Computational and Statistical Approaches to Genomics

[1]  Robert A. Weinberg,et al.  A checkpoint on the road to cancer , 1998, Nature.

[2]  M Wahde,et al.  Coarse-grained reverse engineering of genetic regulatory networks. , 2000, Bio Systems.

[3]  M. Álvarez,et al.  Characterization of yeast DNA sequences capable of directing transcription in Streptomyces and Escherichia coli. , 1994, FEMS microbiology letters.

[4]  S. Catts,et al.  Increased levels of expression of an NMDAR1 splice variant in the superior temporal gyrus in schizophrenia , 2000, Neuroreport.

[5]  P. Underhill,et al.  The Werner syndrome gene and global sequence variation. , 2001, Genomics.

[6]  Sikandar G. Khan,et al.  An intronic poly (AT) polymorphism of the DNA repair gene XPC and risk of squamous cell carcinoma of the head and neck: a case-control study. , 2001, Cancer research.

[7]  Borodovsky MYu,et al.  A general rule for ranged series of codon frequencies in different genomes. , 1989, Journal of biomolecular structure & dynamics.

[8]  B. Pan,et al.  Solution structure of the single-strand break repair protein XRCC1 N-terminal domain , 1999, Nature Structural Biology.

[9]  Peter J. Russell,et al.  Fundamentals of Genetics , 1994 .

[10]  S. Skiena,et al.  Identifying gene regulatory networks from experimental data , 1999, RECOMB.

[11]  Sui Huang.  Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery , 1999, Journal of Molecular Medicine.

[12]  S. Altschul,et al.  SAGEmap: a public gene expression resource. , 2000, Genome research.

[13]  Eddy Mayoraz,et al.  Improved Pairwise Coupling Classification with Correcting Classifiers , 1998, ECML.

[14]  Michael G. Rosenfeld,et al.  Alternative RNA processing in calcitonin gene expression generates mRNAs encoding different polypeptide products , 1982, Nature.

[15]  J. Stec,et al.  Global Gene Expression Changes During Neoadjuvant Chemotherapy for Human Breast Cancer , 2002, Cancer journal.

[16]  D. Black,et al.  Alternative RNA splicing in the nervous system , 2001, Progress in Neurobiology.

[17]  J. Ward.  Radiation mutagenesis: the initial DNA lesions responsible. , 1995, Radiation research.

[18]  K Sivakumar,et al.  General nonlinear framework for the analysis of gene interaction via multivariate expression arrays. , 2000, Journal of biomedical optics.

[19]  J. Monod,et al.  Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.

[20]  K. Furge,et al.  Gene expression profiling of clear cell renal cell carcinoma: Gene identification and prognostic classification , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Y. Rao,et al.  Regulation of Ich-1 pre-mRNA alternative splicing and apoptosis by mammalian splicing factors. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[23]  R. Punnett,et al.  The Genetical Theory of Natural Selection , 1930, Nature.

[24]  W. V. D. Van de Ven,et al.  Calcitonin gene related peptide coding sequence is conserved in the human genome and is expressed in medullary thyroid carcinoma. , 1984, The Journal of clinical endocrinology and metabolism.

[25]  Yves Grandvalet.  Least Absolute Shrinkage is Equivalent to Quadratic Penalization , 1998 .

[26]  Yusuke Nakamura,et al.  Identification of Rad51 alteration in patients with bilateral breast cancer , 2000, Journal of Human Genetics.

[27]  Marcel J. T. Reinders,et al.  Genetic network models: a comparative study , 2001, SPIE BiOS.

[28]  M. Tockman,et al.  Polymorphisms of the DNA repair gene XRCC1 and lung cancer risk. , 2001, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[29]  M. Spitz,et al.  Reduced DNA repair capacity in lung cancer patients. , 1996, Cancer research.

[30]  C. J. Stone,et al.  Consistent Nonparametric Regression , 1977 .

[31]  E. P. van Someren.  Searching for Limited Connectivity in Genetic Network Models , 2004 .

[32]  A. Prentice,et al.  p53 intronic point mutation, aberrant splicing and telomeric associations in a case of B‐chronic lymphocytic leukaemia , 2000, British journal of haematology.

[33]  D. Cooper,et al.  The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: Causes and consequences , 1992, Human Genetics.

[34]  R. Guigó,et al.  GeneID in Drosophila. , 2000, Genome research.

[35]  A T Look,et al.  Splice-site mutation of the p53 gene in a family with hereditary breast-ovarian cancer. , 1994, Oncogene.

[36]  T. Weinert.  A DNA Damage Checkpoint Meets the Cell Cycle Engine , 1997, Science.

[37]  M. Boguski,et al.  Functional genomics: it's all how you read it. , 1997, Science.

[38]  D. Evans,et al.  Germ-line mutations of TP53 in Li-Fraumeni families: an extended study of 39 families. , 1997, Cancer research.

[39]  R. Kole,et al.  Modification of alternative splicing by antisense therapeutics. , 2004, Oligonucleotides.

[40]  M. Spitz,et al.  XPD/ERCC2 polymorphisms and risk of head and neck cancer: a case-control analysis. , 2000, Carcinogenesis.

[41]  Dana Angluin,et al.  Learning Regular Sets from Queries and Counterexamples , 1987, Inf. Comput..

[42]  Qing Zhou,et al.  AsMamDB: an alternative splice database of mammals , 2001, Nucleic Acids Res..

[43]  J. Barker,et al.  Large-scale temporal gene expression mapping of central nervous system development. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[44]  A. J. Lopez,et al.  Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. , 1998, Annual review of genetics.

[45]  R. Guigó,et al.  Evaluation of gene structure prediction programs. , 1996, Genomics.

[46]  S. Knudsen,et al.  Prediction of human mRNA donor and acceptor sites from the DNA sequence. , 1991, Journal of molecular biology.

[47]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.

[48]  J. Stec,et al.  RNA yield from needle biopsies for cDNA microarray analysis of breast cancer prior to neoadjuvant chemotherapy , 2001 .

[49]  R. Gupta,et al.  Background DNA damage for endogenous and unavoidable exogenous carcinogens: a basis for spontaneous cancer incidence? , 1999, Mutation research.

[50]  E. Friedberg.  How nucleotide excision repair protects against cancer , 2001, Nature Reviews Cancer.

[51]  B. Graveley.  Alternative splicing: increasing diversity in the proteomic world. , 2001, Trends in genetics : TIG.

[52]  M. Spitz,et al.  Repair of tobacco carcinogen-induced DNA adducts and lung cancer risk: a molecular epidemiologic study. , 2000, Journal of the National Cancer Institute.

[53]  A. Krämer,et al.  The structure and function of proteins involved in mammalian pre-mRNA splicing. , 1996, Annual review of biochemistry.

[54]  C I Amos,et al.  Modulation of nucleotide excision repair capacity by XPD polymorphisms in lung cancer patients. , 2001, Cancer research.

[55]  Marcel J. T. Reinders,et al.  A Comparison of Genetic Network Models , 2000, Pacific Symposium on Biocomputing.

[56]  C. Fuller,et al.  Fluorescence In Situ Hybridization (FISH) in Diagnostic and Investigative Neuropathology , 2002, Brain pathology.

[57]  E. Devilard,et al.  BCL-X and the apoptotic machinery of lymphoma cells. , 1998, Leukemia & lymphoma.

[58]  A V Carrano,et al.  Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes. , 1996, Genomics.

[59]  Bruce P. Neri,et al.  Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes , 1999, Nature Biotechnology.

[60]  Victor V. Solovyev,et al.  Identification of Human Gene Structure Using Linear Discriminant Functions and Dynamic Programming , 1995, ISMB.

[61]  R Kahavi,et al.  Wrapper for feature subset selection , 1997 .

[62]  J. Hurwitz,et al.  Isolation and characterization of two human transcription factor IIH (TFIIH)-related complexes: ERCC2/CAK and TFIIH. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[63]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[64]  F. Baas,et al.  The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains , 2001, Science.

[65]  T. Powles,et al.  Prediction of response to neoadjuvant chemoendocrine therapy in primary breast carcinomas. , 1997, Clinical cancer research : an official journal of the American Association for Cancer Research.

[66]  J. Fang,et al.  [Expression of standard and variant CD44 in human lung cancer]. , 1998, Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases.

[67]  J. Claverie.  Computational methods for the identification of genes in vertebrate genomic sequences. , 1997, Human molecular genetics.

[68]  J. Valcárcel,et al.  Alternative pre-mRNA splicing: the logic of combinatorial control. , 2000, Trends in biochemical sciences.

[69]  Kai Hwang,et al.  Advanced computer architecture - parallelism, scalability, programmability , 1992 .

[70]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[71]  J. Mesirov,et al.  Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. , 1999, Science.

[72]  A Sureau,et al.  SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs , 2001, The EMBO journal.

[73]  G. Evan,et al.  Proliferation, cell cycle and apoptosis in cancer , 2001, Nature.

[74]  Satoru Miyano,et al.  Identification of gene regulatory networks by strategic gene disruptions and gene overexpressions , 1998, SODA '98.

[75]  F. Gilliland,et al.  The XRCC1 399 glutamine allele is a risk factor for adenocarcinoma of the lung. , 2001, Mutation research.

[76]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[77]  Araceli M. Huerta,et al.  From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[78]  L. Stubbs,et al.  Analysis of homologous XRCC1-linked zinc-finger gene families in human and mouse: evidence for orthologous genes. , 1998, Genomics.

[79]  Temple F. Smith,et al.  Prediction of gene structure. , 1992, Journal of molecular biology.

[80]  Vladimir A. Kuznetsov,et al.  Distribution Associated with Stochastic Processes of Gene Expression in a Single Eukaryotic Cell , 2001, EURASIP J. Adv. Signal Process..

[81]  H P Friedman,et al.  Searching for evidence of altered gene expression: a comment on statistical analysis of microarray data. , 1999, Journal of the National Cancer Institute.

[82]  A. Collins.  Oxidative DNA damage, antioxidants, and cancer , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[83]  B. Ghetti,et al.  Tau Gene Mutations in Frontotemporal Dementia and Parkinsonism Linked to Chromosome 17 (FTDP‐17): Their Relevance for Understanding the Neurogenerative Process , 2000, Annals of the New York Academy of Sciences.

[84]  S. Batalov,et al.  A Comparison of the Celera and Ensembl Predicted Gene Sets Reveals Little Overlap in Novel Genes , 2001, Cell.

[85]  J. Welsh,et al.  Molecular classification of human carcinomas by use of gene expression signatures. , 2001, Cancer research.

[86]  A. Bindereif,et al.  In vitro selection of exonic splicing enhancer sequences: identification of novel CD44 enhancers. , 2001, Nucleic acids research.

[87]  C. Dang,et al.  Cancer genetics: Tumor suppressor meets oncogene , 1999, Current Biology.

[88]  P. Pevzner,et al.  Gene recognition via spliced sequence alignment. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[89]  J. Karras,et al.  Antisense inhibition of membrane-bound human interleukin-5 receptor-alpha chain does not affect soluble receptor expression and induces apoptosis in TF-1 cells. , 2000, Antisense & nucleic acid drug development.

[90]  G. Fuller,et al.  Insulin‐like Growth Factor Binding Protein 2: Gene Expression Microarrays and the Hypothesis‐generation Paradigm , 2002, Brain pathology.

[91]  Jaakko Astola,et al.  On the Use of MDL Principle in Gene Expression Prediction , 2001, EURASIP J. Adv. Signal Process..

[92]  Wentian Li,et al.  Random texts exhibit Zipf's-law-like word frequency distribution , 1992, IEEE Trans. Inf. Theory.

[93]  D. Ruppert.  The Elements of Statistical Learning: Data Mining, Inference, and Prediction , 2004 .

[94]  A. Mannermaa,et al.  A Finnish BRCA1 exon 12 4216‐2nt A to G splice acceptor site mutation causes aberrant splicing and frameshift, leading to protein truncation , 2000, Human mutation.

[95]  L. Zardi,et al.  Transformed human cells release different fibronectin variants than do normal cells , 1986, The Journal of cell biology.

[96]  M. Spitz,et al.  Polymorphisms of DNA repair gene XRCC1 in squamous cell carcinoma of the head and neck. , 1999, Carcinogenesis.

[97]  C. Loprinzi,et al.  Understanding the utility of adjuvant systemic therapy for primary breast cancer. , 2001, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[98]  Wentian Li,et al.  Statistical Properties of Open Reading Frames in Complete Genome Sequences , 1999, Comput. Chem..

[99]  V. Rotter,et al.  p53-dependent apoptosis is regulated by a C-terminally alternatively spliced form of murine p53 , 2000, Oncogene.

[100]  J. J. Ramsden,et al.  Zipf-like behavior in procaryotic protein expression , 1998 .

[101]  Marcel J. T. Reinders,et al.  Linear Modeling of Genetic Networks from Experimental Data , 2000, ISMB.

[102]  K H Buetow,et al.  Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project. , 2000, Genome research.

[103]  Jorma Rissanen,et al.  Strong optimality of the normalized ML models as universal codes and information in data , 2001, IEEE Trans. Inf. Theory.

[104]  A. Krainer,et al.  Pre-mRNA splicing in the new millennium. , 2001, Current opinion in cell biology.

[105]  Sikandar G. Khan,et al.  A new xeroderma pigmentosum group C poly(AT) insertion/deletion polymorphism. , 2000, Carcinogenesis.

[106]  N. Shen,et al.  Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis , 1999, Nature Genetics.

[107]  Leslie G. Valiant,et al.  A theory of the learnable , 1984, CACM.

[108]  B. Weir,et al.  Estimating the total number of alleles using a sample coverage method. , 2001, Genetics.

[109]  S. Wuchty.  Scale-free behavior in protein domain networks. , 2001, Molecular biology and evolution.

[110]  S. Henikoff,et al.  Drosophila genomic sequence annotation using the BLOCKS+ database. , 2000, Genome research.

[111]  G. Moran.  ON THE PERIOD-TWO-PROPERTY OF THE MAJORITY OPERATOR IN INFINITE GRAPHS , 1995 .

[112]  P. Sharp.  Split Genes and RNA Splicing (Nobel Lecture) , 1994 .

[113]  H. Lou,et al.  Alternative ribonucleic acid processing in endocrine systems. , 2001, Endocrine reviews.

[114]  T Gaasterland,et al.  MAGPIE: automated genome interpretation. , 1996, Trends in genetics : TIG.

[115]  P. Ravdin,et al.  Survey of breast cancer patients concerning their knowledge and expectations of adjuvant therapy. , 1998, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[116]  E J Duell,et al.  Polymorphisms in the DNA repair gene XRCC1 and breast cancer. , 2001, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[117]  David S. Johnson,et al.  Computers and In stractability: A Guide to the Theory of NP-Completeness. W. H Freeman, San Fran , 1979 .

[118]  Z. Szallasi,et al.  Modeling the normal and neoplastic cell cycle with "realistic Boolean genetic networks": their application for understanding carcinogenesis and assessing therapeutic strategies. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[119]  David I. K. Martin,et al.  Reactivation of heritably silenced gene expression in mice , 2000, Mammalian Genome.

[120]  Jorma Rissanen,et al.  The Minimum Description Length Principle in Coding and Modeling , 1998, IEEE Trans. Inf. Theory.

[121]  S. Eddy.  Non–coding RNA genes and the modern RNA world , 2001, Nature Reviews Genetics.

[122]  R. Tebbs,et al.  Correction of chromosomal instability and sensitivity to diverse mutagens by a cloned cDNA of the XRCC3 DNA repair gene. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[123]  P. Bork,et al.  Alternative splicing of human genes: more the rule than the exception? , 1999, Trends in genetics : TIG.

[124]  T. Ideker,et al.  Mining SNPs from EST databases. , 1999, Genome research.

[125]  S. Tapscott,et al.  Modeling stochastic gene expression: implications for haploinsufficiency. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[126]  R. Roberts,et al.  An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA , 1977, Cell.

[127]  The eMERGE Clinical Annotation Working Group.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001 .

[128]  C. Nusbaum,et al.  Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. , 1998, Science.

[129]  Alok N. Choudhary,et al.  An Efficient Heuristic Scheme for Dynamic Remapping of Parallel Computations , 1993, Parallel Comput..

[130]  G D Schuler,et al.  Molecular profiling of clinical tissue specimens: feasibility and applications. , 2000, The American journal of pathology.

[131]  Christian A. Rees,et al.  Molecular portraits of human breast tumours , 2000, Nature.

[132]  A. Povey.  DNA Adducts: Endogenous and Induced , 2000, Toxicologic pathology.

[133]  S. London,et al.  No association between the XPD (Lys751G1n) polymorphism or the XRCC3 (Thr241Met) polymorphism and lung cancer risk. , 2001, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[134]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[135]  A. E. Hoerl,et al.  Ridge Regression: Applications to Nonorthogonal Problems , 1970 .

[136]  A. Harris,et al.  A variant within the DNA repair gene XRCC3 is associated with the development of melanoma skin cancer. , 2000, Cancer research.

[137]  P Bork,et al.  EST comparison indicates 38% of human mRNAs contain possible alternative splice forms , 2000, FEBS letters.

[138]  H. Mohrenweiser,et al.  Amino acid substitution variants of APE1 and XRCC1 genes associated with ionizing radiation sensitivity. , 2001, Carcinogenesis.

[139]  Michal Linial,et al.  Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..

[140]  T. Lindahl.  Instability and decay of the primary structure of DNA , 1993, Nature.

[141]  L. Bell,et al.  Developmental distribution of female-specific Sex-lethal proteins in Drosophila melanogaster. , 1991, Genes & development.

[142]  E. Dougherty,et al.  Multivariate measurement of gene expression relationships. , 2000, Genomics.

[143]  C. Fizames,et al.  Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence , 2000, Nature Genetics.

[144]  Jorma Rissanen,et al.  MDL Denoising , 2000, IEEE Trans. Inf. Theory.

[145]  F. Gabreëls,et al.  A second common mutation in the methylenetetrahydrofolate reductase gene: an additional risk factor for neural-tube defects? , 1998, American journal of human genetics.

[146]  Jane Y. Wu,et al.  Alternative Splicing and Programmed Cell Death , 1999 .

[147]  D. Botstein,et al.  The transcriptional program in the response of human fibroblasts to serum. , 1999, Science.

[148]  J. Rissanen.  Stochastic Complexity and Modeling , 1986 .

[149]  L. Thompson,et al.  An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III , 1994, Molecular and cellular biology.

[150]  Michael Ruogu Zhang,et al.  An alternative-exon database and its statistical analysis. , 2000, DNA and cell biology.

[151]  F. Couch,et al.  Utilization of gene expression profiling to identify markers of disease recurrence in node-negative breast cancer , 2001 .

[152]  I. M. Jones,et al.  Variation in DNA repair is a factor in cancer susceptibility: a paradigm for the promises and perils of individual and population risk estimation? , 1998, Mutation research.

[153]  I. Ross,et al.  Transcription of individual genes in eukaryotic cells occurs randomly and infrequently , 1994, Immunology and cell biology.

[154]  Thangavel Alphonse Thanaraj.  A clean data set of EST-confirmed splice sites from Homo sapiens and standards for clean-up procedures , 1999, Nucleic Acids Res..

[155]  J. Concordet,et al.  Illegitimate transcription: transcription of any gene in any cell type. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[156]  Satoru Miyano,et al.  Inferring qualitative relations in genetic networks and metabolic pathways , 2000, Bioinform..

[157]  Chien-Jen Chen,et al.  Genetic polymorphisms of XRCC1 and risk of the esophageal cancer , 2001, International journal of cancer.

[158]  D. Black.  Protein Diversity from Alternative Splicing A Challenge for Bioinformatics and Post-Genome Biology , 2000, Cell.

[159]  Jaakko Astola,et al.  Quantization and distance function selecton for discrimination of tumors using gene expression data , 2002, SPIE BiOS.

[160]  M. Kuehl,et al.  RNA splicing generates a variant light chain from an aberrantly rearranged kappa gene. , 1980, Nature.

[161]  A. Krogh.  Two methods for improving performance of an HMM application for gene finding , 1997 .

[162]  D. Cooper.  Retention of CD44 introns in bladder cancer: Understanding the alternative splicing of pre‐mRNA opens new insights into the pathogenesis of human cancers , 1995, The Journal of pathology.

[163]  A. D. McLachlan,et al.  Codon preference and its use in identifying protein coding regions in long DNA sequences , 1982, Nucleic Acids Res..

[164]  W. Yung,et al.  Reactivation of insulin-like growth factor binding protein 2 expression in glioblastoma multiforme: a revelation by parallel gene expression profiling. , 1999, Cancer research.

[165]  Bhagirath Narahari,et al.  Dynamic load balancing schemes for computing accessible surface area of protein molecules , 1998, Proceedings. Fifth International Conference on High Performance Computing (Cat. No. 98EX238).

[166]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[167]  J. Shimazaki,et al.  Alternatively spliced MDM2 transcripts in human breast cancer in relation to tumor necrosis and lymph node involvement , 2000, Pathology international.

[168]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[169]  Peter S. Linsley,et al.  Expression profiling predicts poor outcome of disease in young breast cancer patients , 2001 .

[170]  S. Dudoit,et al.  Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data , 2002 .

[171]  Wei Zhang,et al.  Molecular Classification of Human Diffuse Gliomas by Multidimensional Scaling Analysis of Gene Expression Profiles Parallels Morphology‐Based Classification, Correlates with Survival, and Reveals Clinically‐Relevant Novel Glioma Subsets , 2002, Brain pathology.

[172]  Edward R. Dougherty,et al.  Coefficient of determination in nonlinear signal processing , 2000, Signal Process..

[173]  G. Yule,et al.  A Mathematical Theory of Evolution Based on the Conclusions of Dr. J. C. Willis, F.R.S. , 1925 .

[174]  J. Franco.  Finding Optimal Boolean Classifiers , 2000 .

[175]  S. West,et al.  Complex formation by the human RAD51C and XRCC3 recombination repair proteins , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[176]  E. Davidson,et al.  The hardwiring of development: organization and function of genomic regulatory systems. , 1997, Development.

[177]  S. Tavaré,et al.  Polymorphisms in the human DNA repair gene XPF. , 1999, Mutation research.

[178]  C. Kisker,et al.  Error-Prone DNA Polymerases Novel Structures and the Benefits of Infidelity , 2001, Cell.

[179]  J. Graves,et al.  Did genomic imprinting and X chromosome inactivation arise from stochastic expression? , 2001, Trends in genetics : TIG.

[180]  R. Yamada,et al.  Identification of 187 single nucleotide polymorphisms (SNPs) among 41 candidate genes for ischemic heart disease in the Japanese population , 2000, Human Genetics.

[181]  R C Garner,et al.  The role of DNA adducts in chemical carcinogenesis. , 1998, Mutation research.

[182]  K. Vogan,et al.  An alternative splicing event in the Pax-3 paired domain identifies the linker region as a key determinant of paired domain DNA-binding activity , 1996, Molecular and cellular biology.

[183]  M. Nevalainen,et al.  Increased Expression of FGF-8 Isoforms and FGF Receptors in Human Premalignant Prostatic Intraepithelial Neoplasia Lesions and Prostate Cancer , 2001, Laboratory Investigation.

[184]  S. Avigad,et al.  A novel germ line p53 mutation in intron 6 in diverse childhood malignancies , 1997, Oncogene.

[185]  Umesh V. Vazirani,et al.  An Introduction to Computational Learning Theory , 1994 .

[186]  R. Rozen,et al.  A second genetic polymorphism in methylenetetrahydrofolate reductase (MTHFR) associated with decreased enzyme activity. , 1998, Molecular genetics and metabolism.

[187]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[188]  Christian A. Rees,et al.  Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[189]  P. Kwok.  Approaches to allele frequency determination. , 2000, Pharmacogenomics.

[190]  A. Piazza,et al.  DNA repair gene polymorphisms, bulky DNA adducts in white blood cells and bladder cancer in a case‐control study , 2001, International journal of cancer.

[191]  A. Sancar,et al.  Nucleotide excision repair: from E. coli to man. , 1999, Biochimie.

[192]  Benjamin Ray Seyfarth,et al.  How to Build a Beowulf: A Guide to the Implementation and Application of PC Clusters , 2000, Scalable Comput. Pract. Exp..

[193]  L. Samson,et al.  Global response of Saccharomyces cerevisiae to an alkylating agent. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[194]  M. Sternberg,et al.  Structure of an XRCC1 BRCT domain: a new protein–protein interaction module , 1998, The EMBO journal.

[195]  F. Kittrell,et al.  Stage-specific changes in SR splicing factors and alternative splicing in mammary tumorigenesis , 1999, Oncogene.

[196]  P. Green,et al.  Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags. , 1999, Genome research.

[197]  Y. Chen,et al.  Ratio-based decisions and the quantitative analysis of cDNA microarray images. , 1997, Journal of biomedical optics.

[198]  S. Agrawal,et al.  Antisense oligonucleotides as modulators of pre-mRNA splicing. , 2000, Methods in molecular biology.

[199]  Neal S. Holter,et al.  Fundamental patterns underlying gene expression profiles: simplicity from complexity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[200]  P. Guptasarma,et al.  Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? , 1995, BioEssays : news and reviews in molecular, cellular and developmental biology.

[201]  Kevin Burrage,et al.  ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome , 2000, Nature Genetics.

[202]  Animesh A. Sinha,et al.  Gene Expression Profile Analysis by DNA Microarrays , 2001 .

[203]  P. Peltomäki,et al.  CYCLIN D1 as a genetic modifier in hereditary nonpolyposis colorectal cancer. , 2001, Cancer research.

[204]  L Grossman,et al.  DNA repair and aging in basal cell carcinoma: a molecular epidemiology study. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[205]  P Vineis,et al.  Markers of DNA repair and susceptibility to cancer in humans: an epidemiologic review. , 2000, Journal of the National Cancer Institute.

[206]  Rajiv Kumar,et al.  Single nucleotide polymorphism analyses of the human proliferating cell nuclear antigen (pCNA) and flap endonuclease (FEN1) genes , 2000, International journal of cancer.

[207]  G. Fuller,et al.  Fibroblast growth factor receptor-1 alpha-exon exclusion and polypyrimidine tract-binding protein in glioblastoma multiforme tumors. , 2000, Cancer research.

[208]  P. Underhill,et al.  Global sequence diversity of BRCA2: analysis of 71 breast cancer families and 95 control individuals of worldwide populations. , 1999, Human molecular genetics.

[209]  E. Uberbacher,et al.  Discovering and understanding genes in human DNA sequence using GRAIL. , 1996, Methods in enzymology.

[210]  Ting Chen,et al.  Modeling Gene Expression with Differential Equations , 1998, Pacific Symposium on Biocomputing.

[211]  Toshihide Ibaraki,et al.  Error-Free and Best-Fit Extensions of Partially Defined Boolean Functions , 1998, Inf. Comput..

[212]  Patrik D'haeseleer,et al.  Linear Modeling of mRNA Expression Levels During CNS Development and Injury , 1998, Pacific Symposium on Biocomputing.

[213]  T. Ørntoft,et al.  Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics , 2000, FEBS letters.

[214]  E. Alnemri,et al.  Cloning and Expression of Four Novel Isoforms of Human Interleukin-1β Converting Enzyme with Different Apoptotic Activities (*) , 1995, The Journal of Biological Chemistry.

[215]  D. Barnes,et al.  Reconstitution of DNA base excision‐repair with purified human proteins: interaction between DNA polymerase beta and the XRCC1 protein. , 1996, The EMBO journal.

[216]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[217]  T. Kunkel,et al.  In Vivo Consequences of Putative Active Site Mutations in Yeast DNA Polymerases α, ε, δ, and ζ , 2001 .

[218]  A. Hughes,et al.  Pattern and timing of gene duplication in animal genomes. , 2001, Genome research.

[219]  E. Campo,et al.  Differential Expression of cdc25 Cell-Cycle–Activating Phosphatases in Human Colorectal Carcinoma , 2001, Laboratory Investigation.

[220]  M M Shi,et al.  Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. , 2001, Clinical chemistry.

[221]  E. Lander,et al.  Characterization of single-nucleotide polymorphisms in coding regions of human genes , 1999 .

[222]  Y. Crama,et al.  Cause-effect relationships and partially defined Boolean functions , 1988 .

[223]  A. Lehmann,et al.  Xeroderma pigmentosum and trichothiodystrophy are associated with different mutations in the XPD (ERCC2) repair/transcription gene. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[224]  G. Stormo.  Gene-finding approaches for eukaryotes. , 2000, Genome research.

[225]  C S Robinson,et al.  Transcription occurs in pulses in muscle fibers. , 1998, Genes & development.

[226]  T Shimada,et al.  Random monoallelic expression of three genes clustered within 60 kb of mouse t complex genomic DNA. , 2001, Genome research.

[227]  C. Jacquillat,et al.  [Primary chemotherapy in breast cancer. Preliminary results]. , 1984, Annales de medecine interne.

[228]  C. Benz,et al.  Expression of a truncated 100 kDa HER2 splice variant acts as an endogenous inhibitor of tumour cell proliferation , 2001, Oncogene.

[229]  A. Brazma,et al.  Gene expression data analysis , 2000, FEBS letters.

[230]  U. Vogel,et al.  Polymorphisms in the DNA repair gene XPD: correlations with risk and age at onset of basal cell carcinoma. , 1999, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[231]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[232]  D. Bell,et al.  XRCC1 polymorphisms: effects on aflatoxin B1-DNA adducts and glycophorin A variant frequency. , 1999, Cancer research.

[233]  L. Brooks,et al.  A DNA polymorphism discovery resource for research on human genetic variation. , 1998, Genome research.

[234]  Christopher M. Bishop,et al.  Current address: Microsoft Research, , 2022 .

[235]  C. Rodolfo,et al.  Mutations in the XPD helicase gene result in XP and TTD phenotypes, preventing interaction between XPD and the p44 subunit of TFIIH , 1998, Nature Genetics.

[236]  H. Bartsch,et al.  Metabolic polymorphisms as susceptibility markers for lung and oral cavity cancer. , 2001, IARC scientific publications.

[237]  Allen Gersho,et al.  Vector quantization and signal compression , 1991, The Kluwer international series in engineering and computer science.

[238]  M. Press,et al.  Improved survival benefit from Herceptin (trastuzumab) and chemotherapy in patients selected by fluorescence in situ hybridization. , 2001 .

[239]  D. Haber,et al.  Wilms tumor and the WT1 gene. , 2001, Experimental cell research.

[240]  H. Kimura,et al.  Specialized transcription factories within mammalian nuclei. , 2000, Critical reviews in eukaryotic gene expression.

[241]  M. S. Ko.  Induction mechanism of a single gene molecule: stochastic or deterministic? , 1992, BioEssays : news and reviews in molecular, cellular and developmental biology.

[242]  E. Wagner,et al.  Polypyrimidine Tract Binding Protein Antagonizes Exon Definition , 2001, Molecular and Cellular Biology.

[243]  U. Vogel,et al.  Polymorphisms of the DNA repair gene XPD: correlations with risk of basal cell carcinoma revisited. , 2001, Carcinogenesis.

[244]  M. Johnston,et al.  The yeast genome: on the road to the Golden Age. , 2000, Current opinion in genetics & development.

[245]  T Misteli,et al.  Protein dynamics: implications for nuclear architecture and gene expression. , 2001, Science.

[246]  P. Grabowski.  Splicing Regulation in Neurons: Tinkering with Cell-Specific Control , 1998, Cell.

[247]  J. Mesirov,et al.  Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[248]  P Vineis,et al.  XRCC1, XRCC3, XPD gene polymorphisms, smoking and (32)P-DNA adducts in a sample of healthy subjects. , 2001, Carcinogenesis.

[249]  D. Tomescu,et al.  Nucleotide excision repair gene XPD polymorphisms and genetic predisposition to melanoma. , 2001, Carcinogenesis.

[250]  K. Heider,et al.  Characterization of a high-affinity monoclonal antibody specific for CD44v6 as candidate for immunotherapy of squamous cell carcinomas , 1996, Cancer Immunology, Immunotherapy.

[251]  J. Hoeijmakers.  Genome maintenance mechanisms for preventing cancer , 2001, Nature.

[252]  A Wuensche,et al.  Genomic regulation modeled as a network with basins of attraction. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[253]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[254]  A. Levinson,et al.  Expression of the H-ras proto-oncogene is controlled by alternative splicing , 1989, Cell.

[255]  J. Rissanen,et al.  Modeling By Shortest Data Description* , 1978, Autom..

[256]  D. Hume,et al.  Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. , 2000, Blood.

[257]  R. W. Davis,et al.  Global analysis of ATM polymorphism reveals significant functional constraint. , 2001, American journal of human genetics.

[258]  Rebecca A Betensky,et al.  Histopathological‐Molecular Genetic Correlations in Referral Pathologist‐Diagnosed Low‐Grade “Oligodendroglioma” , 2002, Journal of neuropathology and experimental neurology.

[259]  Sebastian A. Leidel,et al.  Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III , 2000, Nature.

[260]  D. Botstein,et al.  Microarrays in primary breast cancer--lessons from chemotherapy studies. , 2001, Endocrine-related cancer.

[261]  Thomas Werner,et al.  ConsInspector 3.0: new library and enhanced functionality , 1997, Comput. Appl. Biosci..

[262]  Satoru Miyano,et al.  Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model , 1998, Pacific Symposium on Biocomputing.

[263]  Jorma Rissanen,et al.  Universal coding, information, prediction, and estimation , 1984, IEEE Trans. Inf. Theory.

[264]  A. Sancar.  DNA repair in humans. , 1995, Annual review of genetics.

[265]  O. Kallioniemi,et al.  Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. , 2000, Cancer research.

[266]  R. Durbin,et al.  Using GeneWise in the Drosophila annotation experiment. , 2000, Genome research.

[267]  C. Gooding,et al.  Differential alternative splicing activity of isoforms of polypyrimidine tract binding protein (PTB). , 2001, RNA.

[268]  D. Louis,et al.  Specific genetic predictors of chemotherapeutic response and survival in patients with anaplastic oligodendrogliomas. , 1998, Journal of the National Cancer Institute.

[269]  J. Claverie,et al.  What If There Are Only 30,000 Human Genes? , 2001, Science.

[270]  K. Aldape,et al.  Detection of 1p and 19q loss in oligodendroglioma by quantitative microsatellite analysis, a real-time quantitative polymerase chain reaction assay. , 2001, The American journal of pathology.

[271]  George M. Church,et al.  Regulatory Networks Revealed by Transcriptional Profiling of Damaged Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with Proteasomes , 2000, Molecular and Cellular Biology.

[272]  A. Ronen,et al.  Human DNA repair genes , 2001, Environmental and molecular mutagenesis.

[273]  I. Muchnik.  An Implementation of Logical Analysis of Data an Implementation of Logical Analysis of Data , 1996 .

[274]  K. Khanna,et al.  DNA double-strand breaks: signaling, repair and the cancer connection , 2001, Nature Genetics.

[275]  Wei Zhang,et al.  Tissue Microarrays: Applications in Neuropathology Research, Diagnosis, and Education , 2002, Brain pathology.

[276]  Jack A. Taylor,et al.  DNA Repair Gene XRCC 1 Polymorphisms , Smoking , and Bladder Cancer Risk , 2001 .

[277]  N. Murata,et al.  Identification of 142 single nucleotide polymorphisms in 41 candidate genes for rheumatoid arthritis in the Japanese population , 2000, Human Genetics.

[278]  D. Jackson,et al.  The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells , 2000, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[279]  Pao-Ta Yu,et al.  Convergence behavior and root signal sets of stack filters , 1992 .

[280]  E. Uberbacher,et al.  Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[281]  F S Fay,et al.  Visualization of single RNA transcripts in situ. , 1998, Science.

[282]  K. Herbert,et al.  Immunochemical quantitation of UV-induced oxidative and dimeric DNA damage to human keratinocytes , 2000, Free radical research.

[283]  S Fuhrman,et al.  Reveal, a general reverse engineering algorithm for inference of genetic network architectures. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[284]  B. Scheithauer,et al.  Alterations of chromosome arms 1p and 19q as predictors of survival in oligodendrogliomas, astrocytomas, and mixed oligoastrocytomas. , 2000, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[285]  J. Rowley,et al.  Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[286]  Pui-Yan Kwok,et al.  Single-nucleotide polymorphisms in the public domain: how useful are they? , 2001, Nature Genetics.

[287]  R. Stoughton,et al.  Experimental annotation of the human genome using microarray technology , 2001, Nature.

[288]  P. Sharp,et al.  Spliced segments at the 5′ terminus of adenovirus 2 late mRNA* , 1977, Proceedings of the National Academy of Sciences.

[289]  W. K. Alfred Yung.  PATHOLOGY AND GENETICS OF TUMOURS OF THE NERVOUS SYSTEM , 2002 .

[290]  A. Hughes,et al.  Ancient genome duplications did not structure the human Hox-bearing chromosomes. , 2001, Genome research.

[291]  Shahid H. Bokhari,et al.  On the Mapping Problem , 1981, IEEE Transactions on Computers.

[292]  R. Legerski,et al.  Expression cloning of a human DNA repair gene involved in xeroderma pigmentosum group C , 1992, Nature.

[293]  T. Cooper,et al.  The regulation of splice-site selection, and its role in human disease. , 1997, American journal of human genetics.

[294]  J. Sng.  Hereditary breast cancer: a brief overview. , 2000, Annals of the Academy of Medicine, Singapore.

[295]  J. Ross,et al.  A Test Case of Correlation Metric Construction of a Reaction Pathway from Measurements , 1997 .

[296]  Gary D. Stormo,et al.  Modeling Regulatory Networks with Weight Matrices , 1998, Pacific Symposium on Biocomputing.

[297]  Robert L. Martino,et al.  Parallel Algorithms in Molecular Biology , 1997, HPCN Europe.

[298]  D. Housman,et al.  Germline intronic and exonic mutations in the Wilms' tumour gene (WT1) affecting urogenital development , 1992, Nature Genetics.