Infobio01 - References

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Biology/Bioinformatics References

Here are some books and journal articles related to various topics from the ITP INFOBIO program, as provided by various speakers and program participants. They are by no means complete, and are merely intended to guide the uninitiated into the vast literature on these topics. Please email Nick Buchler if you find a good book or review article you would like to share with the rest of the program participants. [NOTE: Journal articles are for the private use only.]
 
 
 

General Background  Sequence Alignment DNA and RNA Protein Folding
Gene Finding  Genome Architecture DNA Motif Finding Molecular Information Processing
Molecular Networks Molecular Evolution Evolution &
Phylogenics		 Algorithms
Gene Expression  Comparative 
Genomics		 Regulation Protein-DNA 
Binding

 

General background reading (The hyperlinks to amazon.com are not marketing schemes but rather portals to more detailed information.)

  • To those uninitiated physicists, the "standard" molecular biology text books Molecular Biology of the Cell (3rd edition) by Alberts et al. and Molecular Cell Biology (4th edition) by Lodish et al. are excellent references for learning everything about modern biology.
  • Freifelder's Essentials for Molecular Biology is much smaller than Alberts, but gives a good intro to most of the important topics.
  • Biological sequence analysis by Durbin et al. describes some of the standard computational methods used in bioinformatics, especially the hidden Markov model approach.
  • Frank-Kamenetskii's Unraveling DNA presents several relevant topics in a way that should appeal to physical scientists.
  • Binding and Linkage by Wyman and Gill that is very good at describing physical chemistry of macromolecular interactions.
  • Walter M. Fitch has written a very nice intro for the quantitative types: An Introduction to Molecular Biology for Mathematicians and Computer Programmers. DIMACS series in Discrete Mathematics and Theoretical Computer Science; Mathematical Support for Molecular Biology, American Mathematical Society, Providence, RI; Editors: Martin Farach.
  • Introduction to Algorithms (MIT Electrical Engineering and Computer Science) by Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest
  • The Eighth Day of Creation : Makers of the Revolution in Biology by Horace Freeland Judson

 

Sequence Alignment

  • Amino acid substitution matrices from protein blocks (Blosum-62), S Henikoff and JG Henikoff, Proc Natl Acad. Sci (USA) 89 : 10915 (1992). [PS]
  • Local Alignment Statitstics, S.F. Altschul and W. Gish, Methods of Enzymology, 266: 460-480 (1996). 
  • Gapped BLAST and PSI-BLAST:  a new generation of protein database search programs, S.F. Altschul, T.L. Madden, A.A. Schaeffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman, Nucleic Acids Res. 25: 3389 (1997). [PDF]
  • Asymmetric exclusion process and extremal statistics of random sequences, R. Bundschuh, cond-mat/9911386, submitted to Phys. Rev. E. [PS]
  • Rapid Significance Estimation in Local Sequence Alignment with Gaps, R. Bundschuh, Proc. Fifth Annual Intn'l Conf. on Comp. Mol. Biology (RECOMB 2001). ACM press, New York (2001) [PS].

DNA and RNA

  • A bound and edited collection of contributed papers and topics on the  RNA World (2nd edition, R.F. Gesteland, T.R. Cech, J.F. Atkins). 
  • Theory of Helix-Coil Transitions in Biopolymers, D. Poland and H.A. Scheraga. Academic Press, New York, 1970.
  • Thermal-denaturation of DNA-molecules:  A comparison of theory with experiment, R.M. Wartell and A.S. Benight, Physics Reports 126: 67 (1985) 
  • On finding all suboptimal foldings of an RNA molecule, M. Zuker, Science 244: 48 (1989)
  • The equilibrium partition-function and base pair binding probabilities for RNA secondary structure, J.S. McCaskill, Biopolymers 29: 1105 (1990) 
  • Identifying constraints on the higher-order structure of RNA:  Continued development and application of comparative sequence analysis methods, R.R. Gutell, A. Power, G.Z. Hertz, E.J. Putz, G.D. Stormo, Nucl. Acids Res. 20: 5785 (1992)
  • Kinetics of conformational fluctuations in DNA hairpin-loops, G. Bonnet, O. Krichevsky, A. Libchaber, Proc. Natl. Acad. Sci. (USA) 95: 8602 (1998) [PDF]
  • How RNA folds, I. Tinoco and C. Bustamante, Journal of Mol. Biology 293: 271 (1999) [PDF]
  • RNA secondary structure formation: a solvable model of heteropolymer folding,, R. Bundschuh, T. Hwa, Phys. Rev. Lett. 83:1479 (1999) [PS]
  • Complete suboptimal folding of RNA and the stability of secondary structures, S. Wuchty, W. Fontana, I.L. Hofacker, P. Schuster, Biopolymers 49: 145 (1999) [PS]
  • Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics, J. Pan, D. Thirumalai, S.A. Woodson, Proc. Natl. Acad. Sci. (USA) 96: 6149 (1999) [PDF]
  • RNA folding at elementary step resolution, C. Flamm, W. Fontana, I.L. Hofacker, P. Schuster, RNA 6: 325 (2000) [PS]
  • Pulling pinned polymers and unzipping DNA, D.K. Lubensky and D.R. Nelson, Phys. Rev. Lett. 85: 1572 (2000) [PDF]
  • Single-molecule studies of DNA mechanics, C. Bustamante, S.B. Smith, J. Liphardt, D. Smith, Curr. Opin. Struct. Biol. 10: 279 (2000) [PDF]
  • One sequence, two ribozymes:  Implications for the emergence of new ribozyme folds, E.A. Schultes and D.P. Bartel, Science 289:  448 (2000) [PS]
  • Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme, H. Isambert and E. D. Siggia, Proc. Natl. Acad. Sci. (USA) 97: 6515  (2000) [PS]
  • Hairpin formation and elongation of biomolecules, A. Montanari and M. Mezard, Phys. Rev. Lett. 86: 2178 (2001) [PDF] 
  • RNA and the small molecule world, Y. Tor, Highlights [PDF]
  • Dynamics of DNA-protein interaction deduced from in vitro DNA evolution, A. Libchaber, Phys. Rev. Lett., in press (2001)
  • Effects of DNA Sequence and Structure on Binding of RecA to Single-Stranded DNA, A. Lichaber, Proc. Natl. Acad. Sci (USA), in press (2001)
  • Force induced denaturation of RNA, U. Gerland, R. Bundshuh, T. Hwa, Biophys J (2001), in press. [PS]

 Protein Folding

  • Side-Chain Entropy Opposes Alpha-Helix Formation but Rationalizes Experimentally Determined Helix-Forming Propensities, T.P. Creamer and G.D. Rose, Proc. Natl. Acad. Sci (USA) 89: 5937 (1992) [PDF]
  • Principles of protein folding - A perspective from simple exact models, K.A. Dill, S. Bromberg, K. Yue, K.M. Fiebig, D.P. Yee, P.D. Thomas and H.S. Chan, Prot. Science 4: 561 (1995) 
  • Emergence of Preferred Structures in a Simple Model of Protein Folding, H. Li, R. Helling, C. Tang, N. Wingreen, Science 273: 666 (1996) 
  • Chaperonin-facilitated protein folding: Optimization of rate and yield by an iterative annealing mechanism, M.J. Todd, G.H. Lorimer, D. Thirumalai, Proc. Natl. Acad. Sci (USA) 93: 4030 (1996) [PDF]
  • From Levinthal to pathways to funnels: The "New View" of protein folding kinetics, K.A. Dill and H.S. Chan, Nature Structural Biology 4: 10 (1997). 
  • Contact order, transition state placement, and the refolding rates of single domain proteins, K.W. Plaxco, K.T. Simons, D. Baker, J. Mol. Biol. 277: 985 (1998) [PDF] 
  • Are protein folds atypical? H. Li, C. Tang, and N.S. Wingreen, Proc. Natl. Acad. Sci (USA) 95: 4987 (1998) [PDF]
  • Chaperonin function: Folding by forced unfolding M. Shtilerman, G.H. Lorimer, S.W. Englander, Science 284: 822 (1999) [PDF]
  • Polymer principles and protein folding, K.A. Dill, Prot. Science 8: 1166 (1999). 
  • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins, C. Clementi, H. Nymeyer, J.N. Onuchic, J. Mol. Biol. 298: 937 (2000) [PDF] 
  • How native-state topology affects the folding of dihydrofolate reductase and interleukin-1 beta, C. Clementi, P.A. Jennings, J.N. Onuchic, Proc. Natl Acad. Sci (USA)97: 5871 (2000) [PDF]
  • Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus, N.E.G Buchler and R.A. Goldstein , J. Chem. Phys. 112: 2533 (2000)  [PDF]
  • The Distribution of Structures in Evolving Protein Populations, D.M. Taverna and R.A. Goldstein, Biopolymers 53: 1 (2000) [PDF]
  • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation, U. Mayor, C.M. Johnson, V. Daggett, A.R. Fersht, Proc. Natl. Acad. Sci. (USA) 97: 13518 (2000) [PDF]
  • Measuring the rate of intramolecular contact formation in polypeptides L.J. Lapidus, W.A. Eaton, J. Hofrichter, Proc. Natl. Acad. Sci (USA) 97: 7220 (2000) [PDF]
  • Construction of protein binding sites in scaffold structures S. Liang, Z. Liu, W. Li, L. Ni, L. Lai, Biopolymers 54: 515 (2000) [PDF]
  • Toward an energy function for the contact map representation of proteins K. Park, M. Vendruscolo, E. Domany, Proteins 40: 237 (2000) [PDF]
  • A surprising simplicity to protein folding D. Baker, Nature 405: 39 (2000)  [PDF]
  • Modeling the third loop of short-chain snake venom neurotoxins:  Roles of the short-range and long-range interactions, Z. Lin, W. Li. H. Zhang, Y. Han, L. Lai, Proteins 42: 6 (2001) [PDF]

Gene Finding

  • Genome Research Journal issue on genome annotation assessment and articles covering the state-of-art in gene finding.
     
  • Finding the genes in genomic DNA, C.B. Burge and S. Karlin, Curr. Opin. Struct. Biol. 8: 346 (1998) [PDF] 
  • Chipping away at the transcriptome, C.B. Burge, Nature Genetics 27:  4 (2001)

Genome Architecture

  • Intron positions correlate with module boundaries in ancient proteins, S.J. de Souza, M. Long, L. Schoenbach, S.W. Roy, W. Gilbert, Proc. Natl. Acad. Sci. (USA)  93: 14632 (1997) [PDF] 
  •  Genome system architecture and natural genetic engineering in evolution, J.A. Shapiro, in Molecular Strategies for Biological Evolution, L. Caporale (ed.), Annal. NY Acad. Sci 870: 23 (1999) 
  • Transposable elements as the key to a 21st century view of evolution J.A. Shapiro, Genetica 107: 171 (1999) [PS]
  • From molecular to modular cell biology, L.H. Hartwell, J.J. Hopfield, S. Leibler, A.W. Murray, Nature 402:  C47, Suppl. (1999) 
  • Fractals related to long DNA sequences and complete genomes, B.-L. Hao, H.C. Lee, S.-Y. Zhang, Chaos, Solitons, Fractals 11: 825 (2000) [PDF]
  • Fractals from genomes - exact solutions of a biology-inspired problem, B.-L. Hao, Physica A 282: 223 (2000) [PDF]
  • Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae, J.L. Gerton, J. DeRisi, R. Shroff, M. Lichten, P.O. Brown, T.D. Petes, Proc. Natl. Acad. Sci (USA) 97:  11383 (2000) [PDF]
  • Genome system architecture and natural genetic engineering, J.A. Shapiro, in Evolution as Computatation, L.F. Landweber and E. Winfree (eds.), Springer, Berlin (2000)
  • Whither genomics?, A.W. Murray,  Genome Biology (2000) [PDF]
  • Alternative splicing: increasing diversity in the proteomic world, B.R. Graveley, Trends in Genetics 17: 100 (2001) [PDF] 
     

DNA motif finding

  • Identifying protein-binding sites from unaligned DNA fragments, G.D. Stormo and G.W. Hartzell, Proc. Natl. Adac. Sci. (USA) 86: 1183 (1989) 
  • Detecting subtle sequence signals - A Gibbs sampling strategy for multiple alignment, C.E. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, F. Neuwald, J.C. Wootton Science 262: 208 (1993) 
  • Unsupervised learning of multiple motifs in biopolymers using expectation maximization, T.L. Bailey and C. Elkan, Mach. Learn. 21: 51 (1995) 
  • Meta-MEME:  Motiff-based hidden Markov models of protein families, W.N. Grundy, T.L. Bailey, C.P. Elkan, M.E. Baker, Comput. Appl. Biosci 13: 397 (1997) 
  • Building a dictionary for genomes:  Identification of presumptive regulatory sites by statistical analysis, H.J Bussemaker, H. Li, E.D. Siggia Proc. Natl. Acad. Sci. (USA) 97: 10096 (2000) [PS] 
  • Regulatory Element Detection Using Correlation with Expression, H. Li, H.J. Bussemaker, E.D. Siggia Nature Genetics 27: 167 (2001)  [PDF] 
     

Molecular Information Processing

  • Kinetic proofreading: New mechanism for reducing errors in biosynthetic processes requiring high specificity, JJ Hopfield, P Natl Acad Sci USA 71 (1974) 4135. [PDF]
  • An integrated model of the transcription complex in elongation, termination, and editing, P.H. von Hippel, Science 281: 660 (1998) [PDF]

Molecular and Genetic Networks

  • Ptashne's Genetic Switch gives a beautiful account of one of the best understood genetic circuits.
  • Davidson's Genomic Regulatory Systems explores the role of evolution in developmental and genetic networks.
     
  • Transcriptional activation by  recruitment., M. Ptashne, A. Gann, Curr. Biology 8: 812 (1998) [PDF]
  • Robustness in simple biochemical networks, N. Barkai and S. Leibler, Nature 387: 913 (1997) 
  • Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene, C.H. Yuh, H. Bolouri, and E.H. Davidson, Science 279:1896 (1998). [PDF] 
  • Imposing specificity by  localization: mechanism and evolvability, M. Ptashne, A. Gann, Curr. Biology 8: 812 (1998) [PDF]
  • Robustness in bacterial chemotaxis, U. Alon, M.G. Surette, N. Barkai, S. Leibler, Nature 397: 168 (1999)
  • Construction of a genetic toggle switch in Escherichia coli, T.S. Gardner, C.R. Cantor, J.J. Collins, Nature 403: 339 (1999)
  • It's a noisy business!  Genetic regulation at the nanomolar scale, H.H. McAdams and A. Arkin, Trends Genet. 15: 65 (1999) [PS]
  • Modeling genetic regulatory dynamics in neural development, M. Wahde, J. Hertz,  [PS] (1999)
  • Coarse-grained reverse engineering of genetic regulatory networks, M. Wahde, J. Hertz, [PS] (1999)
  • A synthetic oscillatory network of transciptional regulators, M.B. Elowitz and S. Leibler, Nature 403: 335 (2000)
  • Gene regulation:  Towards a circuit engineering discipline, H.H. McAdams and A. Arkin, Curr. Biol. 10: R318 (2000) 
  • Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes, D. Endy, L. You, J. Yin, I.J. Molineux, Proc. Natl. Acad. Sci97: 5375 (2000) [PDF] 
  • Cis-regulatory logic in the endo16 gene, C.H. Yuh, H. Bolouri, and E.H. Davidson, Development 128: 617 (2001) [PDF]
  • Modelling cellular behavior, D. Endy, R. Brent, Nature 409: 391 (2001) [PDF]
  • Design principles for elementary gene circuits:  Elements, methods, and examples, M. A. Savageau, Chaos 11: 142 (2001) [PDF] 

Molecular Evolution & Origins of Life

  • Positional dependence, cliques, and predictive motifs in the bHLH protein domain, W.R. Atchley, W. Terhalle, A. Dress, J. Mol. Evolution 48: 501 (1997) [PDF]
  • Testing ancient RNA-protein interactions, L.F. Landweber, Proc. Natl. Acad. Sci (USA) 96: 11067 (1999) [PDF]
  • Selection, history and chemistry: the three faces of the genetic code, R.D. Knight, S.J. Freeland, L.F. Landweber, Trends in Biol. Sci. (1999) [PDF]
  • Non-unity molecular heritability demonstrated by continuous evolution in vitro, T. Schmitt, N. Lehman, Chemistry & Biology 8: 857 (1999) [ PDF]
  • A molecular description of the evolution of resistance, P. Ordoukhanian, G.F. Joyce, Chemistry & Biology 8: 881 (1999) [PDF]
  • Patterns of nucleotide substitution in Drosophila and mammalian genomes, D.A Petrov, D.L. Hartl, Proc. Natl. Acad. Sci. (USA) 96: 1475 (1999) [ PDF]
  • Using Physical-Chemistry Based Mutation Models in Phylogenetic Analyses of HIV-1 Subtypes, J.M Koshi, D.P. Mindell, R.A. Goldstein, Mol. Biol. Evol. 16:  173 (1999) [PDF] 
  • Modeling Evolution at the Protein Level using an Adjustable Amino Acid Fitness Model, M.W. Dimmic, D. P. Mindell, R.A. Goldsteinm PSB  (2000) [PDF]
  • Composing life, D. Segre, D. Lancet, EMBO Reports 1: 217 (2000) [ PDF]
  • Compositional genomes:  Prebiotic information transfer in mutually catalytic noncovalent assemblies, D. Segre, D. Ben-Eli, D. Lancet, Proc. Natl. Acad. Sci (USA) 97: 4112 (2000) [PDF]
  • Evidence for DNA loss as a determinant of genome size, D.A. Petrov, T.A. Sangster, J.S. Johnston, D.L. Hartl, K.L. Shaw, Science 287: 1060 (2000) [ PDF]
  • Testing a biosynthetic theory of the genetic code: Fact or artifact?, T.A. Ronneberg, L.F. Landweber, S.J. Freeland, Proc. Natl. Acad. Sci (USA) 97: 13690 (2000) [ 
  • Molecular computation:   RNA solutions to chess problems, D. Faulhammer, A.R. Cukras, R.J. Lipton, L.F. Landweber, Proc. Natl. Acad. Sci (USA) 97: 1385 (2000) [PDF]
  • Correlations among amino acid sites in bHLH protein domains:  An information theoretic analysis, W.R. Atchley, K.R. Wollenberg, W.M. Fitch, W. Terhalle, A.W. Dress, Mol. Biol. Evol. 17: 164 (2000) [PDF]
  • Consensus temporal order of amino acids and evolution of the triplet code, E. N. Trifonov, Gene 261: 139 (2000) [PS]
  • Distinct stages of protein evolution as suggested by protein sequence analysis, E.N. Trifonov, A. Kirzhner, V.M. Kirzhner, I.N. Berezovsky, J. Mol. Evolution, in press (2001)
  • The lipid world, D. Segre, D. Ben-Eli, D.W. Deamer, D. Lancet Origins of Life and Evolution of the Biosphere 31: 119 (2001) [ ]
  • On the Selection and Evolution of Regulatory DNA Motifs, U. Gerland, T. Hwa (2001), in review []

Macro-Evolution & Phylogenies

  • Punctuated evolution caused by selection of rare beneficial mutations, S.F. Elena, V.S. Cooper, R.E. Lenski, Science 272: 1802 (1996)
  • Continuity in evolution: On the nature of transitions, W. Fontana and P. Schuster, Science 280: 1451 (1998) [PDF] 
  • Genomic evolution during a 10,000-generation experiment with bacteria, D. Papdopoulous, D. Schneider, J. Meier-Eiss, W. Arber, R.E. Lenski, M. Blot, Proc. Natl. Acad. Sci. (USA) 96: 3807 (1999) [PDF]
  • Quasispecies evolution in general mean-field landscapes, L. Peliti, Europhys. Lett. (2001) [PS]

Algorithms

  • Genomic mapping by fingerprinting random clones:  A mathematical analysis , E.S. Lander, M.S. Waterman Genomics 2: 231 (1988) 
  • Exact sampling with coupled Markov chains and applications to statistical mechanics, J.G. Propp, D.B. Wilson, Random Struct. Algorithms 9: 223 (1996)

Gene expression

  • Cluster analysis and display of genome-wide expression patterns, M.B. Eisen, P.T. Spellman, P.O. Brown, D. Botstein,  Proc. Natl. Acad. Sci. (USA)  95: 14863 (1998) [PDF] 
  • Genomics and array technology, J.L. DeRisi, V.R. Iyer, Curr Opin Oncol 11: 76 (1999) 
  • Adsorption of semiflexible polyelectrolytes on charged planar surfaces:  Charge compensation, charge reversal, and multilayer formation, R.R. Netz, J.F. Joanny, Macromolecules 32: 9013 (1999) [PDF] 
  • Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays, U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, A.J. Levin, Proc. Natl. Acad. Sci. (USA) 96: 6745 (1999) [PDF] 
  • Coupled two-way clustering analysis of gene microarray data, G. Getz, E. Levine, E. Domany Proc. Natl. Acad. Sci. (USA) 97: 12079 (2000) [PDF] 
  • Super-paramagnetic clustering of yeast gene expression profiles, G. Getz, E. Levine, E. Domany,  Physica A  279: 457 (2000) [PDF] 
  • Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria, R.E. Hayward, J.L. DeRisi, S. Alfadhli, D.C. Kaslow, P.O. Brown, P.K. Rathod, Mol Microbiol 35: 6 (2000) 
  • Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays, D.A. Notterman, U. Alon, A.J. Sierk, A.J. Levine, Cancer Research 61:  3124 (2001) [PDF]

Comparative Genomics

  • Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences, W. Makalowski, M.S. Boguski, Proc. Natl. Acad. Sci. (USA) 95: 9407 (1998) [PDF] 
  • Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs, N. Jareborg, E. Birney, and R. Durbin, Genome Research 9: 815 (1999) [PDF] 
  • Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence, J.R. Crollius, O. Jaillon, A. Bernot, et al.  Nature Genetics 25: 235 (2000)

Regulation

  • What's up and down with histone deacetylation and transciption?, M.J. Pazin, J.T. Kadonaga, Cell 89:  325 (1997) [PDF]
  • Identification of regulatory regions which confer muscle-specific gene expression, W.W. Wasserman and J.W. Fickett, J Mol Biol 278: 167 (1998)  [PDF] 
  • Going the distance:  A current view of enhancer action, E.M. Blackwood, J.T. Kadonaga, Science 281: 60 (1998) [PDF] 
  • The language of covalent histone modifications, B.B. Strahl, C.D. Allis Nature 403: 41 (2000) [PDF] 
  • Salt-induced DNA-Histone complexation, K.K. Kunze, R.R. Netz Phys. Rev. Lett. 85:  4389 (2000) [PDF]

Protein-DNA/RNA Binding

  • Probability Model for Molecular Recognition in Biological Receptor Repertoires: Significance to the Olfactory System, D. Lancet, E. Sadovsky, and E. Seidemann, Proc. Natl Acad. Sci. (USA) 90: 3715 (1993) [PDF]
  • Specificity, free energy and information content in protein-DNA interactions, G.D. Stormo, D.S. Fields, Trends in Biochem Sci. 23: 109 (1998) [PDF] 
  • Deciphering RNA recognition: aminoglycoside binding to the hammerhead ribozyme, Y. Tor, T. Hermann, E. Westhof, Chem. Bio.  5: R277 (1998) [PDF] 
  • A general model for nucleic acid helicases and their "coupling" within macromolecular machines, P.H. von Hippel, E. De la Goutte, Cell 104: 177 (2001) [PDF] 
  • The complete human olfactory subgenome,G. Glusman, I. Yanai, I. Rubin, D. Lancet, Genome Research in press (2001) [PDF]