Research Topics
Species | Joel RozowskySummaryAffiliation: Yale University Country: USA Publications
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Detail Information
Publications
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing dataAndrea 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...- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controlsJoel 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... - The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel lociJoel 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... - AlleleSeq: analysis of allele-specific expression and binding in a network frameworkJoel 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... - Efficient yeast ChIP-Seq using multiplex short-read DNA sequencingPhilippe Lefrançois
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
BMC Genomics 10:37. 2009.... - A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasetsChao 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... 
Architecture of the human regulatory network derived from ENCODE dataMark 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...- Modeling ChIP sequencing in silico with applicationsZhengdong 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... - Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array dataZhi 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... - Construction and analysis of an integrated regulatory network derived from high-throughput sequencing dataChao 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... 
Divergence of transcription factor binding sites across related yeast speciesAnthony 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...- RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summariesLukas 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/... - Integrative analysis of the Caenorhabditis elegans genome by the modENCODE projectMark 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... - Mapping accessible chromatin regions using Sono-SeqRaymond 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... - Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platformsAnthony 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... - Annotating non-coding regions of the genomeRoger 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... - ACT: aggregation and correlation toolbox for analyses of genome tracksJustin 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. AVAILABILITY: ACT is available at http://act.gersteinlab.org CONTACT: pi@gersteinlab.org... - VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environmentLukas Habegger
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
Bioinformatics 28:2267-9. 2012..AVAILABILITY AND IMPLEMENTATION: VAT is implemented in C and PHP. The VAT web service, Amazon Machine Image, source code and detailed documentation are available at vat.gersteinlab.org... - Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factorsKevin 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... - Variation in transcription factor binding among humansMaya 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... - Understanding transcriptional regulation by integrative analysis of transcription factor binding dataChao 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... - Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarraysMichael 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... - Comparison and calibration of transcriptome data from RNA-Seq and tiling arraysAshish 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... - Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genomeOlof 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... - Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genomeJia 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... - Tiling array data analysis: a multiscale approach using waveletsAlexander 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... - Tilescope: online analysis pipeline for high-density tiling microarray dataZhengdong 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... - Major molecular differences between mammalian sexes are involved in drug metabolism and renal functionJohn 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... - What is a gene, post-ENCODE? History and updated definitionMark 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... - Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identificationThomas 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... - A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledgeJiang Du
Department of Computer Science, Yale University, New Haven, CT 06520, USA
Bioinformatics 22:3016-24. 2006..This latter result has strong implications for the optimum way medium-scale validation experiments should be carried out to verify the results of the genome-scale tiling array experiments... - Design optimization methods for genomic DNA tiling arraysPaul 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... - Global identification of human transcribed sequences with genome tiling arraysPaul 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... - Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologiesGhia 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... - Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologiesThomas 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... - Assessing the need for sequence-based normalization in tiling microarray experimentsThomas 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... - Issues in the analysis of oligonucleotide tiling microarrays for transcript mappingThomas E Royce
NASA ARC
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...