Podell, Sheila, Gaasterland, Terry, Allen, Eric E
Abstract Background The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete...
Computational prediction and experimental validation of Ciona intestinalismicroRNA genes (2007)
Norden-Krichmar, Trina M, Holtz, Janette, Pasquinelli, Amy E, Gaasterland, Terry
Abstract Background This study reports the first collection of validated microRNA genes in the sea squirt, Ciona intestinalis . MicroRNAs are processed from hairpin precursors to ~22 nucleotide RNAs...
DarkHorse: a method for genome-wide prediction of horizontal gene transfer (2007)
Podell, Sheila, Gaasterland, Terry
Abstract A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally...
Dorr, Bonnie, Gaasterland, Terry
This document describes the information used for summarization-inspired temporal-relation extraction [Dorr and Gaasterland, 2007]. We present a set of tense/aspect extraction templates that are...
A computational investigation of kinetoplastid trans-splicing (2005)
Gopal, Shuba, Awadalla, Saria, Gaasterland, Terry, Cross, George AM
Abstract Trans -splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy...
A computational investigation of kinetoplastid trans-splicing (2005)
Gopal, Shuba, Awadalla, Saria, Gaasterland, Terry, Cross, George
Article may be found at: http://genomebiology.com/2005/6/11/r95
A computational investigation of kinetoplastid trans-splicing (2005)
Gopal, Shuba, Awadalla, Saria, Gaasterland, Terry, Cross, George
Article may be found at: http://genomebiology.com/2005/6/11/r95
Special issue on data management, analysis, and mining for the life sciences (2005)
Raschid, Louiqa, Jagadish, H. V., Gaasterland, Terry
Peer Reviewed
Wang, Xiu-Jie, Gaasterland, Terry, Chua, Nam-Hai
Abstract Background Natural antisense transcripts (NAT) are a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to other transcripts. Several lines of evidence have...
Taneri, Bahar, Snyder, Ben, Novoradovsky, Alexey, Gaasterland, Terry
Abstract Background Analyzing proteins in the context of all available genome and transcript sequence data has the potential to reveal functional properties not accessible through protein sequence...
Prediction and identification of Arabidopsis thalianamicroRNAs and their mRNA targets (2004)
Wang, Xiu-Jie, Reyes, José L, Chua, Nam-Hai, Gaasterland, Terry
Abstract Background A class of eukaryotic non-coding RNAs termed microRNAs (miRNAs) interact with target mRNAs by sequence complementarity to regulate their expression. The low abundance of some...
An organism-specific method to rank predicted coding regions in Trypanosoma brucei (2003)
Gopal, Shuba, Cross, George, Gaasterland, Terry
Article may be found at: http://nar.oxfordjournals.org/cgi/reprint/31/20/5877
An organism-specific method to rank predicted coding regions in Trypanosoma brucei (2003)
Gopal, Shuba, Cross, George, Gaasterland, Terry
Article may be found at: http://nar.oxfordjournals.org/cgi/reprint/31/20/5877
Bonnie J. Dorr, Terry Gaasterland
Generating language that reflects the temporal organization of represented knowledge requires a language generation model that integrates contemporary theories of tense and aspect, temporal...
Dorr, Bonnie J., Gaasterland, Terry
Generating language that reflects the temporal organization of represented knowledge requires a language generation model that integrates contemporary theories of tense and aspect, temporal...
Dorr, Bonnie J., Gaasterland, Terry
Generating language that reflects the temporal organization of represented knowledge requires a language generation model that integrates contemporary theories of tense and aspect, temporal...
NOBUKO ARISUE, TETSUO HASHIMOTO, JENNIFER A. LEE, DOROTHY V. MOORE, PAUL GORDON, CHRISTOPH W. SENSEN, ...
The taxonomic position and phylogenetic relationships of the Pelobionta, an amitochondriate amoeboflagellate group, are not yet completely settled. To provide more information, we obtained sequences...
Functional update of the Escherichia coli K-12 genome (2001)
Serres, Margrethe H., Gopal, Shuba, Nahum, Laila A., Liang, Ping, Gaasterland, Terry, Riley, Monica
Author Posting. © 2001 Serres et al. The definitive version was published in Genome Biology 2 (2001): research0035.1–0035.7, doi:10.1186/gb-2001-2-9-research0035.
A functional update of the Escherichia coli K-12 genome (2001)
Serres, Margrethe H, Gopal, Shuba, Nahum, Laila A, Liang, Ping, Gaasterland, Terry, Riley, Monica
Abstract Background Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar...
A functional update of the Escherichia coli K-12 genome (2001)
Serres, Margrethe, Gopal, Shuba, Nahum, Laila, Liang, Ping, Gaasterland, Terry, Riley, Monica
Article may be found at: http://www.biomedcentral.com/content/pdf/gb-2001-2-9-research0035.pdf
A functional update of the Escherichia coli K-12 genome (2001)
Serres, Margrethe, Gopal, Shuba, Nahum, Laila, Liang, Ping, Gaasterland, Terry, Riley, Monica
Article may be found at: http://www.biomedcentral.com/content/pdf/gb-2001-2-9-research0035.pdf
Functional update of the Escherichia coli K-12 genome (2001)
Serres, Margrethe H., Gopal, Shuba, Nahum, Laila A., Liang, Ping, Gaasterland, Terry, Riley, Monica
Author Posting. © 2001 Serres et al. The definitive version was published in Genome Biology 2 (2001): research0035.1–0035.7, doi:10.1186/gb-2001-2-9-research0035.
Gopal, Shuba, Schroeder, Mark, Pieper, Ursula, Sczyrba, Alexander, Aytekin-Kurban, Gulriz, Bekiranov, Stefan, ...
Article may be found at: http://www.nature.com/ng/journal/v27/n3/pdf/ng0301_337.pdf
Gopal, Shuba, Schroeder, Mark, Pieper, Ursula, Sczyrba, Alexander, Aytekin-Kurban, Gulriz, Bekiranov, Stefan, ...
Article may be found at: http://www.nature.com/ng/journal/v27/n3/pdf/ng0301_337.pdf
An Experimental Distributed Deductive Database System (2000)
Claudio Robles, Jorge Lobo, Terry Gaasterland
. In this paper we describe a distributed environment for the evaluation of data intensive queries through deductive rules. The distributed database query answering system has been developed on the...
Qualified Answers That Reflect User Needs and Preferences (2000)
This paper introduces a formalism to describe the needs and preferences of database users. Because of the precise formulation of these concepts, we have found an automatic and very simple mechanism...
Processing Negation and Disjunction in Logic Programs Through Integrity Constraints (2000)
Integrity constraints were initially defined to verify the correctness of the data that is stored in a database. They were used to restrict the modifications that can be applied to a database....
Christoph W. Sensen, Robert L. Charlebois, Cynthia Chow, Ib Groth, Clausen Bruce Curtis, W. Ford, ...
The Sulfolobus solfataricus P2 genome collaborators are poised to sequence the entire 3-Mbp genome of this crenarchaeote archaeon. About 80% of the genome has been sequenced to date, with the rest of...
Genetic Sequence Analysis: The Grand Challenge (1998)
Terry Gaasterland, Ross Overbeek
B B B B B B B B B B B B B P P P P hhhhhh h % % " " ¸ ¸ @ @ @ Pi Pi Pi Pi Pi Pi Pi Gamma Gamma i i i Gamma Gamma Gamma Gamma Z Z fi fi fi fi fi i i i i Gamma Gamma Gamma Gamma X SACCHAROMYCES ZEA...
User Needs and Language Generation Issues in a Cooperative Answering System (1998)
This paper uses the following notation for a rule, a query, and a constraint: "A / B" indicates that B is a precondition for A. A query asking `Q' has the form "/ Q". An integrity constraint saying...
Relaxation as a Platform of Cooperative Answering (1998)
Terry Gaasterland, Parke Godfrey, Jack Minker
this paper, we provide a general notion and definition of query relaxation which is used to extend what is meant by "an answer to a query." We regard returning relaxed queries and their answers to...
Restricting Query Relaxation Through User Constraints (1998)
This paper describes techniques to restrict and to heuristically control relaxation of deductive database queries. The process of query relaxation provides a user with a means to automatically...
An Experimental Distributed Deductive Database System (1998)
Claudio Robles, Jorge Lobo, Terry Gaasterland
In this paper we describe a distributed environment for the evaluation of data intensive queries through deductive rules. The distributed database query answering system has been developed on the IBM...
Terry Gaasterland, Christoph W. Sensen
rom the fact that during the lifetime of a genome sequencing project, the sequence is growing and changing; the public sequence databases are also growing and changing; new and improved software...
Reconstruction of Metabolic Networks Using Incomplete Information (1998)
Terry Gaasterland, Evgeni Selkov
This paper describes an approach that uses methods for automated sequence analysis (Gaasterland et al. August 1994) and multiple databases accessed through an object+attribute view of the data (Baehr...
Using Multiple Tools for Automated Genome Interpretation in an Integrated Environment (1998)
Terry Gaasterland, Christoph Sensen
st genome projects therefore do not have the capacities to analyze the sequence that they generate completely. To address this situation we are developing a prototype for a UNIX-based integrated...
Assigning Function to CDS Through Qualified Query Answering: Beyond Alignment and Motifs (1998)
Guo-hua Chen, Terry Gaasterland, Natalia Maltsev, Jorge Lobo
In this paper, we show how to use qualitative query answering to annotate CDS-to-function relationships with confidence in the score, confidence in the tool, and confidence in the decision about the...
Cooperative Explanation in Deductive Databases (1998)
this paper, we will discuss two mechanisms to augment an initial logic formula which has been produced by the basic cooperative answering system of Gal. The first mechanism ensures that each piece of...
Qualified Answers That Reflect User Needs and Preferences (1998)
This paper introduces a formalism to describe the needs and preferences of database users. Because of the precise formulation of these concepts, we have found an automatic and very simple mechanism...
Selecting Tense, Aspect, and Connecting Words In Language Generation (1998)
Bonnie J. Dorr, Terry Gaasterland
Generating language that reflects the temporal organization of represented knowledge requires a language generation model that integrates contemporary theories of tense and aspect, temporal...
Processing Negation and Disjunction in Logic Programs Through Integrity Constraints (1998)
Integrity constraints were initially defined to verify the correctness of the data that is stored in a database. They were used to restrict the modifications that can be applied to a database....
Knowledge Base Systems - A Deductive Database Approach (1998)
Terry Gaasterland, Jack Minker, Arcot Rajasekar
This paper consists of four sections. In the next section we define our notion of what constitutes a knowledge base system and discuss how it differs from the anatomy of a conventional KBS. Section 3...
An Overview of Cooperative Answering (1998)
Terry Gaasterland, Parke Godfrey, Jack Minker
Databases and information systems are often hard to use because they do not explicitly attempt to cooperate with their users. Direct answers to database and knowledge base queries may not always be...
Terry Gaasterland, Christoph W. Sensen
es from the fact that during the lifetime of a genome sequencing project, the sequence is growing and changing; the public sequence databases are also growing and changing; new and improved software...
MAGPIE: A Responsive System for Data Collection and Analysis (1998)
Terry Gaasterland, Christoph W. Sensen
The MAGPIE system has been designed and implemented to address the data management and analysis problems that arise during the interpretation of whole microbial genomes. The system consists of a...
Using Multiple Tools for Automated Genome Interpretation in an Integrated Environment (1998)
Terry Gaasterland, Christoph Sensen
ases daily. Most genome projects therefore do not have the capacities to analyze the sequence that they generate completely. 1 To address this situation we are developing a prototype for a UNIX-based...
Selecting Tense, Aspect, and Connecting Words In Language Generation (1998)
Bonnie J. Dorr, Terry Gaasterland
Generating language that reflects the temporal organization of represented knowledge requires a language generation model that integrates contemporary theories of tense and aspect, temporal...
Relaxation as a Platform for Cooperative Answering (1998)
Terry Gaasterland, Parke Godfrey, Jack Minker
Responses to queries posed by a user of a database do not always contain the information desired. Database answers to a query, although they may be logically correct, can sometimes be misleading....
This paper describes an approach that uses methods for automated sequence analysis [GLMC94] and multiple databases accessed through an object+attribute view of the data [BDG + 92], together with...
Relaxation as a Platform for Cooperative Answering (1997)
Terry Gaasterland, Parke Godfrey, Jack Minker
Responses to queries posed by a user of a database do not always contain the information desired. Database answers to a query, although they may be logically correct, can sometimes be misleading....
The Metabolic Pathway Collection from EMP: The Enzymes and Metabolic Pathways Database (1996)
Terry Gaasterland, Igor Goryanin, Yuri Gretchkin, Natalia Maltsev, Valeri Nenashev, Ross Overbeek, ...
The Enzymes and Metabolic Pathways database (EMP) is an encoding of the contents of over 10,000 original publications on the topics of enzymology and metabolism. This large body of information has...
Using Multiple Tools for Automated Genome Interpretation in an Integrated Environment (1996)
Terry Gaasterland, Christoph Sensen
st genome projects therefore do not have the capacities to analyze the sequence that they generate completely. To address this situation we are developing a prototype for a UNIX-based integrated...
Selecting Tense, Aspect, and Connecting Words In Language Generation (1996)
Bonnie J. Dorr, Terry Gaasterland
Generating language that reflects the temporal organization of represented knowledge requires a language generation model that integrates contemporary theories of tense and aspect, temporal...
Assigning Function to CDS Through Qualified Query Answering: Beyond Alignment and Motifs (1995)
Guo-hua Chen, Terry Gaasterland, Natalia Maltsev, Jorge Lobo
In this paper, we show how to use qualitative query answering to annotate CDS-to-function relationships with confidence in the score, confidence in the tool, and confidence in the decision about the...
Assigning Function to CDS Through Qualified Query Answering: Beyond Alignment and Motifs (1995)
Guo-hua Chen, Terry Gaasterland, Natalia Maltsev, Jorge Lobo
In this paper, we show how to use qualitative query answering to annotate CDS-to-function relationships with confidence in the score, confidence in the tool, and confidence in the decision about the...
Processing Negation and Disjunction in Logic Programs Through Integrity Constraints (1995)
Integrity constraints were initially defined to verify the correctness of the data that is stored in a database. They were used to restrict the modifications that can be applied to a database....
Qualified Answers That Reflect User Needs and Preferences (1995)
This paper introduces a formalism to describe the needs and preferences of database users. Because of the precise formulation of these concepts, we have found an automatic and very simple mechanism...
An Experimental Distributed Deductive Database System (1995)
Claudio Robles, Jorge Lobo, Terry Gaasterland
. In this paper we describe a distributed environment for the evaluation of data intensive queries through deductive rules. The distributed database query answering system has been developed on the...
A Cooperative Answering System (1970)
Terry Gaasterland, Parke Godfrey, Jack Minker, Lev Novik
Introduction We seek to improve human-computer communication by enabling a computer to respond to questions in a manner that accounts for a user's misconceptions, expectations, desires, and...
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
A functional update of the Escherichia coli K-12 genome
Serres, Margrethe H, Gopal, Shuba, Nahum, Laila A, Liang, Ping, Gaasterland, Terry, Riley, Monica
Complete Sequence of a 184-Kilobase Catabolic Plasmid from Sphingomonas aromaticivorans F199†
Romine, Margaret F., Stillwell, Lisa C., Wong, Kwong-Kwok, Thurston, Sarah J., Sisk, Ellen C., Sensen, Christoph, ...
The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode...
Müller, Miklós, Lee, Jennifer A., Gordon, Paul, Gaasterland, Terry, Sensen, Christoph W.
Inorganic pyrophosphate-dependent phosphofructokinase (PPi-PFK) of the amitochondriate eukaryote Mastigamoeba balamuthi was sequenced and showed about 60% identity to PPi-PFKs from two eubacteria,...
Bapteste, Eric, Brinkmann, Henner, Lee, Jennifer A., Moore, Dorothy V., Sensen, Christoph W., Gordon, Paul, ...
The phylogenetic relationships of amoebae are poorly resolved. To address this difficult question, we have sequenced 1,280 expressed sequence tags from Mastigamoeba balamuthi and assembled a large...
Kim, Unkyu, Siegel, Rachael, Ren, Xiaodi, Gunther, Cary S., Gaasterland, Terry, Roeder, Robert G.
The tissue-specific transcriptional coactivator OCA-B is required for antigen-dependent B cell differentiation events, including germinal center formation. However, the identity of OCA-B target genes...
Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome
Zavolan, Mihaela, Van Nimwegen, Erik, Gaasterland, Terry
We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed...
An organism-specific method to rank predicted coding regions in Trypanosoma brucei
Gopal, Shuba, Cross, George A. M., Gaasterland, Terry
Genome annotation in differently evolved organisms presents challenges because the lack of sequence-based homology limits the ability to determine the function of putative coding regions. To provide...
MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region
Gaasterland, Terry, Sczyrba, Alexander, Thomas, Elizabeth, Aytekin-Kurban, Gulriz, Gordon, Paul, Sensen, Christoph W.
Our challenge in annotating the 2.91-Mb Adh region of the Drosophila melanogaster genome was to identify genetic and genomic features automatically, completely, and precisely within a 6-week period....
Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome
Ravasi, Timothy, Huber, Thomas, Zavolan, Mihaela, Forrest, Alistair, Gaasterland, Terry, Grimmond, Sean, ...
Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by...
Zavolan, Mihaela, Kondo, Shinji, Schönbach, Christian, Adachi, Jun, Hume, David A., Hayashizaki, Yoshihide, ...
We analyzed the FANTOM2 clone set of 60,770 RIKEN full-length mouse cDNA sequences and 44,122 public mRNA sequences. We developed a new computational procedure to identify and classify the forms of...
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
Wang, Xiu-Jie, Reyes, José L, Chua, Nam-Hai, Gaasterland, Terry
Using bioinformatic methods, 83 novel Arabidopsis miRNAs have been predicted. Putative target mRNAs have been identified for most of the candidate genes.
Taneri, Bahar, Snyder, Ben, Novoradovsky, Alexey, Gaasterland, Terry
Splice variants of 461 transcription factor loci were analyzed using a new database of splice variants in the mouse transcriptome, MouSDB3, providing quantitative evidence that alternative splicing...
Wang, Xiu-Jie, Gaasterland, Terry, Chua, Nam-Hai
A new computational method for predicting cis-encoded natural antisense transcripts (NATs) in Arabidopsis identified 1,340 potential NAT pairs. The expression of both sense and antisense transcripts...
A computational investigation of kinetoplastid trans-splicing
Gopal, Shuba, Awadalla, Saria, Gaasterland, Terry, Cross, George AM
A novel computational approach is presented and applied to predicting trans-splicing sites in 2 chromosomes of Leishmania major.
Prediction and Identification of Herpes Simplex Virus 1-Encoded MicroRNAs
Cui, Can, Griffiths, Anthony, Li, Guanglin, Silva, Lindsey M., Kramer, Martha F., Gaasterland, Terry, ...
MicroRNAs (miRNAs) are key regulators of gene expression in higher eukaryotes. Recently, miRNAs have been identified from viruses with double-stranded DNA genomes. To attempt to identify miRNAs...