Motif Evaluation by Leave-one-out Scoring (2008)
Audrey Girouard, Noah W. Smith, Donna K. Slonim
Abstract — We propose a new method for collecting information on regulatory elements found by any motif discovery program. We suggest that combining the results of n leave-oneout motif discovery...
Abstract Class Prediction and Discovery Using Gene Expression Data (2008)
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. L
Classification of patient samples is a crucial aspect of cancer diagnosis and treatment. We present a method for classifying samples by computational analysis of gene expression data. We consider the...
Algorithms for Modeling and Measuring Proteins (2007)
In this paper we investigate efficient algorithms for computing the volume and surface area of protein molecules and for graphically displaying the molecules in real time. Protein molecules are...
Algorithms for Modeling and Measuring Proteins (2007)
In this paper we investigate e cient algorithms for computing the volume and surface area of protein molecules and for graphically displaying the molecules in real time. Protein molecules are modeled...
Baugh, L. Ryan, Hill, Andrew A., Claggett, Julia M., Hill-Harfe, Kate, Wen, Joanne C., Slonim, Donna K., ...
Maternal and zygotic activities of the homeodomain protein PAL-1 specify the identity and maintain the development of the multipotent C blastomere lineage in the C. elegans embryo. To identify PAL-1...
Baugh, L. Ryan, Wen, Joanne C., Hill, Andrew A., Slonim, Donna K., Brown, Eugene L., Hunter, Craig P.
Phenotypic robustness is evidenced when single-gene mutations do not result in an obvious phenotype. It has been suggested that such phenotypic stability results from 'buffering' activities of...
Baugh, L Ryan, Wen, Joanne C, Hill, Andrew A, Slonim, Donna K, Brown, Eugene L, Hunter, Craig P
Abstract Phenotypic robustness is evidenced when single-gene mutations do not result in an obvious phenotype. It has been suggested that such phenotypic stability results from 'buffering' activities...
Hill, Andrew A, Brown, Eugene L, Whitley, Maryann Z, Tucker-Kellogg, Greg, Hunter, Craig P, Slonim, Donna K
Abstract Background Affymetrix oligonucleotide arrays simultaneously measure the abundances of thousands of mRNAs in biological samples. Comparability of array results is necessary for the creation...
Class Prediction and Discovery Using Gene Expression Data (2000)
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. Lander, Eric S. L
Classification of patient samples is a crucial aspect of cancer diagnosis and treatment. We present a method for classifying samples by computational analysis of gene expression data. We consider the...
Learning With Unreliable Boundary Queries (1997)
Avrim Blum, Prasad Chalasani, Sally A. Goldman, Donna K. Slonim
We introduce a model for learning from examples and membership queries in situations where the boundary between positive and negative examples is somewhat ill-defined. In our model, queries near the...
Learning from imperfect data in theory and practice (1996)
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Learning from imperfect data in theory and practice / (1996)
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Learning from imperfect data in theory and practice (1996)
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Learning With Unreliable Boundary Queries (1995)
Avrim Blum, Prasad Chalasani, Sally A. Goldman, Donna K. Slonim
We introduce a model for learning from examples and membership queries in situations where the boundary between positive and negative examples is somewhat ill-defined. In our model, queries near the...
Learning With Unreliable Boundary Queries (1995)
Avrim Blum, Prasad Chalasani, Sally A. Goldman, Donna K. Slonim
We introduce a new model for learning with membership queries in which queries near the boundary of a target concept may receive incorrect or "don't care" responses. In partial...
The power of team exploration: Two robots can learn unlabeled directed graphs (1994)
Michael A. Bender, Donna K. Slonim
We show that two cooperating robots can learn exactly any strongly-connected directed graph with n indistinguishable nodes in expected time polynomial in n. Weintroduce a new type of homing sequence...
Randomly fallible teachers: learning monotone DNF with an incomplete membership oracle (1994)
Abstract. We introduce a new fault-tolerant model of algorithmic learning using an equivalence oracle and an incomplete membership oracle, in which the answers to a random subset of the...
The Power of Team Exploration: Two Robots Can Learn Unlabeled Directed Graphs (1994)
Michael A. Bender, Donna K. Slonim
We show that two cooperating robots can learn exactly any strongly-connected directed graph with n indistinguishable nodes in expected time polynomial in n. We introduce a new type of homing sequence...
The Power of Team Exploration: Two Robots Can Learn Unlabeled Directed Graphs (1994)
Michael Bender, Donna K. Slonim
We show that two cooperating robots can learn exactly any strongly-connected directed graph with n indistinguishable nodes in expected time polynomial in n. We introduce a new type of homing sequence...
The Power of Team Exploration: Two Robots Can Learn Unlabeled Directed Graphs (1994)
Michael A. Bender, Donna K. Slonim
We show that two cooperating robots can learn exactly any strongly-connected directed graph with n indistinguishable nodes in expected time polynomial in n. We introduce a new type of homing sequence...
Learning Monotone DNF with an Incomplete Membership Oracle (1991)
We introduce a new fault-tolerant model of algorithmic learning using an equivalence oracle and an incomplete membership oracle, in which the answers to a random subset of the learner's...
Chemosensitivity prediction by transcriptional profiling
Staunton, Jane E., Slonim, Donna K., Coller, Hilary A., Tamayo, Pablo, Angelo, Michael J., Park, Johnny, ...
In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles...
Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls
Hill, Andrew A, Brown, Eugene L, Whitley, Maryann Z, Tucker-Kellogg, Greg, Hunter, Craig P, Slonim, Donna K
Baugh, L Ryan, Wen, Joanne C, Hill, Andrew A, Slonim, Donna K, Brown, Eugene L, Hunter, Craig P
To identify interactions among genes implicated in posterior patterning of the C. elegans embryo, synthetic lethality following RNA interference of 22 genes was measured in 15 mutant strains. A pair...
Chemosensitivity prediction by transcriptional profiling
Staunton, Jane E., Slonim, Donna K., Coller, Hilary A., Tamayo, Pablo, Angelo, Michael J., Park, Johnny, ...
In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles...
Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls
Hill, Andrew A, Brown, Eugene L, Whitley, Maryann Z, Tucker-Kellogg, Greg, Hunter, Craig P, Slonim, Donna K
Baugh, L Ryan, Wen, Joanne C, Hill, Andrew A, Slonim, Donna K, Brown, Eugene L, Hunter, Craig P
To identify interactions among genes implicated in posterior patterning of the C. elegans embryo, synthetic lethality following RNA interference of 22 genes was measured in 15 mutant strains. A pair...
Yanai, Itai, Baugh, L Ryan, Smith, Jessica J, Roehrig, Casey, Shen-Orr, Shai S, Claggett, Julia M, ...
Biological networks are inherently modular, yet little is known about how modules are assembled to enable coordinated and complex functions. We used RNAi and time series, whole-genome microarray...
Slonim, Donna K., Koide, Keiko, Johnson, Kirby L., Tantravahi, Umadevi, Cowan, Janet M., Jarrah, Zina, ...
To characterize the differences between second trimester Down syndrome (DS) and euploid fetuses, we used Affymetrix microarrays to compare gene expression in uncultured amniotic fluid supernatant...