Mapping 

Informatics 

ELSI 

Infrastructure 

SBIR 
 
FY '94-'95 Projects 

Part II Index 

Glossary 
  
Acronyms 
 

Projects in this section have been completed or did not receive support through the DOE Human Genome Program in FY1996. 

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Sequencing 

Sequencing by Hybridization: Methods to Generate Large Arrays of Oligonucleotides 
Thomas M. Brennan 

Sequencing by Hybridization: Development of an Efficient Large-Scale Methodology 
Radomir Crkvenjakov 

Genomic Instrumentation Development: Detection Systems for Film and HighSpeed GelLess Methods 
Jack B. Davidson and RobertS. Foote 

SingleMolecule Detection Using ChargeCoupled Device Array Technology 
M. Bonner Denton, Richard Keller, Mark E. Baker, Colin W. Earle, and David A. Radspinner 

Coupling Sequencing by Hybridization with Gel Sequencing for Inexpensive Analysis of Genes and Genomes 
Radoje Drmanac, Snezana Drmanac, and Ivan Labat 

Physical Structure and DNA Sequence of Human Chromosomes 
Glen A. Evans 

Using Scanning Tunneling Microscopy to Sequence the Human Genome 
Thomas L. Ferrell, Robert J. Warmack, David P. Allison, K.Bruce Jacobson, Gilbert M. Brown, and Thomas G. Thundat 

DNA Sequence Analysis by SolidPhase Hybridization 
Robert S. Foote, Richard A. Sachleben, and K. Bruce Jacobson 

DNA Sequencing Using Stable Isotopes 
K. Bruce Jacobson, Heinrich F. Arlinghaus, Gilbert M. Brown, Robert S. Foote, Frank W. Larimer, Richard A. Sachleben, 
Norbert Thonnard, and Richard P. Woychik 

Preparation of Oligonucleotide Arrays for Hybridization Studies 
MichaelC. Pirrung, StevenW. Shuey, David C. Lever, Lara Fallon, J.-C. Bradley, and William P. Hawe 

Improvement and Automation of Ligation-Mediated Genomic Sequencing 
Arthur D. Riggs and Gerd P. Pfeifer 

*Analysis of a 53-Kb Nucleotide Sequence from the Right Genome Terminus of the Variola Major Virus Strain India-1967 
Sergei N. Shchelkunov, Vladimir M. Blinov, Sergei M. Resenchuk, Alexei V. Totmenin, Viktor N. Krasnykh, Ludmilla V. Olenina, Oleg I. Serpinsky, and Lev S. Sandakhchiev 

A High-Speed Automated DNA Sequencer 
Lloyd M. Smith 

Characterization and Modification of DNA Polymerases for Use in DNA Sequencing 
Stanley Tabor 


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Mapping 

*Toward Cloning Human Chromosome 19 in Yeast Artificial Chromosomes 
Inga P. Arman, Alexander B. Devin, Svetlana P. Legchilina, Irina G. Efimenko, Marina E. Smirnova, and Dina V. Glazkova 

A Panel of Mouse-Human Monochromosomal Hybrid Cell Lines, Each Containing a Single Different Tagged Human Chromosome 
Arbansjit K. Sandhu, G.Pal Kaur, and Raghbir S. Athwal 

*Preparation of a Set of Molecular Markers for Human Chromosome 5 Using G+C­Rich and Functional Site-Specific Oligonucleotides 
M.L. Filipenko, A.I. Muravlev, E.I. Jantsen, V.V. Smirnova, N.A. Chikaev, V.P. Mishin, and M.A. Ivanovich 

An Improved Method for Producing Radiation Hybrids Applied to Human Chromosome 19 
Cynthia L. Jackson and Hon Fong L. Mark 

Construction of a Human Genome Library Composed of Multimegabase Acentric Chromosome Fragments 
Michael J. Lane, Peter Hahn, and John Hozier 

Reagents for Understanding and Sequencing the Human Genome 
J.R. Korenberg, X-N. Chen, S. Mitchell, S. Gerwehr, Z. Sun, D. Noya, R. Hubert, U-J. Kim, H. Shizuya, X. Wu, J. Silva, B. Birren, T.J. Hudson, P. deJong, E. Lander, and M. Simon 

Development of Diallelic Marker Maps Using PCR/OLA 
Deborah A. Nickerson and Pui-Yan Kwok 

Multiplex Mapping of Human cDNAs 
William C. Nierman, Donna R. Maglott, and Scott Durkin 

Physical Mapping in Preparation for DNA Sequencing 
Andreas Gnirke, Regina Lim, Gane Wong, Jun Yu, Roger Bumgarner, and Maynard Olson 

Construction of a Genetic Map Across Chromosome 21 
Elaine A. Ostrander 

Integrated Physical Mapping of Human cDNAs 
Mihael H. Polymeropoulos 

Sequence-Tagged Sites for Human Chromosome 19 cDNAs 
Michael J. Siciliano and Anthony V. Carrano 

cDNA/STS Map of the Human Genome: Methods Development and Applications Using Brain cDNAs 
James M. Sikela, Akbar S. Khan, Arto K.Orpana, Andrea S. Wilcox, Janet A. Hopkins, and Tamara J. Stevens 

Physical Structure of Human Chromosome 21 
Cassandra L. Smith, Denan Wang, Kaoru Yoshida, Jesus Sainz, Carita Fockler, and Meire Bremer 

Physical Mapping of Human Chromosome 16 
David F. Callen, Sinoula Apostolou, Elizabeth Baker, Helen Kozman, Sharon A. Lane, Julie Nancarrow, Hilary A. Phillips, Scott A.Whitmore, Norman A. Doggett, John C. Mulley, 
Robert I. Richards, and Grant R. Sutherland 

Chromosome Mapping by FISH to Interphase Nuclei 
Barbara J. Trask 

Flow Karyotyping and Flow Instrumentation Development 
Ger vanden Engh and Barbara Trask 

Isolation of Specific Human Telomeric Clones by Homologous Recombination and YAC Rescue 
Geoffrey Wahl and Linnea Brody 

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Informatics 

*A Method for Direct Sequencing of Diploid Genomes on Oligonucleotide Arrays: Theoretical Analysis and Computer Modeling 
Alexander B. Chetverin 

Sampling-Based Methods for the Estimation of DNA Sequence Accuracy 
Gary Churchill and Betty Lazareva 

Computer-Aided Genome Map Assembly with SIGMA (System for Integrated Genome Map Assembly) 
Michael J. Cinkosky, Michael A. Bridgers, William M. Barber, Mohamad Ijadi, and James W. Fickett 

Informatics for the Sequencing by Hybridization Project 
Aleksandar Milosavljevic and Radomir Crkvenjakov 

Sequencing by Hybridization Algorithms and Computational Tools 
Radoje Drmanac, Ivan Labat, and Nick Stavropoulos 

HGIR: Information Management for a Growing Map 
James W. Fickett, Michael J. Cinkosky, Michael A. Bridgers, HenryT. Brown, Christian Burks, Philip E. Hempfner, Tran N. Lai, Debra Nelson, Robert M. Pecherer, Doug Sorenson, 
Peichen H. Sgro, Robert D. Sutherland, Charles D. Troup, and Bonnie C. Yantis 

Identification of Genes in Anonymous DNA Sequences 
Christopher A. Fields and Carol A. Soderlund 

Algorithms in Support of the Human Genome Project 
Dan Gusfield, Jim Knight, Kevin Murphy, Paul Stelling, Lushen Wang, Archie Cobbs, Paul Horton, Richard Karp, and Gene Lawler 

BISP: VLSI Solutions to Sequence-Comparison Problems 
Tim Hunkapiller, Leroy Hood, Ed Chen, and Michael Waterman 

Physical Mapping of DNA Molecules 
Richard M. Karp 

BIOSCI Electronic Newsgroup Network for the Biological Sciences 
David Kristofferson  

Multiple Alignment and Homolog Sequence Database Compilation 
Hwa A. Lim 

Applying Machine Learning Techniques to DNA Sequence Analysis 
Jude W. Shavlik, Michiel O. Noordewier, Geoffrey Towell, Mark Craven, Andrew Whitsitt, Kevin Cherkauer, and Lorien Pratt 

New Approaches to Recognizing Functional Domains in Biological Sequences 
Gary D. Stormo 


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ELSI 

Protecting Genetic Privacy by Regulating the Collection, Analysis, Use, and Storage of DNA and Information Obtained from DNA Analysis 
George J. Annas, Leonard H. Glantz, and Patricia A. Roche 

"The Secret of Life" 
Paula Apsell and Graham Chedd 

Genome Technology and Its Implications: A Hands-On Workshop for Educators 
Diane Baker and Paula Gregory 

Predicting Future Disease: Issues in the Development, Application, and Use of Tests for Genetic Disorders 
Ruth E. Bulger and Jane E. Fullarton 

HUGO International Yearbook: Genetics, Ethics, Law, and Society (GELS) 
Alex Capron and Bartha Knoppers 

The Human Genome: Science and the Social Consequences; Interactive Exhibits and Programs on Genetics and the Human Genome 
Charles C. Carlson 

International Conference Working Group: The Social Costs and Medical Benefits of Human Genetic Information 
Betsy Fader 

"Medicine at the Crossroads" 
George Page and Stefan Moore 

Pilot Senior Research Fellowship Program: Bioethical Issues in Molecular Genetics 
Declan Murphy and Claudette Cyr Friedman 

Studies of Genetic Discrimination 
Marvin Natowicz 

DNA Banking and DNA Data Banking: Legal, Ethical, and Public Policy Issues 
Philip Reilly 

Mechanical Interactive Exhibits on Biotechnology 
Elizabeth Sharpe 

Impact of Technology Derived from the Human Genome Project on Genetic Testing, Screening, and Counseling: Cultural, Ethical, and Legal Issues 
Ralph W. Trottier, Lee A. Crandall, David Phoenix, Mwalimu Imara, and RayE. Mosley 

Social Science Concepts and Studies of Privacy: A Comprehensive Inventory and Analysis for Considering Privacy, Confidentiality, and Access Issues in the Use of Genetic Tests and Applications of Genetic Data 
Alan F. Westin 

Human Genetics and Genome Analysis: A Practical Workshop for Public Policymakers and Opinion Leaders 
Jan Witkowski, David A. Micklos, and Margaret Henderson 


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SBIR Phase I  

A Graphical Ad Hoc Query Interface Capable of Accessing Heterogenous Public Genome Databases 
J. Clarke Anderson 

Techniques for Screening Large-Insert Libraries 
Saika Aytay 

Interactive DNA Sequence Processing for a Microcomputer 
Wayne Dettloff and Holt Anderson 

High-Performance Searching and Pattern Recognition for Human Genome Databases 
Douglas J. Eadline 

Estimating, Encoding, and Using Uncertainties in Sequence Data 
John R. Hartman  

Low-Cost Massively Parallel Neurocomputing for Pattern Recognition in Macromolecular Sequences 
John R. Hartman 

Electrophoretic Separation of DNA Fragments in Ultrathin Planar-Format Linear Polyacrylamide 
Michael T. MacDonell and Darlene B. Roszak 

An Acoustic Plate Mode DNA Biosensor 
Douglas J. McAllister 

Piezoelectric Biosensor Using Peptide Nucleic Acids for Triplex Capture 
Douglas McAllister 

Pedigree Software for the Presentation of Human Genome Information for Genetic Education and Counseling 
Charles L. Manske 

A High-Spatial-Resolution Spectrograph for DNA Sequencing 
Cathy D. Newman 

Nonradioactive Detection Systems Based on Enzyme-Fragment Complementation 
Peter Richterich 

Separation Media for DNA Sequencing 
David S. Soane and Herbert H. Hooper 


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SBIR Phase II  

Increased Speed in DNA Sequencing by Utilizing LARIS and SIRIS to Localize Multiple Stable IsotopeLabeled Fragments 
Heinrich F. Arlinghaus  

Rapid, High-Throughput DNA Sequencing Using Confocal Fluorescence Imaging of Capillary Arrays 
David L. Barker and Jay Flatley 

Spatially Defined Oligonucleotide Arrays 
Stephen P.A. Fodor 

Site-Specific Endonucleases for Human Genome Mapping 
George Golumbeski, Kimberly Knoche, Susanne Selman, Tim Hartnett, Lydia Hung, and Peter Bayne 

High-Performance DNA and Protein Sequence Analysis on a Low-Cost Parallel-Processor Array 
John R. Hartman and David L. Solomon 

Chemiluminescent Multiprimed DNA Sequencing 
Chris S. Martin, Corinne E.M. Olesen, and 
Irena Bronstein 

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Note:  The proceedings of the 1997 DOE Human Genome Program Contractor-Grantee Workshop VI, which include updated research abstracts, can be found at:  
http://www.ornl.gov/hgmis/publicat/97santa/santafe.shtml