Statistical Topics in Genetics and Genomics (140.668)

References, Second Term, 2004-2005

Meiosis, recombination, interference (Nov 1)

• Broman KW, Murray JC, Sheffield VC, White RL, Weber JL (1998) Comprehensive human genetic maps: Individual and sex-specific variation in recombination. Am J Hum Genet 63:861-869 [pdf]
• Broman KW, Weber JL (2000) Characterization of human crossover interference. Am J Hum Genet 66:1911-1926 [pdf]
• Broman KW, Rowe LB, Churchill GA, Paigen K (2002) Crossover interference in the mouse. Genetics 60:1123-1131 [pdf]
• Cox DR (1962) Renewal theory. Methuen, London.
• Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR, Stefansson K (2002) A high-resolution recombination map of the human genome. Nat Genet 31:241-247. [pdf]
• Kong A, Barnard J, Gudbjartsson DF, Thorleifsson G, Jonsdottir G, Sigurdardottir S, Richardsson B, Jonsdottir J, Thorgeirsson T, Frigge ML, Lamb NE, Sherman S, Gulcher JR, Stefansson K (2004) Recombination rate and reproductive success in humans. Nat Genet [pdf]
• McPeek MS, Speed TP (1995) Modeling interference in genetic recombination. Genetics 139:1031-1044 [pdf]
• McPeek MS (1996) An introduction to recombination and linkage analysis. In: Speed T, Waterman MS (eds) Genetic Mapping and DNA sequencing. Vol 81: IMA Volumes in Mathematics and Its Applications. Springer, New York, pp 1-14
• Speed TP (1996) What is a genetic map function? In: Speed T, Waterman MS (eds) Genetic Mapping and DNA sequencing. Vol 81: IMA Volumes in Mathematics and Its Applications. Springer, New York, pp 65-88
• Speed TP (1997) Genetic map functions. In: Encyclopedia of Biostatistics [pdf]
• Zhao H, Speed TP (1996) On genetic map functions. Genetics 142:1369-1377 [pdf]

QTL mapping in mice (Nov 8)

• Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185-199 [pdf]
• Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963-971 [pdf]
• Broman KW (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Animal 30:44-52 [pdf]
• Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm (with discussion). Journal of the Royal Statistical Society Series B 39:1-38 [pdf]

QTL mapping in mice (Nov 10)

• Broman KW, Speed TP (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion). J Roy Stat Soc B 64:641-656, 731-775 [pdf (326k) | discussion (519k)]
• Zeng Z-B, Kao C-H, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74:279-289 [pdf]
• KW Broman, GA Churchill, BS Yandell, Z-B Zeng. Statistical methods for mapping quantitative trait loci, in preparation. Chapter on hidden Markov models. [pdf]
• Baum LE, Petrie T, Soules G, Weiss N (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. The Annals of Mathematical Statistics 41:164-171 [pdf]
• Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77:257-286 [pdf]

Parametric linkage in humans (Nov 15)

• Ott J (1999) Analysis of human genetic linkage, 3rd edition. Johns Hopkins University Press
• Elston RC, Stewart J (1971) A general model for the genetic analysis of pedigree data. Human Heredity 21:523-542
• Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proceedings of the National Academy of Sciences USA 84:2363-2367 [pdf]
• Liang K-Y, Rathouz PJ, Beaty TH (1996) Determining linkage and mode of inheritance: Mod scores and other methods. Genetic Epidemiology 13:575-593
• Clerget-Darpoux F, Bonati-Pelli C, Hochez J (1986) Effects of misspecifying genetic parameters in lod score analysis. Biometrics 42:393-399 [pdf]
• Elston RC (1989) Man bites dog? The validity of maximizing lod scores to determine mode of inheritance. American Journal of Medical Genetics 34:487-488
• Hodge SE, Elston RC (1994) Lods, wrods, and mods: The interpretation of lod scores calculated under different models. Genetic Epidemiology 11:329-342

Nonparametric linkage in humans (Nov 17)

• Whittemore AS (1996) Genome scanning for linkage: An overview. American Journal of Human Genetics 59:704-716
• McPeek MS (1999) Optimal allele-sharing statistics for genetic mapping using affected relatives. Genetic Epidemiology 16:225-249 [pdf]
• Kong A, Cox NJ (1997) Allele-sharing models: LOD scores and accurate linkage tests. American Journal of Human Genetics 61:1179-1188 [pdf]

QTL mapping in humans (Nov 22)

• Kruglyak L, Lander ES (1995) Complete multipoint sib-pair analysis of qualitative and quantitative traits. American Journal of Human Genetics 57:439-454
• Amos CI (1994) Robust variance-components approach for assessing genetic linkage in pedigrees. American Journal of Human Genetics 54:535-543
• Haseman JK, Elston RC (1972) The investigation of linkage between a quantitative trait and a marker locus. Behavior Genetics 2:3-19
• Almasy L, Blangero J (1998) Multipoint quantitative-trait linkage analysis in general pedigrees. American Journal of Human Genetics 62:1198-1211 [pdf]

Principles of Protein Structure (Nov 29 & Dec 1)

• Branden C and Tooze J (1999) Introduction to protein structure. Garland Publishing; 2nd edition.
• Creighton TE (1992) Proteins: structures and molecular properties. WH Freeman; 2nd edition.
• Nelson DL and Cox MM (2004) Lehninger principles of biochemistry. WH Freeman; 4th edition.

Mass spectrometry (Dec 6)

• Petricoin EF et al (2002) Use of proteomic patterns in serum to identify ovarian cancer. The Lancet 359:572-577 [pdf]
  Check also PUBMED for some immediate responses to the article.
• Baggerly KA et al (2004) Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 20:777-785 [pdf]

Protein structure and data bases (Dec 8)

• Great webpages on NMR and X-ray crystallography.
• Andreeva A et al (2004) SCOP database in 2004: refinements integrate structure and sequence family data Nucleic Acids Research 32:D226-229 [pdf]
• Berman HM et al (2000) The Protein Data Bank. Nucleic Acids Research, 28:235-242 Bioinformatics 20:777-785 [pdf]
• Bourne P and Weissig H (2003) Structural Bioinformatics. Wiley-Liss.
• Holm L and Sander C (1993) Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology 233:123-138. [pdf]
• Holm L and Sander C (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Research 26:316-319 [pdf]
• Hubbard TJ, Ailey B, Brenner SE, Murzin AG, and Chothia C (2004) SCOP: a structural classification of proteins database. Nucleic Acids Research 27:254-256 [pdf]
• Pearl FMG et al (2000) Assigning genomic sequences to CATH. Nucleic Acids Research 28:277-282 [pdf]

Classification and prediction (Dec 12 & 14)

We will discuss the Siepen paper [pdf] and the Yasui paper [pdf] in class.

• Breiman L (1996) Bagging predictors. Machine Learning, 24:123-140. [pdf]
• Breiman L (2001) Random forests. Machine Learning, 45:5-32. [pdf]
• Breiman L (2001) Statistical modeling: The two cultures. Statistical Science, 16:199-215.
• Breiman L, Friedman JH, Olshen RA, and Stone CJ (1984) Classification and regression trees. Kluwer Academic Publishers.
• Dietterich T (2000) An experimental comparison of three methods for constructing ensembles of decision trees: bagging, boosting, and randomization. Machine Learning 40:139-157. [pdf]
• Freund Y and Schapire RE (1996) Experiments with a new boosting algorithm. Machine Learning: Proceedings of the Thirteenth International Conference, 148-156. [pdf]
• Friedman JH (1991) Multivariate adaptive regression splines. Annals of Statistics 19:1-141.
• Hastie T, Tibshirani R, and Friedman J (2001) The elements of statistical learning. Springer, NY.
• Saunders CT and Baker D (2002) Evaluation of structural and evolutionary contributions to deleterious mutation prediction. Journal of Molecular Biology 322:891-901. [pdf]
• Siepen JA, Radford SE, and Westhead DR (2003) Beta edge strands in protein structure prediction and aggregation. Protein Science 12:2348-2359. [pdf]
• Therneau TM and Atkinson EJ (2000) An introduction to recursive partitioning using the RPART routines. Technical Report Series No 61, Department of Health Science Research, Mayo Clinic, Rochester, Minnesota [pdf]
• Venables WN and Ripley BD (2002) Modern applied statistics with S. Springer NY, 4th edition.
• Yasui Y et al (2003) A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. Biostatistics 4:449-463. [pdf]
• The random forests webpage.
• The open rasmol webpage.

Protein structure prediction (Dec 20 & 22)

• Cheng B, and Titterington DM (1994) Neural Networks: A Review from a Statistical Perspective. Statistical Science, 9:2-30. [pdf]
• van Laarhoven PJ, and Aarts EH (1987) Simulated Annealing: Theory and Applications. Kluwer Academic Publishers.
• Otten RH, and Ginneken LP (1989) The Annealing Algoritm. Kluwer Academic Publishers.
• Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng. 12:85-94. [pdf]
• Simons KT, Kooperberg C, Huang E, and Baker D (1997) Assembly of Protein Tertiary Structures from Fragments with Similar Local Sequences using Simulated Annealing and Bayesian Scoring Functions. Journal of Molecular Biology, 268:209-25. [pdf]
• Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystroff C, and Baker D (1999) Improved Recognition of Native-like Protein Structures using a Combination of Sequence-dependent and Sequence-independent Features of Proteins. Proteins, 34:82-95. [pdf]
• The Baker lab webpage
• The Dunbrack lab webpage.
• The PHD secondary structure prediction webpage and the predict protein web server.
• The CASP webpage.
• The CASP 5 evaluation.

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Last modified: Fri Apr 4 10:57:39 2008