master.bib

%
% Master bibliography
%
% This bibliography is large and is kept sorted; it is easiest
% to add entries by creating a small file and merging it with
% "bibmerge", rather than editing the master itself.
%
% SRE, Mon Aug  2 16:57:13 1993
% Cambridge

% Journal abbreviations
% These must all be one-line entries: bibdistill.pl relies on it.
@string{ARB    = "Annu. Rev. Biochem."}
@string{ARBBC  = "Annu. Rev. Biophys. Biophys. Chem."}
@string{ARCB   = "Annu. Rev. Cell Biol."}
@string{ARG    = "Annu. Rev. Genet."}
@string{ARGHG  = "Annu. Rev. Genomics Hum. Genet."}
@string{ARI    = "Annu. Rev. Immunol."}
@string{ARN    = "Annu. Rev. Neurosci."}
@string{ARP    = "Annu. Rev. Physiol."}
@string{BBA    = "Biochem. Biophys. Acta"}
@string{BBRC   = "Biochem. Biophys. Res. Commun."}
@string{CABIOS = "Comput. Applic. Biosci."}
@string{CACM   = "Communications of the ACM"}
@string{COCB   = "Curr. Opin. Cell Biol."}
@string{COGD   = "Curr. Opin. Genet. Dev."}
@string{COM    = "Curr. Opin. Microbiol."}
@string{COSB   = "Curr. Opin. Struct. Biol."}
@string{CSHSQB = "Cold Spring Harbor Symp. Quant. Biol."}
@string{CURRB  = "Curr. Biol."}
@string{DEV    = "Development"}
@string{DEVB   = "Devel. Biol."}
@string{EMBO   = "EMBO J."}
@string{FEBS   = "FEBS J."}
@string{FOCS   = "Found. Comp. Sci."}
@string{GDEV   = "Genes Dev."}
@string{GR     = "Genome Res."}
@string{IRC    = "Int. Rev. Cytol."}
@string{ISMB   = "Proc. Int. Conf. Intell. Syst. Mol. Biol."}
@string{JBACT  = "J. Bacteriol."}
@string{JBC    = "J. Biol. Chem."}
@string{JBSD   = "J. Biomol. Struct. Dyn."}
@string{JCB    = "J. Cell. Biol."}
@string{JCompB = "J. Comput. Biol."}
@string{JMB    = "J. Mol. Biol."}
@string{JME    = "J. Mol. Evol."}
@string{JNEUR  = "J. Neurosci."}
@string{JTB    = "J. Theor. Biol."}
@string{MBE    = "Mol. Bio. Evol."}
@string{MCB    = "Mol. Cell. Biol."}
@string{METH   = "Meth. Enzymol."}
@string{MGG    = "Mol. Gen. Genet."}
@string{NAR    = "Nucl. Acids Res."}
@string{NBT    = "Nat. Biotechnol."}
@string{NRG    = "Nat. Rev. Genet."}
@string{PNARMB = "Prog. Nucl. Acids Res. Mol. Biol."}
@string{PNAS   = "Proc. Natl. Acad. Sci. USA"}
@string{PROTS  = "Protein Sci."}
@string{PSB    = "Pac. Symp. Biocomput."}
@string{SIAMJC = "SIAM Journal of Computing"}
@string{TIBTECH= "Trends Biotech."}
@string{TIBS   = "Trends Biochem. Sci."}
@string{TICB   = "Trends Cell Biol."}
@string{TIGS   = "Trends Genet."}


@Article{AWM-84a,
  author = 	"R. M. Arbarbanel and P. R. Wieneke and E. Mansfield
		 and D. A. Jaffe and D. L. Brutlag",
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  journal = 	NAR,
  year = 	1984,
  volume = 	12,
  number = 	1,
  pages = 	"263-280"
}

@PhdThesis{Abedon90,
  author = 	"Stephen Tobias Abedon",
  title = 	"The Ecology of Bacteriophage {T4}",
  school = 	"University of Arizona",
  year = 	1990
}

@ARTICLE {Abelson79,
AUTHOR = "John Abelson",
TITLE = "{RNA} Processing and the Intervening Sequence Problem",
JOURNAL = ARB,
VOLUME = 48,
PAGES = "1035-1069",
YEAR = 1979}

@Article{Abouelhoda04,
  author={M.I. Abouelhoda and S. Kurtz and E. Ohlebusch},
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  year={2004}
}

@Article{Abrahams90,
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  filed =        {Pleij}
}

@BOOK {Abramowitz,
AUTHOR = {M. Abramowitz and I. A. Stegun (eds.)},
TITLE  = {Handbook of mathematical functions, 9th printing},
PUBLISHER = {Dover},
ADDRESS = {New York},
YEAR = 1972
}

@InBook{Abramowitz822,
  editor = 	{M. Abramowitz and I. A. Stegun},
  title = 	{Handbook of mathematical functions, 9th printing},
  chapter = 	{Binomial Coefficients, 24.1.1},
  publisher = 	{Dover},
  pages =	{822},
ADDRESS = {New York},
  year = 	1972,
}

@Article{Abril00,
  author = 	 {J. F. Abril and R. Guig\'{o}},
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  year = 	 2000,
  volume =	 16,
  pages =	 {743-744},
  filed =	 {Guigo},
  pmid =	 11099262
}

@Article{AdachiHasegawa96,
  author = 	 {J. Adachi and M. Hasegawa},
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  volume =	 42,
  pages =	 {459-468},
  filed =	 {Hasegawa},
  pmid =	 8642615
}

@Article{Adams00,
  author =       {M. D. Adams and S. E. Celniker and R. A. Holt and
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                  S. M. Dietz and K. Dodson and L. E. Doup and
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                  C. Ferraz and S. Ferriera and W. Fleischmann and
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                  F. Gong and J. H. Gorrell and Z. Gu and P. Guan and
                  M. Harris and N. L. Harris and D. Harvey and
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                  K. A. Ketchum and B. E. Kimmel and C. D. Kodira and
                  C. Kraft and S. Kravitz and D. Kulp and Z. Lai and
                  P. Lasko and Y. Lei and A. A. Levitsky and J. Li and
                  Z. Li and Y. Liang and X. Lin and X. Liu and
                  B. Mattei and T. C. McIntosh and M. P. McLeod and
                  D. McPherson and G. Merkulov and N. V. Milshina and
                  C. Mobarry and J. Morris and A. Moshrefi and
                  S. M. Mount and M. Moy and B. Murphy and L. Murphy
                  and D. M. Muzny and D. L. Nelson and D. R. Nelson
                  and K. A. Nelson and K. Nixon and D. R. Nusskern and
                  J. M. Pacleb and M. Palazzolo and G. S. Pittman and
                  S. Pan and J. Pollard and V. Puri and M. G. Reese
                  and K. Reinert and K. Remington and R. D. Saunders
                  and F. Scheeler and H. Shen and B. C. Shue and
                  I. Siden-Kiamos and M. Simpson and M. P. Skupski and
                  T. Smith and E. Spier and A. C. Spradling and
                  M. Stapleton and R. Strong and E. Sun and
                  R. Svirskas and C. Tector and R. Turner and
                  E. Venter and A. H. Wang and X. Wang and Z. Y. Wang
                  and D. A. Wassarman and G. M. Weinstock and
                  J. Weissenbach and S. M. Williams and  and
                  K. C. Worley and D. Wu and S. Yang and Q. A. Yao and
                  J. Ye and R. F. Yeh and J. S. Zaveri and M. Zhan and
                  G. Zhang and Q. Zhao and L. Zheng and X. H. Zheng
                  and F. N. Zhong and W. Zhong and X. Zhou and S. Zhu
                  and X. Zhu and H. O. Smith and R. A. Gibbs and
                  E. W. Myers and G. M. Rubin and J. C. Venter},
  title =        {The Genome Sequence of \emph{{D}rosophila melanogaster}},
  journal =      {Science},
  year =         2000,
  volume =       287,
  pages =        {2185--2195},
  pmid =         10731132,
}

@BOOK {Adams59,
AUTHOR = "Mark H. Adams",
TITLE  = "Bacteriophages",
PUBLISHER = "Interscience",
ADDRESS = "New York",
YEAR = 1959}

@Article{Aflalo91,
  author = 	 "Claude Aflalo",
  title = 	 "Biologically Localized Firefly Luciferase: A Tool to
		  Study Cellular Processes",
  journal = 	 IRC,
  year = 	 1991,
  volume = 	 130,
  pages = 	 "269-323"
}

@Article{AgarwalStates94,
  author = 	 {P. Agarwal and D. J. States},
  title = 	 {The Repeat Pattern Toolkit ({RPT}): Analyzing the
                  Structure and Evolution of the {\emph{C. elegans}} Genome},
  journal = 	 ISMB,
  year = 	 1994,
  volume =	 2,
  pages =	 {1--9},
  pmid =	 7584377,
  muid =	 96038997,
}

@Article{AhC-75a,
  author = 	"A. V. Aho and M. J. Corasick",
  title = 	"Efficient String Matching: An Aid to Bibliographic Search",
  journal = 	CACM,
  year = 	1975,
  volume = 	18,
  number = 	6,
  pages = 	"333-340",
  month = 	"June",
}

@InBook{Aho-80a,
  author = 	"A. V. Aho",
  title = 	"Formal Language Theory",
  chapter = 	"Pattern matching in strings",
  publisher = 	"Academic Press",
  year = 	1980,
}

@Unpublished{Aho-89a,
  author = 	"Alfred V. Aho",
  title = 	"Algorithms for Finding Patterns in Strings",
  note = 	"preprint of book chapter",
  year = 	1989
}

@Article{AhrensDieter73,
  author = 	 {J. H. Ahrens and U. Dieter},
  title = 	 {Extensions of {F}orsythe's Method for Random Sampling
                  from the Normal Distribution},
  journal = 	 {Math. Comput.},
  year = 	 1973,
  volume =	 27,
  pages =	 {927--937}
}

@Article{AibaMizushima87,
  author =       {H. Aiba and S. Matsuyama and T. Mizuno and S. Mizushima},
  title =        {Function of {MicF} as an Antisense {RNA} in
                  Osmoregulatory Expression of the {OmpF} Gene in
                  \emph{{E}scherichia coli}},
  journal =      JBACT,
  year =         1987,
  volume =       169,
  pages =        {3007--3012},
  filed =	 {Mizushima},
  pmid =	 2439487,
}

@ARTICLE {Akins87,
AUTHOR = "Robert A. Akins and Alan M. Lambowitz",
TITLE = "A Protein Required for Splicing Group {I} Introns in
	 {{\em Neurospora}} Mitochondria is Mitochondrial
	 Tyrosyl-{tRNA} Synthetase or a Derivative Thereof",
JOURNAL = {Cell},
VOLUME = 50,
PAGES = "331-345",
YEAR = 1987}

@Article{AkmaevStormo00,
  author =       {V. R. Akmaev and S. T. Kelley and G. D. Stormo},
  title =        {Phylogenetically Enhanced Statistical Tools for {RNA} Structure Prediction},
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  year =         2000,
  volume =       16,
  pages =        {501--512},
  pmid =	 10980147,
}

@Article{Albert00,
  author =       {R. Albert and H. Jeong and A. L. Barabasi},
  title =        {Error and Attack Tolerance of Complex Networks},
  journal =      {Nature},
  year =         2000,
  volume =       406,
  pages =        {378--382},
  filed =	 {Barabasi},
  mynote =	 {scale-free networks},
  pmid =	 10935628,
}

@Article{AlbertGreen03,
  author = 	 {T. J. Albert and J. Norton and M. Ott and T. Richond
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  pmid =	 12655023
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@Book{Alberts,
  author =	 {Bruce Alberts and Dennis Bray and Julian Lewis and
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  year = 	 1994,
  isbn = 	 {0815316194}
}

@Article{Albertson84,
  author = 	 "Donna G. Albertson",
  title = 	 "Localization of the Ribosomal Genes in
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  volume = 	 3,
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@Article{Albertson85,
  author = 	 "Donna G. Albertson",
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  volume = 	 4,
  pages = 	 "2493-2498"
}

@Unpublished{Albertson92,
  author = 	 "Donna G. Albertson",
  title = 	 "Mapping Chromosome Rearrangement Breakpoints to
		  Physically Mapped {YAC}s in {{\em Caenorhabditis elegans}}
		  by Fluorescent in situ Hybridization",
  note = 	 "in preparation",
  year = 	 1992
}

@Article{Alexandersson03,
  author =       {M. Alexandersson and S. Cawley and L. Pachter},
  title =        {{SLAM:} Cross-Species Gene Finding and Alignment
                  With a Generalized Pair Hidden {Markov} Model},
  journal =      {Genome Res.},
  year =         2003,
  volume =       13,
  pages =        {496--502},
  pmid =	 12618381,
}

@Article{Alien06,
   author =       {J. E. Alien and W. H. Majoros and S. L. Salzberg},
   title =        {{JIGSAW}, {GeneZilla}, and {GlimmerHMM}: Puzzling
                  Out the Features of Human Genes in {ENCODE}
                  Regions},
   journal =      {Genome Biol.},
   year =         2006,
   volume =       7,
   pages =        {S9.1--S9.13},
   pmid =         16925843,
}

@Article{Allen06,
   author =       {J. E. Allen and W. H. Majoros and S. L. Salzberg},
   title =        {{JIGSAW}, {GeneZilla}, and {GlimmerHMM}: Puzzling
                  Out the Features of Human Genes in {ENCODE}
                  Regions},
   journal =      {Genome Biol.},
   year =         2006,
   volume =       7,
   pages =        {S9.1--S9.13},
   pmid =         16925843,
}

@TechReport{Allison93,
  author = 	 "L. Allison and C. S. Wallace",
  title = 	 "The Posterior Probability Distribution of Alignments
		  and its Application to Parameter Estimation of
		  Evolutionary Trees and to Optimisation of Multiple Alignments",
  institution =  "Monash University Computer Science",
  year = 	 1993,
  number = 	 "TR 93/188"
}

@Article{Allison94,
  author = 	 "L. Allison and C. S. Wallace",
  title = 	 "The Posterior Probability Distribution of Alignments
		  and Its Application to Parameter Estimation of
		  Evolutionary Trees and to Optimization of Multiple
		  Alignments",
  journal = 	 "J. Mol. Evol.",
  year = 	 1994,
  volume = 	 39,
  pages = 	 "418-430"
}

@Article{Almakarem12,
  author = 	 {A. S. {Abu Almakarem} and A. I.  Petrov and J. Stombaugh and C. L.  Zirbel and N. B. Leontis},
  title = 	 {Comprehensive survey and geometric classification of base triples in {RNA} structure},
  journal = 	 NAR,
  year = 	 2012,
  volume = 	 40,
  pages = 	 {1407-1423},
}

@InCollection{Altman99,
  author = 	 {S. Altman and L. Kirsebom},
  title = 	 {Ribonuclease {P}},
  booktitle = 	 {The {RNA} World, Second Edition},
  pages =	 {351-380},
  publisher =	 {Cold Spring Harbor Laboratory Press},
  year =	 1999,
  editor =	 {R. F. Gesteland and T. R. Cech and J. F. Atkins},
  address =	 {New York}
}

@article{Altschuh87,
  title={Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus},
  author={Altschuh, D. and Lesk, A. M. and Bloomer, A. C. and Klug, A.},
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  number={4},
  pages={693--707},
  year={1987},
  publisher={Elsevier}
}

@article{Altschuh88,
  title={Coordinated amino acid changes in homologous protein families},
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  volume={2},
  number={3},
  pages={193--199},
  year={1988},
  publisher={Oxford Univ Press}
}

@Article{Altschul01,
  author =       {S. F. Altschul and R. Bundschuh and R. Olsen and T. Hwa},
  title =        {The Estimation of Statistical Parameters for Local
                  Alignment Score Distributions},
  journal =      NAR,
  year =         2001,
  volume =       29,
  pages =        {351--361},
  pmid =	 11139604,
}

@Article{Altschul05,
  author =       {S. F. Altschul and J. C. Wootton and E. M. Gertz and
                  R. Agarwala and A. Morgulis and A. A. Sch\"{a}ffer and
                  Y. K. Yu},
  title =        {Protein Database Searches Using Compositionally
                  Adjusted Substitution Matrices},
  journal =      FEBS,
  year =         2005,
  volume =       272,
  pages =        {5101--5109},
  filed =	 {Altschul},
  pmid =	 16218944,
}

@Article{Altschul11,
  author =       {X. Ye and  G. Wang  and S. F. Altschul},
  title =        {An assessment of substitution scores for protein profile-profile comparison},
  journal =      Bioinformatics,
  year =         2011,
  volume =       27,
  pages =        {3356--3363},
}

@Article{Altschul89,
  author = 	 "S. F. Altschul and R. J. Carroll and D.
		  J. Lipman",
  title = 	 "Weights for Data Related by a Tree",
  journal = 	 JMB,
  year = 	 1989,
  volume = 	 207,
  pages = 	 "647-653",
  filed =        "Altschul"
}

@Article{Altschul90,
  author = 	 "S. F. Altschul and W. Gish and W. Miller
		  and E. W. Myers and D. J. Lipman",
  title = 	 "Basic Local Alignment Search Tool",
  journal = 	 JMB,
  year = 	 1990,
  volume = 	 215,
  pages = 	 "403-410",
  filed =        "Altschul",
  pmid =         2231712,
}

@Article{Altschul91,
  author = 	 "S. F. Altschul",
  title = 	 "Amino Acid Substitution Matrices from an Information
		  Theoretic Perspective",
  journal = 	 JMB,
  year = 	 1991,
  volume = 	 219,
  pages = 	 "555-565",
  filed =        "Altschul",
  pmid =         2051488,
  muid =         91269329,
}

@Article{Altschul93,
  author = 	 {S. F. Altschul},
  title = 	 {A Protein Alignment Scoring System Sensitive at All Evolutionary Distances},
  journal = 	 {J. Mol. Evol.},
  year = 	 1993,
  volume = 	 36,
  pages = 	 {290--300},
}

@Article{Altschul94,
  author = 	 "S. F. Altschul and M. S. Boguski and W.
		  Gish and J. C. Wooton",
  title = 	 "Issues in Searching Molecular Sequence Databases",
  journal = 	 "Nature Genetics",
  year = 	 1994,
  volume = 	 6,
  pages = 	 "119-129",
  filed =        "Altschul"
}

@Article{Altschul97,
  author = 	 {S. F. Altschul and T. L. Madden and A. A. Schaffer and
                  J. Zhang and Z. Zhang and W. Miller and D. J. Lipman},
  title = 	 {Gapped {BLAST} and {PSI-BLAST}: A New Generation of
                  Protein Database Search Programs},
  journal = 	 NAR,
  year = 	 1997,
  volume =	 25,
  pages =	 {3389-3402},
  filed =        {Altschul}
}

@Article{Altschul98,
  author =       {S. F. Altschul},
  title =        {Generalized Affine gap Costs for Protein Sequence Alignment},
  journal =      {Proteins},
  year =         1998,
  volume =       32,
  pages =        {88--96},
  pmid =	 9672045,
}

@Article{AltschulErickson85,
  author = 	 {S. F. Altschul and B. W. Erickson},
  title =        {Significance of Nucleotide Sequence Alignments: a
                  Method for Random Sequence Permutation That
                  Preserves Dinucleotide and Codon Usage},
  journal =      MBE,
  year =         1985,
  volume =       2,
  pages =        {526--538},
  pmid =	 3870875,
}

@Article{AltschulErickson86,
  author = 	 {S. F. Altschul and B. W. Erickson},
  title = 	 {Optimal Sequence Alignment Using Affine Gap Costs},
  journal = 	 {Bull. Math. Biol.},
  year = 	 1986,
  volume =	 48,
  pages =	 {603-616},
  filed =        "lost! Graeme has it..."
}

@Article{AltschulGish96,
  author = 	 {S. F. Altschul and W. Gish},
  title = 	 {Local Alignment Statistics},
  journal = 	 METH,
  year = 	 1996,
  volume =	 266,
  pages =	 {460-480},
  filed =	 {bookshelf}
}

@Article{AltschulLipman89,
  author = 	 {S. F. Altschul and D. J. Lipman},
  title = 	 {Trees, Stars, and Multiple Biological Sequence Alignment},
  journal = 	 {SIAM J. Appl. Math.},
  year = 	 1989,
  volume =	 49,
  pages =	 {197-209},
  filed =        "Altschul"
}

@Article{Altshuler00,
  author = 	 {D. Altshuler and M. Daly and L. Kruglyak},
  title = 	 {Guilt by Association},
  journal = 	 {Nature Genetics},
  year = 	 2000,
  volume =	 26,
  pages =	 {135-137},
  filed =	 {Altshuler},
  pmid =	 11017062
}

@Article{Altuvia04,
  author =       {S. Altuvia},
  title =        {Regulatory Small {RNAs:} the key to Coordinating
                  Global Regulatory Circuits},
  journal =      JBACT,
  year =         2004,
  volume =       186,
  pages =        {6679--6680},
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% ts and am mutant isolations
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% minimal MOPS medium
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% NapIV construction
@ARTICLE {Nelson82,
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% td8, td9 isolation
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@Article{SleutelsBarlow02,
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@Article{Smith96,
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@Article{SmithJohnson07,
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@Article{SmithMattick13,
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%% Lab guides: we sometimes use these as references, but we 
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%% Lab guides: we sometimes use these as references, but we
%% don't want them in lab.bib where the web site scripts would
%% see them and try to add them to our online reference lists.
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