Publications

Rubin AF and Green P: Expression-based segmentation of the Drosophila genome. BMC Genomics 14:812 (2013).

Gordon D and Green P: Consed: a graphical editor for next-generation sequencing. Bioinformatics 29(22):2936-37 (2013).

Green P and Ewing B: Comment on “Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions.”. Science 340(6133):682 (2013).

Thompson O, Edgley M, Strasbourger P, Flibotte S, Ewing B, Adair R, Au V, Chaudry I, Fernando L, Hutter H, Kieffer A, Lau J, Lee N, Miller A, Raymant G, Shen B, Shendure J, Taylor J, Turner EH, Hillier LW, Moerman DG and Waterston RH: The Million Mutation Project: A new approach to genetics in Caenorhabditis elegans.. Genome Research 23:1749-62 (2013).

Gerstein, MB et al., Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science 330:1775-87 (2010).

McVicker G and Green P: Genomic signatures of germline gene expression. Genome Research 20:1503-11 (2010).

Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T: Visualizing genomes: techniques and challenges. Nature Methods 7(3 Suppl):S5-S15 [Epub 2010 Feb 25]. Review (2010).

Rubin AF and Green P: Mutation patterns in cancer genomes. Proceedings of the National Academy of Sciences U.S.A. 106(51):21766-70 [Epub 2009 Dec 7] (2009).

McVicker G, Gordon D, Davis C, and Green P: Widespread genomic signatures of natural selection in hominid evolution. PLoS Genetics 5(5): e1000471 [Epub 2009 May 8] (2009).

Hillier LW, Reinke V, Green P, Hirst M, Marra M, and Waterston RH: Massively parallel sequencing of the poly-adenylated transcriptome of C. elegans. Genome Research 19(4):657-66 [Epub 2009 Jan 30] (2009).

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium: Unlocking the secrets of the genome. Nature 459(7249):927-30 (2009).

Ley TJ,...,Gordon D,...,Wilson K: DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456:66-72 (2008).

Merrihew, GE, Davis, C, Ewing, B, Williams, G, Kall, L, Frewen, BE, Noble, WS, Green, P, Thomas, JH, and MacCoss, MJ: Use of shotgun proteomics for the identification, confirmation and correction of C. elegans gene annotations. Genome Research 18(10):1660-9 [Epub ahead of print 2008 July 24] (2008).

Siepel A, Diekhans M, Brejova B, Langton L, Stevens M, Comstock CLG, Davis C, Ewing B, Ooommen S, Lau C, Yu H-C, Li J, Roe BA, Green P, Gerhard DS, Temple G, Haussler D, Brent MR : Targeted discovery of novel human exons by comparative genomics. Genome Research 17(12):1763-73 [Epub 2007 November 7] (2007).

Saunders CT and Green P: Insights from modeling protein evolution with context-dependent mutation and asymmetric amino acid selection. Molecular Biology and Evolution 24(12): 2632-47. [Epub 2007 September 28] (2007).

Green P: 2X genomes--does depth matter? Genome Research 17(11):1547-49 (2007).

Rubin AF and Green P: Comment on "the consensus coding sequences of human breast and colorectal cancers". Science 317 (5855): 1500c (2007).

Garg K and Green P: Differing patterns of selection in alternative and constitutive splice sites. Genome Research 17:1015-1022 [Epub 2007 June 7] (2007).

Baek D, Davis C, Ewing B, Gordon D and Green P: Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Research 17(2):145-55 [Epub 2007 Jan 8] (2007).

Bubb KL, Boyee D, Buckley D, Haugen E, Kibukawa M, et al.: Scan of human genome reveals no new loci under ancient balancing selection. Genetics 173(4):2165-77 [Epub 2006 June 4] (2006).

Baek D and Green P: Sequence conservation, relative isoform frequencies and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proceedings of the National Academy of Sciences U.S.A. 102:12813-12818 (2005).

Hwang DG and Green P: Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proceedings of the National Academy of Sciences U.S.A. 101:13994-14001 (2004). Download Ambiore [220K].

Gordon D: Viewing and Editing Assembled Sequences Using Consed. In Current Protocols in Bioinformatics (AD Baxevanis and DB Davison, eds). Section 11.2.1-11.2.43 (2004).

Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, et al.: Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788-793 (2003).

Green P, Ewing B, Miller W, Thomas PJ, NISC Comparative Sequencing Program, Green ED: Transcription-associated mutational asymmetry in mammalian evolution. Nature Genetics 33:514-517 (2003). Download PDF file [93 kbytes].

Green, P: Whole-genome disassembly. Proceedings of the National Academy of Sciences U.S.A. 99:4143-4144 (2002).

Gordon D, Desmarais C, Green P: Automated finishing with Autofinish. Genome Res 11:614-625 (2001).

Ewing B, Green P: Analysis of expressed sequence tags indicates 35,000 human genes. Nature Genetics 25:232-234 (2000). Download PDF file [112 kbytes]. Additional information is available at EST Assembly Methods and Contig Files.

Green P, Koonin E (eds): Genomes and evolution: glimpses of an emerging synthesis. Curr Opin Genet Dev 9:621-623 (1999).

Garg K, Green P, Nickerson DA: Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags. Genome Research 9:1087-1092 (1999).

Olson MV, Green P: A “quality-first” credo for the Human Genome Project. Genome Research 8:414-415 (1998).

Green P: Human genome project: Data quality. Science 279:1113 (1998).

Gordon D, Abajian C, Green P: Consed: a graphical tool for sequence finishing. Genome Research 8:195-202 (1998).

Ewing B, Green P: Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Research 8:186-194 (1998).

Ewing B, Hillier L, Wendl M, Green P: Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research 8:175-185 (1998).

Green P: Against a whole-genome shotgun. Genome Research 7:410-417 (1997).

Green E, Braden V, Fulton R, Lim R, Ueltzen M, Peluso D, Mohr-Tidwell R, Idol J, Smith L, Chumakov I, Le Paslier D, Cohen D, Featherstone T, Green P: A human chromosome 7 yeast artificial chromosome resource: construction, characterization, and screening. Genomics 25:170-183 (1995).

Green P: Ancient conserved regions in gene sequences. Current Opinion in Structural Biology 4:404-412 (1994).

Wilson R, Ainscough R, Anderson K, Baynes C, Berks M, Bonfield J, Burton J, Connell M, Copsey T, Cooper J, Coulson A, Craxton M, Dear S, Du Z, Durbin R, Favello A, Fraser A, Fulton L, Gardner A, Green P, Hawkins T, Hillier L, Jier M, Johnston L, Jones M, Kershaw J, Kirsten J, Laisster N, Latreille P, Lightning J, Lloyd C, Mortimore B, O'Callaghan M, Parsons J, Percy C, Rifken L, Roopra A, Saunders D, Shownkeen R, Sims M, Smaldon N, Smith A, Sonnhammer E, Staden R, Sulston J, Thierry-Mieg J, Thomas K, Vaudin M, Vaughan K, Waterston R, Watson A, Weinstock L, Wilkinson-Sproat J, Wohldman P: 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature 368:32-38 (1994).

Waterston R, Ainscough R, Anderson K, Berks M, Blair D, Connell M, Cooper J, Coulson A, Craxton M, Dear S, Du Z, Durbin R, Favello A, Fulton L, Green P, Halloran N, Hawkins T, Hillier L, Huynh C, Johnston L, Kershaw J, Kirsten J, Kozono Y, Laister N, Latreille P, Mortimore B, Panussis D, Percy C, Rifkin L, Roopra A, Shownkeen R, Smaldon N, Smith A, Smith M, Staden R, Sulston J, Thierry-Mieg J, Vaudin M, Vaughan K, Weinstock L, Wohldmann P, Wilson R: The genome of the nematode Caenorhabditis elegans. Cold Spring Harbor Symposia on Quantitative Biology 58: in press (1993).

Neuwald AF, Green P: Detecting patterns in protein sequences. J. Mol. Biol. 239:698-712 (1994).

Olson MV, Green P: Criterion for the completeness of large-scale physical maps of DNA. Cold Spring Harbor Symposia on Quantitative Biology 58:349-355 (1993).

Green P, Lipman D, Hillier L, Waterston R, States D, Claverie J-M: Ancient conserved regions in new gene sequences and the protein databases. Science 259:1711-1716 (1993).

Waterston R, Martin C, Craxton M, Huynh C, Coulson A, Hillier L, Durbin R, Green P, Shownkeen R, Halloran N, Metzstein M, Hawkins T, Wilson R, Berks M, Du Z, Thomas K, Thierry-Mieg J, Sulston J: A survey of expressed genes in Caenorhabditis elegans. Nature Genetics 1:114-123 (1992).

Sulston J, Du Z, Thomas K, Wilson R, Hillier L, Staden R, Halloran N, Green P, Thierry-Mieg J, Qiu L, Dear S, Coulson A, Craxton M, Durbin R, Berks M, Metzstein M, Hawkins T, Ainscough R, Waterston R: The C. elegans genome sequencing project: A beginning. Nature 356:37-41 (1992).

Green P: Population genetic issues in DNA fingerprinting. Am J Human Genetics 50:440-441 (1992). (refereed letter to editor)

Green ED, Green P: Sequence-tagged site (STS) content mapping of human chromosomes: theoretical considerations and early experiences. PCR Methods and Applications 1:77-90 (1991).

Hillier L, Green P: OSP: A computer program for choosing PCR and DNA sequencing primers. PCR Methods and Applications 1:124-128 (1991).

Chen E, Cheng A, Lee A, Kuang W-J, Hillier L, Green P, Schlessinger D, Ciccodicola A, D'Urso M: Sequence of human glucose-6-phosphate dehydrogenase cloned in plasmids and a yeast artificial chromosome. Genomics 10:792-800 (1991).

Green P, Lander E: Forensic DNA tests and Hardy-Weinberg equilibrium. Science 253:1038-1039 (1991).

Green P: Genetic Analysis Workshop 7: mapping chromosome 21 linkage markers. Cytogenet. Cell Genet. 59:77-79 (1992).

Green P: Construction and comparison of chromosome 21 radiation hybrid and linkage maps using CRI-MAP. Cytogenet. Cell Genet. 59:122-124 (1992).

Lander E, Green P: Counting algorithms for linkage: correction to Morton and Collins. Ann Hum Genet 55:33-38 (1991).

Keats B, Sherman S, Morton N, Robson E, Buetow K, Cartwright P, Chakravarti A, Francke U, Green P, Ott J: Guidelines for human linkage maps: An international system for human linkage maps (ISLM 1990). Genomics 9:557-560 (1991).

Barnett L, Gillett W, Green P: Probabilistic analysis of random clone restriction mapping. 14th Annual Symposium on Computer Applications in Medical Care (IEEE Computer Society Press), 99-103, (1990).

Keith T, Green P, Reeders S, Brown V, Phipps P, Bricker A, Falls K, Rediker K, Powers J, Hogan C, Nelson C, Knowlton R, Donis-Keller H: Genetic linkage map of 46 DNA markers on human chromosome 16. Proc Natl Acad Sci 87:5754-5758 (1990).

Green P: The human genome. Encyclopedia of Human Biology (Academic Press Inc.), vol. 3:869-879 (1991).

Drury H, Green P, McCauley B, Olson M, Politte D, Thomas L: Spatial normalization of one-dimensional electrophoretic gel images. Genomics 8:119-126 (1990).

Murray J, Nishimura D, Buetow K, Ardinger H, Spence M, Sparkes R, Falk R, Falk P, Gardner R, Harkness E, Glinski L, Pauli R, Nakamura Y, Green P, Schinzel A: Linkage of an autosomal dominant clefting syndrome (Van der Woude) to loci on chromosome 1q. Am J Human Genetics 46:486-491 (1990).

White R, Lalouel J, Nakamura Y, Donis-Keller H, Green P, Bowden D, Mathew C, Easton D, Robson R, Morton N, Gusella J, Haines J, Retief A, Kidd K, Murray J, Lathrop M, Cann H: The CEPH consortium primary linkage map of human chromosome 10. Genomics 6:393-412 (1990).

Wells R, Green P, Reeders S: Simultaneous genetic mapping of multiple human minisatellite sequences using DNA fingerprinting. Genomics 5:761-772 (1989).

Green P: Genetic linkage and complex diseases: a comment. Genetic Epid 7:25-27 (1990).

Page D, Disteche C, Simpson E, de la Chapelle A, Andersson M, Alitalo T, Brown L, Green P, Akots G: Chromosomal localization of ZFX — a human gene that escapes X inactivation — and its murine homologs. Genomics 7:37-46 (1990).

Bowden D, Gravius T, Green P, Falls K, Wurster-Hill D, Noll W, Muller-Kahle H, Donis-Keller H: A genetic linkage map of 32 loci on human chromosome 10. Genomics 5:718-726 (1989).

Green P, Helms C, Weiffenbach B, Stephens K, Keith T, Bowden D, Smith D, Donis-Keller H: Construction of a linkage map of the human genome, and its application to mapping genetic diseases. Clinical Chem 35/7(B):33-37 (1989).

Drabkin H, Sage M, Helms C, Green P, Gemmill R, Smith D, Erickson P, Hart I, Ferguson-Smith A, Ruddle F, Tommerup N: Regional and physical mapping studies characterizing the Greig polysyndactyly 3;7 chromosome translocation, t(3;7) (p21.1;p13). Genomics 4:518-529 (1989).

Fulton T, Bowcock A, Smith D, Daneshvar L, Green P, Cavalli-Sforza L, Donis-Keller H: A 12 megabase restriction map at the cystic fibrosis locus. Nucl Acids Res 17:271-284 (1989).

Bale S, Dracopoli N, Tucker M, Clark W, Fraser M, Stanger B, Green P, Donis-Keller H, Housman D, Greene M: Mapping the gene for hereditary cutaneous malignant melanoma/dysplastic nevus to chromosome 1p. New Engl J Med 320:1367-1372 (1989).

Bowden D, Muller-Kahle H, Gravius TC, Helms C, Watt-Morgan D, Green P, Donis-Keller H: Identification and characterization of 23 restriction fragment length polymorphic loci by screening random cosmid genomic clones. Am J Human Genetics 44:671-678 (1989).

Stephens K, Green P, Riccardi VM, Ng S, Rising M, Barker D, Darby J, Falls K, Collins FS, Willard H, Donis-Keller H: Genetic analysis of eight loci tightly linked to neurofibromatosis 1. Am J Human Genetics 44:13-19 (1989).

Goldgar D, Green P, Parry D, Mulvihill J: Multipoint linkage analysis in Neurofibromatosis Type I: An international collaboration. Am J Human Genetics 44:6-12 (1989).

Donis-Keller H, Barker D, Knowlton R, Schumm J, Braman J, Green P: Highly polymorphic RFLP probes as diagnostic tools. In Cold Spring Harbor Symposia on Quantitative Biology, vol LI (1986).

Nugent C, Gravius T, Green P, Larsen J, MacMillin M, Donis-Keller H: Prenatal diagnosis of cystic fibrosis by chorionic villus sampling using 12 polymorphic deoxyribonucleic acid markers. Obstetrics and Gynecology 71:213-215 (1988).

Green P, Barker D, Knowlton R, Schumm J, Lander E, Oliphant A, Willard H, Akots G, Brown V, Gravius T, Helms C, Nelson C, Parker C, Rediker K, Rising M, Watt D, Weiffenbach B, Donis-Keller H: A genetic linkage map of chromosome 7 including the cystic fibrosis region. In Cellular and Molecular Basis of Cystic Fibrosis (G. Mastella and P. Quinton, eds). San Francisco Press (1987).

Reeders S, Keith T, Green P, Germino G, Barton N, Lehmann O, Brown V, Phipps P, Morgan J, Bear J, Parfrey P: Regional localisation of the autosomal dominant polycystic kidney disease locus. Genomics 3:150-155(1988).

Stephens K, Riccardi VM, Rising M, Ng S, Green P, Collins FS, Rediker KS, Powers JA, Parker C, Donis-Keller H: Linkage studies with chromosome 17 DNA markers in 45 neurofibromatosis 1 families. Genomics 1:353-357 (1987).

Donis-Keller H, Green P, Helms C, Cartinhour S, Weiffenbach B, Stephens K, Keith T, Bowden D, Smith D, Lander E, Botstein D, Akots G, Rediker K, Gravius T, Brown V, Rising M, Parker C, Powers J, Watt D, Kauffman E, Bricker A, Phipps P, Muller-Kahle H, Fulton T, Ng S, Schumm J, Braman J, Knowlton R, Barker D, Crooks S, Lincoln S, Daly M, Abrahamson J: A genetic linkage map of the human genome. Cell 51:319-337 (1987).

Lander E, Green P, Abrahamson J, Barlow A, Daly M, Lincoln S, Newburg L: Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181 (1987).

Barker D, Green P, Knowlton R, Schumm J, Lander E, Oliphant A, Willard H, Akots G, Brown V, Gravius T, Helms C, Nelson C, Parker C, Rediker K, Watt D, Weiffenbach B, Donis-Keller H: Genetic linkage map of human chromosome 7 with 63 DNA markers. Proc. Natl. Acad. Sci. USA 84:8006-8010 (1987).

Nordeen SK, Green P, Fowlkes D: A rapid, sensitive, and inexpensive assay for chloramphenicol acetyltransferase. DNA 6:173-178 (1987).

Lander E, Green P: Construction of multi-locus genetic linkage maps in humans. Proc. Natl. Acad. Sci. USA 84:2363-2367 (1987).

Green P, Manucci PM, Briet E, Ljung R, Kasper CK, Essien EM, Chediak J, Rizza CR, Graham JB: Carrier Detection in Hemophilia "A", A Cooperative International Study, II: The efficacy of a universal linear discriminant. Blood 67:1560-1567 (1986).

Graham JB, Rizza CR, Chediak J, Manucci PM, Briet E, Ljung R, Kasper CK, Essien EM, Green P: Carrier Detection in Hemophilia "A", A Cooperative International Study, I: The carrier phenotype. Blood 67:1554-1559 (1986).

Graham JB, Green P, McGraw RA, Davis LM: Application of molecular genetics to prenatal diagnosis and carrier detection in the hemophilias: some limitations. Blood 66:759-764 (1985).

Heuch I, Namboodiri KK, Green P, Kaplan EB, Laskarzewski P, Glueck CJ, Elston RC: A multivariate analysis of familial associations of lipoprotein levels in the Lipid Research Clinics Collaborative Family Study: I. Familial correlation and regression analyses. Genetic Epidem. 2:283-300 (1985).

Namboodiri KK, Kaplan EB, Heuch I, Elston RC, Green P, Rao DC, Laskarzewski P, Glueck CJ, Rifkind BB: The Collaborative Lipid Research Clinics Family Study: Biological and cultural determinants of familial resemblance for plasma lipids and lipoproteins. Genetic Epidem. 2:227-254 (1985).

Greenberg RA, Green P, Roggenkamp KJ, Barrett-Connor E, Tyroler HA, Heiss G: The constancy of parent-offspring similarity of total cholesterol throughout childhood and early adult life. J. Chron. Dis. 37: 833-838 (1984).

Green P, Owen ARG, Namboodiri K, Hewitt D, Williams LR, Elston RC: The Collaborative Lipid Research Clinics Program Family Study: Detection of major genes influencing lipid levels by examination of heterogeneity of familial variances. Genetic Epidem. 1:123-141 (1984).

Namboodiri KK, Green P, Kaplan EB, Morrison JA, Chase GA, Elston RC, Owen ARG, Rifkind BM, Glueck CJ, Tyroler HA: The Collaborative Lipid Research Clinics Program Family Study. IV. Familial associations of plasma lipids and lipoproteins. Am. J. Epidem. 119:975-996 (1984).

Green P, Namboodiri KK, Hannan P, Martin J, Owen ARG, Chase GA, Kaplan EB, Williams L, Elston RC: The Collaborative Lipid Research Clinics Program Family Study. III. Transformations and covariate adjustments of lipid and lipoprotein levels. Am. J. Epidem. 119:959-974 (1984).

Namboodiri KK, Green P, Walden C, Kaplan EB, Dawson D, Kelly K, Maciolowski M, Morrison JA, Elston RC, Austin M, Rifkind BM, Thomas R: The Collaborative Lipid Research Clinics Program Family Study. II. Response rates, representativeness of the sample, and stability of lipid and lipoprotein levels. Am. J. Epidem. 119:944-958 (1984).

Namboodiri KK, Green P, Kaplan EB, Tyroler HA, Morrison JA, Chase GA, Elston RC, Rifkind BM, Glueck CJ: Family aggregation of high density lipoprotein cholesterol: The Collaborative Lipid Research Clinics Program Family Study. Arteriosclerosis 3:616-626 (1983).

Morrison JA, Namboodiri K, Green P, Martin J, Glueck CJ: Familial aggregation of lipids and lipoproteins and early identification of dyslipoproteinemia: The Collaborative Lipid Research Clinics Family Study. JAMA 250:1860-1868 (1983).

Criqui MH, Haskell WL, Heiss G, Tyroler HA, Green P, Rubenstein CJ: Predictors of systolic blood pressure response to treadmill exercise:The Lipid Research Clinics Program Prevalence Study. Circulation 68: 225-233 (1983).

Ash A, Grayson D, Green P: Computations of cuspidal cohomology of congruence subgroups of SL(3,Z). J. of Number Theory 19:412-436 (1984).

Green P: Twisted crossed products, the “Mackey machine”, and the Effros-Hahn conjecture. Proceedings of Symposia in Pure Math. v. 38:327-336 (1982).

Green P: Equivariant K-theory and crossed product C*-algebras. Proceedings of Symposia in Pure Math v. 38:337-338 (1982).

Green P: The structure of imprimitivity algebras. J. Functional Analysis 37:88-104 (1980).

Green P: Square integrable representations and the dual topology. J. Functional Analysis 35:279-294 (1980).

Green P: A primitive C*-algebra with no non-trivial projections. Indiana Univ. Math. J. 28:349-351 (1979).

Green P: Minimal primitive ideals of GCR C*-algebras. Proc. Amer. Math. Soc. 73:209-210 (1979).

Green P: The local structure of twisted covariance algebras. Acta Math. 140:191-250 (1978).

Brown LG, Green P, Rieffel M: Stable isomorphism and strong Morita equivalence of C*-algebras. Pacific J. Math. 71:349-363 (1977).

Green P: C*-algebras of transformation groups with smooth orbit space. Pacific J. Math. 72:71-97 (1977).