Publications

Papers

2008

Sundquist A, Fratkin E, Do CB, Batzoglou S. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Research, in press.

    Abstract accepted in RECOMB 2008

Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple network alignment. Accepted in RECOMB 2008.

2007

Sundquist A, Bigdeli S, Jalili R, El-Sayed YY, Taslimi MM, Druzin ML, Waller S, Pullen KM, Batzoglou S, Ronaghi M. Bacterial flora typing with deep, targeted, chip-based Pyrosequencing. BMC Microbiology, 7:108, 2007.

Gross SS, Do CB, Sirota M, Batzoglou S. A discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biology, 8:R269, 2007.

Drosophila Comparative Genome Sequencing and Analysis Consortium. Evolution of genes and genomes in the context of the Drosophila phylogeny. Nature 450: 203-218, 2007.

Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S.  Current progress in network research: toward reference networks for key model organisms.  Briefings in Bioinformatics 8(5): 318-32, 2007.

The ENCODE Project Consortium.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.  Nature 447: 799-816, 2007.

Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high-throughput short-read technologies.  PLOS One, 2(5): e484.

Margulies E, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Lytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bieckl P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Schuler G, Church D, Rosenbloom KR, Kent WJ, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, UCSC Genome Browser Team, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research 17 (6): 760-774, 2007.

Gross SS, Russakovsky O, Do CB, Batzoglou S.  Training conditional random fields for maximum parse accuracy. NIPS 2006.

2006

Phuong TM, Do CB, Edgar RC, Batzoglou S.  Multiple alignment of protein sequences with repeats and rearrangements.  Nucleic Acids Research 34(20): 5932-5942, 2006.

Naughton B, Fratkin E, Batzoglou S, Brutlag DL.  A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.  Nucleic Acids Research 34(20): 5730-5739, 2006.

Srinivasan BS, Do CB, Batzoglou S. RECOMB 2006: Evidence for Intelligent (Algorithm) Design. Genome Biology, 7:322, 2006.

Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S.  Graemlin: General and Robust Alignment of Multiple Large Interaction Networks.  Genome Research, 16:1169–1181, 2006.

Davydov E, Batzoglou S.  A computational model for RNA multiple structural alignment.  Theoretical Computer Science, Special Issue on Combinatorial Pattern Matching, in press.

Do CB, Woods DA, Batzoglou S.  CONTRAfold: RNA Secondary Structure Prediction without Physics-Based Models.  ISMB 2006 Conference Proceedings, Bioinformatics 22:e90–e98, 2006.  Best Paper Award ISMB 2006.

Fratkin E, Naughton B, Brutlag DL, Batzoglou S.  MotifCut: Finding Regulatory Motifs with Maximum Density Subgraphs.  ISMB 2006 Conference Proceedings, Bioinformatics 22: e150–e157, 2006.

Edgar RC, Batzoglou S.  Multiple Sequence Alignment.  Current Opinion in Structural Biology, 16: 368–373, 2006.

Do CB, Gross SS, Batzoglou S.  CONTRAlign: Discriminative Training for Protein Sequence Alignment.  Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB 2006), pp. 160–164.

Srinivasan BS, Novak A, Flannick J, Batzoglou S, McAdams H.  Integrated Protein Interaction Networks for 11 Microbes.  Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB 2006), pp. 1–14.

2005

Galagan JE, Calvo SE, Cuomo C, Ma L-J, Wortman J, Batzoglou S, Lee S-I, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D’Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peņalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren B.  Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.  Nature 438:1105–1115, 2005.

Flannick J, Batzoglou S.  Using multiple alignments to improve seeded local alignment algorithms.  Nucleic Acids Research 33(14): 4563–4577, 2005.

Manohar A, Batzoglou S.  TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.  Proceedings of the CSB 2005, pp 111–119.

Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A.  Distribution and intensity of constraint in mammalian genomic sequence.  Genome Research 15: 901–913, 2005.

Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: probabilistic consistency-based multiple alignment of amino acid sequences.  Genome Research 15: 330–340, 2005.

Batzoglou S. The many faces of sequence alignment.  Briefings in Bioinformatics 1: 6–22, 2005.

Batzoglou S. Algorithmic Challenges in Mammalian Genome Sequence Assembly.  Special Review, In: Dunn M, Jorde L, Little P, Subramaniam S, editors. Encyclopedia of genomics, proteomics and bioinformatics. Hoboken (New Jersey): John Wiley and Sons, 2005.

2004

The ENCODE Project Consortium.  The ENCODE (ENCyclopedia Of DNA Elements) Project.  Science 306: 636–640, 2004.

Sundararajan M, Brudno M, Small K, Sidow A, Batzoglou S. Chaining algorithms for alignment of draft sequence.  WABI 2004.

 Do CB, Brudno M, Batzoglou S. ProbCons: probabilistic consistency-based multiple alignment of amino acid sequences.  Extended Abstract in Abstract in the Nineteenth National Conference on Artificial Intelligence AAAI p. 703, 2004. ISMB/ECCB 2004, online.  Best Paper Award, ISMB/ECCB 2004.

Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu S. A suit of web-based programs to search for transcription regulatory motifs.  Nucleic Acids Research 32: W204–W207, 2004.

Davydov E, Batzoglou S. A computational model for RNA multiple structural alignment.  Combinatorial Pattern Matching 2004.

 Rat Genome Sequencing Project Consortium (RGSPC).  Genome sequence of the Brown Norway Rat yields insights into mammalian evolution.  Nature 428: 493–521, 2004.

Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I. Automated whole-genome multiple alignment of Rat, Mouse, and Human.  Genome Research 14: 685–692, 2004.

Cooper GM, Brudno M, Stone ES, Dubchak I, Batzoglou S, Sidow A. Characterization of evolutionary rates and constraints in three mammalian genomes.  Genome Research 14: 539–548, 2004.

Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S. Eukaryotic regulatory element conservation and identification using comparative genomics.  Genome Research, 14: 451–458, 2004.

2003

Lee S-I, Batzoglou S.  ICA-based clustering of genes from microarray expression data.  In Advances in Neural Information Processing Systems (NIPS), Vancouver, British Columbia, Canada, December 2003.  Poster.

Lee S-I, Batzoglou S. Application of independent component analysis to microarrays.  Genome Biology 2003, 4:R76.

Shan N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Joy S, Bethel W, Rubin EM, Hamann B, Dubchak I. Phylo-VISTA: an interactive visualization tool for multiple DNA sequence alignments.  Bioinformatics 19: 1575–1577, 2003.

Brudno M, Chapman MA, Gottgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences.  BMC Bioinformatics 4:66, 2003.

Brudno M, Malde S, Poliakov A, Do C, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment.  Special Issue on the Proceedings of the ISMB 2003, Bioinformatics 19: 54i–62i, 2003.

Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou M, Morgenstern B. AgenDA: homology-based gene prediction. Bioinformatics, 19:1575–1577, 2003.

Khambata-Ford S, Liu Y, Gleason C, Dickson M, Altman RB, Batzoglou S, Myers RM. Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. Genome Research 13:1765–1774, 2003.

Cooper GM, Brudno M, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.  Genome Research 13:813–820, 2003.

Brudno M, Do C, Cooper GM, Kim MF, Davydov E, NISC Comparative Sequencing Program, Green ED, Sidow A, Batzoglou S. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Research 13: 721–731, 2003.

2002 and before

Batzoglou S, Jaffe D, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: A whole genome shotgun assembler.  Genome Research 12:177–189, 2002.

Lander ES et al. Initial sequencing and analysis of the human genome.  Nature 409:860–921, 2001.

Batzoglou S, Pachter L, Mesirov JP, Berger B,. Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction.  Genome Research 10:950–958, 2000.

Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction.  Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, (RECOMB 2000) p.46–53.

Batzoglou S, Mesirov JP, Berger B, Lander ES. Sequencing a genome by walking with clone-ends: A mathematical analysis.  Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, (RECOMB 2000) p.45.

Istrail S, Hurd A, Lippert RA, Walenz B, Batzoglou S, Conway JH, Peyerl FW. Prediction of Self-Assembly of Energetic Tiles and Dominos: Experiments, Mathematics and Software.  Sandia Labs Technical Report, March 2000.

Batzoglou S, Mesirov JP, Berger B, Lander ES.  Sequencing a genome by walking with clone-ends: A mathematical analysis.  Genome Research 9:1163–1174, 1999.

Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B.  A dictionary based approach to gene annotation.  Journal of Computational Biology 6:419–430, 1999.

Pachter L, Batzoglou S, Spitkovsky VI, Beebee W, Lander ES, Berger B, Kleitman DJ. A dictionary based approach to gene annotation.  Proceedings of the Third Annual International Conference on Computational Molecular Biology, (RECOMB 1999), 285–294.

Batzoglou S, Istrail S.  Physical mapping with repeated probes: The hypergraph superstring problem.  Lecture Notes in Computer Science 1645:66 ff, 1999, Special Issue on Combinatorial Pattern Matching 1999.

Batzoglou S, Berger B, Kleitman DJ, Lander ES, Pachter L. Recent developments in computational gene recognition.  Documenta Mathematica, Extra Volume ICM I, 649–658, 1998.

Agarwala R, Batzoglou S, Dancik V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan M, Skiena S. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Journal of Computational Biology 4: 275–296, 1997.

Agarwala R, Batzoglou S, Dancik V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan S, Skiena S.  Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model.  Proceedings of the 8th Annual ACM-SIAM Symposium on Discrete Algorithms, (SODA ’97) 390–399.

Agarwala R, Batzoglou S, Dancik V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan S, Skiena S. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model.  Proceedings of the First Annual International Conference on Computational Molecular Biology, (RECOMB 1997) 1–2.

Decatur S, Batzoglou S. Protein folding in the hydrophobic-polar model on the 3D triangular lattice. Proceedings of the 6th Annual MIT Student Workshop on Computing Technology, 1997.

 

 

Abstracts of Conference Talks

Novak AF, Flannick JA, Srinivasan B, McAdams HH, Batzoglou S.  NUKE: fast and scalable multiple alignment of protein interaction networks.  CSHL Conference Genome Informatics, October 28-November 1, 2005, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2005.

Srinivasan B, Novak AF, Flannick JA, Batzoglou S, McAdams HH.  Integrated protein interaction networks for 230 microbes.  In BCATS 2005 Symposium Proceedings, p. 26, 2005.

Fratkin E, Naughton B, Brutlag D, Batzoglou S.  Motif finding in DNA sequences using maximum density subgraphs.  2nd Moscow Conference in Computational Molecular Biology (MCCMB), 2005.

Asimenos G, Cooper GM, Holbert D, Sidow A, Batzoglou S.  A reference mammalian whole-genome alignment.  The Biology of Genomes, CSHL, May 2005.

Dubchak I, Brudno M, Poliakov A, Kislyuk A, Sundararajan M, Batzoglou S.  Glocal (global/local) alignment methods for comparison of DNA sequences and whole genome assemblies utilized in VISTA tools. 2nd RECOMB Comparative Genomics Satellite Workshop, 16–19 October, Bertinoro (Forli), Italy, 2004.

Liu Y, Batzoglou S, Kim SK.  Global identification of Caenorhabditis elegans regulatory motifs.  In BCATS 2004 Symposium Proceedings, p. 26, 2004.

Do CB, Brudno M, Batzoglou S.  ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences.  Intelligent Systems in Molecular Biology (ISMB) 2004.  Best Paper Award.

Do CB, Brudno M, Batzoglou S.  Probabilistic consistency-based multiple alignment of proteins.  In BCATS 2003 Symposium Proceedings, 2003.

Liu Y, Liu XS, Stuart JM, Kim SK, Batzoglou S.  Predicting the Activity of Transcription Factor Binding Motifs.  In BCATS 2003 Symposium Proceedings, 2003.

Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S.  Glocal alignment: finding rearrangements during alignment.  Joint CSHL/Wellcome Trust Conference Genome Informatics May 7–11 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2003.

Brudno M, Poliakov A, Couronne O, Do CB, Batzoglou S, Dubchak I.  Multiple alignment of whole genomes: a pipeline approach.  Joint CSHL/Wellcome Trust Conference Genome Informatics May 7–11 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2003.

Brudno M, Do CB, Cooper GM, Kim M, Davydov E. NISC Comparative Sequencing Program, Green ED, Sidow A, Batzoglou S.  Multiple genomic sequence alignment.  Advances in Genome Biology and Technology (AGBT) Marco Island, Florida, February 2003.

Brudno M, Do CB, Kim M, Batzoglou S.  Multiple genomic sequence alignment.  In BCATS 2002 Symposium Proceedings, p.23, 2002.

Brudno M, Kim M, Batzoglou S.  Multiple alignment of genomic sequences.  Joint CSHL/Wellcome Trust Conference Genome Informatics September 4–8 p.6. Wellcome Trust Genome Campus, Hinxton, United Kingdom, 2002.

Couronne O, Bray N, Khatib F, Dubchak I, Batzoglou S, Pachter L.  Comparative whole genome shotgun assembly.  Abstracts of papers presented at the Joint CSHL/Wellcome Trust Conference Genome Sequencing and Biology May 7–11 p.63, p.123. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2002.

Jaffe D, Batzoglou B, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES.  ARACHNE: A whole genome shotgun assembler.  Abstracts of papers presented at the Joint CSHL/Wellcome Trust Conference Genome Informatics August 8–12 p.10. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2001.

Batzoglou S, Jaffe D, Stanley K, Berger B, Mesirov JP, Lander ES.  ARACHNE: A whole genome shotgun assembler.  Abstracts of papers presented at the 2001 meeting on Genome Sequencing and Biology May 9–13 p.199. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2001.

Batzoglou S, Jaffe D, Stanley K, Berger B, Mesirov JP, Lander ES.  ARACHNE: A whole-genome shotgun assembler.  Advances in Genome Biology and Technology (AGBT) Marco Island, Florida, February 2001.

Batzoglou S., Istrail S.  Physical mapping with repeated probes: the hypergraph superstring problem.  In Ninth SIAM Conference on Discrete Mathematics, Toronto, Canada, July 1998.

 

 

Conference Posters

Gross SS, Russakovsky O, Do CB, Batzoglou S. Training Conditional Random Fields for Maximum Labelwise Accuracy. NIPS 2006.

Gross SS, Do CB, Batzoglou S.  De novo gene prediction using a semi-Markov conditional random field.  RECOMB 2006.

Do CB, Woods DA, Batzoglou S.  CONTRAfold: RNA secondary structure prediction without physics-based models.  RECOMB 2006.

Flannick J, Batzoglou S.  Using multiple alignments to improve seeded local alignment algorithms.  CSHL Conference Genome Informatics, October 28-November 1, 2005, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2005.

Srinivasan B, Novak AF, Flannick JA, Batzoglou S, McAdams HH.  Integrated protein interaction networks for 230 microbes.  CSHL Conference Genome Informatics, October 28-November 1, 2005, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2005. Best Poster Award.

Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S.  A strategy for whole-genome sequencing and assembly with high-throughput, short-read technologies. CSHL Conference Genome Informatics, October 28-November 1, 2005, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2005.

Do CB, Gross SS, Edgar RC, Batzoglou S. CONTRAlign: a discriminative framework for protein sequence alignment.  In BCATS 2005 Symposium Proceedings, p. 45, 2005. Best Poster Award.

Gross SS, Do CB, Batzoglou S.  CONTRAST: de novo gene prediction using a semi-Markov conditional random field.  In BCATS 2005 Symposium Proceedings, p. 82, 2005.

Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S.  A strategy for whole-genome sequencing and assembly with high-throughput, short-read technologies. In BCATS 2005 Symposium Proceedings, p. 38, 2005.

Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A.  Characterization of the effects of purifying selection in a sample of the human genome.  The Biology of Genomes, CSHL, May 2005.

Davydov E, Batzoglou S. A computational model for RNA multiple structural alignment.  In BCATS 2004 Symposium Proceedings, p. 42, 2004.

Brudno M, Sundararajan M, Poliakov A, Kislyuk A, Dubchak I, Batzoglou S.  Constructing synteny maps for whole-genome alignments.  Joint CSHL/Wellcome Trust Conference Genome Informatics September 22–26, 2004.

Do CB, Brudno M, Batzoglou S.  LAGAN2: Probabilistic global alignment of DNA under multiple conservation models.  Intelligent Systems in Molecular Biology (ISMB) 2003.

Lee S, Batzoglou S.  Discovering biological processes from microarray data using independent component analysis.   Joint CSHL/Wellcome Trust Conference Genome Informatics May 7–11 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2003.

Do C, Brudno M, Batzoglou S.  The draft problem: genomic sequence alignment reconsidered.  In BCATS 2002 Symposium Proceedings, p.41, 2002.

Taher L, Rinner O, Garg S, Brudno M, Batzoglou S, Morgenstern B.  AGenDA: A WWW server for gene recognition by comparative sequence analysis.  In Thomas Lengauer, Hans-Peter Lenhof, Ruth Christmann (editors) European Conference on Computational Biology 2002, Poster Abstracts pp. 236–238, 2002.

Vinson J, Jaffe D, Stange-Thomann N, Galagan J, Batzoglou S, Nusbaum C, Birren B, Zody M, Mesirov J, Sidow A, Lander ES.  Highly polymorphic genomes: a challenge for assembly and an opportunity for comparative genomics. Joint CSHL/Wellcome Trust Conference Genome Informatics September 4–8 p.86. Wellcome Trust Genome Campus, Hinxton, United Kingdom, 2002.

Vinson J, Jaffe D, Sidow A, Batzoglou S, Butler J, Nusbaum C, Birren B, Stange-Thomann N, Zody M, Mesirov J, and Lander ES.  Assembly of the highly polymorphic genome of Ciona savigny.  Abstracts of papers presented at the Joint CSHL/Wellcome Trust Conference Genome Sequencing and Biology May 7–11 p.291. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2002.

Nusbaum C, Endrizzi M, Calvo S, Foley K, Stange-Thomann N, Sachs M, Kinsey J, Staben C, Jaffe D, Batzoglou S, Galagan J, and Birren B.  Sequencing the Neurospora Genome.  Abstracts of papers presented at the 2001 meeting on Genome Sequencing and Biology May 9–13 p.182. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2001.

 

 

Other Manuscripts

PhD THESIS.  Serafim Batzoglou. Computational Genomics: Mapping, Comparison, and Annotation of Genomes. Ph.D. Dissertation, Department of Electrical Engineering and Computer Science, MIT, June 2000.   Here is my thesis is pdf format. Please note that I had to reformat it a little (merge files from the time where PCs had only 64 Mb RAM and I had to split a Word document into many files...)  Computational Genomics: Mapping, Comparison, and Annotation of Genomes.

Area Exam.  Serafim Batzoglou. DNA Computing and Molecular Self-Assembly.  Area examination, Department of Electrical Engineering and Computer Science, MIT, December 1999.  Note: I seem to have lost the figures that show the NP-completeness gadgets.

Solutions Manual.  Serafim Batzoglou and Victor Boyko. Discrete Algorithms: A solutions manual. Morgan Kauffman, 1998.