Joel Rozowsky

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
    Andrea Sboner
    Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, New Haven, CT 06511, USA
    Genome Biol 11:R104. 2010
  2. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
  3. pmc AlleleSeq: analysis of allele-specific expression and binding in a network framework
    Joel Rozowsky
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Mol Syst Biol 7:522. 2011
  4. pmc The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
    Joel S Rozowsky
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:732-45. 2007
  5. pmc Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    Chao Cheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 22:1658-67. 2012
  6. pmc Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
    Philippe Lefrançois
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    BMC Genomics 10:37. 2009
  7. pmc A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets
    Chao Cheng
    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA
    Genome Biol 12:R15. 2011
  8. ncbi request reprint Architecture of the human regulatory network derived from ENCODE data
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Nature 489:91-100. 2012
  9. pmc Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
    Zhi John Lu
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 21:276-85. 2011
  10. pmc Modeling ChIP sequencing in silico with applications
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS Comput Biol 4:e1000158. 2008

Collaborators

Detail Information

Publications37

  1. pmc FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
    Andrea Sboner
    Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, New Haven, CT 06511, USA
    Genome Biol 11:R104. 2010
    ..It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements...
  2. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information...
  3. pmc AlleleSeq: analysis of allele-specific expression and binding in a network framework
    Joel Rozowsky
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Mol Syst Biol 7:522. 2011
    ..Furthermore, we investigate the coordination between ASE and ASB from multiple transcription factors events using a regulatory network framework. Correlation analyses and network motifs show mostly coordinated ASB and ASE...
  4. pmc The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
    Joel S Rozowsky
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:732-45. 2007
    ..Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously...
  5. pmc Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    Chao Cheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 22:1658-67. 2012
    ..The models imply that these features regulate transcription in a highly coordinated manner...
  6. pmc Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
    Philippe Lefrançois
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    BMC Genomics 10:37. 2009
    ....
  7. pmc A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets
    Chao Cheng
    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA
    Genome Biol 12:R15. 2011
    ..Moreover, our framework reveals the positional contribution around genes (upstream or downstream) of distinct chromatin features to the overall prediction of expression levels...
  8. ncbi request reprint Architecture of the human regulatory network derived from ENCODE data
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Nature 489:91-100. 2012
    ..The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease...
  9. pmc Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
    Zhi John Lu
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 21:276-85. 2011
    ..Overall, our study identifies many new potential ncRNAs in C. elegans and provides a method that can be adapted to other organisms...
  10. pmc Modeling ChIP sequencing in silico with applications
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS Comput Biol 4:e1000158. 2008
    ..This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion...
  11. pmc Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data
    Chao Cheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
    PLoS Comput Biol 7:e1002190. 2011
    ..As more and more genome-wide ChIP-Seq and RNA-Seq data becomes available in the near future, our methods of data integration have various potential applications...
  12. ncbi request reprint Divergence of transcription factor binding sites across related yeast species
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Science 317:815-9. 2007
    ..Transcription factor binding sites have therefore diverged substantially faster than ortholog content. Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species...
  13. pmc RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
    Lukas Habegger
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    Bioinformatics 27:281-3. 2011
    ..Availability and implementation: RSEQtools is implemented in C and the source code is available at http://rseqtools.gersteinlab.org/...
  14. pmc Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
    Science 330:1775-87. 2010
    ..Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome...
  15. pmc Mapping accessible chromatin regions using Sono-Seq
    Raymond K Auerbach
    Program in Computational Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 106:14926-31. 2009
    ..Furthermore, our results provide insights into the mapping of binding sites by using ChIP-Seq experiments and the value of reference samples that should be used in such experiments...
  16. pmc Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    Kevin Y Yip
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R48. 2012
    ..While this large amount of data creates a valuable resource, it is nonetheless overwhelmingly complex and simultaneously incomplete since it covers only a small fraction of all human transcription factors...
  17. pmc VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
    Lukas Habegger
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 28:2267-9. 2012
    ..Finally, in order to enable on-demand access and to minimize unnecessary transfers of large data files, VAT can be run as a virtual machine in a cloud-computing environment...
  18. ncbi request reprint Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Funct Integr Genomics 7:335-45. 2007
    ..The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available...
  19. doi request reprint Annotating non-coding regions of the genome
    Roger P Alexander
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Nat Rev Genet 11:559-71. 2010
    ..Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis...
  20. pmc ACT: aggregation and correlation toolbox for analyses of genome tracks
    Justin Jee
    Program in Computational Biology and Bioinformatics, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
    Bioinformatics 27:1152-4. 2011
    ..Here, we explain the components of the toolbox in more detail and apply them in various contexts...
  21. pmc Variation in transcription factor binding among humans
    Maya Kasowski
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 328:232-5. 2010
    ..Our results indicate that many differences in individuals and species occur at the level of TF binding, and they provide insight into the genetic events responsible for these differences...
  22. pmc Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays
    Ashish Agarwal
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    BMC Genomics 11:383. 2010
    ..Understanding the relative merits of these technologies will help researchers select the appropriate technology for their needs...
  23. pmc Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays
    Michael Seringhaus
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    BMC Genomics 9:635. 2008
    ..Here, we present the results of two large-scale microarray experiments on S. cerevisiae and H. sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions...
  24. pmc Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
    Olof Emanuelsson
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:886-97. 2007
    ..Finally, our experiments reveal a significant amount of novel transcription outside of known genes, and an appreciable sample of this was validated by independent experiments...
  25. pmc Tilescope: online analysis pipeline for high-density tiling microarray data
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 8:R81. 2007
    ..The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis...
  26. pmc Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome
    Jia Qian Wu
    Molecular, Cellular and Developmental Biology Department, KBT918, Yale University, New Haven, Connecticut 06511, USA
    Genome Biol 9:R3. 2008
    ..However, there is still much uncertainty regarding precisely what portion of the genome is transcribed, the exact structures of these novel transcripts, and the levels of the transcripts produced...
  27. pmc Tiling array data analysis: a multiscale approach using wavelets
    Alexander Karpikov
    Diagnostic Radiology, Yale University, New Haven, CT, USA
    BMC Bioinformatics 12:57. 2011
    ..In doing this, we used specific wavelet basis functions, Coiflets, since their triangular shape closely resembles the expected profiles of true ChIP-chip peaks...
  28. ncbi request reprint Major molecular differences between mammalian sexes are involved in drug metabolism and renal function
    John L Rinn
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Dev Cell 6:791-800. 2004
    ..We conclude that there are persistent differences in gene expression between adult males and females. These molecular differences have important implications for the physiological differences between males and females...
  29. ncbi request reprint What is a gene, post-ENCODE? History and updated definition
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
    Genome Res 17:669-81. 2007
    ..It also manifests how integral the concept of biological function is in defining genes...
  30. ncbi request reprint A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
    Jiang Du
    Department of Computer Science, Yale University, New Haven, CT 06520, USA
    Bioinformatics 22:3016-24. 2006
    ..Here we propose a supervised framework for doing this. It has the advantage of explicitly incorporating validated biological knowledge into the model and allowing for formal training and testing...
  31. pmc Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification
    Thomas E Royce
    Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, USA
    Nucleic Acids Res 35:e99. 2007
    ..Taken together, our results provide proof-of-principle for probing nucleic acid targets with off-target, nearest-neighbor features...
  32. pmc Design optimization methods for genomic DNA tiling arrays
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CN 06520, USA P50 HG02357
    Genome Res 16:271-81. 2006
    ..A Web resource has also been developed, accessible at http://tiling.gersteinlab.org, to generate optimal tile paths from user-provided DNA sequences...
  33. ncbi request reprint Global identification of human transcribed sequences with genome tiling arrays
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8103, USA
    Science 306:2242-6. 2004
    ..A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins...
  34. pmc Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies
    Ghia M Euskirchen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    Genome Res 17:898-909. 2007
    ..Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies...
  35. ncbi request reprint Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies
    Thomas E Royce
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
    Methods Enzymol 411:282-311. 2006
    ..In so doing, we will assume little or no prior training in statistics of the reader. Areas covered include background correction, intensity normalization, spatial normalization, and the testing of statistical significance...
  36. ncbi request reprint Assessing the need for sequence-based normalization in tiling microarray experiments
    Thomas E Royce
    Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 23:988-97. 2007
    ..Any biases in tiling array signals must be systematically removed to achieve this goal...
  37. pmc Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    Thomas E Royce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Trends Genet 21:466-75. 2005
    ..We introduce the informatics challenges arising in the analysis of tiling microarray experiments as open problems to the scientific community and present initial approaches for the analysis of this nascent technology...