    Martin C Frith
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:189-200. 2004
    ..Detection of transcription factor-binding motifs is limited by the motifs' intrinsic subtlety rather than by inadequacy of the alignment optimization procedure...
  34. pmc The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome
    Yutao Fu
    Bioinformatics Program, Boston University, Boston, Massachusetts, USA
    PLoS Genet 4:e1000138. 2008
    ..We suggest that binding of CTCF provides an anchor point for positioning nucleosomes, and chromatin remodeling is an important component of CTCF function...
  35. pmc PromoSer: improvements to the algorithm, visualization and accessibility
    Anason S Halees
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W191-4. 2004
    ..PromoSer now also supports queries using a SOAP-based interface and XML-based responses. The service is publicly available at http://biowulf.bu.edu/zlab/PromoSer...
  36. ncbi request reprint CisML: an XML-based format for sequence motif detection software
    Peter M Haverty
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Bioinformatics 20:1815-7. 2004
    ..AVAILABILITY: http://zlab.bu.edu/CisML/ SUPPLEMENTARY INFORMATION: Example CisML-formatted data and XSL stylesheets for report generation are available along with the sample output...
  37. pmc Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1
    Hualin Xi
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 17:798-806. 2007
    ..We also discuss the evolutionary advantages of housing a transcriptional element inside the transcript in terms of the migration of these genes in the human genome...
  38. pmc Detection of functional DNA motifs via statistical over-representation
    Martin C Frith
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:1372-81. 2004
    ..It also demonstrates superior performance over two contingency table based over-representation methods. In conclusion, Clover has the potential to greatly accelerate characterization of signals that regulate transcription...
  39. pmc Identification of functional modules that correlate with phenotypic difference: the influence of network topology
    Jui Hung Hung
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA
    Genome Biol 11:R23. 2010
    ..We present a method that takes account of such information - expressed in terms of the topology of a correlation network - and we apply the method in the context of current procedures for gene set enrichment analysis...
  40. pmc Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC
    Jaafar N Haidar
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 74:948-60. 2009
    ..Four of the point mutations that improved binding were then combined to give a mutant TCR that binds the pepMHC 99 times more strongly than the wild-type TCR...
  41. pmc Structure, function, and evolution of transient and obligate protein-protein interactions
    Julian Mintseris
    Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 102:10930-5. 2005
    ..In contrast, the plasticity inherent in transient interactions leads to an increased rate of substitution for the interface residues and leaves little or no evidence of correlated mutations across the interface...
  42. pmc PromoSer: A large-scale mammalian promoter and transcription start site identification service
    Anason S Halees
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 31:3554-9. 2003
    ..The service is publicly available at http://biowulf.bu.edu/zlab/PromoSer/...
  43. ncbi request reprint Systematic detection of statistically overrepresented DNA motif association rules
    Jane Marie Lin
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Genome Inform 17:124-33. 2006
    ..Applying CAYCE to human promoters in 1% of the human genome, we discover that motif clusters containing five repetitions of SP1 are the most statistically significant...
  44. ncbi request reprint Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 47:281-94. 2002
    ..If combined with a post-processing method, our algorithm may provide a general solution to the unbound docking problem. Our program, called ZDOCK, is freely available to academic users (http://zlab.bu.edu/~rong/dock/)...
  45. ncbi request reprint ZDOCK predictions for the CAPRI challenge
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 52:68-73. 2003
    ..Implications of the treatment of prior biological information as well as contributions of manual inspection to docking predictions are also discussed...
  46. pmc A computational framework for optimal masking in the synthesis of oligonucleotide microarrays
    Simon Kasif
    Center for Advanced Genomic Technology, Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 30:e106. 2002
    ..The problem was introduced by Hubbell et al. Here, we formalize the problem, obtain precise bounds on its complexity and devise several computational solutions...
  47. pmc A combination of rescoring and refinement significantly improves protein docking performance
    Brian Pierce
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 72:270-9. 2008
    ..This shows the effective combination of independently developed docking protocols (ZDOCK/ZRANK, and RosettaDock), indicating that using diverse search and scoring functions can improve protein docking results...
  48. ncbi request reprint Characterization of genomic organization of the adenosine A2A receptor gene by molecular and bioinformatics analyses
    Liqun Yu
    Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
    Brain Res 1000:156-73. 2004
    ..This raises the possibility of generating multiple tissue-specific A(2A)R mRNA species by alternative promoters with varying regulatory susceptibility...
  49. ncbi request reprint ZRANK: reranking protein docking predictions with an optimized energy function
    Brian Pierce
    Bioinformatics Program, Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 67:1078-86. 2007
    ..ZRANK can be applied either as a refinement protocol in itself or as a preprocessing stage to enrich the well-ranked hits prior to further refinement...
  50. ncbi request reprint Optimizing protein representations with information theory
    Julian Mintseris
    Bioinformatics Program, Boston University, Boston MA 02215, USA
    Genome Inform 15:160-9. 2004
    ..Implications for further structural studies are discussed...
  51. ncbi request reprint A simple method for improving the specificity of anti-methyl histone antibodies
    Caroline Connor
    Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA
    Epigenetics 5:392-5. 2010
    ....
  52. ncbi request reprint Atomic contact vectors in protein-protein recognition
    Julian Mintseris
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 53:629-39. 2003
    ..With this method, we arrive at a nonredundant set of 209 recognition complexes--the largest set reported so far...
  53. pmc SeqVISTA: a graphical tool for sequence feature visualization and comparison
    Zhenjun Hu
    Bioinformatics Program, Boston University, Boston, MA, 02215, USA
    BMC Bioinformatics 4:1. 2003
    ..But now you want to see what other features have been annotated close by, and this information is buried several screenfuls higher up the web page...
  54. pmc Quantitative analysis of single nucleotide polymorphisms within copy number variation
    SooHyun Lee
    Bioinformatics Program, Boston University, Boston, MA, USA
    PLoS ONE 3:e3906. 2008
    ..This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE...
  55. pmc HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues
    Peter M Haverty
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02115, USA
    Nucleic Acids Res 30:214-7. 2002
    ..We provide interactive tools for researchers to query and visualize our data over the Internet. To facilitate data analysis, we cross-reference each gene on the array with its annotation in the LocusLink database at NCBI...
  56. pmc Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells
    Zarmik Moqtaderi
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Struct Mol Biol 17:635-40. 2010
    ..Our results suggest that human Pol III complexes associate preferentially with regions near functional Pol II promoters and that TFIIIC-mediated recruitment of TFIIIB is regulated in a locus-specific manner...
  57. pmc In silico meets in vivo
    Zhiping Weng
    Bioinformatics Program, Boston University, Cummington Street, Boston, MA 02215, USA
    Genome Biol 9:302. 2008
    ..A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007...
  58. ncbi request reprint Identification and validation of a novel cell-recognition site (KNEED) on the 8th type III domain of fibronectin
    Joyce Y Wong
    Department of Biomedical Engineering, Boston University, MA 02215, USA
    Biomaterials 23:3865-70. 2002
    ..As more sequence and crystallographic data become available, computational approaches may aid in the identification of new targets for applications where biorecognition plays a key role...
  59. pmc Nucleosome positioning signals in genomic DNA
    Heather E Peckham
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Genome Res 17:1170-7. 2007
    ..Finally, we show that intrinsic nucleosome positioning signals are both more inhibitory and more variable in promoter regions than in open reading frames in S. cerevisiae...
  60. ncbi request reprint Protein therapeutics: promises and challenges for the 21st century
    Zhiping Weng
    Biomedical Engineering Department and Bioinformatics Program, Boston University, Boston MA 02215, USA
    Trends Biotechnol 20:29-35. 2002
    ..Taken collectively, these advances will usher in an era of predictive medicine, which will move medical practice from reactive therapy after disease onset, to proactive prevention...
  61. pmc Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences
    Martin C Frith
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston MA 02215, USA
    Nucleic Acids Res 30:3214-24. 2002
    ..Thus, discovery of additional signals that belong to these regulatory regions will be the key to future progress...
  62. pmc Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays
    Ben McNally
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Nano Lett 10:2237-44. 2010
    ..We show that signals from multiple nanopores can be detected simultaneously, allowing straightforward parallelization to large nanopore arrays...
  63. pmc Gene discovery in the auditory system: characterization of additional cochlear-expressed sequences
    Barbara L Resendes
    Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women s Hospital, Boston, MA 02115, USA
    J Assoc Res Otolaryngol 3:45-53. 2002
    ..Identification of additional known genes, ESTs, and cochlear-specific ESTs provides new candidate genes for both syndromic and nonsyndromic deafness disorders...
  64. ncbi request reprint A global map of p53 transcription-factor binding sites in the human genome
    Chia Lin Wei
    Genome Institute of Singapore, Singapore 138672
    Cell 124:207-19. 2006
    ....
  65. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  66. ncbi request reprint Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules
    Bjorn Peters
    Institut fur Biochemie, Charite, Humboldt Universitat Berlin, Monbijoustr 2, 10117 Berlin, Germany
    Bioinformatics 19:1765-72. 2003
    ..g. artificial neural networks). We aim to compare the prediction accuracies of these methods, and quantify the impact of interactions between peptide positions...
  67. pmc Global mapping of c-Myc binding sites and target gene networks in human B cells
    Karen I Zeller
    Department of Medicine and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 103:17834-9. 2006
    ....
  68. pmc Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    David S Johnson
    Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
    Genome Res 18:393-403. 2008
    ..The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated...
  69. ncbi request reprint Main-chain conformational tendencies of amino acids
    Robert J Anderson
    Serono Reproductive Biology Institute, One Technology Place, Rockland, Massachusetts, USA
    Proteins 60:679-89. 2005
    ..In addition to these conclusions, we here present an amino acid substitution table derived from experimental data...
  70. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  71. pmc High-resolution mapping and characterization of open chromatin across the genome
    Alan P Boyle
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Cell 132:311-22. 2008
    ..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
  72. ncbi request reprint Ancestral and consensus envelope immunogens for HIV-1 subtype C
    Denise L Kothe
    Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Virology 352:438-49. 2006
    ..These results establish the utility of centralized HIV-1 subtype C Env immunogens and warrant their continued evaluation as potential components of future AIDS vaccines...
  73. pmc Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:787-97. 2007
    ..Data sets associated with histone modifications have particularly strong correlations. Finally, we show how the correlations between factors change when only regulatory elements far from the transcription start sites are considered...
  74. pmc Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies
    Xiaodong Zhang
    Department of Genetics and Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Nat Methods 5:163-5. 2008
    ..The knock-in approach provides a general solution for the study of proteins to which antibodies are substandard or not available...
  75. pmc Antigenicity and immunogenicity of HIV-1 consensus subtype B envelope glycoproteins
    Denise L Kothe
    Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Virology 360:218-34. 2007
    ....

Research Grants2

  1. Identification of Transcriptional Factor Binding Sites in Human Promoters
    Zhiping Weng; Fiscal Year: 2007
    ..The data generated in this project will be the first systematic functional analysis of TF binding sites at base-pair resolution. ..