microarray
human genetic analysis (real data)
human genetic analysis (methodology)
dna sequence analysis
zipf's law
searching W.L. in scholar.google
TALK:
"The less, the better": another trend
in genomic and genetic analysis
Genetic Analysis (Real Data, Mostly Human)
Human Genetic Analysis (Methodology)
DNA Sequence Analysis
TALK: A Study of 500kb Oscillation of GC% in Human Chromosome 21
Zipf's Law and Other Scalings
(Hersey
Computational Biology and Bioinformatics Seminar,
Cold Spring Harbor Lab, Feb 2006)
[powerpoint]
TALK:
"The More, The Better" or "The Less, The Better"? Conflicting Trends
in Genomic and Genetic Analysis
(Department of Biomathematics, Mt. Sinai School of Medicine,
May 2005)
[power-point]
TALK: Gene Selection Criterion for Discriminant Microarray
Data Analysis Based on Extreme Value Distributions
(International Conference on Research in Computational Molecular
Biology (RECOMB)'2003, Berlin, April 2003)
[PDF]
[citation via google]
TALK: Zipf's Law in Importance of Genes for Cancer Classification
Using Microarray Data
(Second Conference of Chinese Bioinformatics Society, Beijing, China,
July 2002)
[PDF] (almost identical with my Barcelona talk)
TALK: Introduction to Microarray Data Analysis
(pre-CCB02 course, Beijing, China, June 2002)
[PDF]
TALK: Zipf's Law in Importance of Genes for Cancer Classification
Using Microarray Data
(UPF/IMIM, Barcelona, Spain, April 2002)
[PDF]
TALK: Low- and High-Level Analysis of Affymetrix Chip Data
(Pharmacia Research Center, Nerviano/Milano, November 2001)
[PDF]
TALK: Gene Selection in Discriminant Microarray Data Analysis
(Department of Physiology and Biophysics Seminar, Albert Einstein
College of Medicine, April 2001)
[MS PowerPoint]
TALK: How Many Genes Are Needed for a Discriminant Microarray
Data Analysis?
(Critical Assessment of Techniques for Microarray Data Mining Workshop,
December 2000)
[PDF]
Wentian Li, Young Ju Suh, Jingshan Zhang
"Does logarithm transformation of microarray data affect ranking order
of differentially expressed genes?",
arXiv preprint, q-bio.QM/0606018.
[abstract]
[abstract]
"Overlapping probabilities of top ranking gene lists, hypergeometric
distribution, and stringency of gene selection criterion",
Conference proceedings of Annual International Conference of the
IEEE Engineering in Medicine and Biology Society, pp. 5531-5541 (IEEE)
[abstract]
[PDF]
see also,
arXiv preprint, q-bio.QM/0606017.
[abstract]
"Monoclonal antibody classification based on epitope binding using
differential antigen disruption",
Journal of Immunological Methods, 314:9-20.
[abstract]
[PDF]
"The-more-the-better and the-less-the-better",
Bioinformatics, 22(18):2187-2188.
[abstract]
[PDF]
[citations]
[ citation via google]
"Microarray analyses of peripheral blood cells identifies
unique expression signature in psoriatic arthritis",
Molecular Medicine, 11(1-12):21-29.
[PDF]
"Peripheral blood gene expression profiling in rheumatoid arthritis"
Genes and Immunity, 6(5):388-397.
[abstract]
[PDF]
"Extreme-value distribution based gene selection
criteria for discriminant microarray data analysis
using logistic regression",
Journal of Computational Biology, 11(2-3):215-226.
[abstract]
[PDF]
[citations]
[citation via google]
[abstract from arXiv preprint]
"Gene discovery in bladder cancer progression using cDNA microarrays",
American Journal of Pathology, 163:505-516.
[abstract]
[PDF]
[citations]
[citation via google]
"Gene selection criterion for discriminant microarray
data analysis based on extreme value distributions",
RECOMB03: Proceedings of the Seventh Annual International Conference on
Computational Biology, pp. 217-223 (ACM Press).
[RECOMB'03 homepage]
[PDF]
[citation via google]
"Zipf's law in importance of genes for cancer classification
using microarray data",
Journal of Theoretical Biology, 219(4):539-551.
[abstract]
[PDF]
[citations]
[entry in CiteSeer]
[citation via google]
"How many genes are needed for a discriminant microarray
data analysis",
in Methods of Microarray Data Analysis ,
eds SM Lin and KF Johnson (Kluwer Academic), pp.137-150
[ PDF ]
[ MS-WORD]
[CAMDA homepage]
[CAMDA'00 homepage]
[citation via google]
[a compilation of citations]
[abstract]
[abstract]
[abstract]
PLoS Medicine, 3(12):e491.
Genes and Immunity, 7:533-543.
[abstract]
[PDF]
"High-density SNP analysis of 642 caucasian families with rheumatoid
arthritis identifies two new linkage regions on 11p12 and 2q33",
Genes and Immunity, 7(4):277-286.
[abstract]
[PDF]
Genes and Immunity, 7(5):335-341.
[abstract]
Arthritis & Rheumatism , 52(12):3813-3818.
[PDF]
[citations]
[citation via google]
"Analysis of families in the Multiple Autoimmune Disease Genetics
Consortium (MADGC): the PTPN22 620W allele associates with multiple
autoimmune phenotypes",
American Journal of Human Genetics, 76:561-571.
[PDF]
[citations]
[citation via google]
"The PTPN22 R620W polymorphism associates with RF positive rheumatoid
arthritis in a dose-dependent manner but not with HLA-SE status",
Genes and Immunity, 6(2):129-133.
[abstract]
[PDF]
[citations]
[citation via google]
"Analysis of CARD15/NOD2 haplotypes fails to identify common
variants associated with rheumatoid arthritis susceptibility",
Scandinavian Journal of Rheumatology, 34(3):198-203.
[abstract]
[PDF]
[citation via google]
"Identification of two novel female-specific non-MHC loci
regulating collagen-induced arthritis severity and chronicity,
and evidence for epistasis"
Arthritis & Rheumatism , 50(8):2695-2705.
[abstract]
[citation via google]
"Dissecting the genetic complexity of the association between
human leukocyte antigens and rheumatoid arthritis",
American Journal of Human Genetics, 71:585-594.
[abstract]
[PDF]
[html]
[citations]
[citation via google]
"Candidate genes involved in cardiovascular risk factors
by a family-based association study on the island of
Kosrae, Federated States of Micronesia",
American Journal of Medical Genetics, 110(3):234-242.
[abstract]
[ PDF]
[citations]
[citation via google]
"Linkage disequilibrium and founder effect analysis of the NF1
gene in French Canadians from the Quebec population"
Annales de Genetique, 45:39-44.
[abstract]
[PDF]
[citations]
[citation via google]
"Genotype analysis of the NF1 gene in the French Canadians
from the Quebec population",
American Journal of Medical Genetics, 104:189-198.
[abstract(via pubmed)]
[ PDF]
[citation via google]
"Progressive supranuclear gaze palsy
is in linkage disequilibrium with the tau and not the
alpha-synuclein gene",
Neurology, 50(1):270-273.
[abstract]
[citation via google]
"Genetic mapping of GLCLC, the human gene encoding the
catalytic subunit of gamma-glutamylcysteine synthetase, to chromosome
6p12 and characterization of a polymorphic trinucleotide
repeat within its 5' untranslated region",
Cytogenetics and Cell Genetics, 75(1):14-16.
[abstract(via pubmed)]
[citation via google]
(NSF Sponsored International Conference on Bioinformatics, Hangzhou, China, Jun 2007)
POSTER:
"Using pedigree founders only or using all pedigree members?
-- A comparison of SNP-expression regression results",
(with YJ Suh, HS Lee, F Batliwalla)
(Genetic Analysis Workshop 15, St. Pete Beach, FL, Nov 2006)
[PDF]
POSTER:
Genotype-based case-control analysis, violation of
Hardy-Weinberg equilibrium, and phase diagrams
(North Shore LIJ retreat, October 2006)
[PDF]
POSTER:
Inferring causal relationships among intermediate
phenotypes and biomarkers: a case study of rheumatoid
arthritis
(North Shore LIJ retreat, October 2006)
[PDF]
TALK: Causal Inference for Genetic and Microarray Data
(International Workshop on Exploring the Mechanisms and Landscapes
of Cellular Networks, Telluride, CO, August 2006)
TALK: Causal Inference of Intermediate Phenotypes and
Biomarkers in Rheumatoid Arthritis: An Application of
Machine Learning Techniques in Genetic Epidemiology
(Fuwai Hospital/Chinese National Human Genome Ceneter, Beijing,
China, May 2006)
[MS PowerPoint]
POSTER:
Effective Sample Size of Affected Sib Pairs
in Case-Control Analyses
(North Shore LIJ retreat, September 2005)
[PDF]
TALK: Association studies to locate human disease genes
(Symposium on pharmacogenomics, Guadalajara, Mexico, March 2005).
[MS PowerPoint]
POSTER:
Computer reconstructed haplotypes in pedigrees may not be
trusted
(North Shore LIJ retreat, May 2003)
[PDF]
TALK: Applications of Akaike and Bayesian Information Criteria
in Epidemiology, Linkage analysis, Microarray Data Analysis, and
DNA Sequence Analysis
(Genetic Epidemiology Seminar, Columbia University, December 2000)
[PDF]
TALK: Reducing Complexity in Biological and Genetic Data
(Medical Informatics Seminar, Columbia University, November 2000)
[PDF]
TALK: Applying Artificial Neural Networks in Pedigree Analysis
of Complex Genetic Diseases
(Beijing Bioinformatics Workshop, July 1999)
[PDF]
POSTER: A Revised Li-Sacks Formula For Calculating
the Probability of Identity-by-Descent Proportion
(Annual Meeting of American Society of Human Genetics, Denver CO, Oct 1998)
[PDF]
Wentian Li, Yaning Yang, Elaine Remmers, Chukwuma Ogunwole, Daniel Kastner,
Peter K. Gregersen
"effective sample size: quick estimation of the effect of relative pairs
in genetic case-control association analyses",
Nature precedings preprint, document 400
[abstract]
or, arXiv preprint, q-bio.QM/0611093
[abstract]
"Comparison of two-phase analyses for case-control genetic association studies"
Statistics in Medicine, to appear.
"Three lectures on case-control genetic association analysis",
Briefings in Bioinformatics, 9:1-13.
[abstract]
"A comparison of founder-only and all-pedigree-members genotype-expression
association by regression analysis",
BMC Proceedings, 1(suppl 1):S8.
[abstract]
"Genotype-based case-control analysis, violation of Hardy-Weinberg
equilibrium, and phase diagram",
Proceedings of the 5th Asia-Pacific Bioinformatics Conference,
pp.185-194 (Imperial College Press).
[abstract]
[
abstract from arXiv preprint (second version in March 2008 with
an error corrected)]
"Inferring causal relationships among intermediate
phenotypes and biomarkers: a case study of rheumatoid
arthritis",
Bioinformatics, 22(12):1503-1507.
[abstract ]
[PDF]
[citations]
[citation via google]
"Comparing single-nucleotide-polymorphism marker-based
and microsatellite marker-based
linkage analyses"
BMC Genetics, 6(suppl 1):S13.
[PDF]
[citations]
[citation via google]
"Reconstructing haplotypes in pedigrees:
the importance of parental information",
American Journal of Medical Genetics, 124A:107-109.
[abstract]
[ PDF]
[citations]
"Correlation between quantitative traits and correlation
between corresponding LOD scores: detection of pleiotropic
effects",
BMC Genetics, 4(suppl 1):S60.
[abstract]
[PDF]
[citation via google]
"Marker selection by Akaike information criterion and
Bayesian information criterion",
Genetic Epidemiology, 21(supp 1):S272-S277.
[abstract (via pubmed)]
[MS-WORD]
[PDF]
[citations]
[citation via google]
"Two approaches for consolidating results from genome scans
of complex traits: selection methods and scan statistics",
Genetic Epidemiology, 21(supp 1):S396-S402.
"A complete enumeration and classification
of two-locus disease models,"
Human Heredity, 50(6):334-349.
[abstract]
[PDF]
[citations]
[citation via google]
"Design of artificial neural network and its application to
the analysis of alcoholism data,"
Genetic Epidemiology, 17(suppl 1):S223-S228.
[abstract (via pubmed)]
[citations]
[citation via google]
"Low-order polynomial trends of female-to-male map distance
ratios along human chromosomes,"
Human Heredity, 48(5):266-270.
[abstract]
[citations]
[citation via google]
"Affected-sib-pair analysis of bipolar disorder using
data on chromosome 18",
Genetic Epidemiology, 14:641-646.
[abstract]
[citations]
[citation via google]
(Center for Theoretical Biology, Beijing University, Beijing, China, May 2006)
TALK: Ohno's Evolution by Duplication and
DNA Correlation
(Institute of Botany, Chinese Academy of Science, Beijing, China,
May 2006)
TALK: A Study of 500kb Oscillation of GC% in Human Chromosome 21
(Institute of Biophysics, Hebei University of Technology, Tianjing, China, May 2006)
TALK: Universal 1/f spectra in DNA sequences
(Universaity of Central Florida, December 2005)
[PDF]
TALK:
The 500kb Oscillation of GC% and Its Possible
Connection to Down Syndrome
(6th Anton Dohrn Workshop on Evolutionary Genomics,
Ischia, Naples, November 2005)
[PDF]
TALK:
Ohno's evolution by duplication and DNA correlations
(Instituto de Investigaciones Biomedicas,
Universidad Nacional Autonoma de Mexico, March 2005)
[MS PowerPoint]
TALK:
Some Recent Progresses in Genome-Wide DNA Sequence Analysis
(Instituto de Fisica,
Universidad Nacional Autonoma de Mexico, November 2004)
[PDF]
TALK: 1/f Spectrum is a Universal Feature of Human Genome DNA Sequences
(Texas A&M, April 2004)
[PDF]
TALK: Statistical Properties of Human Isochore Sequences
(International Workshop on Molecular Evolution, Beijing, June 2002)
TALK: Are Spectral Analyses Useful for DNA Sequence Analysis?
(International Conference on DNA in Chromatin, Arcachon, France, March 2002)
[PDF]
TALK: Five Applications of Recursive Segmentation in DNA Sequence Analysis
(Istituto Superiore di Sanita, Roma, October 2001)
[PDF]
TALK: Are Isochore Sequences Homogeneous?
(5th Anton Dohrn Workshop on Natural Selection and the Neutral Theory,
Ischia, Naples, October 2001)
[PDF]
TALK: DNA Segmentation as a Model Selection Process
(International Conference on Research in Computational Molecular
Biology'2001, April, 2001)
[MS PowerPoint]
TALK: Selecting Mathematical Models of DNA Sequences by Akaike
Information Criterion
(Center for Bioinformatics, Beijing University, July 2000)
[PDF ]
TALK: Correlations, Domains, and Periodicities in DNA Sequences
(Beijing Bioinformatics Workshop, July 1999)
[PDF]
"Large-scale oscillation of structure-related DNA sequence
features in human chromosome 21",
Physical Review E, 74:021912.
[abstract]
[PDF]
"Universal 1/f noise , crossovers of scaling exponents, and
chromosome-specific patterns of guanine-cytosine content in DNA
sequences of the human genome"
Physical Review E, 71:041910.
[abstract]
[abstract from arXiv preprint]
[PDF]
[ citations ]
[citation via google]
"An unusual 500,000 bases long oscillation of guanine and cytosine content
in human chromosome 21",
Computational Biology and Chemistry, 28(5-6):393-399.
[abstract]
[abstract from arXiv preprint]
[PDF]
[ citations ]
[citation via google]
"Spectral analysis of guanine and cytosine fluctuation of mouse
genomic DNA",
Fluctuation and Noise Letters, 4(3):L453-L464.
[abstract]
[abstract from arXiv preprint]
[ citations ]
[PDF]
"Isochores merit the prefix 'iso'" ,
Computational Biology and Chemistry, 27(1):5-10.
[abstract]
[ PDF]
[entry in CiteSeer]
[ citations ]
[citation via google]
also the preprint version:
Genome Biology, 3:preprint0009 (2002) .
"Simplifying the mosaic description of DNA sequences",
Physical Review E, 66:031913.
[abstract]
[PDF]
[citation via google]
"Are isochore sequences homogeneous?",
Gene, 300(1-2):129-139.
[abstract]
[PDF]
[citations]
[citation via google]
"Applications of recursive segmentation to the analysis of DNA sequences"
Computers & Chemistry (genome and informatics special issue), 26(5):491-510.
[abstract]
[PDF]
[entry in CiteSeer]
[citations]
[citaion via google]
[ supplement materials]
"Delineating relative homogeneous G+C domains in DNA sequences"
Gene, 276:57-72
[abstract]
[PDF]
[citations]
[
citation via google]
"New stopping criteria for segmenting DNA sequences",
Physical Review Letters, 86(25):5815-5818.
[abstract]
[ PDF]
[ citations ]
[citation via google]
"DNA segmentation as a model selection process",
RECOMB01: Proceedings of the Fifth Annual International Conference on
Computational Biology, pp. 204-210 (ACM Press).
[RECOMB'01 homepage]
[PDF]
[citation via google]
[entry in CiteSeer]
"Statistical properties of open reading frames in complete
genome sequences,"
Computers & Chemistry (informatics and the genome special issue), 23(3-4):283-301.
[abstract]
[PDF]
[entry in CiteSeer]
[citations]
[
citation via google]
Wentian Li (1999, unpublished)
"Large-scale patterns in DNA texts,"
Unused manuscript for Scientific American.
[PDF]
"Compositional heterogeneity within, and uniformity
between, DNA sequences of yeast chromosomes,"
Genome Research, 8(9):916-928.
[abstract]
[ PDF ]
[entry in CiteSeer]
[ citations ]
[ citation via google]
"Comments on "Simplicity and complexity in gene
evolution," (letters to the editor),
Complexity, 3(5):10.
[PDF]
[entry in CiteSeer]
Wentian Li (2003)
Reply to "On words and genes" by A.A. Tsonis and P.A.Tsonis
(letters to the editor),
Complexity, 8(5):13-14.
[PDF]
"The complexity of DNA: the measure of compositional heterogeneity
in DNA sequences and measures of complexity,"
Complexity, 3(2):33-37.
[abstract]
[PDF]
[entry in CiteSeer]
[citation via google]
"The study of correlation structures of DNA sequences
- a critical review",
Computers & Chemistry (open problems of computational molecular
biology special issue), 21(4):257-272.
[abstract]
[PDF]
[citations]
[citation via google]
"Rapid self-organized criticality: fractal evolution in
extreme environments",
Physical Review E, 70:036118.
[abstract]
[PDF]
[citation via google]
"Comments on 'Linguistic features in eukaryotic genomes',"
(letters to the editor)
Complexity, 9(4):10-11.
"Zipf's law everywhere",
Glottometrics, 5:14-21.
[ PDF]
[ MS-WORD]
[citations]
[citation via google]
Comments on "Zipf's law and the structures and evolution
of natural languages" (letters to the editor),
Complexity, 3(5):9-10.
[PDF]
Wentian Li (2003)
Reply to "On words and genes" by A.A. Tsonis and P.A.Tsonis
(letters to the editor),
Complexity, 8(5):13.
[PDF]
"Comments on "Bell curves and monkey languages" (letters to the editor),
Complexity, 1(6):6.
[PDF (preprint version) ]
[entry in CiteSeer]