Bloom, Joshua S, Khan, Zia, Kruglyak, Leonid, Singh, Mona, Caudy, Amy A
Abstract Background High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring...
A Cost-Aggregating Integer Linear Program for Motif Finding (2009)
Carl Kingsford, Elena Zaslavsky, Mona Singh
Abstract. In the motif finding problem one seeks a set of mutually similar subsequences within a collection of biological sequences. This is an important and widely-studied problem, as such shared...
Applying Mixed-Initiative Interaction in User Interfaces for Communicators (2009)
Communicators are small handheld devices that combine the features of PDAs and palmtop computers with those of telephones. They are widely believed to be the next big wave of devices to gain market...
Yanover, Chen, Singh, Mona, Zaslavsky, Elena
Motivation: Identifying regulatory elements in genomic sequences is a key component in understanding the control of gene expression. Computationally, this problem is often addressed by motif...
Khan, Zia, Bloom, Joshua S., Kruglyak, Leonid, Singh, Mona
Motivation: High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences...
Predicting DNA recognition by Cys2His2 zinc finger proteins (2009)
Persikov, Anton V., Osada, Robert, Singh, Mona
Motivation: Cys2His2 zinc finger (ZF) proteins represent the largest class of eukaryotic transcription factors. Their modular structure and well-conserved protein-DNA interface allow the development...
Methods A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes (2008)
Kam Jim, Kush Parmar, Mona Singh, Saeed Tavazoie
We present a computational method for de novo identification of gene function using only cross-organismal distribution of phenotypic traits. Our approach assumes that proteins necessary for a set of...
Piecemeal Graph Exploration by a Mobile Robot (2008)
Baruch Awerbuchy, Margrit Betke, Ronald L. Rivest, Mona Singh
Abstract We study how a mobile robot can piecemeal learn an unknown environment. The robot's goal is to learn a complete map of its environment, while satisfying the constraint that it must...
NetGrep: fast network schema searches in interactomes (2008)
Banks, Eric, Nabieva, Elena, Peterson, Ryan, Singh, Mona
Abstract NetGrep ( http://genomics.princeton.edu/singhlab/netgrep/ ) is a system for searching protein interaction networks for matches to user-supplied 'network schemas'. Each schema consists of...
Paul Jose Palathingal, Munindar Singh, Peng Ning, Mona Singh
System for Knowlegde Management. (Under the direction of Dr. Munindar Singh.) Social networks potentially form a huge repository of private knowledge that is unavailable on any search engine. The...
ASemidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies (2008)
Bernard Chazelle, Carl Kingsford, Mona Singh
Side chain positioning is an important subproblem of the general protein-structure-prediction problem, with applications in homology modeling and protein design. The side chain positioning problem...
Bernard Chazelle, Mona Singh, Carl Kingsford
Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a rotamer...
Predicting Protein Secondary and Supersecondary Structure (2008)
29.1 Introduction............................................ 29-1 Background • Difficulty of general protein structure prediction • A bottom-up approach 29.2 Secondary...
Abstract. The Temporal Structure of Narratives: A Semantic Approach (2008)
Computing the temporal structure of narratives is an important milestone in understanding stories and discourses. We propose structured representations for events based on their algebraic properties....
A Natural Language Interface to Information Retrieval Systems (2008)
. Increasing attention is being focused on Information Retrieval (IR) systems. Even as IR systems become more powerful, users of such systems encounter great difficulty in using them. This is because...
Organization of Physical Interactomes as Uncovered by Network Schemas (2008)
Eric Banks, Elena Nabieva, Bernard Chazelle, Mona Singh
Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning. We introduce network schemas to elucidate shared mechanisms within...
Characterization and prediction of residues determining protein functional specificity (2008)
Motivation: Within a homologous protein family, proteins may be grouped into subtypes that share specific functions that are not common to the entire family. Often, the amino acids present in a small...
Piecemeal Graph Exploration byaMobile Robot (2007)
Baruchawerbuch Margrit Betke, Baruch Awerbuch, Margrit Betke, Ronald L. Rivest, Mona Singh
We study how a mobile robot can piecemeal learn an unknown environment. The robot's goal is to learn a complete map of its environment, while satisfying the constraint that it must return every...
Piecemeal Graph Exploration by a Mobile Robot (Extended Abstract) (2007)
Baruch Awerbuch, Margrit Betke, Ronald L. Rivest, Mona Singh
) Baruch Awerbuch y Margrit Betke Ronald L. Rivest Mona Singh Laboratory for Computer Science Massachusetts Institute of Technology Cambridge, MA 02139 Abstract We study the problem of learning a...
The Role of Semantic Context in the Temporal Interpretation of Events (2007)
The temporal interpretation of utterances is crucial to many applications of natural language understanding. The interpretation of utterances clearly depends on both the linguistics or semantic...
Thematic Roles, Word Order, and Definiteness (2007)
this paper, I present rules that unambiguously determine the definiteness of bare NPs in the article-less language, Hindi. These rules involve the thematic roles and the syntactic positions of the...
Spoken Dialogue Interfaces for Patient Care (2007)
Mona Singh, James Barnett, Munindar P. Singh
There is an increasing interest in containing the costs of healthcare without having to compromise its quality. Patient care refers to the component of healthcare that deals with patients prior to,...
Designing a Portable Spoken Dialogue System (2007)
. Spoken dialogue systems enable the construction of complex applications involving extended, meaningful interactions with users. Building an effective, generic dialogue system requires techniques...
Piecemeal Graph Exploration by aMobile Robot (2007)
Baruch Awerbuch, Margrit Betke, Ronald L. Rivest, Mona Singh
We study how a mobile robot can piecemeal learn an unknown environment. The robot's goal is to learn a complete map of its environment, while satisfying the constraint that it must return every...
Ronald L. Rivest, Frederic R. Morgenthaler, Mona Singh, Mona Singh
of Philosophy We consider three problems in machine learning: ffl concept learning in the PAC model ffl mobile robot environment learning ffl learning-based approaches to protein structure prediction...
The Temporal Structure of Narratives: A Semantic Approach (2007)
. Computing the temporal structure of narratives is an important milestone in understanding stories and discourses. We propose structured representations for events based on their algebraic...
Predicting functionally important residues from sequence conservation (2007)
Motivation: All residues in a protein are not equally important. Some are essential for the proper structure and function of the protein, whereas others can be readily replaced. Conservation analysis...
A combinatorial optimization approach for diverse motif finding applications (2006)
Abstract Background Discovering approximately repeated patterns, or motifs, in biological sequences is an important and widely-studied problem in computational molecular biology. Most frequently,...
Nabieva, Elena, Jim, Kam, Agarwal, Amit, Chazelle, Bernard, Singh, Mona
Motivation: Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its...
Predicting specificity in bZIP coiled-coil protein interactions (2004)
Fong, Jessica H, Keating, Amy E, Singh, Mona
Abstract We present a method for predicting protein-protein interactions mediated by the coiled-coil motif. When tested on interactions between nearly all human and yeast bZIP proteins, our method...
Carleton L. Kingsford, Bernard Chazelle, Mona Singh
Motivation: Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a...
Osada, Robert, Zaslavsky, Elena, Singh, Mona
Motivation: An important step in unravelling the transcriptional regulatory network of an organism is to identify, for each transcription factor, all of its DNA binding sites. Several approaches are...
Osada, Robert, Zaslavsky, Elena, Singh, Mona
Motivation: An important step in unravelling the transcriptional regulatory network of an organism is to identify, for each transcription factor, all of its DNA binding sites. Several approaches are...
Solving and analyzing side-chain positioning problems using linear and integer programming (2004)
Kingsford, Carleton L., Chazelle, Bernard, Singh, Mona
Motivation: Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a...
A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes (2004)
Jim, Kam, Parmar, Kush, Singh, Mona, Tavazoie, Saeed
We present a computational method for de novo identification of gene function using only cross-organismal distribution of phenotypic traits. Our approach assumes that proteins necessary for a set of...
Osada, Robert, Zaslavsky, Elena, Singh, Mona
Motivation: An important step in unravelling the transcriptional regulatory network of an organism is to identify, for each transcription factor, all of its DNA binding sites. Several approaches are...
Solving and analyzing side-chain positioning problems using linear and integer programming (2004)
Kingsford, Carleton L., Chazelle, Bernard, Singh, Mona
Motivation: Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a...
Brooks, Dawn J., Fresco, Jacques R., Lesk, Arthur M., Singh, Mona
To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral...
Towards predicting coiledcoil protein interactions (2001)
Protein-protein interactions play a central role in many cellular functions, and as whole-genome data accumulates, computational methods for predicting these interactions become increasingly...
Sequence Comparison: Global Sequence Alignments (1999)
Mona Singh, Lecturer Mona Singh, Scribe Robert Phillips
Introduction In comparisons of biomolecular sequences (i.e., those of DNA, RNA, and protein), regions of high sequence similarity often indicate signicant functional or structural similarity as well....
Piecemeal Learning of an Unknown Environment, (1998)
Betke, Margrit, Rivest, Ronald L., Singh, Mona
We introduce a new learning problem: leaning a graph by piecemeal search, in which the learner must return every so often to its starting point (for refueling, say). We present two linear-time...
Enhancing Conversational Moves for Portable Dialogue Systems (1997)
Mona Singh, James H. Barnett, Munindar P. Singh
Spoken dialogue interfaces are finding usage in a number of important applications. Conversational moves are the atoms of the interaction between a user and the computer system. We are building a...
Automating Spoken Dialogue Systems (1997)
Mona Singh, James Barnett, Munindar P. Singh
. Spoken dialogue interfaces apply in a number of applications. Engaging in meaningful conversation presupposes the ability to recognize and generate different conversational moves, and to adaptively...
On the Temporal Structure of Events (1997)
The temporal interpretation of events is crucial to many applications of natural language understanding. Interpreting events as described in individual utterances and discourse requires both semantic...
Automating spoken dialogue systems (1997)
Mona Singh, James Barnett, Munindar P. Singh
Abstract. Spoken dialogue interfaces apply in a number of applications. Engaging in meaningful conversation presupposes the ability to recognize and generate di erent conversational moves, and to...
Learning algorithms with applications to robot navigation and protein folding / (1995)
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Learning algorithms with applications to robot navigation and protein folding (1995)
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Learning algorithms with applications to robot navigation and protein folding (1995)
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Piecemeal graph exploration by a mobile robot (1995)
Baruch Awerbuch, Margrit Betke, Ronald L. Rivest, Mona Singh
We study how a mobile robot can piecemeal learn an unknown environment. The robot's goal is to learn a complete map of its environment, while satisfying the constraint that it must return every...
Piecemeal graph exploration by a mobile robot (1995)
Baruch Awerbuch, Margrit Betke, Ronald L. Rivest, Mona Singh
We study how a mobile robot can learn an unknown environment in a piecemeal manner. The robot's goal is to learn a complete map of its environment, while satisfying the constraint that it must...
Piecemeal Learning of an Unknown Environment (1995)
Margrit Betke, Ronald L. Rivest, Mona Singh
We introduce a new learning problem: learning a graph by piecemeal search, in which the learner must return every so often to its starting point (for refueling, say). We present two linear-time...
Piecemeal graph exploration by a mobile robot (1995)
Baruch Awerbuch, Margrit Betke, Ronald L. Rivest, Mona Singh
We study how a mobile robot can learn an unknown environment in a piecemeal manner. The robot's goal is to learn a complete map of its environment, while satisfying the constraint that it must...
Piecemeal Learning of an Unknown Environment (1994)
Betke, Margrit, Rivest, Ronald L., Singh, Mona
We introduce a new learning problem: learning a graph by piecemeal search, in which the learner must return every so often to its starting point (for refueling, say). We present two linear-time...
Piecemeal Learning of an Unknown Environment (1994)
Betke, Margrit, Rivest, Ronald L., Singh, Mona
We introduce a new learning problem: learning a graph by piecemeal search, in which the learner must return every so often to its starting point (for refueling, say). We present two linear-time...
Machine Learning - Lecture 26 (1994)
Introduction to the piecemeal learning problem ffl Linear time algorithm for piecemeal learning of city-block graphs ffl Nearly linear time algorithm for piecemeal learning of general graphs 26.2...
Piecemeal learning of an unknown environment (1993)
Margrit Betke, Ronald L. Rivest, Mona Singh
This publication can be retrieved by anonymous ftp to publications.ai.mit.edu. We introduce a new learning problem: learning a graph by piecemeal search, inwhich the learner must return every so...
Piecemeal learning of an unknown environment (1993)
Ronald L. Rivest, Mona Singh, Sally Goldman
Abstract. We introduce a new learning problem: learning a graph by piecemeal search, in which the learner must return every so often to its starting point (for refueling, say). We present two...
Piecemeal learning of an unknown environment (1993)
Ronald L. Rivest, Mona Singh, Sally Goldman
Abstract. Weintroduce a new learning problem: learning a graph by piecemeal search, in which the learner must return every so often to its starting point (for refueling, say). We present two...
Computing the temporal structure of events in natural language (1992)
Abstract. Akey step in Natural Language Processing is creating representations of sentences and discourses. Sentences describe states and events. Thus a crucial component of semantically interpreting...
Computing the Temporal Structure of Events in Natural Language (1992)
. A key step in Natural Language Processing is creating representations of sentences and discourses. Sentences describe states and events. Thus a crucial component of semantically interpreting them...
Computing the Temporal Structure of Events in Natural Language (1992)
. A key step in Natural Language Processing is creating representations of sentences and discourses. Sentences describe states and events. Thus a crucial component of semantically interpreting them...
An Event-Based Analysis of Causatives (1992)
this paper I present an analysis of morphological causatives that is motivated by considerations of Dowty's recent theory of Proto-Roles, as also by philosophical action theory. The proposed...
Computing the temporal structure of events in natural language (1992)
Abstract. Akey step in Natural Language Processing is creating representations of sentences and discourses. Sentences describe states and events. Thus a crucial component of semantically interpreting...
Hydrogen transfer mediated by organoaluminum and nickel(0) compounds / (1991)
Thesis (Ph. D.)--State University of New York at Binghamton, Dept. of Chemistry, 1992.
The Perfective Aspect: An Algebraic Analysis (1991)
this paper, I discuss the neutral perfective in the context of Hindi. As we have seen, the perfective in Hindi is intimately connected with the phenomenon of compound verbs, which I will now describe...
The Perfective Paradox: Or How to Eat Your Cake and Have it Too (1991)
this paper, I discuss the perfective paradox in the context of Hindi. The perfective in Hindi is intimately connected with the phenomenon of
The Aspectual Content Of Compound Verbs (1990)
this paper I look at the interaction of the perfective aspect with the four situation types. The importance of this interaction is explained in the following sections. Examples are cited from Hindi,
Structural characterization of the human respiratory syncytial virus fusion protein core
Zhao, Xun, Singh, Mona, Malashkevich, Vladimir N., Kim, Peter S.
Human respiratory syncytial virus (HRSV) is a major cause of a number of severe respiratory diseases, including bronchiolitis and pneumonia, in infants and young children. The HRSV F protein, a...
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains
Singh, Mona, Berger, Bonnie, Kim, Peter S., Berger, James M., Cochran, Andrea G.
The recent rapid growth of protein sequence databases is outpacing the capacity of researchers to biochemically and structurally characterize new proteins. Accordingly, new methods for recognition of...
The trimer-of-hairpins motif in membrane fusion: Visna virus
Malashkevich, Vladimir N., Singh, Mona, Kim, Peter S.
Structural studies of viral membrane fusion proteins suggest that a “trimer-of-hairpins” motif plays a critical role in the membrane fusion process of many enveloped viruses. In this motif, a...
A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes
Jim, Kam, Parmar, Kush, Singh, Mona, Tavazoie, Saeed
We present a computational method for de novo identification of gene function using only cross-organismal distribution of phenotypic traits. Our approach assumes that proteins necessary for a set of...
Predicting specificity in bZIP coiled-coil protein interactions
Fong, Jessica H, Keating, Amy E, Singh, Mona
A method to predict interactions between coiled-coil dominas, which is based on sequence and biophysical data.
Structural characterization of the human respiratory syncytial virus fusion protein core
Zhao, Xun, Singh, Mona, Malashkevich, Vladimir N., Kim, Peter S.
Human respiratory syncytial virus (HRSV) is a major cause of a number of severe respiratory diseases, including bronchiolitis and pneumonia, in infants and young children. The HRSV F protein, a...
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains
Singh, Mona, Berger, Bonnie, Kim, Peter S., Berger, James M., Cochran, Andrea G.
The recent rapid growth of protein sequence databases is outpacing the capacity of researchers to biochemically and structurally characterize new proteins. Accordingly, new methods for recognition of...
The trimer-of-hairpins motif in membrane fusion: Visna virus
Malashkevich, Vladimir N., Singh, Mona, Kim, Peter S.
Structural studies of viral membrane fusion proteins suggest that a “trimer-of-hairpins” motif plays a critical role in the membrane fusion process of many enveloped viruses. In this motif, a...
A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes
Jim, Kam, Parmar, Kush, Singh, Mona, Tavazoie, Saeed
We present a computational method for de novo identification of gene function using only cross-organismal distribution of phenotypic traits. Our approach assumes that proteins necessary for a set of...
Predicting specificity in bZIP coiled-coil protein interactions
Fong, Jessica H, Keating, Amy E, Singh, Mona
A method to predict interactions between coiled-coil dominas, which is based on sequence and biophysical data.
Organization of Physical Interactomes as Uncovered by Network Schemas
Banks, Eric, Nabieva, Elena, Chazelle, Bernard, Singh, Mona
Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning. We introduce network schemas to elucidate shared mechanisms within...
NetGrep: fast network schema searches in interactomes
Banks, Eric, Nabieva, Elena, Peterson, Ryan, Singh, Mona
NetGrep is a system for searching protein interaction networks for matches to user-supplied network schemas.
Characterization and prediction of residues determining protein functional specificity
Motivation: Within a homologous protein family, proteins may be grouped into subtypes that share specific functions that are not common to the entire family. Often, the amino acids present in a small...
Protein quantification across hundreds of experimental conditions
Khan, Zia, Bloom, Joshua S., Garcia, Benjamin A., Singh, Mona, Kruglyak, Leonid
Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds...