Research Topics
Genomes and Genes | Cheng LiSummaryAffiliation: Harvard University Country: USA Publications
Research Grants
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Detail Information
Publications
Major copy proportion analysis of tumor samples using SNP arraysCheng 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...- Automating dChip: toward reproducible sharing of microarray data analysisCheng 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... - Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arraysRameen 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... - Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplificationJ 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... 
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanomaLevi 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...- Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysisXiaojun 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... - An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arraysXiaojun 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... - Temporal gene expression following prosthetic arterial graftingDavid 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... 
Significant biological role of sp1 transactivation in multiple myelomaMariateresa 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...- dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity dataMing Lin
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
Bioinformatics 20:1233-40. 2004..harvard.edu/complab/dchip/snp/ SUPPLEMENTARY INFORMATION: The breast cancer data are provided by Andrea L. Richardson, Zhigang C. Wang and James D. Iglehart... - Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancersZhenyu 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... - Genome-wide analysis of neuroblastomas using high-density single nucleotide polymorphism arraysRani 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... - Growth arrest, apoptosis, and telomere shortening of Barrett's-associated adenocarcinoma cells by a telomerase inhibitorMasood A Shammas
VA Boston Health Care System, Boston, MA, USA
Gastroenterology 126:1337-46. 2004.... - High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell linesPasi 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... - Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec dataYuhyun 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... - Lessons from a decade of integrating cancer copy number alterations with gene expression profilesNorman 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... - SNP array analysis in hematologic malignancies: avoiding false discoveriesStefan 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... - Identification of genes regulated by 2-methoxyestradiol (2ME2) in multiple myeloma cells using oligonucleotide arraysDharminder 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... - Comparative linkage analysis and visualization of high-density oligonucleotide SNP array dataIgor 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... - Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancersZhigang 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... - Copy number abnormalities, MYC activity, and the genetic fingerprint of normal B cells mechanistically define the microRNA profile of diffuse large B-cell lymphomaCheng 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... - The dChip survival analysis module for microarray dataSamir 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... - Estimation of genotype error rate using samples with pedigree information--an application on the GeneChip Mapping 10K arrayKe 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... - Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip Human Mapping 10K arrayKe 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... - Gene regulation and DNA damage in the ageing human brainTao 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... - In vitro and in vivo activity of the maytansinoid immunoconjugate huN901-N2'-deacetyl-N2'-(3-mercapto-1-oxopropyl)-maytansine against CD56+ multiple myeloma cellsPierfrancesco 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... - Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinomaJin 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.... - Novel pheochromocytoma susceptibility loci identified by integrative genomicsPatricia 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... - Global gene expression profiling in whole-blood samples from individuals exposed to metal fumesZhaoxi 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... - A plasma biomarker signature of immune activation in HIV patients on antiretroviral therapyAnupa 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... - Expression of heat shock proteins and heat shock protein messenger ribonucleic acid in human prostate carcinoma in vitro and in tumors in vivoDan Tang
Department of Radiation Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
Cell Stress Chaperones 10:46-58. 2005.... - Phenotypic and functional effects of heat shock protein 90 inhibition on dendritic cellJooeun Bae
Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
J Immunol 178:7730-7. 2007.... - Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNPMarshall 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... - Utilization of a whole genome SNP panel for efficient genetic mapping in the mouseJennifer 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... - Telomerase inhibition and cell growth arrest after telomestatin treatment in multiple myelomaMasood A Shammas
Boston VA Health Care System, Boston, Massachusetts, USA
Clin Cancer Res 10:770-6. 2004.... - Evolution of the aging brain transcriptome and synaptic regulationPatrick 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... - Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's diseaseMarta 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... - Computational inference of mRNA stability from histone modification and transcriptome profilesChengyang 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... - Molecular diversity of astrocytes with implications for neurological disordersRobert 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.... - 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 infiltratePrzemyslaw 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... - Temporal genetic program following B-cell receptor cross-linking: altered balance between proliferation and death in healthy and malignant B cellsLaurent 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... - Determinants of antigenicity and specificity in immune response for protein sequencesYulong 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.... - Bioconductor: open software development for computational biology and bioinformaticsRobert 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... - Temporal genomics of vein bypass grafting through oligonucleotide microarray analysisJeffrey 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... - Ovarian cancer is a heterogeneous diseaseVivian 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... - Adjusting batch effects in microarray expression data using empirical Bayes methodsW 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/... - Identifying rare variants using a Bayesian regression approachAimin 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... - Identification of genes modulated in multiple myeloma using genetically identical twin samplesNikhil 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... - ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysisSheng 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/... - The vascular endothelial growth factor receptor tyrosine kinase inhibitor PTK787/ZK222584 inhibits growth and migration of multiple myeloma cells in the bone marrow microenvironmentBoris 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... - Integration of global SNP-based mapping and expression arrays reveals key regions, mechanisms, and genes important in the pathogenesis of multiple myelomaBrian 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... - Insights into the multistep transformation of MGUS to myeloma using microarray expression analysisFaith 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... - Allele-specific amplification in cancer revealed by SNP array analysisThomas 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... - A global expression-based analysis of the consequences of the t(4;14) translocation in myelomaAnn M Dring
Academic Unit of Haematology and Oncology, University of Leeds, Leeds, United Kingdom
Clin Cancer Res 10:5692-701. 2004..A number of non-t(4;14) cases also express MMSET consistent with this gene playing a role in myeloma pathogenesis... - The RhoGAP protein DLC-1 functions as a metastasis suppressor in breast cancer cellsSteve 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... - Whole genome loss of heterozygosity profiling on oral squamous cell carcinoma by high-density single nucleotide polymorphic allele (SNP) arrayXiaofeng Zhou
Cancer Genet Cytogenet 151:82-4. 2004 - A fully automated nanoelectrospray tandem mass spectrometric method for analysis of Caco-2 samplesColleen 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... - Significance and relationship between infiltrating inflammatory cell and tumor angiogenesis in hepatocellular carcinoma tissuesShao 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...
Research Grants
- dChip:Analysis and Visualization of Oligonucleotide Expression and SNP ArraysCheng Li; Fiscal Year: 2010....
- dChip:Analysis and Visualization of Oligonucleotide Expression and SNP ArraysCheng Li; Fiscal Year: 2009....