Peter J Park

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. ncbi request reprint MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism
    Erica Larschan
    Howard Hughes Medical Institute, Brigham and Women s Hospital, 75 Francis Street, Boston, MA 02115, USA
    Mol Cell 28:121-33. 2007
  2. pmc A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome
    Artyom A Alekseyenko
    Harvard Partners Center for Genetics and Genomics, Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Cell 134:599-609. 2008
  3. pmc Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation
    Marnie E Gelbart
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Struct Mol Biol 16:825-32. 2009
  4. pmc Estimating enrichment of repetitive elements from high-throughput sequence data
    Daniel S Day
    Harvard MIT Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Genome Biol 11:R69. 2010
  5. pmc Combining gene expression data from different generations of oligonucleotide arrays
    Kyu Baek Hwang
    School of Computer Science and Engineering, Seoul National University, Seoul 151 742, Korea
    BMC Bioinformatics 5:159. 2004
  6. pmc ChIP-seq: advantages and challenges of a maturing technology
    Peter J Park
    Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
    Nat Rev Genet 10:669-80. 2009
  7. ncbi request reprint Linking gene expression data with patient survival times using partial least squares
    Peter J Park
    Children s Hospital Informatics Program and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
    Bioinformatics 18:S120-7. 2002
  8. ncbi request reprint Comparing expression profiles of genes with similar promoter regions
    Peter J Park
    Informatics Program and Division of Endocrinology, Children s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
    Bioinformatics 18:1576-84. 2002
  9. ncbi request reprint Epigenetics meets next-generation sequencing
    Peter J Park
    Harvard Medical School Center for Biomedical Informatics, Harvard Partners Center for Genetics and Genomics, HST Informatics Program at Children s Hospital Boston, Boston, Massachusetts 02115, USA
    Epigenetics 3:318-21. 2008
  10. pmc Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context
    Artyom A Alekseyenko
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 8:e1002646. 2012

Research Grants

Detail Information

Publications93

  1. ncbi request reprint MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism
    Erica Larschan
    Howard Hughes Medical Institute, Brigham and Women s Hospital, 75 Francis Street, Boston, MA 02115, USA
    Mol Cell 28:121-33. 2007
    ..Our results support a model in which MSL complex uses high-affinity sites to initially recognize the X chromosome and then associates with many of its targets through sequence-independent features of transcribed genes...
  2. pmc A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome
    Artyom A Alekseyenko
    Harvard Partners Center for Genetics and Genomics, Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Cell 134:599-609. 2008
    ..These results provide strong evidence for both sequence-dependent and -independent steps in MSL targeting of dosage compensation to the male X chromosome...
  3. pmc Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation
    Marnie E Gelbart
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Struct Mol Biol 16:825-32. 2009
    ....
  4. pmc Estimating enrichment of repetitive elements from high-throughput sequence data
    Daniel S Day
    Harvard MIT Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Genome Biol 11:R69. 2010
    ....
  5. pmc Combining gene expression data from different generations of oligonucleotide arrays
    Kyu Baek Hwang
    School of Computer Science and Engineering, Seoul National University, Seoul 151 742, Korea
    BMC Bioinformatics 5:159. 2004
    ..However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform...
  6. pmc ChIP-seq: advantages and challenges of a maturing technology
    Peter J Park
    Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
    Nat Rev Genet 10:669-80. 2009
    ..ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms...
  7. ncbi request reprint Linking gene expression data with patient survival times using partial least squares
    Peter J Park
    Children s Hospital Informatics Program and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
    Bioinformatics 18:S120-7. 2002
    ..The algorithm is fast, as it does not involve any matrix decompositions in the iterations. We apply our method to data sets from lung carcinoma and diffuse large B-cell lymphoma studies to verify its effectiveness...
  8. ncbi request reprint Comparing expression profiles of genes with similar promoter regions
    Peter J Park
    Informatics Program and Division of Endocrinology, Children s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
    Bioinformatics 18:1576-84. 2002
    ..We consider the problem in the opposite direction: we seek to find the genes that have similar promoter regions and determine the extent to which these genes have similar expression profiles...
  9. ncbi request reprint Epigenetics meets next-generation sequencing
    Peter J Park
    Harvard Medical School Center for Biomedical Informatics, Harvard Partners Center for Genetics and Genomics, HST Informatics Program at Children s Hospital Boston, Boston, Massachusetts 02115, USA
    Epigenetics 3:318-21. 2008
    ..ChIP-seq generates considerably larger quantities of data and the most challenging aspect for investigators will be computational and statistical analysis necessary to uncover biological insights hidden in the data...
  10. pmc Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context
    Artyom A Alekseyenko
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 8:e1002646. 2012
    ..Our analysis can serve as a model for identifying chromatin and local sequence features that may contribute to selection of functional protein binding sites in the genome...
  11. pmc The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome
    Tuba H Sural
    Harvard Partners Center for Genetics and Genomics, Division of Genetics, Department of Medicine, Brigham and Women s Hospital, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Struct Mol Biol 15:1318-25. 2008
    ..Our results support a model in which activating complexes, similarly to their silencing counterparts, use the nucleosomal binding specificity of their respective chromodomains to spread from initiation sites to flanking chromatin...
  12. pmc Expression profiling of uterine leiomyomata cytogenetic subgroups reveals distinct signatures in matched myometrium: transcriptional profilingof the t(12;14) and evidence in support of predisposing genetic heterogeneity
    Jennelle C Hodge
    Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Hum Mol Genet 21:2312-29. 2012
    ..This suggests an underlying constitutional genetic predisposition to these somatic changes which could potentially lead to improved personalized management and treatment...
  13. pmc X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila
    Erica Larschan
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Nature 471:115-8. 2011
    ..Improving transcriptional output downstream of typical gene-specific controls may explain how dosage compensation can be imposed on the diverse set of genes along an entire chromosome...
  14. pmc Design and analysis of ChIP-seq experiments for DNA-binding proteins
    Peter V Kharchenko
    Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, Massachusetts 02115, USA
    Nat Biotechnol 26:1351-9. 2008
    ..We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites...
  15. pmc Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
    Peter V Kharchenko
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 471:480-5. 2011
    ..This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function...
  16. pmc nuScore: a web-interface for nucleosome positioning predictions
    Michael Y Tolstorukov
    Harvard Partners Center for Genetics and Genomics, Brigham and Women s Hospital, Boston, MA 02115, USA
    Bioinformatics 24:1456-8. 2008
    ..The interface allows the user to specify a number of options such as selecting from several structural templates for threading calculations and adding random sequences to the analysis...
  17. pmc A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity
    Bing Zhang
    Department of Cardiology, Boston Children s Hospital, Boston, Massachusetts 02115, USA
    Genome Res 23:917-27. 2013
    ..Further, our study implicates global epigenetic modifications in rapid, signal-responsive transcriptional regulation...
  18. pmc Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells
    Michael Y Tolstorukov
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 47:596-607. 2012
    ..Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing...
  19. doi request reprint Numb regulates glioma stem cell fate and growth by altering epidermal growth factor receptor and Skp1-Cullin-F-box ubiquitin ligase activity
    Xiuli Jiang
    Department of Neurosurgery, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Stem Cells 30:1313-26. 2012
    ..Thus, decreased Numb promotes glioblastoma growth, but the remaining Numb establishes a phenotypically diverse stem-like cell hierarchy that increases tumor aggressiveness and therapeutic resistance...
  20. doi request reprint Upregulation of proapoptotic microRNA mir-125a after massive small bowel resection in rats
    Anita Balakrishnan
    Department of Surgery, Brigham and Women s Hospital, Boston, MA 02115, USA
    Ann Surg 255:747-53. 2012
    ..To identify new treatments we focused on postresection changes in microRNAs--short noncoding RNAs, which suppress target genes--and suggest a previously undiscovered role for microRNA-125a (mir-125a) in intestinal adaptation...
  21. pmc Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X
    Andrey A Gorchakov
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genes Dev 23:2266-71. 2009
    ..We conclude that a long-sought specific DNA sequence within X-linked genes is not obligatory for MSL binding. Instead, linkage and transcription play the pivotal roles in MSL targeting irrespective of gene origin and DNA sequence...
  22. pmc Alternative splicing of CHEK2 and codeletion with NF2 promote chromosomal instability in meningioma
    Hong Wei Yang
    Department of Neurosurgery, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Neoplasia 14:20-8. 2012
    ..Taken together, these data indicate that alternative splicing and frequent codeletion of CHEK2 and NF2 contribute to the genomic instability and associated development of aggressive biologic behavior in meningiomas...
  23. pmc Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship
    Hyunsoo Kim
    Department of Medicine, Harvard Partners Center for Genetics and Genomics, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 107:2183-8. 2010
    ..Thus, hsa-miR-26a, CDK4, and CENTG1 comprise a functionally integrated oncomir/oncogene DNA cluster that promotes aggressiveness in human cancers by cooperatively targeting the RB1, PI3K/AKT, and JNK pathways...
  24. pmc Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters
    Michael Y Tolstorukov
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 110:10165-70. 2013
    ..Collectively, these findings define a direct relationship between chromatin-remodeling complexes, chromatin structure, and transcriptional regulation...
  25. pmc Diverse mechanisms of somatic structural variations in human cancer genomes
    Lixing Yang
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Cell 153:919-29. 2013
    ....
  26. pmc Normalization and experimental design for ChIP-chip data
    Shouyong Peng
    Howard Hughes Medical Institute, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    BMC Bioinformatics 8:219. 2007
    ..However, several issues in the processing and analysis of ChIP-chip data have not been resolved fully, including the effect of background (mock control) subtraction and normalization within and across arrays...
  27. pmc ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis
    Joshua W K Ho
    Department of Medicine, Brigham and Women s Hospital, and Harvard Medical School, Boston, MA, USA
    BMC Genomics 12:134. 2011
    ....
  28. pmc Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
    Ruibin Xi
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:E1128-36. 2011
    ..We propose this statistical approach as a principled yet practical and efficient method to estimate CNVs in whole-genome sequencing data...
  29. pmc A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs
    Tae Min Kim
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA
    Cancer Res 71:3387-99. 2011
    ....
  30. pmc Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes
    Tae Min Kim
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 23:217-27. 2013
    ..Taken together, our comprehensive view of copy number alterations provides a framework for understanding the functional significance of various genomic alterations in cancer genomes...
  31. pmc Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance
    Peter J Park
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, Center of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 25:3121-7. 2009
    ..We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance...
  32. pmc A region of the human HOXD cluster that confers polycomb-group responsiveness
    Caroline J Woo
    Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
    Cell 140:99-110. 2010
    ..We conclude that D11.12 is a Polycomb-dependent regulatory region with similarities to Drosophila PREs, indicating conservation in the mechanisms that target PcG function in mammals and flies...
  33. pmc "Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts
    Francesco Ferrari
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Cell Rep 5:629-36. 2013
    ..Our results highlight facilitated transcriptional elongation as a key mechanism for the coordinated regulation of a diverse set of genes. ..
  34. pmc CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms
    Weil Lai
    Harvard Partners Center for Genetics and Genomics and Informatics Program, Children s Hospital, Boston, MA 02139, USA
    Bioinformatics 24:1014-5. 2008
    ..The web interface calls algorithms written in the statistical language R. We encourage developers of new algorithms to submit their routines to be incorporated into the website...
  35. pmc rSW-seq: algorithm for detection of copy number alterations in deep sequencing data
    Tae Min Kim
    Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, Massachusetts 02115, USA
    BMC Bioinformatics 11:432. 2010
    ..A robust and reliable method for screening chromosomal alterations would allow a detailed characterization of the cancer genome with unprecedented accuracy...
  36. pmc Quantized correlation coefficient for measuring reproducibility of ChIP-chip data
    Shouyong Peng
    Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    BMC Bioinformatics 11:399. 2010
    ..However, the correlation coefficient can be misleading because it is affected not only by the reproducibility of the signal but also by the amount of binding signal present in the data...
  37. pmc Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation
    JESSICA L DERMODY
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
    PLoS ONE 3:e3273. 2008
    ..This work defines a novel role for Npl3 in elongation and its regulation by phosphorylation...
  38. pmc CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays
    Sek Won Kong
    Bauer Center for Genomics Research, Harvard University, Cambridge, MA, USA
    Bioinformatics 21:2116-7. 2005
    ..Our website supports a within-species comparison for human and mouse GeneChip arrays...
  39. pmc Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers
    Jonathan M Dreyfuss
    Partners Healthcare Center for Personalized Genetic Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Mol Cancer 8:71. 2009
    ..Although genomewide profiling of expression levels with microarrays can be used to identify differentially expressed genes between these tumor types, comparative studies so far have resulted in gene lists that show little overlap...
  40. pmc Phase II study of neoadjuvant bevacizumab and radiotherapy for resectable soft tissue sarcomas
    Sam S Yoon
    Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
    Int J Radiat Oncol Biol Phys 81:1081-90. 2011
    ..We sought to examine the safety and efficacy of bevacizumab (BV) and RT in soft tissue sarcomas and explore biomarkers to help determine the treatment response...
  41. pmc Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters
    Caroline J Woo
    Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
    Mol Cell Biol 33:3274-85. 2013
    ..These elements, however, have diverse requirements for binding factors, which, combined with previous data on other loci, speaks to the complexity of PcG targeting in mammals. ..
  42. pmc Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila
    Artyom A Alekseyenko
    Division of Genetics, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genes Dev 27:853-8. 2013
    ..We found evidence for the creation of new CESs, with the analogous sequence and spacing as in D. melanogaster, providing strong support for the spreading model in the establishment of dosage compensation...
  43. pmc A multivariate approach for integrating genome-wide expression data and biological knowledge
    Sek Won Kong
    Department of Cardiology 300 Longwood Avenue, Boston, MA 02115, USA
    Bioinformatics 22:2373-80. 2006
    ..However, most such methods are based on a series of univariate statistical tests and do not properly account for the complex structure of gene interactions...
  44. pmc Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes
    Hyunju Lee
    Harvard Partners Center for Genetics and Genomics, Informatics Program, Children s Hospital, Department of Cardiology, Children s Hospital, Boston, MA, USA
    Bioinformatics 24:889-96. 2008
    ..Most studies so far have focused on how a CNA affects the expression levels of those genes contained within that CNA...
  45. doi request reprint Differential H3K4 methylation identifies developmentally poised hematopoietic genes
    Keith Orford
    Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
    Dev Cell 14:798-809. 2008
    ..These data reveal distinct epigenetic regulation of CGI and non-CGI genes during development and indicate an interactive relationship between DNA sequence and differential H3K4 methylation in lineage-specific differentiation...
  46. pmc Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes
    Michael Y Tolstorukov
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:967-77. 2009
    ..We also find that human H2A.Z nucleosomes protect only approximately 120 bp of DNA from MNase digestion and exhibit specific sequence preferences, suggesting a novel mechanism of nucleosome organization for the H2A.Z variant...
  47. pmc Nucleosome positioning in human HOX gene clusters
    Peter V Kharchenko
    Harvard Partners Center for Genetics and Genomics, Boston, Massachusetts 02115, USA
    Genome Res 18:1554-61. 2008
    ..Through comparison of different cell lines, we find that active transcription is correlated with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes...
  48. doi request reprint Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome
    Teresa Davoli
    Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Division of Genetics, Brigham and Women s Hospital, Boston, MA 02115, USA
    Cell 155:948-62. 2013
    ..We propose that the cancer genome is shaped through a process of cumulative haploinsufficiency and triplosensitivity...
  49. pmc Primate genome architecture influences structural variation mechanisms and functional consequences
    Omer Gokcumen
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115
    Proc Natl Acad Sci U S A 110:15764-9. 2013
    ..Differences in the present day activity of SV formation mechanisms that our study revealed may contribute to ongoing diversification and adaptation of great ape and Old World monkey lineages. ..
  50. doi request reprint A survey of copy-number variation detection tools based on high-throughput sequencing data
    Ruibin Xi
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
    Curr Protoc Hum Genet . 2012
    ..In this unit, we give an overview of available computational tools for detection of CNVs and discuss comparative advantages and disadvantages of different approaches...
  51. pmc High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome
    Artyom A Alekseyenko
    Howard Hughes Medical Institute, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genes Dev 20:848-57. 2006
    ..Distinguishing expressed genes from the bulk of the genome is likely to be an important function common to many chromatin organizing and modifying activities...
  52. pmc MicroRNA mir-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts
    Anita Balakrishnan
    Department of Surgery, Brigham and Women s Hospital, Boston, MA 02115, USA
    Exp Cell Res 316:3512-21. 2010
    ..The regulatory mechanisms behind these rhythms remain largely unknown. We hypothesized that microRNAs are involved in mediating these rhythms, and studied the role of microRNAs specifically in modulating intestinal proliferation...
  53. pmc Identifying the molecular signature of the interstitial deletion 7q subgroup of uterine leiomyomata using a paired analysis
    Jennelle C Hodge
    Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Genes Chromosomes Cancer 48:865-85. 2009
    ..This study provides a molecular signature of the del(7q) UL subgroup and will serve as a platform for future studies of tumor pathogenesis...
  54. pmc Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis
    Jussi Pihlajamaki
    Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
    Cell Metab 14:208-18. 2011
    ..Together, our results indicate that reduced expression of SFRS10, as observed in tissues from obese humans, alters LPIN1 splicing, induces lipogenesis, and therefore contributes to metabolic phenotypes associated with obesity...
  55. pmc Nozzle: a report generation toolkit for data analysis pipelines
    Nils Gehlenborg
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 29:1089-91. 2013
    ..The package can be applied to any project where user-friendly reports need to be created...
  56. pmc Expression, circulation, and excretion profile of microRNA-21, -155, and -18a following acute kidney injury
    Janani Saikumar
    Department of Medicine, Renal Division, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Toxicol Sci 129:256-67. 2012
    ..Taken together, these results suggest that miRNA-21 and -155 could potentially serve as translational biomarkers for detection of AKI and may play a critical role in the pathogenesis of kidney injury and tissue repair process...
  57. pmc Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells
    Matthias Stadtfeld
    Massachusetts General Hospital Center for Regenerative Medicine, Harvard Stem Cell Institute, Boston, Massachusetts, USA
    Nat Genet 44:398-405, S1-2. 2012
    ..More generally, these findings indicate that culture conditions during cellular reprogramming can strongly influence the epigenetic and biological properties of the resultant iPSCs...
  58. pmc iSyTE: integrated Systems Tool for Eye gene discovery
    Salil A Lachke
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard edical School, Boston, Massachusetts, USA
    Invest Ophthalmol Vis Sci 53:1617-27. 2012
    ....
  59. pmc Gene expression analysis reveals the cell cycle and kinetochore genes participating in ischemia reperfusion injury and early development in kidney
    Tae Min Kim
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 6:e25679. 2011
    ..The molecular mechanisms that mediate the ischemia-reperfusion (I/R) injury in kidney are not completely understood. It is also largely unknown whether such mechanisms overlap with those governing the early development of kidney...
  60. doi request reprint Experimental design and data analysis for array comparative genomic hybridization
    Peter J Park
    Children s Hospital Informatics Program, Harvard Partners Center for Genetics and Genomics, Boston, Massachusetts, USA peter
    Cancer Invest 26:923-8. 2008
    ..We also describe integration of copy number data with other types of data to identify functional significance of observed aberrations...
  61. pmc Detecting structural variations in the human genome using next generation sequencing
    Ruibin Xi
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Brief Funct Genomics 9:405-15. 2010
    ..In this review, we will describe some of the sequencing-based algorithms for detection of structural variations and discuss the key issues in future development...
  62. pmc Vector algebra in the analysis of genome-wide expression data
    Finny G Kuruvilla
    Howard Hughes Medical Institute, Bauer Center for Genomics Research, Department of Chemistry, Harvard University, Cambridge, MA 02138, USA
    Genome Biol 3:RESEARCH0011. 2002
    ..In particular, concepts from vector algebra have proven useful in the study of genome-wide expression data...
  63. ncbi request reprint A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    Winston Patrick Kuo
    Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, Massachusetts 02115, USA
    Nat Biotechnol 24:832-40. 2006
    ..We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms...
  64. pmc Improving identification of differentially expressed genes in microarray studies using information from public databases
    Richard D Kim
    Harvard Partners Center for Genetics and Genomics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Genome Biol 5:R70. 2004
    ..Our results are further improved by weighting the results of our approach with the regularized t-test results in a hybrid method...
  65. pmc Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming
    Effie Apostolou
    Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, 185 Cambridge Street, Boston, MA 02114, USA
    Cell Stem Cell 12:699-712. 2013
    ..Our results document a complex, pluripotency-specific chromatin "interactome" for Nanog and suggest a functional role for long-range genomic interactions in the maintenance and induction of pluripotency...
  66. pmc Systematic identification of synergistic drug pairs targeting HIV
    Xu Tan
    Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Biotechnol 30:1125-30. 2012
    ..MuSIC can be applied to a wide variety of disease-relevant screens to facilitate efficient identification of compound combinations...
  67. doi request reprint Advances in analysis of transcriptional regulatory networks
    Tae Min Kim
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA
    Wiley Interdiscip Rev Syst Biol Med 3:21-35. 2011
    ..Finally, we will discuss the types of biological insights that can be obtained from a network-level understanding of transcription regulation as well as future challenges in the field...
  68. pmc Landscape of somatic retrotransposition in human cancers
    Eunjung Lee
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Science 337:967-71. 2012
    ....
  69. doi request reprint A Wnt-bmp feedback circuit controls intertissue signaling dynamics in tooth organogenesis
    Daniel J O'Connell
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Sci Signal 5:ra4. 2012
    ....
  70. pmc Thyroid hormone-related regulation of gene expression in human fatty liver
    Jussi Pihlajamaki
    Research Division, Joslin Diabetes Center, One Joslin Place, Boston, Massachusetts 02215, USA
    J Clin Endocrinol Metab 94:3521-9. 2009
    ..Fatty liver is an important complication of obesity; however, regulatory mechanisms mediating altered gene expression patterns have not been identified...
  71. pmc KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs
    Alexandros Tzatsos
    Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
    J Clin Invest 123:727-39. 2013
    ..These results defined epigenetic programs through which KDM2B subverts cellular differentiation and drives the pathogenesis of an aggressive subset of PDAC...
  72. pmc Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain
    Gilad D Evrony
    Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
    Cell 151:483-96. 2012
    ..Single-neuron sequencing allows systematic assessment of genomic diversity in the human brain...
  73. ncbi request reprint A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma
    Fenghua Liu
    Department of Neurological Surgery, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
    Cancer Res 66:10815-23. 2006
    ..This novel genome-wide approach greatly expanded the list of target genes in glioblastoma and represents a powerful new strategy to identify the upstream determinants of tumor phenotype in a range of human cancers...
  74. pmc Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data
    Weil R Lai
    Harvard Partners Center for Genetics and Genomics 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Bioinformatics 21:3763-70. 2005
    ..While a large number of approaches have been proposed for analyzing the large array CGH datasets, the relative merits of these methods in practice are not clear...
  75. ncbi request reprint Microarrays and clinical dentistry
    Winston Patrick Kuo
    Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Mass 02115, USA
    J Am Dent Assoc 134:456-62. 2003
    ....
  76. pmc Impact of chromatin structure on sequence variability in the human genome
    Michael Y Tolstorukov
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Struct Mol Biol 18:510-5. 2011
    ..These findings indicate an increased level of conservation for the sequences associated with epigenetically modified nucleosomes, highlighting complex organization of the human chromatin...
  77. pmc Specific genes expressed in association with progesterone receptors in meningioma
    Elizabeth B Claus
    Department of Neurosurgery, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Cancer Res 68:314-22. 2008
    ..These findings suggest that PR status may be a clinical marker for genetic subgroups of meningioma and warrant further examination in a larger data set...
  78. ncbi request reprint Postmeiotic sex chromatin in the male germline of mice
    Satoshi H Namekawa
    Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, 02114, USA
    Curr Biol 16:660-7. 2006
    ..We conclude that chromosome-wide X silencing continues from meiosis to the end of spermiogenesis, and we discuss implications for proposed mechanisms of imprinted X-inactivation...
  79. doi request reprint A pharmacoepidemiological network model for drug safety surveillance: statins and rhabdomyolysis
    Ben Y Reis
    Childrens Hospital Informatics Program, Harvard MIT Division of Health Sciences and Technology, Childrens Hospital, Harvard Medical School, Boston, MA, USA
    Drug Saf 35:395-406. 2012
    ..These data are typically analysed by comparing the adverse event rates associated with a drug of interest to those of a single comparable reference drug...
  80. pmc Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster
    Fumika N Hamada
    Howard Hughes Medical Institute, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genes Dev 19:2289-94. 2005
    ..We found that expression of many genes from the X chromosome decreased, while expression from the autosomes was largely unchanged. We conclude that the primary role of the MSL complex is to up-regulate the male X chromosome...
  81. pmc MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues
    Seth Blackshaw
    Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute, 200 Longwood Avenue, Boston, MA 02115, USA
    Genome Biol 4:R17. 2003
    ..Serial analysis of gene expression using small amounts of starting material (microSAGE) has not yet been conclusively shown to be representative, reproducible or accurate...
  82. pmc Efficacy of sunitinib and radiotherapy in genetically engineered mouse model of soft-tissue sarcoma
    Sam S Yoon
    Department of Surgery, Division of Surgical Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
    Int J Radiat Oncol Biol Phys 74:1207-16. 2009
    ..The present study examined SU and radiotherapy (RT) in a genetically engineered mouse model of soft tissue sarcoma (STS)...
  83. pmc Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood
    Xiu Ping Wang
    Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Development 136:1939-49. 2009
    ..In addition, we identify Fgf8, a known tooth initiation marker, as a direct target of Wnt/beta-catenin signaling. These studies identify key mechanistic features responsible for supernumerary tooth formation...
  84. pmc The Lkb1 metabolic sensor maintains haematopoietic stem cell survival
    Sushma Gurumurthy
    Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 468:659-63. 2010
    ..Instead, these data define a central role for Lkb1 in restricting HSC entry into cell cycle and in broadly maintaining energy homeostasis in haematopoietic cells through a novel metabolic checkpoint...
  85. pmc Surface antigen phenotypes of hematopoietic stem cells from embryos and murine embryonic stem cells
    Shannon L McKinney-Freeman
    Division of Pediatric Hematology Oncology, Manton Center for Orphan Diseases, Stem Cell Transplantation Program, Children s Hospital, Boston, MA 02115, USA
    Blood 114:268-78. 2009
    ..The prospective fractionation of ESC-HSCs will facilitate studies of HSC maturation essential for normal functional engraftment in irradiated adults...
  86. ncbi request reprint Angiogenic profile of soft tissue sarcomas based on analysis of circulating factors and microarray gene expression
    Sam S Yoon
    Department of Surgery, Massachusetts General Hospital, Division of Surgical Oncology, Harvard Medical School, Boston, Massachusetts, USA
    J Surg Res 135:282-90. 2006
    ..The aim of this study was to develop profiles of angiogenesis-related gene and protein expression for various histologic subtypes of soft tissue sarcomas (STS) growing in different sites...
  87. ncbi request reprint Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference
    Peter J Park
    Children s Hospital Informatics Program and Harvard Medical School, 320 Longwood Ave, Boston, MA 02115, USA
    J Biotechnol 112:225-45. 2004
    ..Finally, the reliability of using a universal RNA reference for two-channel microarrays was tested and the results suggest that comparisons of multiple experimental conditions using the same control can be accurate...
  88. ncbi request reprint Interferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis
    Steven A Greenberg
    Department of Neurology, Division of Neuromuscular Disease, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Ann Neurol 57:664-78. 2005
    ....
  89. pmc Discovering statistically significant pathways in expression profiling studies
    Lu Tian
    Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 North Lake Shore Drive, Chicago, IL 60611, USA
    Proc Natl Acad Sci U S A 102:13544-9. 2005
    ..These predictions have been subsequently corroborated by immunohistochemistry...
  90. pmc Pathway analysis of primary central nervous system lymphoma
    Han W Tun
    Department of Hematology and Oncology, Mayo Clinic Jacksonville, FL 32224, USA
    Blood 111:3200-10. 2008
    ..The gene expression signature discovered in our study may represent a true "CNS signature" because we contrasted PCNSL with wide-spectrum non-CNS DLBCL on a genomic scale and performed an in-depth bioinformatic analysis...
  91. pmc Network-based analysis of affected biological processes in type 2 diabetes models
    Manway Liu
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
    PLoS Genet 3:e96. 2007
    ....
  92. pmc Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential
    Louise A Koopman
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    J Exp Med 198:1201-12. 2003
    ..Additionally, two secreted proteins, galectin-1 and progestagen-associated protein 14, known to have immunomodulatory functions, were selectively expressed in dNK cells...
  93. pmc The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression
    Jacob L Mueller
    Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:794-9. 2008
    ..Thus, not only is the mouse X chromosome enriched for spermatogenesis genes functioning before meiosis, but in addition, approximately 18% of mouse X-linked genes are expressed in postmeiotic cells...

Research Grants5

  1. Integrative Analysis of Multiple Genomic Data Sets
    Peter J Park; Fiscal Year: 2010
    ..The tools developed will also allow investigators to see unexpected connections among diseases at the molecular level and thus contribute to the development of treatments. ..
  2. Integrative Analysis of Multiple Genomic Data Sets
    Peter Park; Fiscal Year: 2007
    ..The tools developed will also allow investigators to see unexpected connections among diseases at the molecular level and thus contribute to the development of treatments. ..