ARTICLE An STS-Based Map of the Human Genome (2008)
Thomas J. Hudson, Lincoln D. Stein, Sebastian S. Gerety, Junli Ma, Andrew B. Castle, ...
A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases. The project involved assembly of a radiation hybrid...
C++-Based Object-Oriented DBMS (2008)
Nathan Goodman, Steve Rozen, Lincoln Stein
MapBase is a laboratory information system that has been supporting a high-throughput genome-mapping operation for the last three years. We chose to build MapBase around a C++-based OODBMS because,...
Edgar H. Sibley, Steve Rozen, Dennis Shasha
Developers of a Wall Street financial application were able to exploit a relational DBMS to advantage for some data management tasks (the good). For others, the relational system was not helpful (the...
Abstract Splicing UNIX into a Genome Mapping Laboratory (2008)
Lincoln Stein, Andre Marquis, Ert Dredge, Mary Pat Reeve, Mark Daly, Steve Rozen, ...
Research is responsible for a number of large genome mapping efforts, the scale of which create problems of data and workflow management that dictate reliance on computer support. Two years ago, when...
Steve Rozen, Bruce A. Shapiro, Dennis Shasha, Zhiyuan Wang, Maisheng Yin
Key words: algorithms, consensus sequence, pattern matching, tools for computational biology, DNA sequence recognition
Lincoln Stein, Andre Marquis, Ert Dredge, Mary Pat Reeve, Mark Daly, Steve Rozen, ...
Research is responsible for a number of large genome mapping efforts, the scale of which create problems of data and workflow management that dictate reliance on computer support. Two years ago, when...
High mutation rates have driven extensive structural among human Y chromosomes (2006)
Laura G Brown, Cindy M Korver, Julian Lange, Janet D Marszalek, Tatyana Pyntikova, ...
Although much structural polymorphism in the human genome has been catalogued 1–5, the kinetics of underlying change remain largely unexplored. Because human Y chromosomes are clonally inherited,...
Sun, Chao, Skaletsky, Helen, Rozen, Steve, Gromoll, Jörg, Nieschlag, Eberhard, Oates, Robert, ...
Deletion of any of three regions of the human Y chromosome results in spermatogenic failure and infertility. We previously sequenced one of these regions, azoospermia factor a (AZFa) and found that...
New techniques for DNA sequence classification (1999)
Steve Rozen, Bruce A. Shapiro, Dennis Shasha, Zhiyuan Wang, Maisheng Yin
DNA sequence classification is the activity of determining whether or not an unlabeled sequence S belongs to an existing class C. This paper proposes two new techniques for DNA sequence...
A High-Density Integrated Genetic Linkage and Radiation Hybrid Map of the Laboratory Rat (1999)
Steen, Robert G., Kwitek-Black, Anne E., Glenn, Christopher, Gullings-Handley, Jo, Van Etten, William, Atkinson, O. Scott, ...
A High-Density Integrated Genetic Linkage and Radiation Hybrid Map of the Laboratory Rat (1999)
Steen, Robert G., Kwitek-Black, Anne E., Glenn, Christopher, Gullings-Handley, Jo, Van Etten, William, Atkinson, O. Scott, ...
A Map of 75 Human Ribosomal Protein Genes (1998)
Kenmochi, Naoya, Kawaguchi, Tomoko, Rozen, Steve, Davis, Elizabeth, Goodman, Nathan, Hudson, Thomas J., ...
LabFlow-1: a database benchmark for high-throughput workflow management (1996)
Anthony Bonner, Adel Shru, Steve Rozen
Abstract. Work ow management is a ubiquitous task faced by many organizations, and entails the coordination of various activities. This coordination is increasingly carried out by software systems...
LabFlow-1: a Database Benchmark for High-Throughput Workflow Management (1996)
Anthony Bonner Bonner, Adel Shrufi, Steve Rozen
. Workflow management is a ubiquitous task faced by many organizations, and entails the coordination of various activities. This coordination is increasingly carried out by software systems called...
Database Requirements for Workflow Management in a High-Throughput Genome Laboratory (1996)
Anthony J. Bonner, Adel Shrufi, Steve Rozen
This paper discusses the requirements of this DBMS. The discussion centers on LabFlow-1 [3, 2], a recently developed database benchmark for highthroughput workflow management systems (WFMSs), i:e:,...
LabFlow-1: a Database Benchmark for High-Throughput Workflow Management (1996)
Anthony Bonner, Adel Shrufi, Steve Rozen
. Workflow management is a ubiquitous task faced by many organizations, and entails the coordination of various activities. This coordination is increasingly carried out by software systems called...
Database requirements for work ow managment in a high-thoroughput genome laboratory (1996)
Anthony J. Bonner, Adel Shru, Steve Rozen
This and related papers are available at the following web page:
Database- and Workflow-Management Challenges Posed by the Human Genome Project (1995)
Nathan Goodman, Steve Rozen, Lincoln Stein
The human genome project depends intensively on electronic collection and dissemination of information. In this respect, it arguably foreshadows much future scientific research. Its dependence on...
LabFlow-1: a Database Benchmark for High-Throughput Workflow Management (1995)
Anthony J. Bonner, Adel Shrufi, Steve Rozen, Ms A
Workflow management is a ubiquitous task faced by many organizations, and entails the coordination of various activities. This coordination is increasingly carried out by software systems called...
Benchmarking Object-Oriented DBMSs for Workflow Management (1995)
Anthony Bonner, Adel Shrufi, Steve Rozen
This paper addresses the performance requirements of this DBMS, and examines the ability of object database technology to meet these requirements. The LabFlow-1 benchmark concisely describes the...
LabBase: A Database to Manage Laboratory Data in a Large-Scale Genome-Mapping Project (1995)
Steve Rozen, Lincoln Stein, Nathan Goodman
The central task of managing laboratory data is keeping track of laboratory samples, the experimental steps performed on them, and the results of these experiments. This task engenders several...
Managing Laboratory Workflow With Labbase (1995)
Lincoln Stein, Steve Rozen, Nathan Goodman
We have designed and implemented a system for managing workflow in large semiautomated laboratory projects. This system sits on top of LabBase, a database management system specialized for...
Workflow Management Software for Genome-Laboratory Informatics (1995)
Steve Rozen, Genome-laboratory Informatics, Nathan Goodman, Steve Rozen, Lincoln D. Stein
y automation becomes the modus operandi for genome laboratories, a software component whose primary function is workflow management will become a critical factor in managing operational complexity....
Benchmarking Object-Oriented DBMSs for Workflow Management (1995)
Anthony J. Bonner, Adel Shrufi, Steve Rozen
This paper addresses the performance requirements of this DBMS, and examines the ability of object database technology to meet these requirements. The LabFlow-1 benchmark concisely describes the...
Genome-map: Real-world test data and queries for logic databases (1995)
Steve Rozen, Mark J. Daly, Mary-pat Reeve, Nathan Goodman
In the process of trying to nd a logic query language to use with our genomemapping database we extracted test data from our database and developed a set of representative queries over the data. We...
Benchmarking object-oriented DBMSs for workflow management (1995)
Anthony J. Bonner, Adel Shru, Steve Rozen
This and related papers are available at the following web page:
LabBase User Manual, Version 1.0 (1994)
Steve Rozen, Lincoln Stein, Nathan Goodman
LabBase is a generic database management system for implementation of laboratory information systems. This manual constitutes both a tutorial introduction to and a reference manual for LabBase. 1...
Genome Informatics Systems, Nathan Goodman, Steve Rozen
This document and others on OPM available at URL
Building a Laboratory Information System around a C++-Based Object-Oriented DBMS (1994)
Nathan Goodman, Steve Rozen, Lincoln Stein
MapBase is a laboratory information system that has been supporting a high-throughput genome-mapping operation for the last three years. We chose to build MapBase around a C++-based OODBMS because,...
Requirements For A Deductive Query Language In The Mapbase Genome-Mapping Database (1994)
Nathan Goodman, Steve Rozen And Lincoln Stein, Steve Rozen, Lincoln Stein
MapBase is a database that stores information about short DNA sequences called markers and about the positions of markers along the chromosomes of an organism. It also stores information about...
Constructing a Domain-Specific DBMS Using a Persistent Object System (1994)
Steve Rozen, Lincoln Stein, Nathan Goodman
e considerations that led to this choice, and we describe LabBase's design and our experiences implementing it. We use our experiences with LabBase to illuminate the advantages and disadvantages...
Splicing UNIX into a Genome Mapping Laboratory (1994)
Lincoln Stein, Andre Marquis, Ert Dredge, Mary Pat Reeve, Mark Daly, Steve Rozen, ...
The Whitehead Institute/MIT Center for Genome Research is responsible for a number of large genome mapping efforts, the scale of which create problems of data and workflow management that dictate...
A Glimpse at the DBMS Challenges Posed by the Human Genome Project (1994)
Nathan Goodman, Steve Rozen, Lincoln Stein
This paper provides a brief overview of database requirements in the genome field, and explains some of the subtleties that make it difficult to use standard database technology. We begin in Section...
Constructing a domain-speci c DBMS using a persistent object system (1994)
Steve Rozen, Lincoln Stein, Nathan Goodman
Constructing a light-weight domain-speci c database management system (DBMS) is one way \...to design applications that e ectively exploit...persistent technology". We have implemented a...
AFreely Sharable Database Management System Designed for Use in Component-Based, Modular (1994)
Genome Informatics Systems, Nathan Goodman, Steve Rozen
To produce and disseminate a freely sharable, domain-speci c database management system (DBMS) suitable for use as a component of a genome informatics system. Over the past three-and-a-half years we...
Automating physical database design : an extensible approach / (1993)
Thesis (Ph.D.)--New York University, Graduate School of Arts and Sciences, 1993.
Automating Physical Database Design: An Extensible Approach (1993)
In a high-level query language such as SQL, queries yield the same result no matter how the logical schema is physically implemented. Nevertheless, a query's cost can vary by orders of magnitude...
Global Optimization for a Coagulating Code Generator: Final Technical Report* (1991)
Michael Karr, Walter G. Morris, Steve Rozen
The Coagulating Code Generator (CCG) is designed to generate highly efficient code in terms of instruction selection, register usage, and procedure calls. These are not the only determinants of code...
Valter G. L'\orris, Steve Rozen
£-L is an experimental software engineering environment and a programming language. An E-L program can be translated into executable code for the MC68020 by means of a Coagulating Code Generator...
Repping, Sjoerd, Skaletsky, Helen, Lange, Julian, Silber, Sherman, Van der Veen, Fulco, Oates, Robert D., ...
It is widely believed that at least three nonoverlapping regions of the human Y chromosome—AZFa, AZFb, and AZFc (“azoospermia factors” a, b, and c)—are essential for normal spermatogenesis....