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Functional discovery via a compendium of expression profiles.

by Timothy R Hughes , Matthew J Marton , Allan R Jones , Christopher J Roberts , Roland Stoughton , Christopher D Armour , Holly A Bennett , Ernest Coffey , Hongyue Dai , Ross-Macdonald , Yudong D He , Matthew J Kidd , Amy M King , Michael R Meyer , David Slade , Pek Y Lum , Sergey B Stepaniants , Daniel D Shoemaker , Julian Simon , Martin Bard - Cell, , 2000
"... provided that the cellular transcriptional response to frames encode proteins required for sterol metabodisruption of different steps in the same pathway is lism, cell wall function, mitochondrial respiration, or similar, and that there are sufficiently unique transcripprotein synthesis. We also sh ..."
Abstract - Cited by 547 (9 self) - Add to MetaCart
show that the compendium tional responses to the perturbation of most cellular can be used to characterize pharmacological perturpathways, systematic characterization of novel mutants bations by identifying a novel target of the commonly could be carried out with a single genome-wide expresused drug

Gene selection for cancer classification using support vector machines

by Isabelle Guyon, Jason Weston, Stephen Barnhill, Vladimir Vapnik, Nello Cristianini - Machine Learning
"... Abstract. DNA micro-arrays now permit scientists to screen thousands of genes simultaneously and determine whether those genes are active, hyperactive or silent in normal or cancerous tissue. Because these new micro-array devices generate bewildering amounts of raw data, new analytical methods must ..."
Abstract - Cited by 1115 (24 self) - Add to MetaCart
available training examples from cancer and normal patients, we build a classifier suitable for genetic diagnosis, as well as drug discovery. Previous attempts to address this problem select genes with correlation techniques. We propose a new method of gene selection utilizing Support Vector Machine methods

Embryonic stem cell lines derived from human blastocysts

by James A. Thomson, Joseph Itskovitz-eldor, Er S. Shapiro, Michelle A. Waknitz, Jennifer J. Swiergiel, Vivienne S. Marshall, Jeffrey M. Jones - Tissue Engineering For Peer Review , 1998
"... Human blastocyst-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express cell surface markers that characterize primate embryonic stem cells but do not characterize other early lineages. After undifferentiated proliferation i ..."
Abstract - Cited by 470 (6 self) - Add to MetaCart
, and stratiÞed squamous epithelium (ectoderm). These cell lines should be useful in human develop-mental biology, drug discovery, and transplantation medicine. Embryonic stem (ES) cells are derived from totipotent cells of the early mamma-lian embryo and are capable of unlimited, undifferentiated proliferation

New Algorithms for Fast Discovery of Association Rules

by Mohammed Javeed Zaki, Srinivasan Parthasarathy, Mitsunori Ogihara, Wei Li - In 3rd Intl. Conf. on Knowledge Discovery and Data Mining , 1997
"... Association rule discovery has emerged as an important problem in knowledge discovery and data mining. The association mining task consists of identifying the frequent itemsets, and then forming conditional implication rules among them. In this paper we present efficient algorithms for the discovery ..."
Abstract - Cited by 397 (26 self) - Add to MetaCart
for the discovery of frequent itemsets, which forms the compute intensive phase of the task. The algorithms utilize the structural properties of frequent itemsets to facilitate fast discovery. The related database items are grouped together into clusters representing the potential maximal frequent itemsets

Scalable Algorithms for Association Mining

by Mohammed J. Zaki - IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING , 2000
"... Association rule discovery has emerged as an important problem in knowledge discovery and data mining. The association mining task consists of identifying the frequent itemsets, and then forming conditional implication rules among them. In this paper we present efficient algorithms for the discovery ..."
Abstract - Cited by 259 (23 self) - Add to MetaCart
for the discovery of frequent itemsets, which forms the compute intensive phase of the task. The algorithms utilize the structural properties of frequent itemsets to facilitate fast discovery. The items are organized into a subset lattice search space, which is decomposed into small independent chunks or sub

Combinatorial approaches to finding subtle signals in DNA sequences,”

by Pavel A Pevzner , Sing-Hoi Sze - in Proceedings of the 8th International Conference on Intelligient Systems for Molecular Biology, , 2000
"... Abstract Signal finding (pattern discovery in unaligned DNA sequences) is a fundamental problem in both computer science and molecular biology with important applications in locating regulatory sites and drug target identification. Despite many studies, this problem is far from being resolved: most ..."
Abstract - Cited by 258 (5 self) - Add to MetaCart
Abstract Signal finding (pattern discovery in unaligned DNA sequences) is a fundamental problem in both computer science and molecular biology with important applications in locating regulatory sites and drug target identification. Despite many studies, this problem is far from being resolved

Worms: Identifying Impacts on Education and Health in the presence of Treatment Externalities

by Edward Miguel, Michael Kremer - ECONOMETRICA , 2004
"... Intestinal helminths—including hookworm, roundworm, whipworm, and schistosomiasis—infect more than one-quarter of the world’s population. Studies in which medical treatment is randomized at the individual level potentially doubly underestimate the benefits of treatment, missing externality benefits ..."
Abstract - Cited by 251 (13 self) - Add to MetaCart
to the comparison group from reduced disease transmission, and therefore also underestimating benefits for the treatment group. We evaluate a Kenyan project in which school-based mass treatment with deworming drugs was randomly phased into schools, rather than to individuals, allowing estimation of overall program

The induction of dynamical recognizers

by Jordan B. Pollack - Machine Learning , 1991
"... A higher order recurrent neural network architecture learns to recognize and generate languages after being "trained " on categorized exemplars. Studying these networks from the perspective of dynamical systems yields two interesting discoveries: First, a longitudinal examination of the le ..."
Abstract - Cited by 225 (14 self) - Add to MetaCart
A higher order recurrent neural network architecture learns to recognize and generate languages after being "trained " on categorized exemplars. Studying these networks from the perspective of dynamical systems yields two interesting discoveries: First, a longitudinal examination

ChEMBL: a large-scale bioactivity database for drug discovery

by Anna Gaulton, Louisa J. Bellis, A. Patricia Bento, Jon Chambers, Mark Davies, Anne Hersey, Yvonne Light, Shaun Mcglinchey, David Michalovich, Bissan Al-lazikani, John P. Overington - Nucleic Acids Research 40(Database issue):D1100–D1107 DOI 10.1093/nar/gkr777 , 2012
"... ChEMBL is an Open Data database containing bind-ing, functional and ADMET information for a large number of drug-like bioactive compounds. These data are manually abstracted from the primary pub-lished literature on a regular basis, then further curated and standardized to maximize their quality and ..."
Abstract - Cited by 148 (8 self) - Add to MetaCart
and utility across a wide range of chemical biology and drug-discovery research problems. Currently, the database contains 5.4 million bioactivity meas-urements for more than 1 million compounds and 5200 protein targets. Access is available through a web-based interface, data downloads and web ser-vices at:

Development and testing of a general amber force field.

by Junmei Wang , Romain M Wolf , James W Caldwell , Peter A Kollman , David A Case - J Comput Chem;25:1157–1174. , 2004
"... Abstract: We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogen ..."
Abstract - Cited by 214 (4 self) - Add to MetaCart
minimized structures, with a root-mean-square displacement of 0.26 Å, which is comparable to that of the Tripos 5.2 force field (0.25 Å) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Å, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs
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