Cheng Li

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers
    Zhenyu Yan
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
    Nucleic Acids Res 40:e135. 2012
  2. pmc Major copy proportion analysis of tumor samples using SNP arrays
    Cheng Li
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, 3 Blackfan Circle, Boston, MA 02115, USA
    BMC Bioinformatics 9:204. 2008
  3. pmc Automating dChip: toward reproducible sharing of microarray data analysis
    Cheng Li
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    BMC Bioinformatics 9:231. 2008
  4. pmc Allele-specific amplification in cancer revealed by SNP array analysis
    Thomas LaFramboise
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
    PLoS Comput Biol 1:e65. 2005
  5. pmc Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification
    J Guillermo Paez
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Nucleic Acids Res 32:e71. 2004
  6. ncbi request reprint Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma
    Levi A Garraway
    Department of Medical Oncology, and Melanoma Program in Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nature 436:117-22. 2005
  7. ncbi request reprint Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis
    Xiaojun Zhao
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Cancer Res 65:5561-70. 2005
  8. pmc The shaping and functional consequences of the dosage effect landscape in multiple myeloma
    Mehmet K Samur
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
    BMC Genomics 14:672. 2013
  9. pmc Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays
    Rameen Beroukhim
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    PLoS Comput Biol 2:e41. 2006
  10. pmc canEvolve: a web portal for integrative oncogenomics
    Mehmet Kemal Samur
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS ONE 8:e56228. 2013

Detail Information

Publications62

  1. pmc Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers
    Zhenyu Yan
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
    Nucleic Acids Res 40:e135. 2012
    ..The results and analysis web server are available at http://www.canevolve.org/dChip-GemiNi...
  2. pmc Major copy proportion analysis of tumor samples using SNP arrays
    Cheng Li
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, 3 Blackfan Circle, Boston, MA 02115, USA
    BMC Bioinformatics 9:204. 2008
    ..We have previously used Hidden Markov Models (HMM) to analyze SNP array data for inferring copy numbers and loss-of-heterozygosity (LOH) from paired normal and tumor samples and unpaired tumor samples...
  3. pmc Automating dChip: toward reproducible sharing of microarray data analysis
    Cheng Li
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    BMC Bioinformatics 9:231. 2008
    ..Improvement is also needed when the dChip user support team tries to identify the causes of reported analysis errors or bugs from users...
  4. pmc Allele-specific amplification in cancer revealed by SNP array analysis
    Thomas LaFramboise
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
    PLoS Comput Biol 1:e65. 2005
    ..An R software package containing the methods described in this paper is freely available at http://genome.dfci.harvard.edu/~tlaframb/PLASQ...
  5. pmc Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification
    J Guillermo Paez
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Nucleic Acids Res 32:e71. 2004
    ..These results suggest that phi29MDA yields high fidelity, near-complete genome representation suitable for high resolution genetic analysis...
  6. ncbi request reprint Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma
    Levi A Garraway
    Department of Medical Oncology, and Melanoma Program in Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nature 436:117-22. 2005
    ..Together, these data suggest that MITF represents a distinct class of 'lineage survival' or 'lineage addiction' oncogenes required for both tissue-specific cancer development and tumour progression...
  7. ncbi request reprint Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis
    Xiaojun Zhao
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Cancer Res 65:5561-70. 2005
    ..EGFR amplification was shown to be independent of kinase domain mutational status...
  8. pmc The shaping and functional consequences of the dosage effect landscape in multiple myeloma
    Mehmet K Samur
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
    BMC Genomics 14:672. 2013
    ....
  9. pmc Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays
    Rameen Beroukhim
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    PLoS Comput Biol 2:e41. 2006
    ..We have developed a method for analyzing high-density oligonucleotide SNP array data to accurately identify of regions of LOH and retention in tumors without the need for paired normal samples...
  10. pmc canEvolve: a web portal for integrative oncogenomics
    Mehmet Kemal Samur
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS ONE 8:e56228. 2013
    ..We have built the canEvolve web portal to meet this need...
  11. pmc Heat shock protein 90 is critical for regulation of phenotype and functional activity of human T lymphocytes and NK cells
    Jooeun Bae
    Department of Medical Oncology, The Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    J Immunol 190:1360-71. 2013
    ..Therefore, these observations demonstrate the need to closely monitor immune function in patients being treated with a Hsp90 inhibitor and may provide a potential therapeutic application in autoimmune diseases...
  12. ncbi request reprint An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays
    Xiaojun Zhao
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Cancer Res 64:3060-71. 2004
    ..The simultaneous measurement of DNA copy number changes and loss of heterozygosity events by SNP arrays should strengthen our ability to discover cancer-causing genes and to refine cancer diagnosis...
  13. ncbi request reprint Temporal gene expression following prosthetic arterial grafting
    David J Willis
    Department of Surgery, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
    J Surg Res 120:27-36. 2004
    ..This study evaluates temporal gene expression at the distal anastomosis of prosthetic arterial grafts using microarray analysis...
  14. ncbi request reprint dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data
    Ming Lin
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 20:1233-40. 2004
    ..Recently, this technology has been applied to loss-of-heterozygosity (LOH) analysis of paired normal and tumor samples. However, methods and software for analyzing such data are not fully developed...
  15. doi request reprint Significant biological role of sp1 transactivation in multiple myeloma
    Mariateresa Fulciniti
    Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Clin Cancer Res 17:6500-9. 2011
    ..We here provide experimental and clinical evidence that Sp1 plays an important regulatory role in multiple myeloma (MM) cell growth and survival...
  16. ncbi request reprint Identification of genes modulated in multiple myeloma using genetically identical twin samples
    Nikhil C Munshi
    Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston MA 02115, USA
    Blood 103:1799-806. 2004
    ..By identifying genes uniquely altered in MM cells compared with normal PCs in an identical genotypic background, the current study provides the framework to identify novel therapeutic targets...
  17. ncbi request reprint High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines
    Pasi A Janne
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Oncogene 23:2716-26. 2004
    ..Using this array, we identified small regions of LOH that were not detected by lower density SNP arrays or by standard microsatellite marker panels...
  18. pmc Genome-wide analysis of neuroblastomas using high-density single nucleotide polymorphism arrays
    Rani E George
    Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
    PLoS ONE 2:e255. 2007
    ..We analyzed paired blood and primary tumor samples from 22 children with high-risk neuroblastoma for loss of heterozygosity (LOH) and DNA copy number change using the Affymetrix 10K single nucleotide polymorphism (SNP) array...
  19. ncbi request reprint Growth arrest, apoptosis, and telomere shortening of Barrett's-associated adenocarcinoma cells by a telomerase inhibitor
    Masood A Shammas
    VA Boston Health Care System, Boston, MA, USA
    Gastroenterology 126:1337-46. 2004
    ..The purpose of this study was to evaluate effects of telomerase inhibition on BEAC...
  20. pmc Copy number abnormalities, MYC activity, and the genetic fingerprint of normal B cells mechanistically define the microRNA profile of diffuse large B-cell lymphoma
    Cheng Li
    Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
    Blood 113:6681-90. 2009
    ..In conclusion, we created a comprehensive map of the miRNA genome in DLBCL and, in the process, have uncovered and mechanistically elucidated the basis for additional molecular heterogeneity in this tumor...
  21. pmc The dChip survival analysis module for microarray data
    Samir B Amin
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Ave, Boston, MA 02215, USA
    BMC Bioinformatics 12:72. 2011
    ..However, there is no software that can perform survival analysis using SNP array data or draw survival curves interactively for expression-based sample clusters...
  22. pmc Lessons from a decade of integrating cancer copy number alterations with gene expression profiles
    Norman Huang
    Department of Biostatistics and Computational Biology, CLS 11075, Dana Farber Cancer Institute, Harvard School of Public Health, CLS 11075 3 Blackfan Circle, Boston, MA 02115, USA
    Brief Bioinform 13:305-16. 2012
    ..We conclude by providing suggestions for building efficient data integration methodologies and asking further biological questions...
  23. ncbi request reprint Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data
    Yuhyun Park
    Department of Biostatistics, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
    Bioinformatics 23:1451-8. 2007
    ..Most of the statistical techniques for comparing two groups are based on qualitative measures such as P-value. A quantitative way such as interval estimation for the contrasts of two groups is more appealing...
  24. pmc Expression of heat shock proteins and heat shock protein messenger ribonucleic acid in human prostate carcinoma in vitro and in tumors in vivo
    Dan Tang
    Department of Radiation Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Cell Stress Chaperones 10:46-58. 2005
    ....
  25. ncbi request reprint Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers
    Zhigang C Wang
    Departments of Surgery and Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Cancer Res 64:64-71. 2004
    ..Furthermore, exclusive association between biological subclasses and restricted LOH events provides rationale to search for targeted genes...
  26. pmc SNP array analysis in hematologic malignancies: avoiding false discoveries
    Stefan Heinrichs
    Departmentsof Pediatric Oncology, Farber Cancer Institute, Boston, MA 02115, USA
    Blood 115:4157-61. 2010
    ..Comparisons between matched tumor and normal samples will continue to be critical as the field moves from high resolution array analysis to deep sequencing to detect abnormalities in the cancer genome...
  27. pmc A plasma biomarker signature of immune activation in HIV patients on antiretroviral therapy
    Anupa Kamat
    Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
    PLoS ONE 7:e30881. 2012
    ..Here, we identify a plasma inflammatory biomarker signature that distinguishes between both viremic and aviremic HIV patients on cART and healthy controls and examine relationships of this signature to markers of disease progression...
  28. pmc Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data
    Igor Leykin
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    BMC Genet 6:7. 2005
    ..For example, the haplotyping results are commonly represented in the text format...
  29. ncbi request reprint Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip Human Mapping 10K array
    Ke Hao
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Eur J Hum Genet 12:1001-6. 2004
    ..We also suggest that as low as 50 random SNPs with heterozygosity >40% should be sufficient as genomic controls...
  30. ncbi request reprint Gene regulation and DNA damage in the ageing human brain
    Tao Lu
    Department of Neurology and Division of Neuroscience, The Children s Hospital and Harvard Medical School, Enders 260, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 429:883-91. 2004
    ..Thus, DNA damage may reduce the expression of selectively vulnerable genes involved in learning, memory and neuronal survival, initiating a programme of brain ageing that starts early in adult life...
  31. ncbi request reprint Estimation of genotype error rate using samples with pedigree information--an application on the GeneChip Mapping 10K array
    Ke Hao
    Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
    Genomics 84:623-30. 2004
    ..The GeneChip Mapping 10K array has a low overall error rate, which is consistent with the results obtained from alternative genotyping assays...
  32. pmc Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease
    Marta M Lipinski
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 107:14164-9. 2010
    ..Finally, we provide a list of candidate drug targets that can be used to safely modulate levels of autophagy without causing cell death...
  33. ncbi request reprint Identification of human leucocyte antigen (HLA)-A*0201-restricted cytotoxic T lymphocyte epitopes derived from HLA-DO╬▓ as a novel target for multiple myeloma
    Yoon Joong Kang
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA Cancer Vaccine Center, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA Department of Biomedical Science, Jungwon University, Chungcheongbuk Do, South Korea
    Br J Haematol 163:343-51. 2013
    ..Taken together, based on the physical presence on tumour cell surface and high immunogenicity, HLA-DOB232-240 might be useful for developing a novel immunotherapy against MM. ..
  34. ncbi request reprint Telomerase inhibition and cell growth arrest after telomestatin treatment in multiple myeloma
    Masood A Shammas
    Boston VA Health Care System, Boston, Massachusetts, USA
    Clin Cancer Res 10:770-6. 2004
    ..The aim of this study was to test the efficacy of telomestatin, an intramolecular G-quadruplex intercalating drug with specificity for telomeric sequences, as a potential therapeutic agent for multiple myeloma...
  35. ncbi request reprint Phenotypic and functional effects of heat shock protein 90 inhibition on dendritic cell
    Jooeun Bae
    Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    J Immunol 178:7730-7. 2007
    ....
  36. ncbi request reprint In vitro and in vivo activity of the maytansinoid immunoconjugate huN901-N2'-deacetyl-N2'-(3-mercapto-1-oxopropyl)-maytansine against CD56+ multiple myeloma cells
    Pierfrancesco Tassone
    Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, VA Boston Healthcare System, Harvard Medical School, Boston, Massachusetts 02115, USA
    Cancer Res 64:4629-36. 2004
    ..Taken together, these data provide the framework for clinical trials of this agent to improve patient outcome in MM...
  37. pmc Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma
    Jin Li
    Department of Radiation Oncology, Division of DNA Repair and Genome Stability, Dana Farber Brigham and Women s Cancer Center, Harvard Medical School, Boston, Massachusetts 02115, USA
    Hum Mutat 30:1583-90. 2009
    ....
  38. ncbi request reprint Novel pheochromocytoma susceptibility loci identified by integrative genomics
    Patricia L M Dahia
    Department of Cancer Biology and Biostatistics, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
    Cancer Res 65:9651-8. 2005
    ..Similarly, complex traits may also be involved in other familial cancer syndromes...
  39. pmc Global gene expression profiling in whole-blood samples from individuals exposed to metal fumes
    Zhaoxi Wang
    Department of Environmental Health, Occupational Health Program, Harvard School of Public Health, Boston, Massachusetts, USA
    Environ Health Perspect 113:233-41. 2005
    ..This technique can be applied to evaluate the host response to other forms of environmental exposures...
  40. pmc BAL1 and BBAP are regulated by a gamma interferon-responsive bidirectional promoter and are overexpressed in diffuse large B-cell lymphomas with a prominent inflammatory infiltrate
    Przemyslaw Juszczynski
    Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Mol Cell Biol 26:5348-59. 2006
    ..IFN-gamma-induced BAL1/BBAP expression contributes to the molecular signature of HR DLBCLs and highlights the interplay between the inflammatory infiltrate and malignant B cells in these tumors...
  41. pmc Temporal genetic program following B-cell receptor cross-linking: altered balance between proliferation and death in healthy and malignant B cells
    Laurent D Vallat
    Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
    Blood 109:3989-97. 2007
    ..Analysis of gene expression profiling over time may be used to identify genes that might be rational targets to perturb these pathways...
  42. pmc Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse
    Jennifer L Moran
    Genetics Division, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 16:436-40. 2006
    ..By using this approach, we identified DNA sequence changes in two ethylnitrosourea-induced mutants...
  43. pmc Evolution of the aging brain transcriptome and synaptic regulation
    Patrick M Loerch
    Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
    PLoS ONE 3:e3329. 2008
    ..Thus, repression of neuronal gene expression is a prominent and recently evolved feature of brain aging in humans and rhesus macaques that may alter neural networks and contribute to age-related cognitive changes...
  44. pmc ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis
    Sheng Zhong
    Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
    Nucleic Acids Res 31:3483-6. 2003
    ..It also has functions for computing related summary statistics of probe sets and Gene Ontology terms. ChipInfo is available at http://biosun1.harvard.edu/complab/chipinfo/...
  45. pmc Computational inference of mRNA stability from histone modification and transcriptome profiles
    Chengyang Wang
    Department of Bioinformatics, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China
    Nucleic Acids Res 40:6414-23. 2012
    ..In summary, we represent the first computational model of mRNA stability inference that compares transcriptome and epigenome profiles, and provides an alternative strategy for directing experimental measurements...
  46. pmc Molecular diversity of astrocytes with implications for neurological disorders
    Robert M Bachoo
    Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 101:8384-9. 2004
    ....
  47. ncbi request reprint Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP
    Marshall E Lieberfarb
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Cancer Res 63:4781-5. 2003
    ..This organizational strategy revealed apparently distinct genetic subsets of prostate cancer...
  48. pmc Determinants of antigenicity and specificity in immune response for protein sequences
    Yulong Wang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston 02115 MA, USA
    BMC Bioinformatics 12:251. 2011
    ....
  49. ncbi request reprint Ovarian cancer is a heterogeneous disease
    Vivian Wang
    Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women s Hospital, Dana Farber Harvard Cancer Center, Harvard Medical School, Boston, MA 02115, USA
    Cancer Genet Cytogenet 161:170-3. 2005
    ..We conclude that ovarian cancer is a heterogeneous disease in which histologic phenotypes correlate with distinct genetic patterns...
  50. ncbi request reprint Temporal genomics of vein bypass grafting through oligonucleotide microarray analysis
    Jeffrey A Kalish
    Department of Surgery, Division of Vascular Surgery, Beth Israel Deacones Medical Center, Boston, MA 02115, USA
    J Vasc Surg 39:645-54. 2004
    ..Despite excellent patency, these conduits undergo remodeling over time. The purpose of this study was to identify temporal gene expression in vein grafts versus control veins through microarray analysis...
  51. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
    ..We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples...
  52. ncbi request reprint Adjusting batch effects in microarray expression data using empirical Bayes methods
    W Evan Johnson
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
    Biostatistics 8:118-27. 2007
    ..We illustrate our methods using two example data sets and show that our methods are justifiable, easy to apply, and useful in practice. Software for our method is freely available at: http://biosun1.harvard.edu/complab/batch/...
  53. ncbi request reprint Identification of genes regulated by 2-methoxyestradiol (2ME2) in multiple myeloma cells using oligonucleotide arrays
    Dharminder Chauhan
    The Jerome Lipper Multiple Myeloma Center, The Department of Medical Oncology, Cancer Biology, Boston Veteran Affairs Healthcare System, Boston, MA, USA
    Blood 101:3606-14. 2003
    ..These studies may therefore allow improved therapeutic use of 2ME2, based upon targeting genes that regulate MM cell growth and survival...
  54. pmc Identifying rare variants using a Bayesian regression approach
    Aimin Yan
    Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
    BMC Proc 5:S99. 2011
    ..However, the model also generated several apparent false positives and missed many true positives, suggesting that there is room for improvement in this model...
  55. ncbi request reprint The vascular endothelial growth factor receptor tyrosine kinase inhibitor PTK787/ZK222584 inhibits growth and migration of multiple myeloma cells in the bone marrow microenvironment
    Boris Lin
    Jerome Lipper Multiple Myeloma Center, Department of Adult Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Cancer Res 62:5019-26. 2002
    ..The demonstrated anti-MM activity of PTK787, coupled with its antiangiogenic effects, provides the framework for clinical trials of this agent to overcome drug resistance and improve outcome in MM...
  56. ncbi request reprint Insights into the multistep transformation of MGUS to myeloma using microarray expression analysis
    Faith E Davies
    Academic Unit of Haematology and Oncology, Algernon Firth Bldg, School of Medicine, University of Leeds, Leeds, United Kingdom
    Blood 102:4504-11. 2003
    ..Understanding the molecular pathogenesis of MM by gene expression profiling has demonstrated sequential genetic changes from N to malignant PCs and highlighted important pathways involved in the transformation of MGUS to MM...
  57. ncbi request reprint Integration of global SNP-based mapping and expression arrays reveals key regions, mechanisms, and genes important in the pathogenesis of multiple myeloma
    Brian A Walker
    Section of Haemato oncology, Institute for Cancer Research, 15 Cotswold Rd, Sutton, Surrey, United Kingdom
    Blood 108:1733-43. 2006
    ..We have documented these genes, providing a focus for further studies to identify and characterize those that are key in the pathogenesis of myeloma...
  58. ncbi request reprint A global expression-based analysis of the consequences of the t(4;14) translocation in myeloma
    Ann M Dring
    Academic Unit of Haematology and Oncology, University of Leeds, Leeds, United Kingdom
    Clin Cancer Res 10:5692-701. 2004
    ..Our purpose in this report was to define genes and pathways dysregulated as a consequence of the t(4;14) in myeloma, and to gain insight into the downstream functional effects that may explain the different prognosis of this subgroup...
  59. pmc The RhoGAP protein DLC-1 functions as a metastasis suppressor in breast cancer cells
    Steve Goodison
    Department of Pathology, University of Florida Health Science Center, Shands Hospital, Jacksonville, Florida 32209 6511, USA
    Cancer Res 65:6042-53. 2005
    ..The finding that DLC-1 can act as a metastasis-suppressor gene supports an influential role for GTPase signaling in tumor progression...
  60. ncbi request reprint Significance and relationship between infiltrating inflammatory cell and tumor angiogenesis in hepatocellular carcinoma tissues
    Shao Hua Peng
    Department of Pathology, Medical College, Hunan Normal University, Changsha 410006, Hunan Province, China
    World J Gastroenterol 11:6521-4. 2005
    ..To investigate the relationship between infiltrating inflammatory cell and tumor angiogenesis in hepatocellular carcinoma (HCC) tissues and their clinicopathological features...
  61. ncbi request reprint A fully automated nanoelectrospray tandem mass spectrometric method for analysis of Caco-2 samples
    Colleen K Van Pelt
    Advion BioSciences, Inc, 15 Catherwood Road, Ithaca, NY 14850, USA
    Rapid Commun Mass Spectrom 17:1573-8. 2003
    ..The permeability and recovery data of the two compounds analyzed in this study obtained from conventional LC/MS/MS and by automated nanoESI-MS/MS were in excellent agreement...
  62. ncbi request reprint Whole genome loss of heterozygosity profiling on oral squamous cell carcinoma by high-density single nucleotide polymorphic allele (SNP) array
    Xiaofeng Zhou
    Cancer Genet Cytogenet 151:82-4. 2004