Papers by Stanley Letovsky
Nucleic Acids Research, 1998
The Genome Database (GDB, http://www.gdb.org ) is a public repository of data on human genes, clo... more The Genome Database (GDB, http://www.gdb.org ) is a public repository of data on human genes, clones, STSs, polymorphisms and maps. GDB entries are highly cross-linked to each other, to literature citations and to entries in other databases, including the sequence databases, OMIM, and the Mouse Genome Database. Mapping data from large genome centers and smaller mapping efforts are added to GDB on an ongoing basis. The database can be searched by a variety of methods, ranging from keyword searches to complex queries. Major functionality extensions in the last year include the ongoing computation of integrated human genome maps, called Comprehensive Maps, and the use of those maps to support positional queries and graphic displays. The capabilities of the GDB map viewer (Mapview) have been extended to include map printing and the graphical display of ad hoc query results. The HUGO Nomenclature Committee continues to curate the proposed and official gene symbols and related data in collaboration with GDB. As genome research shifts its emphasis from mapping to sequencing and functional analysis, the scope of the GDB schema is being extended. We are in the process of adding representations of gene function and expression, and improving our representation of human polymorphism and mutation.
Genomics, Mar 31, 1992
Gene mapping assigns chromosomal coordinates to genetic loci based on analysis of fragmentary ord... more Gene mapping assigns chromosomal coordinates to genetic loci based on analysis of fragmentary ordering and metric data. In assembling genetic maps, geneticists use rules of inference to derive new facts about order and distance between loci from experimentally derived conclusions about order and distance. They construct comprehensive maps by merging related sets of data and resolving conflicts between them. In this article we describe software that formalizes and automates some of these rules of inference to yield a useful map construction utility called CPROP. o 1992 Academic press, I~C. 435 osss-7543/92 $3.00
Genetics, May 1, 1992
COTRANS is a program for analyzing cotransduction data. It calculates distances from pairwise cot... more COTRANS is a program for analyzing cotransduction data. It calculates distances from pairwise cotransduction frequencies, computes crossovers required to obtain each observed recombinant class, and applies rules to draw conclusions about order. The rules are based on the correlation between the frequency of the classes and the number of required crossovers for each possible ordering compatible with the distance calculations. The procedure emulates a geneticist's stepwise analysis of the data by first calculating distances, then looking for obvious three-point ordering conclusions, and finally proceeding to a complete crossover analysis. It reports results from each step of the analysis and an overall conclusion. COTRANS provides significant gains in speed and convenience over hand analysis, particularly for multipoint crosses with several recombinant classes.
Empirical Studies of Programmers Second Workshop, Dec 1, 1987
Lecture Notes in Computer Science, 1996
We present an approach for analyzing the morphology of anatomical structures of the brain, which ... more We present an approach for analyzing the morphology of anatomical structures of the brain, which uses an elastic transformati on to normalize brain images into a reference space. The properties of this transf ormation are used as a quantitative description of the size and shape of brain str uctures; inter-subject comparisons are made by comparing the transformations themselves. The utility
Lecture Notes in Computer Science, 1996
Scienti c databases are used to accession objects representing the results of scienti c inquiry, ... more Scienti c databases are used to accession objects representing the results of scienti c inquiry, such as genes and DNA sequences. These objects must have stable identi ers that can be used as references in scienti c papers and other databases. The requirement for stable object identi ers, however, con icts with the tendency of scienti c data to evolve over time. We present in this paper version management facilities that allow scienti c databases to achieve a balance between stable object identi ers and evolving data.
PLoS Biology, 2013
. These authors contributed equally to this work.
Nucleic Acids Research, 2011
COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation o... more COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids.
Nucleic Acids Research, 1996
Version 6.0 of the Human Genome Data Base introduces a number of significant improvements over pr... more Version 6.0 of the Human Genome Data Base introduces a number of significant improvements over previous releases of GDB. The most important of these are revised data representations for genes and genomic maps and a new curatorial model for the database. GDB 6.0 is the first major genomic database to provide read/write access directly to the scientific community, including capabilities for third-party annotation. The revised database can represent all major categories of genetic and physical maps, along with the underlying order and distance information used to construct them. The improved representation permits more sophisticated map queries to be posed and supports the graphical display of maps. In addition, the new GDB has a richer model for gene information, better suited for supporting cross-references to databases describing gene function, structure, products, expression and associated phenotypes.
Nucleic Acids Research, 1998
The Genome Database (GDB, http://www.gdb.org ) is a public repository of data on human genes, clo... more The Genome Database (GDB, http://www.gdb.org ) is a public repository of data on human genes, clones, STSs, polymorphisms and maps. GDB entries are highly cross-linked to each other, to literature citations and to entries in other databases, including the sequence databases, OMIM, and the Mouse Genome Database. Mapping data from large genome centers and smaller mapping efforts are added to GDB on an ongoing basis. The database can be searched by a variety of methods, ranging from keyword searches to complex queries. Major functionality extensions in the last year include the ongoing computation of integrated human genome maps, called Comprehensive Maps, and the use of those maps to support positional queries and graphic displays. The capabilities of the GDB map viewer (Mapview) have been extended to include map printing and the graphical display of ad hoc query results. The HUGO Nomenclature Committee continues to curate the proposed and official gene symbols and related data in collaboration with GDB. As genome research shifts its emphasis from mapping to sequencing and functional analysis, the scope of the GDB schema is being extended. We are in the process of adding representations of gene function and expression, and improving our representation of human polymorphism and mutation.
Nucleic Acids Research, 1992
Nucleic Acids Research, 1997
The value of the Genome Database (GDB) for the human genome research community has been greatly i... more The value of the Genome Database (GDB) for the human genome research community has been greatly increased since the release of version 6.0 last year. Thanks to the introduction of significant technical improvements, GDB has seen dramatic growth in the type and volume of information stored in the database. This article summarizes the types of data that are now available in the Genome Database, demonstrates how the database is interconnected with other biomedical resources on the World Wide Web, discusses how researchers can contribute new or updated information to the database, and describes our current efforts as well as planned improvements for the future.
... No Digital Version Available: Request from CASI. Author: Soloway, Elliot; Pinto, Jeannine; Fe... more ... No Digital Version Available: Request from CASI. Author: Soloway, Elliot; Pinto, Jeannine; Fertig, Scott; Letovsky, Stan; Lampert, Robin; Littman, David; Ewing, Ken. Collection: NASA. NASA Center: NASA (Unspecified Center). Publication Date: Dec 1, 1986. Publication Year: 1986 ...
Journal of Systems and Software, 1987
This paper reports on an empirical study of the cognitive processes involved in program comprehen... more This paper reports on an empirical study of the cognitive processes involved in program comprehension. Verbal protocols were gathered from professional programmers as they were engaged in a program-understanding task. Based on analysis of these protocols, several types of interesting cognitive events were identified. These include asking questions and conjecturing facts about the code. We describe these event types and use them to derive a computational model of the programmers' mental processes.
Journal of Computer Assisted Tomography, 1996
A new technique for analyzing the morphology of the corpus callosum is presented, and it is appli... more A new technique for analyzing the morphology of the corpus callosum is presented, and it is applied to a group of elderly subjects. The proposed approach normalizes subject data into the Talairach space using an elastic deformation transformation. The properties of this transformation are used as a quantitative description of the callosal shape with respect to the Talairach atlas, which is treated as a standard. In particular, a deformation function measures the enlargement/shrinkage associated with this elastic deformation. Intersubject comparisons are made by comparing deformation functions. This technique was applied to eight male and eight female subjects. Based on the average deformation functions of each group, the posterior region of the female corpus callosum was found to be larger than its corresponding region in the males. The average callosal shape of each group was also found, demonstrating visually the callosal shape differences between the two groups in this sample. The proposed methodology utilizes the full resolution of the data, rather than relying on global descriptions such as area measurements. The application of this methodology to an elderly group indicated sex-related differences in the callosal shape and size.
Journal of Computational Biology, 2010
The rapid adoption of high-throughput next generation sequence data in biological research is pre... more The rapid adoption of high-throughput next generation sequence data in biological research is presenting a major challenge for sequence alignment tools-specifically, the efficient alignment of vast amounts of short reads to large references in the presence of differences arising from sequencing errors and biological sequence variations. To address this challenge, we developed a short read aligner for high-throughput sequencer data that is tolerant of errors or mutations of all types-namely, substitutions, deletions, and insertions. The aligner utilizes a multi-stage approach in which template-based indexing is used to identify candidate regions for alignment with dynamic programming. A template is a pair of gapped seeds, with one used with the read and one used with the reference. In this article, we focus on the development of template families that yield error-tolerant indexing up to a given error-budget. A general algorithm for finding those families is presented, and a recursive construction that creates families with higher error tolerance from ones with a lower error tolerance is developed.
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Papers by Stanley Letovsky