@String{JCS = "J. Cell Sci."}
#String{JCS = "Journal of Cell Science"}
@String{JCP = "The Journal of Chemical Physics"}
+@String{JCPPCB = "J. Chim. Phys."}
+#String{JCPPCB = "Journal de Chimie Physique et de Physico-Chimie Biologique"}
@String{JMB = "J. Mol. Biol."}
+#String{JMB = "Journal of Molecular Biology"}
@String{JPCM = "Journal of Physics: Condensed Matter"}
@String{LANG = "Langmuir"}
@String{NANOTECH = "Nanotechnology"}
@Article{bell78,
author = "G. I. Bell",
title = "Models for the specific adhesion of cells to cells",
- journal = "Science",
+ journal = SCI,
year = "1978",
month = may,
day = "12",
MCarrionVazquez #" and "# AOberhauser #" and K. Schulten
and "# JFernandez,
title = "Mechanical unfolding intermediates in titin modules",
- journal = "Nature",
- year = "1999",
+ journal = NAT,
+ year = 1999,
month = nov,
- day = "04",
- volume = "402",
- number = "6757",
+ day = 04,
+ volume = 402,
+ number = 6757,
pages = "100--103",
keywords = "Biomechanics",
keywords = "Computer Simulation",
and "# CBustamante,
title = "Folding-unfolding transitions in single titin
molecules characterized with laser tweezers",
- journal = "Science",
- year = "1997",
+ journal = SCI,
+ year = 1997,
month = may,
- day = "16",
- volume = "276",
- number = "5315",
+ day = 16,
+ volume = 276,
+ number = 5315,
pages = "1112--1116",
keywords = "Amino Acid Sequence",
keywords = "Elasticity",
title = "Overstretching {B}-{DNA}: the elastic response of
individual double-stranded and single-stranded {DNA}
molecules",
- journal = "Science",
- year = "1996",
+ journal = SCI,
+ year = 1996,
month = feb,
- day = "09",
- volume = "271",
- number = "5250",
+ day = 09,
+ volume = 271,
+ number = 5250,
pages = "795--799",
keywords = "Base Composition",
keywords = "Chemistry, Physical",
Bensimon and V. Croquette",
title = "The elasticity of a single supercoiled {DNA}
molecule",
- journal = "Science",
- year = "1996",
+ journal = SCI,
+ year = 1996,
month = mar,
- day = "29",
- volume = "271",
- number = "5257",
+ day = 29,
+ volume = 271,
+ number = 5257,
pages = "1835--1837",
keywords = "Bacteriophage lambda",
keywords = "DNA, Superhelical",
wider range of researchers and experimental systems.},
url = "http://arxiv.org/abs/0912.5370",
}
+
+@Article{wolfsberg01,
+ author = "T. G. Wolfsberg and J. McEntyre and G. D. Schuler",
+ title = "Guide to the draft human genome.",
+ journal = NAT,
+ year = 2001,
+ month = feb,
+ day = 15,
+ volume = 409,
+ number = 6822,
+ pages = "824--826",
+ keywords = "Amino Acid Sequence",
+ keywords = "Chromosome Mapping",
+ keywords = "Computational Biology",
+ keywords = "Genes",
+ keywords = "Genetic Variation",
+ keywords = "Genome, Human",
+ keywords = "Human Genome Project",
+ keywords = "Humans",
+ keywords = "Internet",
+ keywords = "Molecular Sequence Data",
+ keywords = "Sequence Analysis, DNA",
+ abstract = "There are a number of ways to investigate the
+ structure, function and evolution of the human genome.
+ These include examining the morphology of normal and
+ abnormal chromosomes, constructing maps of genomic
+ landmarks, following the genetic transmission of
+ phenotypes and DNA sequence variations, and
+ characterizing thousands of individual genes. To this
+ list we can now add the elucidation of the genomic DNA
+ sequence, albeit at 'working draft' accuracy. The
+ current challenge is to weave together these disparate
+ types of data to produce the information infrastructure
+ needed to support the next generation of biomedical
+ research. Here we provide an overview of the different
+ sources of information about the human genome and how
+ modern information technology, in particular the
+ internet, allows us to link them together.",
+ ISSN = "0028-0836",
+ doi = "10.1038/35057000",
+ url = "http://www.nature.com/nature/journal/v409/n6822/full/409824a0.html",
+ eprint = "http://www.nature.com/nature/journal/v409/n6822/pdf/409824a0.pdf",
+}
+
+@Article{mcpherson01,
+ author = "J. D. McPherson and M. Marra and L. Hillier and R. H.
+ Waterston and A. Chinwalla and J. Wallis and M. Sekhon
+ and K. Wylie and E. R. Mardis and R. K. Wilson and R.
+ Fulton and T. A. Kucaba and C. Wagner-McPherson and W.
+ B. Barbazuk and S. G. Gregory and S. J. Humphray and L.
+ French and R. S. Evans and G. Bethel and A. Whittaker
+ and J. L. Holden and O. T. McCann and A. Dunham and C.
+ Soderlund and C. E. Scott and D. R. Bentley and G.
+ Schuler and H. C. Chen and W. Jang and E. D. Green and
+ J. R. Idol and V. V. Maduro and K. T. Montgomery and E.
+ Lee and A. Miller and S. Emerling and Kucherlapati and
+ R. Gibbs and S. Scherer and J. H. Gorrell and E.
+ Sodergren and K. Clerc-Blankenburg and P. Tabor and S.
+ Naylor and D. Garcia and P. J. de Jong and J. J.
+ Catanese and N. Nowak and K. Osoegawa and S. Qin and L.
+ Rowen and A. Madan and M. Dors and L. Hood and B. Trask
+ and C. Friedman and H. Massa and V. G. Cheung and I. R.
+ Kirsch and T. Reid and R. Yonescu and J. Weissenbach
+ and T. Bruls and R. Heilig and E. Branscomb and A.
+ Olsen and N. Doggett and J. F. Cheng and T. Hawkins and
+ R. M. Myers and J. Shang and L. Ramirez and J. Schmutz
+ and O. Velasquez and K. Dixon and N. E. Stone and D. R.
+ Cox and D. Haussler and W. J. Kent and T. Furey and S.
+ Rogic and S. Kennedy and S. Jones and A. Rosenthal and
+ G. Wen and M. Schilhabel and G. Gloeckner and G.
+ Nyakatura and R. Siebert and B. Schlegelberger and J.
+ Korenberg and X. N. Chen and A. Fujiyama and M. Hattori
+ and A. Toyoda and T. Yada and H. S. Park and Y. Sakaki
+ and N. Shimizu and S. Asakawa and K. Kawasaki and T.
+ Sasaki and A. Shintani and A. Shimizu and K. Shibuya
+ and J. Kudoh and S. Minoshima and J. Ramser and P.
+ Seranski and C. Hoff and A. Poustka and R. Reinhardt
+ and H. Lehrach",
+ title = "A physical map of the human genome.",
+ journal = NAT,
+ year = 2001,
+ month = feb,
+ day = 15,
+ volume = 409,
+ number = 6822,
+ pages = "934--941",
+ keywords = "Chromosomes, Artificial, Bacterial",
+ keywords = "Cloning, Molecular",
+ keywords = "Contig Mapping",
+ keywords = "DNA Fingerprinting",
+ keywords = "Gene Duplication",
+ keywords = "Genome, Human",
+ keywords = "Humans",
+ keywords = "In Situ Hybridization, Fluorescence",
+ keywords = "Repetitive Sequences, Nucleic Acid",
+ abstract = "The human genome is by far the largest genome to be
+ sequenced, and its size and complexity present many
+ challenges for sequence assembly. The International
+ Human Genome Sequencing Consortium constructed a map of
+ the whole genome to enable the selection of clones for
+ sequencing and for the accurate assembly of the genome
+ sequence. Here we report the construction of the
+ whole-genome bacterial artificial chromosome (BAC) map
+ and its integration with previous landmark maps and
+ information from mapping efforts focused on specific
+ chromosomal regions. We also describe the integration
+ of sequence data with the map.",
+ ISSN = "0028-0836",
+ doi = "10.1038/35057157",
+ url = "http://www.nature.com/nature/journal/v409/n6822/full/409934a0.html",
+ eprint = "http://www.nature.com/nature/journal/v409/n6822/pdf/409934a0.pdf",
+}
+
+@Article{venter01,
+author = "Venter, J. C. and Adams, M. D. and Myers, E. W. and Li,
+ P. W. and Mural, R. J. and Sutton, G. G. and Smith, H. O. and
+ Yandell, M. and Evans, C. A. and Holt, R. A. and Gocayne, J. D. and
+ Amanatides, P. and Ballew, R. M. and Huson, D. H. and Wortman,
+ J. R. and Zhang, Q. and Kodira, C. D. and Zheng, X. H. and Chen,
+ L. and Skupski, M. and Subramanian, G. and Thomas, P. D. and Zhang,
+ J. and Gabor Miklos, G. L. and Nelson, C. and Broder, S. and Clark,
+ A. G. and Nadeau, J. and McKusick, V. A. and Zinder, N. and Levine,
+ A. J. and Roberts, R. J. and Simon, M. and Slayman, C. and
+ Hunkapiller, M. and Bolanos, R. and Delcher, A. and Dew, I. and
+ Fasulo, D. and Flanigan, M. and Florea, L. and Halpern, A. and
+ Hannenhalli, S. and Kravitz, S. and Levy, S. and Mobarry, C. and
+ Reinert, K. and Remington, K. and Abu-Threideh, J. and Beasley,
+ E. and Biddick, K. and Bonazzi, V. and Brandon, R. and Cargill,
+ M. and Chandramouliswaran, I. and Charlab, R. and Chaturvedi, K. and
+ Deng, Z. and Di Francesco, V. and Dunn, P. and Eilbeck, K. and
+ Evangelista, C. and Gabrielian, A. E. and Gan, W. and Ge, W. and
+ Gong, F. and Gu, Z. and Guan, P. and Heiman, T. J. and Higgins,
+ M. E. and Ji, R. R. and Ke, Z. and Ketchum, K. A. and Lai, Z. and
+ Lei, Y. and Li, Z. and Li, J. and Liang, Y. and Lin, X. and Lu,
+ F. and Merkulov, G. V. and Milshina, N. and Moore, H. M. and Naik,
+ A. K. and Narayan, V. A. and Neelam, B. and Nusskern, D. and Rusch,
+ D. B. and Salzberg, S. and Shao, W. and Shue, B. and Sun, J. and
+ Wang, Z. and Wang, A. and Wang, X. and Wang, J. and Wei, M. and
+ Wides, R. and Xiao, C. and Yan, C. and Yao, A. and Ye, J. and Zhan,
+ M. and Zhang, W. and Zhang, H. and Zhao, Q. and Zheng, L. and
+ Zhong, F. and Zhong, W. and Zhu, S. and Zhao, S. and Gilbert,
+ D. and Baumhueter, S. and Spier, G. and Carter, C. and Cravchik,
+ A. and Woodage, T. and Ali, F. and An, H. and Awe, A. and Baldwin,
+ D. and Baden, H. and Barnstead, M. and Barrow, I. and Beeson,
+ K. and Busam, D. and Carver, A. and Center, A. and Cheng, M. L. and
+ Curry, L. and Danaher, S. and Davenport, L. and Desilets, R. and
+ Dietz, S. and Dodson, K. and Doup, L. and Ferriera, S. and Garg,
+ N. and Gluecksmann, A. and Hart, B. and Haynes, J. and Haynes,
+ C. and Heiner, C. and Hladun, S. and Hostin, D. and Houck, J. and
+ Howland, T. and Ibegwam, C. and Johnson, J. and Kalush, F. and
+ Kline, L. and Koduru, S. and Love, A. and Mann, F. and May, D. and
+ McCawley, S. and McIntosh, T. and McMullen, I. and Moy, M. and Moy,
+ L. and Murphy, B. and Nelson, K. and Pfannkoch, C. and Pratts,
+ E. and Puri, V. and Qureshi, H. and Reardon, M. and Rodriguez,
+ R. and Rogers, Y. H. and Romblad, D. and Ruhfel, B. and Scott,
+ R. and Sitter, C. and Smallwood, M. and Stewart, E. and Strong,
+ R. and Suh, E. and Thomas, R. and Tint, N. N. and Tse, S. and Vech,
+ C. and Wang, G. and Wetter, J. and Williams, S. and Williams,
+ M. and Windsor, S. and Winn-Deen, E. and Wolfe, K. and Zaveri,
+ J. and Zaveri, K. and Abril, J. F. and Guig{\'o}, R. and Campbell,
+ M. J. and Sjolander, K. V. and Karlak, B. and Kejariwal, A. and Mi,
+ H. and Lazareva, B. and Hatton, T. and Narechania, A. and Diemer,
+ K. and Muruganujan, A. and Guo, N. and Sato, S. and Bafna, V. and
+ Istrail, S. and Lippert, R. and Schwartz, R. and Walenz, B. and
+ Yooseph, S. and Allen, D. and Basu, A. and Baxendale, J. and Blick,
+ L. and Caminha, M. and Carnes-Stine, J. and Caulk, P. and Chiang,
+ Y. H. and Coyne, M. and Dahlke, C. and Mays, A. and Dombroski,
+ M. and Donnelly, M. and Ely, D. and Esparham, S. and Fosler, C. and
+ Gire, H. and Glanowski, S. and Glasser, K. and Glodek, A. and
+ Gorokhov, M. and Graham, K. and Gropman, B. and Harris, M. and Heil,
+ J. and Henderson, S. and Hoover, J. and Jennings, D. and Jordan,
+ C. and Jordan, J. and Kasha, J. and Kagan, L. and Kraft, C. and
+ Levitsky, A. and Lewis, M. and Liu, X. and Lopez, J. and Ma, D. and
+ Majoros, W. and McDaniel, J. and Murphy, S. and Newman, M. and
+ Nguyen, T. and Nguyen, N. and Nodell, M. and Pan, S. and Peck,
+ J. and Peterson, M. and Rowe, W. and Sanders, R. and Scott, J. and
+ Simpson, M. and Smith, T. and Sprague, A. and Stockwell, T. and
+ Turner, R. and Venter, E. and Wang, M. and Wen, M. and Wu, D. and
+ Wu, M. and Xia, A. and Zandieh, A. and Zhu, X.",
+title="The sequence of the human genome.",
+journal=SCI,
+year=2001,
+month="Feb",
+day=16,
+volume=291,
+number=5507,
+pages="1304--1351",
+keywords="Algorithms",
+keywords="Animals",
+keywords="Chromosome Banding",
+keywords="Chromosome Mapping",
+keywords="Chromosomes, Artificial, Bacterial",
+keywords="Computational Biology",
+keywords="Consensus Sequence",
+keywords="CpG Islands",
+keywords="DNA, Intergenic",
+keywords="Databases, Factual",
+keywords="Evolution, Molecular",
+keywords="Exons",
+keywords="Female",
+keywords="Gene Duplication",
+keywords="Genes",
+keywords="Genetic Variation",
+keywords="Genome, Human",
+keywords="Human Genome Project",
+keywords="Humans",
+keywords="Introns",
+keywords="Male",
+keywords="Phenotype",
+keywords="Physical Chromosome Mapping",
+keywords="Polymorphism, Single Nucleotide",
+keywords="Proteins",
+keywords="Pseudogenes",
+keywords="Repetitive Sequences, Nucleic Acid",
+keywords="Retroelements",
+keywords="Sequence Analysis, DNA",
+keywords="Species Specificity",
+abstract="A 2.91-billion base pair (bp) consensus sequence of the
+euchromatic portion of the human genome was generated by the
+whole-genome shotgun sequencing method. The 14.8-billion bp DNA
+sequence was generated over 9 months from 27,271,853 high-quality
+sequence reads (5.11-fold coverage of the genome) from both ends of
+plasmid clones made from the DNA of five individuals. Two assembly
+strategies-a whole-genome assembly and a regional chromosome
+assembly-were used, each combining sequence data from Celera and the
+publicly funded genome effort. The public data were shredded into
+550-bp segments to create a 2.9-fold coverage of those genome regions
+that had been sequenced, without including biases inherent in the
+cloning and assembly procedure used by the publicly funded group. This
+brought the effective coverage in the assemblies to eightfold,
+reducing the number and size of gaps in the final assembly over what
+would be obtained with 5.11-fold coverage. The two assembly strategies
+yielded very similar results that largely agree with independent
+mapping data. The assemblies effectively cover the euchromatic regions
+of the human chromosomes. More than 90\% of the genome is in scaffold
+assemblies of 100,000 bp or more, and 25\% of the genome is in
+scaffolds of 10 million bp or larger. Analysis of the genome sequence
+revealed 26,588 protein-encoding transcripts for which there was
+strong corroborating evidence and an additional approximately 12,000
+computationally derived genes with mouse matches or other weak
+supporting evidence. Although gene-dense clusters are obvious, almost
+half the genes are dispersed in low G+C sequence separated by large
+tracts of apparently noncoding sequence. Only 1.1\% of the genome is
+spanned by exons, whereas 24\% is in introns, with 75\% of the genome
+being intergenic DNA. Duplications of segmental blocks, ranging in
+size up to chromosomal lengths, are abundant throughout the genome and
+reveal a complex evolutionary history. Comparative genomic analysis
+indicates vertebrate expansions of genes associated with neuronal
+function, with tissue-specific developmental regulation, and with the
+hemostasis and immune systems. DNA sequence comparisons between the
+consensus sequence and publicly funded genome data provided locations
+of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair
+of human haploid genomes differed at a rate of 1 bp per 1250 on
+average, but there was marked heterogeneity in the level of
+polymorphism across the genome. Less than 1\% of all SNPs resulted in
+variation in proteins, but the task of determining which SNPs have
+functional consequences remains an open challenge.",
+issn="0036-8075",
+doi="10.1126/science.1058040",
+url="http://www.sciencemag.org/cgi/content/short/291/5507/1304",
+eprint="http://www.sciencemag.org/cgi/content/pdf/291/5507/1304",
+}
+
+@Article{claverie01,
+ author = "J. M. Claverie",
+ title = "Gene number. What if there are only 30,000 human
+ genes?",
+ journal = SCI,
+ year = 2001,
+ month = feb,
+ day = 16,
+ volume = 291,
+ number = 5507,
+ pages = "1255--1257",
+ keywords = "Animals",
+ keywords = "Computational Biology",
+ keywords = "Drug Industry",
+ keywords = "Expressed Sequence Tags",
+ keywords = "Gene Expression",
+ keywords = "Gene Expression Regulation",
+ keywords = "Genes",
+ keywords = "Genetic Techniques",
+ keywords = "Genome, Human",
+ keywords = "Genomics",
+ keywords = "Human Genome Project",
+ keywords = "Humans",
+ keywords = "Models, Genetic",
+ keywords = "Polymorphism, Single Nucleotide",
+ keywords = "Proteins",
+ keywords = "RNA, Messenger",
+ ISSN = "0036-8075",
+ url = "http://www.sciencemag.org/cgi/content/full/291/5507/1255",
+}
+
+@Article{collins03,
+ author = "Francis S. Collins and Michael Morgan and Aristides
+ Patrinos",
+ title = "The Human Genome Project: lessons from large-scale
+ biology.",
+ journal = SCI,
+ year = 2003,
+ month = apr,
+ day = 11,
+ volume = 300,
+ number = 5617,
+ pages = "286--290",
+ keywords = "Access to Information",
+ keywords = "Computational Biology",
+ keywords = "Databases, Nucleic Acid",
+ keywords = "Genome, Human",
+ keywords = "Genomics",
+ keywords = "Government Agencies",
+ keywords = "History, 20th Century",
+ keywords = "Human Genome Project",
+ keywords = "Humans",
+ keywords = "International Cooperation",
+ keywords = "National Institutes of Health (U.S.)",
+ keywords = "Private Sector",
+ keywords = "Public Policy",
+ keywords = "Public Sector",
+ keywords = "Publishing",
+ keywords = "Quality Control",
+ keywords = "Sequence Analysis, DNA",
+ keywords = "United States",
+ ISSN = "1095-9203",
+ doi = "10.1126/science.1084564",
+ url = "http://www.sciencemag.org/cgi/content/summary/300/5617/277",
+ eprint = "http://www.sciencemag.org/cgi/reprint/300/5617/286.pdf",
+ note = "See also: \href{http://www.ornl.gov/sci/techresources/Human_Genome/project/journals/journals.shtml}{Landmark HPG Papers}",
+}
+
+@Article{levinthal68,
+ author = "Levinthal, Cyrus",
+ title = "Are there pathways for protein folding?",
+ journal = JCPPCB,
+ volume = 65,
+ number = 1,
+ pages = "44--45",
+ year = 1968,
+ eprint = "http://www.biochem.wisc.edu/courses/biochem704/Reading/Levinthal1968.pdf",
+ note = "\emph{Not} Levinthal's paradox.",
+}
+
+@Inproceedings{levinthal69,
+ author = "Levinthal, Cyrus",
+ title = "How to Fold Graciously.",
+ booktitle = "Mossbauer Spectroscopy in Biological Systems",
+ year = 1969,
+ editor = {Debrunner, P. and Tsibris, J.C.M. and M\"unck, E.},
+ pages = "22--24",
+ address = "Allerton House, Monticello, IL",
+ publisher = "University of Illinois Press, Urbana",
+ url = "http://www-miller.ch.cam.ac.uk/levinthal/levinthal.html"
+}
+
+@Article{zwanzig92,
+ author = "R. Zwanzig and A. Szabo and B. Bagchi",
+ title = "Levinthal's paradox.",
+ journal = PNAS,
+ year = 1992,
+ month = jan,
+ day = 01,
+ volume = 89,
+ number = 1,
+ pages = "20--22",
+ keywords = "Mathematics",
+ keywords = "Models, Theoretical",
+ keywords = "Protein Conformation",
+ keywords = "Proteins",
+ abstract = "Levinthal's paradox is that finding the native folded
+ state of a protein by a random search among all
+ possible configurations can take an enormously long
+ time. Yet proteins can fold in seconds or less.
+ Mathematical analysis of a simple model shows that a
+ small and physically reasonable energy bias against
+ locally unfavorable configurations, of the order of a
+ few kT, can reduce Levinthal's time to a biologically
+ significant size.",
+ ISSN = "0027-8424",
+ url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC48166/",
+ eprint = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC48166/pdf/pnas01075-0036.pdf",
+}
projects / thesis.git / commitdiff